XNA ?(xylo nucleic acid): A summary and new derivatives

FULL PAPER

XNA^[‡](xylo Nucleic Acid): A Summary and New Derivatives

B. Ravindra Babu,^[a]Raunak,^[a,b]Nicolai E. Poopeiko,^[a]Martin Juhl,^[c]Andrew D. Bond,^[d]

Virinder S. Parmar,^[b]and Jesper Wengel*^[a]

Keywords: xylo Nucleic acid (XNA) / 2Ј-Deoxy-xylo nucleic acid (dXNA) / Locked nucleic acid / Triple helix / Preferential

RNA hybridization / xylo-Clamp

Fully modified homopyrimidine 2Ј-deoxy-xylo nucleic acid

(dXNA) form triple helixes with complementary DNA/RNA

with thermal stabilities comparable to those of the corre-

sponding DNA:DNA and DNA:RNA duplexes. However, a

single or few insertions of dXNA monomers in a DNA strand

significantly lower duplex stabilities. The dXNA monomers

are known to adopt predominantly an N-type furanose con-

formation in solution. With a desire to increase the binding

affinity, seven sugar-modified XNA monomers (H, F, N, M,

K, P and Q) have been synthesised and their effect on hybrid-

ization towards DNA and RNA complements studied. The in-

troduction of 2Ј-fluoro and 2Ј-hydroxy substituents was ex-

pected to induce conformational restriction towards C3Ј-

endo-type furanose conformation of monomer F derived from

D

-xylofuranosyl]thymine (monomer P), 1-(4-C-piperazinyl-

methyl-β- -xylofuranosyl)thymine (monomer Q), 1-(4-C-hy-

droxymethyl-β- -xylofuranosyl)thymine (monomer M) and

9-(4-C-hydroxymethyl-β- -xylofuranosyl)adenine (monomer

D

K) was studied, with monomer N being locked in an N-type

furanose conformation. Besides, an efficient synthesis of

known xylo-LNA phosphoramidite 19, required for the incor-

poration of 1-(2Ј-O,4Ј-C-methylene-β-D-xylofuranosyl)thy-

mine (monomer L) is described. For comparison, hydridi-

zation data of various XNAs reported in the literature are

included in the discussion section. The thermal denaturation

studies show that XNAs containing conformationally locked

monomers (N and L) display improved binding affinity, and

that partially modified DNA/XNA chimera, or fully modified

1-(2Ј-deoxy-2Ј-fluoro-β-

mer H derived from 1-(β-

ence of functionalites facing the minor groove as in 1-(2Ј-

amino-2Ј-deoxy-2Ј-N,4Ј-C-methylene-β- -xylofuranosyl)thy-

D-xylofuranosyl)thymine and mono- XNA display preferential hybridization towards RNA com-

D-xylofuranosyl)thymine. The pres-

plements.

D

Germany, 2005)

mine (monomer N), 1-[4-C-(N-methylpiperazinyl)methyl-β-

adopt an N-type furanose conformation as opposed to the

S-type of their 2Ј-deoxy-ribo counterparts.^[1]Notably, oligo-

mers containing dXNA monomers possess a higher stability

towards exonucleases.^[1,2,5]A single replacement of the reg-

ular 2Ј-deoxynucleotides by their xylo-configured counter-

parts results generally in a significant decrease in the duplex

stability.^[2]However, with the RNA complement, the ther-

mal stability of the duplex was comparable with the refer-

ence DNA:RNA duplex.^[7,8]The increased binding affinity

towards RNA has been attributed to the tendency of these

nucleotides to adopt a C3Ј-endo conformation, giving ther-

mally stable A-type duplexes. This hypothesis was con-

firmed by the thermal denaturation studies of xylo-

LNA,^[9,10]that contains monomer with sugar conformation

locked in an N-type, leading to preferential hybridization

towards RNA.

Whereas the introduction of a few dXNA monomers into

a DNA strand had a very negative influence on the hybrid-

ization properties,^[2,3,7,8,11]an almost fully modified pyrimi-

dine dXNA displayed comparable, or even significantly in-

creased, binding affinity towards DNA or RNA comple-

ments when compared to the reference duplex,^[1,2,5–8]and a

fully modified self-complementary dXNA formed a com-

Introduction

2Ј-Deoxy-xylo-configured oligonucleotides (2Ј-deoxy-

xylo nucleic acid, dXNA)^[1–6]form complexes with DNA/

RNA complements that substantially differ from the un-

modified counterparts in structure due to the inversion of

the configuration at C3Ј of the xylo monomers (3ЈR config-

uration) as compared to regular DNA/RNA monomers

(3ЈS configuration). The dXNA monomers predominantly

[‡] We have defined an XNA as an oligonucleotide containing one

or more nucleotide monomers with a xylofuranosyl configura-

tion and internucleotide phospho diester linkages linked via the

O3Ј and O5Ј atoms of the monomers.

[a] Nucleic Acid Center, Department of Chemistry, University of

Southern Denmark,

5230 Odense M, Denmark

Fax: +45-66158780

E-mail: jwe@chem.sdu.dk

[b] Bioorganic Laboratory, Department of Chemistry, University

of Delhi,

Delhi 110007, India

[c] Department of Chemistry, University of Copenhagen,

Universitetsparken 5, 2100 Copenhagen, Denmark

[d] Department of Chemistry, University of Southern Denmark,

5230 Odense M, Denmark

Supporting information for this article is available on the

WWW under http://ww w .eurjoc.org or from the author.

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DOI: 10.1002/ejoc.200500023

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plex of similar stability to that formed by the corresponding ous molecular entities,^[16,17]e.g., intercalators, lipophilic

DNA.^[5]Recently, we^[7,8]and Bertrand et al.^[12]have shown groups, amines or a third strand. Incorporation of 4Ј-C-

that dXNA are able to form higher order complexes (i.e. (hydroxymethyl)uridine into an oligonucleotide resulted in

triplexes) with single-stranded DNA and RNA targets. Gel moderate to strong destabilization of the duplex with com-

retardation experiments,^[7,12]UV melting experiments^[7,8,12]plementary DNA, whereas only a small decrease in the

and circular dichroism studies^[11]have shown that in the melting temperature was observed with complementary

triple helices formed by homopyrimidine dXNAs with com- RNA as target.^[18]This, combined with the preferential hy-

plementary DNA or RNA strands, one dXNA strand is bridization of dXNA towards RNA complements relative

antiparallel (Watson–Crick pairing) and the other parallel to DNA complements, inspired the synthesis of 4Ј-C-hy-

(Hoogsteen pairing) with respect to the DNA/RNA target. droxymethyl xylo-configured RNA-like monomers M and

Surprisingly, neither antiparallel nor parallel duplex forma- K (Figure 1). Furthermore, oligonucleotides containing 4Ј-

tion between homopyrimidine dXNAs and their DNA/ C-substituted nucleotides have shown increased resistance

RNA targets was observed. The triplexes formed were towards enzymatic degradation,^[15,18,19]most pronounced

stable at pH 7, but less stable than at pH 5.^[12]

for oligonucleotides containing modified nucleotides with

The main objective of the present work is to present an an amino group.^[20,21]Besides, as the 4Јα position of the

overview of known sugar-modified XNAs, and evaluate the nucleotides is close to the internucleotide phospho diester

opportunities to improve the binding affinity of XNA by linkages, the attachment of alkylamines anticipated to be

either restricting their furanose conformation in an N-type protonated under physiological conditions is attractive as

or by covalently attaching functionalities to the XNA.^[7]We a strategy for increasing the binding affinity towards the

undertook the synthesis of xylo-configured RNA-like mo- negatively charged target strands. Recently, based on similar

nomer H, conformationally restricted 2Ј-deoxy-2Ј-fluoro considerations, we have successfully introduced basic piper-

XNA monomer F and conformationally locked 2Ј-amino- azinyl moieties, pointing either towards the minor or major

xylo-LNA monomer N. In addition we report a convenient groove of duplexes.^[22]Thus, in an attempt to increase the

synthesis of the precursor amidite 19 for the incorporation binding affinity of XNA, we decided to synthesize and eval-

of xylo-LNA monomer L. We speculated that the introduc- uate oligonucleotides containing 4Ј-C-piperazinylmethyl

tion of an electronegative fluoro substituent at the 2Ј posi- XNA monomers P and Q.

tion of dXNA monomer could increase the contribution

from the N-type furanose conformation due to stereoelec-

tronic effect, and that the presence of the secondary amine

functionality in 2Ј-amino-xylo-LNA would be of potential

Results and Discussion

interest as a conjugation site and as a protonation site.

The known dXNA thymine phosphoramidite 1 was pre-

Oligonucleotides containing 4Ј-C-hydroxymethyl nucleo- pared from thymidine following the reported procedure^[1,23]

tide monomers hybridize with both complementary DNA and used for the incorporation of monomer X into oligonu-

and RNA with similar binding affinity as the corresponding cleotides.

unmodified DNA strand.^[15,16]The additional C-alkyl

Synthesis of 2Ј-Fluoro-dXNA Monomer F:^[7]Conversion

branch faces the minor groove allowing attachment of vari- of known methyl 2-deoxy-3,5-di-O-benzoyl-2-fluoro-β-d-

Figure 1. Structures of nucleotide monomers studied: DNA, dXNA thymine monomer (X), XNA thymine monomer (H), 2Ј-deoxy-2Ј-

fluoro XNA thymine monomer (F), xylo-LNA thymine monomer (L), 2Ј-amino-xylo-LNA thymine monomer (N), 4Ј-C-hydroxymethyl

XNA monomers (M and K), 4Ј-C-piperazinylmethyl XNA monomers (P and Q), α-L-LNA thymine monomer (^αLT^L)^[9,13]and LNA

adenine monomer (A^L).^[14]The short notations shown are used in Tables 1–3. T = thymin-1-yl, A = adenin-9-yl.

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XNA (xylo Nucleic Acid): A Summary and New Derivatives

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Scheme 1. Reagents and conditions (yields): (i) AcOH/Ac₂O/concd. H₂SO₄(3.8:1:0.3, v/v/v), room temp., 75 min (97%); (ii) thymine,

BSA, TMS-triflate, 1,2-dichloroethane, reflux, 3 h (4a: 24%, 4b: 49%); (iii) saturated methanolic ammonia, room temp., 12 h (5a: 75%,

5b: 83%); (iv) DMTCl, pyridine, room temp., 14 h (90%); (v) NC(CH₂)₂OP(Cl)N(iPr)₂, EtN(iPr)₂, CH₂Cl₂, room temp., 30 min. (81%);

(vi) DNA synthesizer.

xylofuranoside (2)^[24]into a suitable phosphoramidite build- steps) suitable for incorporation of monomer H into oligo-

ing block for synthesis of XNAs with monomeric unit F nucleotides (Scheme 2).

was performed as depicted in Scheme 1. Acetolysis of 2 af-

forded the anomeric mixture 3, which was coupled with bis-

O-(trimethylsilyl)thymine in the presence of TMS-triflate to

give the isomers 4 (α-anomer 4a and β-anomer 4b, in a ratio

4a/4b = 1:2 after isolation as individual compounds by col-

umn chromatography) in a total yield of 73%. Deprotection

of nucleosides 4a and 4b with saturated ammonia in meth-

anol afforded α-anomer 5a and β-anomer 5b in 75% and

83% yields, respectively. The anomeric configuration of 5a

1

and 5b was assigned by H NMR spectroscopy. For the β-

Scheme 2. Reagents and conditions (yields): (i) Ac₂O, pyridine,

room temp., 12 h (97%); (ii) 80% aq. AcOH, 65 °C to room temp.,

14 h (84%); (iii) DMTCl, pyridine, room temp., 12 h (90%); (iv)

NC(CH₂)₂OP(Cl)N(iPr)₂, EtN(iPr)₂, CH₂Cl₂, room temp., 30 min.

anomer 5b, the signal of H1Ј (δ, 6.02) appeared as a doublet

with a large coupling constant (³J_H1Ј,F= 21.4 Hz). The lack

of a significant coupling between protons H1Ј and H2Ј is

characteristic of a trans-1Ј,2Ј-configuration in furanose de-

rivatives,^[25]thus confirming the β-configuration. On the

other hand, in the α-anomer 5a, the signal of H1Ј (δ, 6.24)

(87%); (v) DNA synthesizer.

New Strategy for Synthesis of xylo-LNA Monomer L: We

appeared as a double doublet with a significant coupling have earlier reported the synthesis of phosphoramidite

constant between H1Ј and H2Ј (³J_H1Ј,H2Ј= 3.3 Hz). More- 19^[9,30]that was used for incorporation of xylo-LNA mono-

over in the spectrum of 5a, the signal for H4Ј is shifted mer L into oligonucleotides. Although significant duplex

Ϸ0.4 ppm downfield when compared to the corresponding destabilization by the introduction of one or few xylo-LNA

signal in the spectrum of 5b which further supports the an- monomers L into a DNA strand was observed, strong bind-

omeric assignments.^[26]Selective protection of the 5Ј-hy- ing affinity was obtained for an almost fully modified xylo-

droxy group of diol 5b by the treatment of DMTCl in pyri- LNA towards DNA or RNA complements^[10](T_m+3.1 and

dine gave nucleoside 6 in 90% yield. The H1Ј signal of nu- +4.3 °C per modification, respectively), which has not been

cleoside 6 appears as a doublet (³J_H1Ј,F= 21.1 Hz), and the reported for other XNA derivatives. Inconveniently phos-

3

absence of J_H1Ј,H2Јcoupling confirms the configurational phoramidite 19 was synthesized from 3-O-benzyl-4-C-hy-

assignments and indicates an N-type furanose conforma- droxymethyl-1,2-O-isopropylidene-α-d-xylofuranose (13)^[31]

tion^[27,28]for 6 (and therefore also for monomer F). Phos- in an overall yield of only 3.3%.^[30]Therefore, we have de-

phitylation of 6 by the standard protocol afforded phos- veloped a new strategy for the synthesis of this interesting

phoroamidite 7 (81% yield) that was used to incorporate phosphoramidite that significantly improves the overall

monomer F into oligonucleotides.

yield to 14.3% (Scheme 3). Furanose 14 was obtained from

Synthesis of XNA Monomer H: For the synthesis of 13 in 50% yield following the known literature pro-

XNAs with monomeric unit H, 1,2-O-isopropylidene-α-d- cedure.^[32]Coupling of 14 with thymine in the presence of

xylofuranose was selected as the starting material, and it BSA and TMS-triflate in acetonitrile afforded nucleoside 15

was converted in five steps in 42% overall yield to 1-(3,5-O- in 72% yield. Subsequent refluxing of 15 with a large excess

isopropylidene-β-d-xylofuranosyl)thymine (8) following the of NaOH in EtOH afforded nucleoside 16, as a result of a

published procedure.^[29]The 2Ј-hydroxy group was acety- reaction cascade involving first 2Ј-deacetylation, then intra-

lated in 97% yield (to give 9) and the 3Ј,5Ј-isopropylidene molecular ring closure and exchange of the mesyloxy group

group was cleaved by refluxing with 80% aq. AcOH to af- at C5Ј with a hydroxy group. Nucleoside 16 was converted

ford nucleoside 10. Selective dimethoxytritylation at the pri- by the standard protocol into its 5Ј-dimethoxytrityl deriva-

mary hydroxy group of 10 by reaction with DMTCl in the tive 17. It has been previously reported that hydrogenolysis

presence of pyridine and subsequent phosphitylation fur- of 17 in the presence of Pd/C in MeOH resulted in concom-

nished the desired phosphoramidite 12 (78% yield, two itant detritylation.^[30]However, when the reaction was car-

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Scheme 3. Reagents and conditions (yields): (i) thymine, BSA, TMS triflate, acetonitrile, reflux, 3 h (72%); (ii) aq. NaOH (2 m), 96%

EtOH, reflux, 60 h (76%); (iii) DMTCl, pyridine, room temp., 12 h (95%); (iv) H₂, Pd(OH)₂, EtOAc/EtOH, 70 °C, 28 h (67%); (v)

NC(CH₂)₂OP(Cl)N(iPr)₂, EtN(iPr)₂, CH₂Cl₂, room temp., 30 min. (82%); (vi) DNA synthesizer.

ried out with Pd(OH)₂/C in a mixture of EtOAc/EtOH, de- advantage of the nucleophilic nature of the O2 position of

tritylation was avoided and nucleoside 18 was obtained in the nucleobase, affording the 2,2Ј-anhydro nucleoside 22.

67% yield. Subsequent conversion of 18 into the phos- Opening of the 2,2Ј-anhydro moiety with retention of con-

phoroamidite 19 completed the optimized synthesis of the figuration at C2Ј was done by refluxing 22 in a mixture of

building block needed for the incorporation of xylo-LNA aqueous sulfuric acid (0.4 m) and acetone (1:1, v/v), which

monomer L into oligonucleotides.

resulted in erythro-configured nucleoside 23 in 98% yield.

Synthesis of 2Ј-Amino-xylo-LNA Monomer N:^[7]The syn- The second inversion was achieved by activation of the 2Ј-

thesis of 2Ј-amino-xylo-LNA phosphoramidite building OH in 23 by reaction with 1.1 equivalents of trifluorome-

block 31 was carried out in twelve steps in an overall yield thanesulfonic anhydride and subsequent nucleophilic dis-

of 13%, starting from nucleoside 15 (Scheme 4). Deprotec- placement by azide furnishing threo-configured nucleoside

tion of the O2Ј acetyl group was carried out using saturated 24. Reduction of the azido group in nucleoside 24 under

methanolic ammonia affording nucleoside 20 in 93% yield. modified Staudinger conditions using trimethylphosphane

In order to obtain the (2ЈR)-2Ј-azido nucleoside 24, a in a mixture of THF and aqueous NaOH and simultaneous

double inversion strategy was applied. The first inversion at in situ intramolecular cyclization afforded the bicyclic nu-

the 2Ј position was carried out using a two-step procedure, cleoside 25 in 53% yield from 23. Nucleophilic displace-

i.e., mesylation of the secondary hydroxy group followed ment of the remaining mesyloxy group in 25 with a benzo-

by displacement of the newly formed mesylate in 21 taking ate group, followed by ester cleavage with saturated meth-

Scheme 4. Reagents and conditions (and yields): (i) saturated NH₃in MeOH, 0 °C to room temp., 45 min (93%); (ii) MsCl, pyridine,

room temp., 4 h (86%); (iii) DBU, CH₃CN, room temp., 1.5 h (89%); (iv) 0.4 m aq. H₂SO₄, acetone, reflux, 14 h (98%); (v) a) Tf₂O,

pyridine, DMAP, CH₂Cl₂, 0 °C, 7 h; b) NaN₃, DMF, room temp., 18 h; (vi) PMe₃, aq. NaOH (2 m), THF, room temp., 72 h (53% from

23); (vii) NaOBz, 15-crown-5, DMF, 120 °C, 30 h; (viii) saturated NH₃in MeOH, room temp., 18 h (48%, 2 steps); (ix) CF₃CO₂Et,

DMAP, MeOH, room temp., 16 h (93%); (x) 10% Pd/C, H₂, MeOH, room temp., 2 h (96%); (xi) DMTCl, pyridine, room temp., 18 h

(94%); (xii) NC(CH₂)₂OP(Cl)N(iPr)₂, DIPEA, CH₂Cl₂, room temp., 8 h (90%); (xiii) DNA synthesizer.

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XNA (xylo Nucleic Acid): A Summary and New Derivatives

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anolic ammonia afforded nucleoside 27. Protection of the 31 from starting material 15 was hereby achieved in an

secondary amino group using ethyl trifluoroacetate, fol- overall yield of 18%. Nucleobase protection of compound

lowed by debenzylation, using catalytic hydrogenation with 15 at the N3 position was carried out with benzyloxymethyl

palladium as the promoter (10% Pd/C), afforded diol 29, chloride (BOMCl) in the presence of diisopropylethylamine

as a (1:2) mixture of rotamers. To prepare for automated to give nucleoside 32 in 86% yield after purification by dry

synthesis of XNAs containing 2Ј-amino-xylo-LNA mono- column vacuum chromatography (DCVC).^[33]Nucleoside

mer N, the primary hydroxy group of nucleoside 29 was 32 was stirred in saturated methanolic ammonia at 0 °C and

selectively dimethoxytritylated followed by phosphitylation then warmed to room temperature over a period of 15–

under standard conditions to furnish the desired phos- 20 min affording the deacetylated nucleoside 33 in 97%

phoramidite building block 31. The assigned configuration yield. Reaction of alcohol 33 with trifluoromethanesulfonic

of nucleoside 29 was confirmed by NOE difference experi- anhydride in the presence of pyridine (10 equivalents) and

ments. Thus selective irradiation of the signal for H5Ј pro- DMAP (4 equivalents) in CH₂Cl₂at 0 °C, followed by the

tons gave a 3% enhancement in the signals of H6 and 3Ј- addition of saturated aqueous NaHCO₃, surprisingly re-

OH. In addition mutual NOE effects were observed be- sulted in the C2Ј inverted alcohol 35 in 72% yield. The in-

tween H1Ј and H5ЈЈ (1%/1%), H3Ј and H5ЈЈ (2%/1%) and version is most likely a consequence of in situ 2,2Ј-anhydro

between H6 and 3Ј-OH (2%/1%), which besides verifying formation (intermediate 34), followed by hydrolysis with re-

the configuration, also suggest that the bicyclic nucleoside tention of configuration. For the synthesis of the desired

adopts the expected N-type (C3Ј-endo) furanose conforma- threo-configured 2Ј-amino xylo-LNA intermediate another

tion.

epimerization at C2Ј was required. Accordingly, activation

Alternative Synthesis of 2Ј-Amino-xylo-LNA Diol 29: The of the 2Ј-OH of 35 by reaction with trifluoromethanesul-

diol 29 was synthesized from nucleoside 15 in an overall fonic anhydride and subsequent substitution with an azide

yield of 16% (Scheme 4). This yield was improved to 21% afforded nucleoside 37 in 58% yield from 35. Reduction of

by following an alternative synthetic route (Scheme 5), the the azide group of nucleoside 37 was carried out by Staud-

key step being a one-pot inversion reaction (35 from 33) inger reaction, using triphenylphosphane in pyridine for

serendipitously discovered in our laboratories. The synthesis 20 h at room temperature followed by the addition of con-

of the 2Ј-amino-xylo-LNA phosphoramidite building block centrated aqueous ammonia to hydrolyze the intermediate

Scheme 5. Reagents and conditions (and yields): (i) BOMCl, DIPEA, CH₂Cl_2,0 °C to room temp., 44 h (86%); (ii) saturated NH₃in

MeOH, 0 °C to room temp., 15 min (94%); (iii) a) Tf₂O, pyridine, DMAP, CH₂Cl₂, 0 °C, 4 h; b) saturated aqueous NaHCO₃(72%); (iv)

Tf₂O, pyridine, DMAP, CH₂Cl₂, 0 °C, 4 h (70%); (v) NaN₃, DMF, room temp., 18 h (83%); (vi) a) PPh₃, pyridine, room temp., 20 h; b)

concd. aqueous NH₃, room temp., 24 h (99%); (vii) NaOBz, 15-crown-5, DMF, 120 °C, 24 h (92%); (viii) saturated NH₃in MeOH, room

temp., 20 h (93%); (ix) CF₃CO₂Et, DMAP, MeOH, room temp., 4 h (78%); (x) a) BCl₃, CH₂Cl₂, –78 °C to room temp., 2 h; b) H₂O,

room temp., 24 h (91%).

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imino-phosphorane, which also resulted in intramolecular ated furanoses. Silylation with the bulky TBDPS group im-

cyclization, affording the bicyclic nucleoside 38 in 99% proved neither the regioselectivity nor the separation of the

yield. Displacement of the remaining mesylate in 38 by ex- isomers by column chromatography. Similar reactivity of

cess sodium benzoate in DMF at 120 °C, followed by cleav- the two primary hydroxyls has been attributed to their pres-

age of the benzoate ester in 39 with saturated methanolic ence in similar environment.^[34]The hydroxy group at C5Ј

ammonia, provided alcohol 40 in 86% yield (from 38). The on the concave face of the bicyclo[3.3.0]octane system is

configuration and conformation of nucleoside 39 was un- expected to be less reactive than the 5-OH on the convex

ambiguously established by NOE difference experiment. Ir- face, while the bulky benzyloxy group at C3 limits the reac-

radiation of the signal for H1Ј proton resulted in enhance- tivity of the 5-OH for steric reasons. We therefore envi-

ment in the signals of H5ЈЈ (1%) and 2Ј-NH (4%). Besides, sioned that removal of the benzyl protection at C3 would

mutual NOE enhancement was observed between H3Ј and enhance the reactivity of 5-OH group. This hypothesis was

H5ЈЈ (2%/5%). Transesterification of 40 proceeded proven to be true when the triol 43^[35]was reacted with 1.1

smoothly with excess (7 equivalents) of ethyl trifluoroacet- equivalent of TBDPSCl resulting in the 5-O-silylated fu-

ate in the presence of 2.5 equivalents of DMAP in MeOH ranose 44 being obtained in almost quantitative yield. Sur-

at room temperature, affording trifluoroacetyl-protected prisingly the formation of the regioisomeric O5Ј-silylated

nucleoside 41 as a mixture of two rotamers in 78% yield. product was not observed while traces of disilylated product

The simultaneous deprotection of the benzyl group at C3Ј and unreacted triol 43 were seen on analytical TLC. The

and the benzyloxymethyl group at N3 by catalytic hydro- unreacted triol 43 was removed by washing the reaction

genation failed. However, Lewis acid-catalyzed deben- mixture with saturated aq. NaHCO₃, whereas the di-

zylation using boron trichloride in CH₂Cl₂resulted in a silylated product was removed by quick fractionation

mixture of the desired nucleoside 29 and nucleoside 42 (ten- through a silica gel column. The configuration of 44 was

tatively assigned as shown in Scheme 5 but neither isolated determined by NOE difference spectroscopy, and was later

nor characterized) in the ratio 1.0:1.5 as judged from NMR confirmed by a single-crystal X-ray diffraction study on fu-

spectra of the crude mixture. The removal of the hy- ranose 54a^[36](Figure 2). Selective irradiation of the signal

droxymethyl group at the N3 position of the nucleobase for H5 of compound 44 induced a 4% enhancement of the

was achieved by stirring the crude mixture (29 + 42) in H₂O signal for 3-OH and vice-versa (1%), which suggested that

at room temperature for 24 h which resulted in complete these protons are positioned at the same side of the fu-

conversion of 42 into 29.

ranose ring. Moreover, significant NOE contacts were ob-

Synthesis of 4-C-Hydroxymethyl-XNA Monomers M and served between H3, H5Ј and 5Ј-OH (3.2%/5.0% between

K: Synthesis of 4-C-hydroxymethyl-XNA monomers M and H3 and H5Јa, 3.0%/3.4% between H3 and H5Јb, 2.1/2.2%

K was achieved by a convergent strategy in which the suita- between H3 and 5Ј-OH) confirming cis positioning of these

bly protected xylofuranose 47 was condensed with the nuc- protons on the furanose ring. The next step was the protec-

leobases under Vogbruggen conditions (Scheme 6). Fu- tion of the remaining hydroxy groups under mild basic con-

ranose 13^[31]was selected as the starting material and ef- ditions (to avoid silyl migration). Selective O5Ј-benzoylation

ficient regioselective modification of the two primary hy- of diol 44 followed by O3-silylation afforded furanose 46 in

droxy groups was critical for the synthesis. Benzylation of 80% yield. In situ acetolysis and acetylation with Ac₂O and

13 using 1 equivalent of BnBr under various conditions AcOH in the presence of catalytic amounts of concd.

gave a ca. 1:1 inseparable mixture of 3,5- and 3,5Ј-dibenzyl- H₂SO₄afforded furanose 47 which served as a common gly-

Scheme 6. Reagents and conditions (yields): (i) HCO₂NH₄, Pd(OH)₂/C, MeOH, reflux, 16 h (89%); (ii) TBDPSCl, Et₃N, CH₂Cl₂, room

temp., 36 h (93%); (iii) BzCl, pyridine, CH₂Cl₂, 0 °C to room temp., 12 h (86%); (iv) TBDPSCl, imidazole, DMAP, anhydrous DMF,

room temp., 12 h (93%); (v) Ac₂O, AcOH, concd. H₂SO₄, room temp., 4 h (87%); (vi) thymine, BSA, TMS-triflate, acetonitrile, reflux,

12 h (48a: 91%) or 6-N-benzoyladenine, SnCl₄, acetonitrile, reflux, 36 h (48b: 66%); (vii) TBAF, THF, room temp. (49a: 93%, 49b: 52%);

(viii) DMTCl, pyridine, room temp., 12 h (50a: 81%, 50b: 88%); (ix) NC(CH₂)₂OP(Cl)N(iPr)₂, EtN(iPr)₂, CH₂Cl₂, room temp., 12 h (51a:

83%, 51b: 86%); (x) DNA synthesizer.

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XNA (xylo Nucleic Acid): A Summary and New Derivatives

FULL PAPER

cosyl donor. Condensation of 47 with silylated thymine in figured nucleoside 48a. Desilylation of 48a, followed by

the presence of TMS-triflate afforded the desired xylo-con- O5Ј-dimethoxytritylation to give 50a and then O3Ј-phos-

phitylation, using standard procedures, furnished the phos-

phoramidite building block 51a (Scheme 6) suitable for the

incorporation of monomer M into oligonucleotides. The

corresponding adenosine derivative was prepared following

the same synthetic route, except that the condensation of

the silylated 6-N-benzoyladenine with 47 required longer re-

action time using SnCl₄as Lewis acid furnishing nucleoside

48b in moderate yield. In order to obtain oligonucleotides

containing monomer K, desilylation of 48b, followed by

O5Ј-dimethoxytritylation and then O3Ј-phosphitylation af-

forded the desired phosphoramidite 51b (Scheme 6).

Synthesis of 4-C-Piperazinylmethyl-XNA Monomers P

and Q: For the synthesis of 4Ј-C-piperazinylmethyl-XNA

monomers P and Q, furanose 52 was selected as the com-

mon precursor obtained by debenzoylation of 46

(Scheme 7). Activation of the 5Ј-hydroxy group by reaction

Figure 2. Molecular structure (ORTEP plot) of 54a.^[36]Only the

numbering of the furanose ring follows the numbering otherwise

used in this text.

Scheme 7. Reagents and conditions (yields): (i) Saturated methanolic ammonia, room temp., 24 h (90%); (ii) a) Tf₂O, pyridine, CH₂Cl₂,

–30 °C to room temp., 12 h; b) N-methylpiperazine, THF, room temp., 12 h (53a: 93%) and (ii) a) Tf₂O, pyridine, CH₂Cl₂, –30 °C to

room temp., 12 h; b) piperazine, THF, room temp., 12 h (53b: 91%); (iii) (CF₃CO)₂O, Et₃N, CH₂Cl₂, room temp., 4 h (87%); (iv) TBAF,

THF, room temp., 12 h (54a: 88%); (v) BzCl, pyridine, CH₂Cl₂, room temp., 12 h (55a: 87%, 55b: 84% from 53c); (vi) a) 80% aq. TFA,

room temp., 3 h; b) Ac₂O, pyridine, room temp., 12 h (56a: 93%, 56b: 91%); (vii) thymine, BSA, TMS-triflate, acetonitrile, reflux, 3 h

(57a: 76%, 57b: 83%); (viii) 10% saturated methanolic ammonia, room temp., 1 h [58: 57%, 57a: 30% (recovered)]; (ix) TBDMSCl,

imidazole, DMAP, anhydrous DMF, 36 °C, 12 h (86%); (x) saturated methanolic ammonia, room temp., 24 h (83%); (xi) DMTCl, pyri-

dine, room temp., 12 h (88%); (xii) NC(CH₂)₂OP(Cl)N(iPr)₂, EtN(iPr)₂, CH₂Cl₂, room temp., 6 h (91%); (xiii) DNA synthesizer; (xiv)

saturated methanolic ammonia, room temp., 36 h (65%).

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Scheme 8. Reagents and conditions (yields): (i) Saturated methanolic ammonia, room temp., 36 h (71%); (ii) ethyl trifluoroacetate, DMAP,

MeOH, room temp., 12 h (84%); (iii) DMTCl, pyridine, room temp., 12 h (89%); (iv) Ac₂O, DMAP, acetonitrile, room temp., 3 h (72%);

(v) NC(CH₂)₂OP(Cl)N(iPr)₂, EtN(iPr)₂, CH₂Cl₂, room temp., 6 h (91%); (vi) DNA synthesizer.

with triflic anhydride followed by nucleophilic displacement 68 suitable for the incorporation of monomer Q into oligo-

with N-methylpiperazine or piperazine furnished 53a and nucleotides (Scheme 8).

53b, respectively. The free amino group of 53b was pro-

Synthesis of XNAs Containing Monomers X, H, M, K, P

tected as its trifluoroacetamide derivative 53c in 87% yield or Q: All XNAs ON8, ON21–ON34, ON36, ON37, ON39

by reaction with trifluoroacetic anhydride. Cleavage of the and ON40 (Tables 1–3) were prepared in 0.2 μmol scale

1,2-O-isopropylidene moieties in 53a and 53c could not be using the phosphoramidite approach (see the experimental

achieved under various conditions, e.g., Ac₂O/AcOH/ section for details). The composition of XNAs was verified

concd. H₂SO₄, 80% aq. TFA or refluxing with 80% aq. by MALDI-MS analysis and their purity (Ͼ80%) by capil-

AcOH (only desilylation was observed). However, after re- lary gel electrophoresis.

placing the silyl groups with benzoyl groups via diols 54a/

Thermal Denaturation Studies: In agreement with litera-

54b, the isopropylidene moieties could be cleaved easily by ture reports,^[1–8,12]a single replacement of a DNA thymine

treatment with 80% aq. TFA for 1 h at room temperature monomer by its 2Ј-deoxy-XNA (dXNA) counterpart X de-

which on subsequent peracetylation afforded the anomeric stabilized the duplex by 6–10 °C when hybridized to com-

mixtures 56a/56b, respectively, suitable for condensation plementary DNA (Table 1, ON2 relative to ON1, ON6 rela-

with nucleobases. Accordingly, the mixture of the anomeric tive to ON5). Preferential binding towards the RNA com-

furanoses 56a/56b was stereoselectively coupled with si- plement was observed (destabilization of the duplex by only

lylated thymine under modified Vorbruggen conditions to 1–4 °C), which can be attributed, in part, to furanose puck-

afford nucleosides 57a and 57b, respectively. Selective O2Ј- ering of the dXNA in an N-type conformation.^[1]Incorpo-

deacetylation of nucleoside 57a was performed with 10% ration of a few isolated X monomers into a DNA strand

saturated methanolic ammonia at room temperature afford- significantly reduced the affinity towards DNA and RNA

ing 58 which upon silylation furnished nucleoside 59 in 49% targets (ON3 relative to ON1), and no cooperative transi-

overall yield from 57a. Zemplen O-debenzoylation of 59 tion above 5 °C could be detected. In contrast, efficient re-

yielded the diol 60 in 83% yield, which was prepared for cognition of both DNA and RNA targets was achieved by

incorporation into oligonucleotides by standard dimeth- an almost fully modified dXNA (ON7), still with preferen-

oxytritylation of the 5Ј-hydoxy group, followed by phos- tial hybridization to the RNA target. Preference of dXNA

phitylation of the 3Ј-hydroxy group to give the phos- for the RNA complement was confirmed when ON7 was

phoramidite building block 62 suitable for the incorpora- hybridized with the RNA-mimicking LNA target (T_m

=

tion of monomer P into oligonucleotides. The correspond- 46 °C), the corresponding DNA-LNA duplex displayed a

ing fully deprotected nucleoside 63 was obtained in 65% T_mof only 38 °C. Efficient binding of the fully modified

yield by stirring 57a in saturated methanolic ammonia pyrimidine XNAs with DNA or RNA complements has

for 36 h at room temperature. For structural confirmation, been shown^[7,12]to be due to triplex formation in which the

an X-ray structure of furanose 54a was obtained^[36]first XNA forms Watson–Crick base pairing with the target

(Figure 2).

while the second XNA is engaged in Hoogsteen base pair-

Efforts towards selective O2Ј-deacetylation of 57b proved ing.

futile as the analysis of the reaction mixture by analytical

For further optimization of the binding properties of

TLC showed the formation of several products. Therefore fully modified dXNA we synthesized the xylo-clamp ON8

57b was completely deacylated, and to avoid N-branching (Table 1) in analogy to similar DNA-clamp oligomers.^[37]

during oligomerization the resulting nucleoside 64 was This molecule, designed for combined Watson–Crick and

treated with ethyl trifluoroacetate to give a 84% yield of Hoogsteen recognition, hybridizes towards both DNA and

trifluoroacetamide derivative 65. Subsequent O5Ј-dimeth- RNA targets more efficiently than the 14-mer dXNA ON7.

oxytritylation followed by selective acetylation of the unhin- However, the xylo-clamp ON8, in contrast to dXNA ON7,

dered 2Ј-hydroxy group (to give nucleoside 67) and then does not display preferred recognition of RNA over DNA.

O3Ј-phosphitylation afforded the desired phosphoramidite The same tendency of increase of thermal stability is ob-

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XNA (xylo Nucleic Acid): A Summary and New Derivatives

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Table 1. Thermal^[a]denaturation experiments of duplexes containing XNA monomers X and F.

DNA target

T_m(ΔT_m) [°C]

RNA target

T_m(ΔT_m) [°C]

LNA target [5Ј-(A^LA)₇]

T_m[°C]

ON1

ON2

ON3

ON4

5Ј-d(GTGATATGC)

5Ј-d(GTGAXATGC)

5Ј-d(GXGAXAXGC)

5Ј-d(GTGAFATGC)

30 (ref.)

24 (–6)^[7]

n.t.^[7]

26 (ref.)

25 (–1)^[7]

n.t.^[7]

25 (–5)^[7]

27 (+1)^[7]

ON5

ON6

ON7

ON8

ON9

ON10

ON11

5Ј-T₁₄

5Ј-T₇XT₆

5Ј-X₁₃T

5Ј-X₁₄ACACAX₁₄C

5Ј-T₇FT₆

5Ј-F₁₃T

5Ј-X₂FX₃FX₃FX₂T

33 (ref.)

29 (ref.)

38

23 (–10)^[7,8]

33 (+0)^[7,8]

43 (+10)

25 (–4)^[7,8]

38 (+9)^[7,8]

42 (+13)

46

53

23 (–10)^[7,8]

36 (+3)^[7,8]

34 (+1)^[7]

25 (–4)^[7,8]

36 (+7)^[7,8]

38 (+9)^[7]

[a] Melting temperatures (T_mvalues) were obtained from the maxima of the first derivatives of the melting curves (A₂₆₀vs. temperature)

recorded in medium salt buffer (10 mm sodium phosphate, 100 mm sodium chloride, 0.1 mm EDTA, pH 7.0) using 1.5 μM concentrations

of the two complementary strands (assuming identical extinction coefficients for all modified and unmodified oligonucleotides); A =

adenin-9-yl monomer, C = cytosin-1-yl monomer, G = guanin-9-yl monomer, T = thymin-1-yl monomer; see Figure 1 for the structures

of 2Ј-deoxy-XNA thymine monomer X, 2Ј-deoxy-2Ј-fluoro-XNA thymine monomer F and adenin-9-yl LNA monomer A^L; “n.t.”: No

cooperative melting transition detected.

served for the complex formed between xylo-clamp ON8 Table 2. Thermal^[a]denaturation experiments of duplexes contain-

ing locked XNA monomers L and N.

and its LNA complement. We anticipate that the complex

DNA target

T_m(ΔT_m) [°C]

RNA target

T_m(ΔT_m) [°C]

formed with xylo-clamp ON8 involves a bimolecular tri-

plex, and that the increased thermal stability relative to

ON7 is due to more favorable entropic changes during tri-

plex formation.

ON1

5Ј-d(GTGATATGC)

31 (ref.)^[7]

28 (–3)^[7]

n.t.

29 (ref.)^[7]

30 (+1)^[7]

19 (–10)^[7]

37 (+8)^[7]

ON12 5Ј-d(GTGANATGC)

ON13 5Ј-d(GNGANANGC)

Next the thermal stability of the complexes involving 2Ј-

fluoro-XNA monomer F was determined (Table 1). We en-

visioned that preorganization of the furanose conformation

in an N-type would enable entropically favored duplex for-

mation. However, in direct comparison with 2Ј-deoxy-XNA

X, no favorable change in the duplex stability was seen for

monomer F. A single insertion of monomer F leads to de-

creased affinity towards unmodified DNA (ΔT_m–5 to

–10 °C, ON4 relative to ON1, ON9 relative to ON5), while

the effect is less detrimental towards RNA (ΔT_m+1 to

–4 °C).^[7,8]The (almost) fully modified 2Ј-fluoro-XNA

(ON10) display T_mvalues in the same range as that of the

reference ON1 and the corresponding dXNA (ON5).^[7,8]

Moreover, it is possible to combine monomer F with dXNA

monomers and still obtain satisfactory hybridization, as

shown for the chimeric XNA ON11.^[7,8]

ON14 5Ј-d(G^αLT^LGANA^αLT^LGC) 28 (–3)^[7]

ON5

ON15 5Ј-T₁₀

5Ј-T₁₄

30^[7]/32^[9,10](ref.) 29^[7]/28^[9,10](ref.)

20^[10](ref.)

19 (–13)^[9]

n.t.^[10]

18^[10](ref.)

24 (–4)^[9]

n.t.^[10]

ON16 5Ј-T₇LT₆

ON17 5Ј-T₅L₄T₅

ON18 5Ј-L₉T

ON19 5Ј-T₇NT₆

ON20 5Ј-X₃(XN)₄X₂T

48 (+28)^[10]

23 (–7)^[7]

39 (+9)^[7]

57 (+39)^[10]

26 (–3)^[7]

45 (+16)^[7]

[a] Melting temperatures (T_mvalues) recorded in medium salt

buffer using 1.5 μM concentrations of the two complementary

strands. See footnote of Table 1 for further details; see Figure 1 for

the structures of 2Ј-deoxy-XNA thymine monomer X, xylo-LNA

thymine monomer L, 2Ј-amino-xylo-LNA thymine monomer N

and α-L-LNA thymine monomer ^αLT^L.

The 2Ј-amino-xylo-LNA monomer N seems to stabilize

the duplex when compared to other sugar-modified XNAs,

Detrimental effect on the thermal stability of duplexes and it displays many interesting features (Table 2). A single

was also seen by the introduction of a single xylo-LNA mo- incorporation induces depression in the duplex stability

nomer L (Table 2),^[9]even though the furanose conforma- (ON12 relative to ON1, ON19 relative to ON5), but even

tion is locked in an N-type. Upon four consecutive incorpo- with three incorporations in a 9-mer, the destabilization

rations of monomer (L) in the middle of a 14-mer (ON17), against RNA target is limited to 10 °C (ON13 relative to

no transition above 5 °C could be detected.^[10]Apparently, ON1).^[7]Another interesting observation was made when

the unnatural xylo-configuration and phospho diester link- this modification was incorporated together with two affin-

ages are nonideal in stereoirregular oligonucleotides, the ity-enhancing α-L-LNA (^αLT^L)^[9,13]monomers in a 9-mer

other monomers being natural ribo-configured DNA mo- strand with a centrally positioned monomer N (ON14). No

nomers. In contrast, the (almost) fully modified xylo-LNA depression of duplex stability was seen against the DNA

(ON18) displayed very strong binding affinity towards target but an increase of +7 °C was observed against the

DNA and RNA complements (ΔT_m+28 and +39 °C, RNA target (ON14 relative to ON12).^[7]Notably, monomer

respectively)^[10]reflecting the importance of conformation- N, locked in an N-type, can also be combined with dXNA

ally locked furanose configuration on the stability of the X, allowing fine tuning of the hybridization properties of

complexes formed in the case of stereoregular XNAs.

XNAs. This was shown by the chimeric XNA ON20, which

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FULL PAPER

against DNA and RNA targets displayed +2.3 and +1.8 °C modified 4Ј-C-hydroxymethyl-XNA ON31 was less stable

increases in melting temperature per modification, respec- compared to the reference duplex (ON5) or to the 2Ј-deoxy

tively (ON20 relative to ON7).^[7]In contrast, monomer F, counterpart (ON7). Whereas no cooperative transition

conformationally restricted (but not locked) in an N-type, above 5 °C was observed between ON31 and DNA, an as-

showed no affinity enhancement in a similar chimeric se- sociation (T_m= 16 °C) was seen between ON31 and RNA.

quence (ON20 compared to ON11).^[7]Finally, thermal de- As described earlier, recognition of DNA or RNA comple-

naturation studies of 9-mers ON12–ON14 were carried out ments by fully modified homopyrimidine XNAs is due to

under different salt conditions (data not shown), but no sig- triplex formation involving two XNA strands. This mode

nificant changes in ΔT_mvalues were observed indicating of binding is not possible with purine XNAs and it is re-

that an affinity-enhancing electrostatic interaction between flected in the fact that no cooperative transition was de-

the 2Ј-amino group of monomer N and the phosphate tected above 5 °C with ON40 against DNA or RNA targets.

backbone is unlikely, and that the increase in melting tem-

peratures observed with this monomer is most likely due to methyl-DNA in a 9-mer mixed sequence, when hybridized

entropically favoured duplex formation. with a DNA target, was shown to increase the duplex sta-

A single incorporation of 4Ј-C-(N-methylpiperazinyl)-

The XNA monomer H seems to stabilize the duplex bility by 4 °C.^[22]The amino group, presumed to be partially

when compared to its 2Ј-deoxy counterpart X, as it shows protonated at physiological pH, is expected to contribute to

increased binding affinity towards the RNA target, both for overall stabilization of the duplex by interacting with the

one and three incorporations (Table 3, ON21 relative to negatively charged phosphate backbone. However, a pipera-

ON2, ON29 relative to ON6 and ON22 relative to ON3). zinylmethyl group covalently attached to XNA (in mono-

The furanose ring of monomer H is preorganized in an N- mers P and Q) has no stabilizing effect.

type conformation (J_1Ј,2Ј= 2 Hz in compound 12 as an ex-

The J_1Ј,2Јcoupling constants of 5.6 Hz (49a), 5.5 Hz

ample), which may contribute to this effect. Introduction of (49b), 5.3 Hz (63) and 5.1 Hz (64) show that these nucleo-

the 4Ј-C-hydroxymethyl group (monomers M and K) sides are not adopting predominantly an N-type furanose

pointing towards the minor groove, has a negative effect conformation in solution but rather exist in an N h S equi-

on the duplex stability (with one or three incorporations) librium. In addition to steric reasons, this can be another

indicating the possibility of an unfavourable steric interac- explanation for the poor hybridization properties of the

tion involving the 4Ј-C-alkyl branch. Even the (almost) fully corresponding monomers (M, K, P and Q).

Table 3.Thermal^[a]denaturation experiments of duplexes containing XNA monomers H, M, K, P and Q.

110 mm [Na]⁺

DNA target

710 mm [Na]⁺

DNA target

RNA target

T_m(ΔT_m) [°C]

ON1

5Ј-d(GTGATATGC)

5Ј-d(GTGAHATGC)

5Ј-d(GHGAHAHGC)

5Ј-d(GTGAMATGC)

5Ј-d(GMGAMAMGC)

5Ј-d(GTGAPATGC)

5Ј-d(GPGAPAPGC)

5Ј-d(GTGAQATGC)

5Ј-d(GQGAQAQGC)

28^b, 30^c(ref.)

27 (–3)^[c]

n.t.

26 (ref.)

30 (+4)

18 (–8)

22 (–4)

n.t.

20 (–6)

n.t.

32 (ref.)

31 (ref.)

ON21

ON22

ON23

ON24

ON25

ON26

ON27

ON28

18 (–10)^[b]

n.t.

19 (–9)^[b]

n.t.

22 (–10)

n.t.

25 (–7)

n.t.

26 (–5)

n.t.

29 (–2)

18 (–13)

19 (–9)^[b]

n.t.

22 (–4)

n.t.

ON5

5Ј-T₁₄

30 (ref.)

18 (–12)

19 (–11)

n.t.

21 (–9)

n.t.

28 (ref.)

23 (–5)

20 (–8)

16 (–12)

20 (–8)

n.t.

41 (ref.)

35 (ref.)

ON29

ON30

ON31

ON32

ON33

ON34

5Ј-T₇HT₆

5Ј-T₇MT₆

5Ј-M₁₃T

5Ј-T₇PT₆

5Ј-X₃(XP)₄X₂T

5Ј-T₇QT₆

31 (–10)

n.t.

31 (–10)

28 (–7)

n.t.

31 (–4)

19 (–11)

22 (–6)

ON35

ON36

ON37

5Ј-d(GCATATCAC)

5Ј-d(GCATKTCAC)

5Ј-d(GCKTKTCKC)

27 (ref.)

13 (–14)

n.t.

25 (ref.)

16 (–9)

n.t.

34

17 (–17)

n.t.

32

22 (–10)

n.t.

ON38

ON39

ON40

5Ј-A₁₄

5Ј-A₇KA₆

5Ј-K₉A

33 (ref.)

23 (–10)

n.t.

47

37 (–10)

n.t.

25

22 (–3)

n.t.

[a] Melting temperatures (T_mvalues) recorded in medium salt buffer or in high salt buffer (10 mm sodium phosphate, 700 mm sodium

chloride, 0.1 mm EDTA, pH 7.0) using 1.0 μM concentrations of the two complementary strands. See footnote of Table 1 for further

details; see Figure 1 for the structures of 2Ј-deoxy-XNA thymine monomer X, XNA thymine monomer H, 4Ј-C-hydroxymethyl-XNA

monomers M and K and 4Ј-C-piperazinylmethyl-XNA thymine monomers P and Q. [b],[c] Determined in different experimental series.

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XNA (xylo Nucleic Acid): A Summary and New Derivatives

FULL PAPER

tive to 85% H₃PO₄as external standard for ³¹P NMR spectroscopy.

Coupling constants (J values) are given in Hertz. Assignments of

Conclusions

We have described here in detail the synthesis and hy- NMR spectra, when given, are based on 2D spectra. Bicyclic com-

pounds are named according to the von Baeyer nomenclature,

whereas the atom numbering in the assignments follow the stan-

dard carbohydrate/nucleoside nomenclature. Fast atom bombard-

ment mass spectra (FAB-MS) were recorded in positive ion mode

on a Kratos MS50TC spectrometer and MALDI-HRMS were re-

corded in positive ion mode on an IonSpec Fourier Transform mass

spectrometer. The composition of the ONs was verified by

MALDI-MS (negative ion mode) on a Micromass Tof Spec E mass

spectrometer using a matrix of diammonium citrate and 2,6-dihy-

droxyacetophenone.

bridization properties of xylo-configured monomers, i.e.,

conformationally restricted 2Ј-deoxy-2Ј-fluoro-XNA (F)

and XNA (H) monomers, conformationally locked 2Ј-

amino-xylo-LNA monomer (N), 4Ј-C-hydroxymethyl-XNA

monomers (M and K) and 4Ј-C-piperazinylmethyl-XNA

monomers (P and Q). We have also described a signifi-

cantly improved synthesis of xylo-LNA phosphoramidite

19 with an overall yield of 10% starting from commercially

available 1,2:5,6-di-O-isopropylidine-α-d-allofuranose. Mo-

nomers M, K, P and Q were synthesised starting from fu-

ranose triol 43, the key step being the stereoselective si-

lylation of the triol 43 to yield furanose 44 in 93% yield.

Various bicyclonucleosides and 4Јα-branched xylo-config-

1-O-Acetyl-2-deoxy-2-fluoro-3,5-di-O-benzoyl-α,β-D-xylofuranose

(3): To a solution of 2-deoxy-3,5-di-O-benzoyl-2-fluoro-β-d-xylofu-

ranoside (2)^[24](709 mg, 1.89 mmol) in a mixture of AcOH and

Ac₂O (7.76 cm³, 3.8:1, v/v) was added concd. H₂SO₄(0.3 cm³) and

ured nucleoside analogues can be synthesised starting from the resulting mixture was stirred at room temp. for 75 min. Then

reaction mixture was slowly poured into ice-cold saturated aq.

NaHCO₃(500 cm³) under vigorous stirring and extraction was per-

formed by CHCl₃(3×150 cm³). The combined organic phase was

washed successively with satd. aqueous NaHCO₃(5×150 cm³) and

H₂O (2×100 cm³), dried, evaporated to dryness and coevaporated

with a mixture of toluene/EtOH (4×50 cm³, 1:1, v/v) to give 0.74 g

(97%) of anomeric mixture 3 as a yellow syrup which was used

in next step without additional purification. R_f0.32 (EtOAc/light

petroleum, 20:80, v/v). ¹H NMR (CDCl₃): δ = 8.09–7.38 (m, 20

H), 6.51 (dd, J = 2.0 and 4.4 Hz, 1 H, 1-Hα), 6.40 (d, J = 12.4 Hz,

intermediate 44. The furanose ring of monomers F and H

adopts an N-type conformation, whereas the furanose ring

in monomers M, K, P and Q likely exists in as N h S

equilibrium. Thermal denaturation studies show that con-

formational restriction of XNA monomers leads to im-

proved binding affinity as most clearly observed for XNAs

ON12, ON14, ON18 and ON20 containing locked xylo-

LNA monomers (N and L). Hybridization data of nine-

mer mixed-base sequences composed of a mixture of XNA

monomers and DNA monomers revealed preferential hy- 1 H, 1-Hβ), 5.97–5.78 (m, 2 H, 3-H), 5.38 (ddd, J = 4.8, 4.9 and

51.7 Hz, 1 H, 2-Hα), 5.20 (dd, J = 0.8 and 48.6 Hz, 1 H, 2-Hβ),

5.00–4.91 (m, 2 H, 4-H), 4.63–4.49 and 4.27–4.17 (m, 4 H, 5-H),

2.18 and 2.09 (3H each, 2s, 2×COCH₃) ppm. ¹³C NMR (CDCl₃,

β-anomer): δ = 169.1, 166.0, 164.9, 133.9, 133.2, 129.8, 129.7,

129.4, 128.6, 128.3, 98.1 (d, J = 25.2 Hz), 97.1 (d, J 247.1), 79.9,

74.0 (d, J = 30.3 Hz), 62.6, 21.0 ppm. MALDI-HRMS: m/z

425.3532 ([M + Na]⁺, C₂₁H₁₉FO₇Na⁺calcd. 425.3539).

bridization towards RNA complements relative to DNA

complements. Importantly, different monomeric nucleo-

tides, including different XNA monomers and LNA mono-

mers, can be combined, allowing fine-tuning of the hybrid-

ization properties of chimeric XNAs (e.g., ON11, ON14

and ON20). It is clear from the results described earlier and

herein that high-affinity targeting of homopurine DNA or

RNA targets can be achieved via triplex formation using

homopyrimidine XNAs; Mixed-sequence target sites, most

efficiently RNA sequences, can be targeted efficiently by

using chimera of XNA monomers and affinity-enhancing

monomers, e.g., LNA or α-L-LNA monomers.

1-(2-Deoxy-2-fluoro-β-D-xylofuranosyl)thymine (5b) and α-Anomer

5a: To a solution of anomeric mixture 3 (803 mg, 2.0 mmol) and

bis(O-trimethylsilyl)thymine [obtained from thymine (277 mg,

2.2 mmol)] in anhydrous 1,2-dichloroethane (30 cm³) was added

TMS-triflate (1.2 cm³, 1.47 g, 6.63 mmol) and the mixture was re-

fluxed for 3 h. The reaction mixture was cooled to room temp.,

diluted with CHCl₃(100 cm³) and washed successively with satu-

rated aq. NaHCO₃(3×75 cm³) and H₂O (100 cm³). The organic

layer was separated, dried and the solvents evaporated to dryness

and the residue obtained was dissolved in a minimum volume of

abs. EtOH and kept in the refrigirator for 3 h. The crystals formed

were filtered, washed with cold EtOH and dried to give 373 mg

(40%) of 4b. R_f0.71 (CHCl₃/EtOH, 20:1, v/v). The mother liquor

was evaporated to dryness under reduced pressure. The residue

(476 mg) was purified by column chromatography using a linear

gradient [0–5% (v/v) MeOH in CHCl₃]. First eluted additional

88 mg (9%) of 4b followed by 120 mg of an inseparable mixture of

Experimental Section

General: Reactions were conducted under nitrogen when anhydrous

solvents were used. All reactions were monitored by thin-layer

chromatography (TLC) using silica-coated plates with fluorescence

indicator (SiO₂-60, F-254) and visualizing under UV light and by

spraying with 5% concd. sulfuric acid in ethanol (v/v) followed by

heating. Silica gel 60 (particle size 0.040–0.063 mm, Merck) was

used for flash column chromatography and Silica gel 60 (particle

size 0.015–0.040 mm, Merck) was used for Dry Column Vacuum 4a and 4b and finally 220 mg (24%) of 4a as a white foam. R_f0.63

Chromatography (DCVC).^[33]Light petroleum of the distillation

range 60–80 °C was used. After column chromatography fractions

containing product were pooled, evaporated to dryness under re-

duced pressure and dried for 12 h under vacuum to give the pro-

duct unless otherwise specified. ¹H NMR spectra were recorded at

(CHCl₃/EtOH, 20:1, v/v). Compound 4b (430 mg, 0.92 mmol) was

stirred with saturated ammonia in MeOH (25 cm³) at room temp.

for 12 h. The reaction mixture was evaporated to dryness under

reduced pressure. The residue obtained was purified by column

chromatography using a linear gradient [0–10% (v/v) MeOH in

300 MHz, ¹³C NMR spectra at 75.5 MHz, and ³¹P NMR spectra CHCl₃] to give 200 mg (83%) of 5b as a colourless syrup. R_f0.35

at 121.5 MHz (unless otherwise stated). Chemical shifts are re-

ported in ppm relative to either tetramethylsilane or the deuterated

solvent as internal standard for ¹H NMR and ¹³C NMR, and rela-

(CHCl₃/EtOH, 90:10, v/v). ¹H NMR (CD₃OD): δ = 7.71 (d, J =

1.1 Hz, 1 H, 6-H), 6.02 (d, J = 21.4 Hz, 1 H, 1Ј-H), 4.95 (d, J =

49.4 Hz, 1 H, 2Ј-H), 4.35 (dd, J = 3.3 and 10.4 Hz, 1 H, 3Ј-H),

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J. Wengel et al.

FULL PAPER

4.23 (ddd, J = 3.3, 6.0 and 8.8 Hz, 1 H, 4Ј-H), 4.00–3.86 (m, 2 H, (s, 1 H, 1Ј-H), 5.10 (s, 1 H, 2Ј-H), 4.31 (m, 1 H, 4Ј-H), 4.19 (br. s,

5Ј-H), 1.86 (d, J = 1.1 Hz, 3 H, 5-CH₃) ppm. ¹³C NMR (CD₃OD): 2 H, 5Ј-H), 4.03 (m, 1 H, 3Ј-H), 2.14 (s, 3 H, COCH₃), 1.95 (s, 3

δ = 163.4, 152.3, 138.5, 110.9, 100.6 (d, J 184.9), 90.4 (d, J =

36.4 Hz), 85.0, 73.8 (d, J = 26.3 Hz), 60.7, 12.6 ppm. MALDI-

HRMS: m/z 283.2153 ([M + Na]⁺, C₁₀H₁₃FN₂O₅Na⁺calcd.

283.2088). Similar debenzoylation of 220 mg (0.47 mmol) of 4a

with saturated ammonia in MeOH (15 cm³) and subsequent

crystallization of the residue from EtOH afforded 91 mg (75%) of

5a as colourless crystals. R_f0.27 (CHCl₃/EtOH, 90:10, v/v). ¹H

NMR (CD₃OD): δ = 7.45 (s, 1 H, 6-H), 6.24 (dd, J = 3.3 and

21.4 Hz, 1 H, 1Ј-H), 5.03 (dd, J = 3.3 and 51.1 Hz, 1 H, 2Ј-H),

4.67–4.64 (m, 2 H, 3Ј-H and 4Ј-H), 3.86 and 3.84 (1H each, 2s, 5Ј-

H), 1.89 (s, 3 H, 5-CH₃) ppm. ¹³C NMR (CD₃OD): δ = 166.4,

152.1, 138.3 (d, J = 2.9 Hz), 110.6, 96.0 (d, J 191.2), 86.9 (d, J =

14.9 Hz), 84.2, 74.6 (d, J = 24.6 Hz), 61.4, 12.4 ppm. MALDI-

HRMS: m/z 283.2033 ([M + Na]⁺, C₁₀H₁₃FN₂O₅Na⁺calcd.

283.2088).

H, 5-CH₃), 1.48 and 1.41 [2s, 3 H each, CH₃(isopropylidene)] ppm.

¹³C NMR (CDCl₃): δ = 169.1, 163.8, 150.2, 136.6, 110.1, 98.2, 89.0,

81.7, 77.2, 73.8, 72.2, 59.9, 28.7, 20.7, 18.5, 12.5 ppm. MALDI-

HRMS: m/z 363.3063 ([M

363.3183).

+

Na]⁺, C₁₅H₂₀N₂O₇Na⁺calcd.

1-(2-O-Acetyl-β-D-xylofuranosyl)thymine (10): A solution of nucle-

oside 9 (251 mg, 0.74 mmol) in 80% AcOH was heated at 65 °C

for 2 h and stirred at room temp. for another 12 h. The reaction

mixture was concentrated to dryness under reduced pressure and

the residue was coevaporated with a mixture of toluene and EtOH

(1:1, v/v, 5×30 cm³). The residue was purified by column

chromatography [1–2% (v/v) EtOH in CHCl₃] to yield 185 mg

(84%) of diol 10 as a colourless syrup. R_f0.1 (CHCl₃/EtOH, 20:1,

v/v). ¹H NMR ([D₆]DMSO): δ = 11.35 (br. s, 1 H), 7.68 (d, J =

1.0 Hz, 1 H), 5.85–5.82 (m, 2 H), 4.95–4.85 (m, 2 H), 4.20 (m, 1

H), 4.01 (m, 1 H), 3.77–3.64 (m, 2 H), 2.08 (s, 3 H), 1.77 (d, J =

1.0 Hz, 3 H) ppm. ¹³C NMR ([D₆]DMSO): δ = 169.4, 163.3, 150.3,

136.5, 109.2, 87.3, 83.0, 81.7, 72.0, 58.8, 20.5, 12.4 ppm. MALDI-

1-[2-Deoxy-5-O-(4,4Ј-dimethoxytrityl)-2-fluoro-β-D-xylofuranosyl]-

thymine (6): To a solution of nucleoside 5b (299 mg, 1.15 mmol) in

anhydrous pyridine (20 cm³) was added dimethoxytrityl chloride

(410 mg, 1.21 mmol) and the mixture was stirred at room temp. for

14 h. The reaction mixture was evaporated to dryness and the resi-

due obtained was dissolved in CHCl₃(100 cm³) and washed suc-

cessively with saturated aq. NaHCO₃(3×50 cm³) and H₂O

(2×50 cm³). The organic layer was separated, dried and the sol-

vents evaporated to dryness under reduced pressure. The crude pro-

duct obtained was purified by column chromatography using a lin-

ear gradient [0–5% (v/v) MeOH in CHCl₃] to give 584 mg (90%)

of nucleoside 6 as a yellow foam. R_f0.57 (CHCl₃/EtOH, 20:1, v/

v). ¹H NMR (CDCl₃): δ = 7.50–7.30 (m, 10 H), 6.86–6.83 (m, 4

H), 6.01 (d, J = 20.9 Hz, 1 H, 1Ј-H), 5.11 (d, J = 48.4 Hz, 1 H, 2Ј-

H), 4.37–4.34 (m, 2 H, 3Ј-H and 4Ј-H), 3.78 (s, 6 H, 2×OCH₃),

3.67–3.58 (m, 2 H, 5Ј-H), 1.72 (s, 3 H, 5-CH₃) ppm. ¹³C NMR

(CDCl₃): δ = 164.1, 158.7, 150.6, 144.2, 137.1, 135.2 (d, J = 4.0 Hz),

130.0, 129.9, 128.0, 127.9, 127.0, 113.3, 110.0, 98.2 (d, J =

185.5 Hz), 90.0 (d, J = 38.4 Hz), 87.1, 81.9, 73.9 (d, J = 28.1 Hz),

61.7, 55.2, 12.4 ppm. MALDI-HRMS: m/z 585.5699 ([M + Na]⁺,

C₃₁H₃₁FN₂O₇Na⁺calcd. 585.5752).

HRMS: m/z 323.2456 ([M

+

Na]⁺, C₁₂H₁₆N₂O₇Na⁺calcd.

323.2544).

1-[2-O-Acetyl-5-O-(4,4Ј-dimethoxytrityl)-β-

D-xylofuranosyl]thymine

(11): To a solution of nucleoside 10 (108 mg, 0.36 mmol) in anhy-

drous pyridine (5 cm³) was added dimethoxytrityl chloride (135 mg,

0.4 mmol) and the resulting mixture was stirred for 12 h at room

temp. The reaction mixture was poured with vigorous stirring into

ice-cold saturated aq. NaHCO₃(100 cm³) and was extracted with

CHCl₃(3×50 cm³). The organic phase was dried and the solvents

evaporated to dryness under reduced pressure. The residue ob-

tained was purified by column chromatography (CHCl₃) to afford

196 mg (90%) of nucleoside 11 as a yellow syrup. R_f0.39 (CHCl₃/

EtOH, 20:1, v/v). ¹H NMR (CDCl₃): δ = 9.14 (br. s, 1 H, NH),

7.50–7.20 (m, 10 H), 6.85–6.82 (m, 4 H), 5.88 (d, J = 2.0 Hz, 1 H,

1Ј-H), 5.13 (m, 1 H, 2Ј-H), 4.22–4.20 (m, 2 H, 3Ј-H and 4Ј-H), 3.78

(s, 6 H, 2×OCH₃), 3.61–3.51 (m, 2 H, 5Ј-H), 2.11 (s, 3 H, COCH₃),

1.80 (d, J = 0.7 Hz, 5-CH₃, 3 H) ppm. ¹³C NMR (CDCl₃): δ =

169.9, 164.1, 158.6, 158.5, 150.4, 144.2, 137.1, 135.3, 130.0, 129.9,

129.1, 127.9, 127.7, 127.6, 127.0, 113.2, 113.1, 110.6, 89.5, 86.9,

82.1, 81.2, 74.5, 61.6, 55.2, 20.7, 12.3 ppm. MALDI-HRMS: m/z

625.6186 ([M + Na]⁺, C₃₃H₃₄N₂O₉Na⁺calcd. 625.6208).

1-{3-O-[2-Cyanoethoxy(diisopropylamino)phosphanyl]-2-O-deoxy-5-

O-(4,4Ј-dimethoxytrityl)-2-fluoro-β-D-xylofuranosyl}thymine (7): 2-

Cyanoethyl N,N-diisopropylphosphoramidochloridite (213 mg,

0.9 mmol) was added dropwise to a stirred solution of nucleoside

6 (338 mg, 0.6 mmol) and diisopropylethylamine (1.0 cm³) in anhy-

drous CH₂Cl₂(5.0 cm³). After stirring for 30 min at room temp.,

the reaction mixture was diluted with EtOAc (50 cm³). Washing

was performed with saturated aq. NaHCO₃(2×25 cm³). The sepa-

rated organic phase was dried (Na₂SO₄), filtered and concentrated

under reduced pressure. The residue obtained was purified by col-

umn chromatography using a linear gradient [10–60% EtOAc in

light petroleum, containing 0.5% Et₃N (v/v/v)] to give amidite 7 as

a white foam (370 mg, 81%). R_f0.73 and 0.58 (EtOAc/CH₂Cl₂/

Et₃N, 50:50:5, v/v/v). ³¹P NMR (CDCl₃): δ = 153.8, 151.2 ppm.

1-{2-O-Acetyl-3-O-[2-cyanoethoxy(diisopropylamino)phosphanyl]-5-

O-(4,4Ј-dimethoxytrityl)-β-D-xylofuranosyl}thymine (12): Phosphit-

ylation of nucleoside 11 (362 mg, 0.6 mmol) with 2-cyanoethyl

N,N-diisopropylphosphoramidochloridite (213 mg, 0.9 mmol) in

the presence of diisopropylethylamine (1.0 cm³) in anhydrous

CH₂Cl₂(5.0 cm³), followed by work-up as described above for am-

idite 7 and purification by column chromatography using a linear

gradient [25–100% EtOAc in light petroleum, containing 0.5%

Et₃N (v/v/v)] afforded amidite 12 as a white foam (420 mg, 87%).

R_f0.67 and 0.52 (EtOAc/CH₂Cl₂/Et₃N, 50:50:5, v/v/v). ³¹P NMR

(CH₃CN): δ = 154.3, 149.9 ppm.

1-(2-O-Acetyl-3,5-O-isopropylidene-β-

D-xylofuranosyl)thymine (9):

1-[2-O-Acetyl-3-O-benzyl-5-O-(methylsulfonyl)-4-C-(methylsulfonyl-

To a solution of 1-(3,5-O-isopropylidene-β-d-xylofuranosyl)thy-

mine (8)^[29](261 mg, 0.88 mmol) in anhydrous pyridine (3.0 cm³)

was added Ac₂O (0.2 cm³) and the resulting mixture was stirred at

room temp. for 12 h. The reaction mixture was evaporated to dry-

ness under reduced pressure and coevaporated with a mixture of

oxymethyl)-α-L-threo-pentofuranosyl]thymine (15): To a solution of

an anomeric mixture of 3-O-benzyl-1,2-di-O-acetyl-5-O-(methylsul-

fonyl)-4-C-(methylsulfonyloxymethyl)-α,β-l-threo-pentofuranose

(14)^[32](2.04 g, 4.0 mmol) in acetonitrile (60 cm³) was added thy-

mine (0.57 g, 4.5 mmol) and N,O-bis(trimethylsilyl)acetamide

toluene and EtOH (1:1, v/v, 6×25 cm³) affording 270 mg (97%) of (2.2 cm³, 1.83 g, 9.0 mmol). The reaction mixture was refluxed for

nucleoside 10 as white foam which was used in the next step with-

out further purification. R_f0.47 (CHCl₃/EtOH, 20:1, v/v). ¹H

NMR (CDCl₃): δ = 8.84 (br. s, 1 H, NH), 7.87 (s, 1 H, 6-H), 6.01

40 min to give a clear solution and then cooled to room temp.

TMS-triflate (2.17 cm³, 2.67 g, 12.0 mmol) was added and the re-

sulting mixture refluxed for 3 h. The reaction mixture was concen-

2308

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Eur. J. Org. Chem. 2005, 2297–2321

XNA (xylo Nucleic Acid): A Summary and New Derivatives

FULL PAPER

trated to dryness under reduced pressure and redissolved in CHCl₃

(500 cm³), washed successively with saturated aq. NaHCO₃

(3×100 cm³) and H₂O (100 cm³), dried and then concentrated to

dryness in vacuo. The residue obtained was purified by column

chromatography (CHCl₃) and then crystallized from EtOH to give

1.89g (72%) of nucleoside 15. R_f0.21 (CHCl₃/EtOH, 20:1, v/v). ¹H

NMR (CDCl₃): δ = 9.36 (s, 1 H, NH), 7.42–7.31 (m, 6 H), 6.29 (d,

J = 3.6 Hz, 1 H, 1Ј-H), 5.36 (dd, J = 2.8 Hz and 3.6, 1 H, 2Ј-H),

4.78 (d, J = 11.3 Hz, 1 H), 4.66 (d, J = 11.3 Hz, 1 H), 4.55 (d, J =

11.2 Hz, 1 H), 4.42 (d, J = 11.2 Hz, 1 H), 4.35 (d, J = 10.7 Hz, 1

H), 4.26 (d, J = 10.7 Hz, 1 H), 4.25 (d, J = 2.8 Hz, 1 H, 3Ј-H), 3.05

and 3.03 (3 H each, 2s, 2×SO₂CH₃), 2.14 (s, 3 H, COCH₃), 1.80

(d, J = 1.0 Hz, 3 H, 5-CH₃) ppm. ¹³C NMR (CDCl₃): δ = 169.8,

163.5, 150.4, 135.8, 135.1, 128.7, 128.7, 128.4, 112.4, 87.6, 84.7,

81.1, 79.4, 73.1, 67.0, 65.4, 37.6, 20.6, 12.3 ppm. MALDI-HRMS:

m/z 599.5180 ([M + Na]⁺, C₂₂H₂₈N₂O₁₂S₂Na⁺calcd. 599.5209).

propylethylamine (1.0 cm³) and anhydrous CH₂Cl₂(5.0 cm³), fol-

lowed by work-up procedure as described above for amidite 7 and

purification by column chromatography using a linear gradient

[25–100% EtOAc in light petroleum, containing 0.5% Et₃N (v/v/

v)] afforded amidite 19 as a white foam (381 mg, 82%) identical in

all the respects with the sample synthesized previously.^[9]

1-[3-O-Benzyl-5-O-(methylsulfonyl)-4-C-(methylsulfonyloxymethyl)-

α-L-threo-pentofuranosyl]thymine (20): Nucleoside 15 (16.18 g,

28.1 mmol) was dissolved in ice-cold saturated methanolic ammo-

nia (250 cm³), where upon the stirred mixture was warmed to room

temp. over a period of 45 min. The reaction mixture was evaporated

to dryness in vacuo. The residue was purified by DCVC [90–100%

(v/v) EtOAc in n-heptane] to give nucleoside 20 (14.0 g, 93%) as a

1

white foam. R_f0.37 (EtOAc/n-heptane, 90:10, v/v). H NMR ([D₆]

DMSO): δ = 11.41 (br. s, 1 H, NH), 7.62 (d, J = 1.1 Hz, 1 H, 6-

H), 7.42–7.28 (m, 5 H), 6.09 (d, J = 5.3 Hz, 1 H, 2Ј-OH), 5.93 (d,

J = 7.3 Hz, 1 H, 1Ј-H), 4.77 [d, J = 11.7 Hz, 1 H, CH₂Ph(a)], 4.69

[d, J = 11.7 Hz, 1 H, CH₂Ph(b)], 4.53 (d, J = 10.6 Hz, 1 H, 5Ј-Ha),

4.48 (ddd, J = 5.3, 5.5 and 6.8 Hz, 1 H, 2Ј-H), 4.41 (d, J = 10.6 Hz,

1 H, 5ЈЈ-Ha), 4.34 (d, J = 10.6 Hz, 1 H, 5Ј-Hb), 4.33 (d, J =

10.6 Hz, 1 H, 5ЈЈ-Hb), 4.22 (d, J = 5.5 Hz, 1 H, 3Ј-H), 3.24 (s, 3

(1S,3R,4R,7R)-7-Benzyloxy-1-(hydroxymethyl)-3-(thymin-1-yl)-2,5-

dioxabicyclo[2.2.1]heptane (16): To a solution of the nucleoside 15

(1.3 g, 2.25 mmol) in EtOH (60 cm³) was added H₂O (6 cm³) and

NaOH pallets (0.5 g, 12.5 mmol). The reaction mixture was re-

fluxed during 60 h, neutralized by adding solid CO₂and the sol-

vents evaporated to dryness. The residue obtained was purified by

column chromatography using a linear gradient (0–10% (v/v)

EtOH in CHCl₃) to yield 0.62 g (76%) of nucleoside 16 as a white

foam. R_f0.08 (CHCl₃/EtOH, 20:1, v/v). ¹H NMR (CDCl₃): δ =

9.57 (br. s, 1 H), 7.42–7.11 (m, 6 H), 5.70 (s, 1 H), 4.56 (d, J =

1.7 Hz, 1 H), 4.49 (d, J = 11.0 Hz, 1 H), 4.31 (d, J = 11.0 Hz, 1

H), 4.17 (d, J = 12.1 Hz, 1 H), 4.12–4.07 (m, 3 H), 3.94 (d, J =

12.1 Hz, 1 H), 1.60 (s, 3 H, 5-CH₃) ppm. ¹³C NMR (CDCl₃): δ =

164.5, 150.2, 136.9, 136.0, 128.5, 128.3, 127.7, 108.2, 88.9, 88.4,

79.9, 76.2, 73.0, 58.5, 12.1 ppm. MALDI-HRMS: m/z 383.3414

([M + Na]⁺, C₁₈H₂₀N₂O₆Na⁺calcd. 383.3510).

H, SO₂CH₃), 3.17 (s, 3 H, SO₂CH₃), 1.76 (s, 3 H, 5-CH₃) ppm. ¹³

C

NMR ([D₆]DMSO): δ = 163.6 (C-4), 150.9 (C-2), 137.7, 135.8 (C-

6), 128.3, 127.8, 127.7, 110.4 (C-5), 85.4 (C-1Ј), 82.8 (C-3Ј), 80.7

(C-4Ј), 75.8 (C-2Ј), 72.4 (CH₂Ph), 69.2 and 68.6 (C-5Ј and C-5ЈЈ),

36.7 and 36.6 (2×SO₂CH₃), 12.0 (5-CH₃) ppm. ESI-MS: m/z 535.1

+

([MH]⁺, C₂₀H₂₇N₂O₁₁S₂calcd. 535.1).

1-[3-O-Benzyl-2,5-di-O-(methylsulfonyl)-4-C-(methylsulfonyloxy-

methyl)-α-L-threo-pentofuranosyl]thymine (21): To a solution of nu-

cleoside 20 (13.98 g, 26.2 mmol) in anhydrous pyridine (50 cm³) at

0 °C, was added methanesulfonyl chloride (4.1 cm³, 52.3 mmol).

The reaction mixture was stirred for 4 h, then ethyl acetate

(200 cm³) was added and the reaction mixture was washed with

saturated aq. NaHCO₃(4×100 cm³). The organic phase was dried

(Na₂SO₄), filtered and the solvent removed in vacuo. The residue

was purified by DCVC [90–100% (v/v) EtcOAc in n-heptane] to

give nucleoside 21 (13.8 g, 86%) as a white foam. R_f0.41 (EtOAc/

n-heptane, 90:10, v/v); ¹H NMR (CDCl₃): δ = 9.39 (br. s, 1 H, NH),

7.40–7.28 (m, 6 H), 6.14 (d, J = 3.4 Hz, 1 H, 1Ј-H), 5.29 (t, J =

3.4 Hz, 1 H, 2Ј-H), 4.75 [d, J = 11.4 Hz, 1 H, CH₂Ph(a)], 4.65 [d,

J = 11.4 Hz, 1 H, CH₂Ph(b)], 4.61 (d, J = 11.2 Hz, 1 H), 4.43 (d,

J = 3.4 Hz, 1 H, 3Ј-H), 4.38 (d, J = 11.2 Hz, 1 H), 4.33 (d, J =

10.8 Hz, 1 H), 4.24 (d, J = 10.8 Hz, 1 H), 3.19 (s, 3 H, SO₂CH₃),

3.05 (s, 3 H, SO₂CH₃), 3.02 (s, 3 H, SO₂CH₃), 1.86 (s, 3 H, 5-CH₃)

ppm. ¹³C NMR (CDCl₃): δ = 163.3 (C-4), 150.5 (C-2), 135.6, 134.6

(C-6), 128.7, 128.7, 128.3, 112.2 (C-5), 88.0 (C-1Ј), 85.1 (C-4Ј), 83.1

(C-2Ј), 80.9 (C-3Ј), 73.3 (CH₂Ph), 66.6 and 66.2 (C-5Ј and C-5ЈЈ),

38.7, 37.6 and 37.5 (3 × SO₂CH₃), 12.2 (5-CH₃) ppm. ESI-MS:

m/z 635.1 ([M + Na]⁺, C₂₁H₂₈N₂O₁₃S₃Na⁺calcd. 635.1).

(1R,3R,4R,7R)-7-Benzyloxy-1-[(4,4Ј-dimethoxytrityl)oxymethyl]-3-

(thymin-1-yl)-2,5-dioxabicyclo[2.2.1]heptane (17): To a solution of

nucleoside 16 (0.6 g, 1.66 mmol) in anhydrous pyridine (20 cm³)

was added freshly crystallized DMTCl (0.62 g, 1.83 mmol) and the

resulting mixture was stirred at room temp. for 12 h. The reaction

mixture was evaporated to dryness under reduced pressure and dis-

solved in CHCl₃(200 cm³), washed successively with saturated aq.

NaHCO₃(3×75 cm³), H₂O (100 cm³) and brine (50 cm³) and dried

(Na₂SO₄). The organic phase was concentrated to dryness and the

residue obtained was purified by column chromatography using a

linear gradient [10–50% (v/v) EtOAc in light petroleum] to afford

1.05 g (95%) of nucleoside 17 as a white foam. R_f0.1 (EtOAc/light

petroleum, 60:40, v/v). All analytical data were identical to those

previously reported.^[30]

(1R,3R,4R,7R)-1-[(4,4Ј-Dimethoxytrityl)oxymethyl]-7-hydroxy-3-(thy-

min-1-yl)-2,5-dioxabicyclo[2.2.1]heptane (18): To a solution of nu-

cleoside 17 (663 mg, 1.0 mmol) in a mixture of EtOAc and abs.

EtOH (30 cm³, 9:1, v/v) was added 10% Pd(OH)₂/C (500 mg). The

mixture was stirred under hydrogen at 70 °C for 28 h. The catalyst

was filtered off and washed with a mixture of EtOAc and EtOH

(2×30 cm³, 9:1, v/v). The combined filtrate was evaporated to dry-

ness and the residue obtained was purified by column chromatog-

raphy using a linear gradient (0–5% (v/v) MeOH in CHCl₃) to give

384 mg (67%) of nucleoside 18. All analytical data were identical

to those previously reported.^[9]

2,2Ј-Anhydro-1-[3-O-benzyl-5-O-(methylsulfonyl)-4-C-(methylsulfo-

nyloxymethyl)-α-L-erythro-pentofuranosyl]thymine (22): To a solu-

tion of nucleoside 21 (12.72 g, 20.8 mmol) in anhydrous acetonitrile

(150 cm³) was added DBU (3.42 cm³, 22.84 mmol) and the reaction

mixture was stirred for 1.5 h during which extensive precipitation

of nucleoside 22 occurred. The reaction mixture was cooled to

–20 °C and filtered. The precipitate was washed several times with

MeOH affording nucleoside 22 (9.57 g, 89%) as a white solid mate-

1

(1R,3R,4R,7R)-7-[2-Cyanoethoxy(diisopropylamino)phosphanyl-

oxy]-1-[(4,4Ј-dimethoxytrityl)oxymethyl]-3-(thymin-1-yl)-2,5-dioxa-

bicyclo[2.2.1]heptane (19): Phosphitilation of nucleoside 18

(344 mg, 0.6 mmol) with 2-cyanoethyl N,N-diisopropylphos-

phoramidochloridite (213 mg, 0.9 mmol) in the presence of diiso-

rial. R_f0.39 (MeOH/CH₂Cl₂,10:90, v/v). H NMR ([D₆]DMSO): δ

= 7.79 (d, J = 1.3 Hz, 1 H, 6-H), 7.45–7.32 (m, 5 H), 6.31 (d, J =

5.7 Hz, 1 H, 1Ј-H), 5.61 (t, J = 5.7 Hz, 1 H, 2Ј-H), 4.77 [d, J =

11.5 Hz, 1 H, CH₂Ph(a)], 4.68 [d, J = 11.5 Hz, 1 H, CH₂Ph(b)],

4.48 (d, J = 5.7 Hz, 1 H, 3Ј-H), 4.38 (d, J = 10.9 Hz, 1 H), 4.32 (d,

Eur. J. Org. Chem. 2005, 2297–2321

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2309

J. Wengel et al.

FULL PAPER

J = 10.9 Hz, 1 H), 4.23 (d, J = 11.5 Hz, 1 H), 4.05 (d, J = 11.5 Hz, 10.8 Hz, 1 H), 4.48 (d, J = 10.8 Hz, 1 H), 4.43–4.37 (m, 3 H), 3.27

1 H), 3.25 (s, 3 H, SO₂CH₃), 3.06 (s, 3 H, SO₂CH₃), 1.79 (s, 3 H, (s, 3 H, SO₂CH₃), 3.19 (s, 3 H, SO₂CH₃), 1.79 (s, 3 H, 5-CH₃) ppm.

5-CH₃) ppm. ¹³C NMR ([D₆]DMSO): δ = 171.3 (C-4), 159.7 (C- ¹³C NMR ([D₆]DMSO): δ = 163.5, 150.7, 137.1, 135.3, 128.4,

2), 137.0, 131.9 (C-6), 128.4, 128.1, 128.0, 117.1 (C-5), 89.4 (C-1Ј),

84.0 (C-4Ј), 80.1 (C-2Ј), 78.8 (C-3Ј), 72.8 (CH₂Ph), 68.9 and 67.6

(C-5Ј and C-5ЈЈ), 37.0 and 36.9 (2×SO₂CH₃), 13.6 (5-CH₃) ppm.

ESI-MS: m/z 517.1 ([MH]⁺, calcd. 517.1). C₂₀H₂₄N₂O₁₀S₂: calcd.

C 46.50, H 4.68, N 5.42; found C 46.27, H 4.54, N 5.43.

128.1, 127.9, 110.9, 82.9, 82.1, 81.1, 73.1, 69.1, 68.1, 65.1, 36.8, 12.1

ppm. ESI-MS: m/z 558.1 ([M – H]^–, C₂₀H₂₄N₅O₁₀S₂^–calcd. 558.1).

(1R,3R,4R,7R)-7-Benzyloxy-1-(methylsulfonyloxymethyl)-3-(thy-

min-1-yl)-2-oxa-5-azabicyclo[2.2.1]heptane (25): To a solution of

nucleoside 24 (1.74 g) in THF (90 cm³) was added aq. NaOH

(2.0 m, 31 cm³, 62 mmol) and trimethylphosphane in THF (1.0 m,

6.2 cm³, 6.2 mmol). After stirring the reaction mixture for 72 h, it

was evaporated to approximately half volume in vacuo and brine

(100 cm³) was added. The aqueous phase was extracted with ethyl

acetate (2×150 cm³) and CH₂Cl₂(6×150 cm³). TLC analysis of

the aqueous phase indicated the presence of product so it was evap-

orated to dryness in vacuo and the residue was extracted with

MeOH (3 × 150 cm³). The two combined organic phases were

mixed and concentrated to dryness under reduced pressure. The

residue was purified by DCVC [3–10% (v/v) MeOH in CH₂Cl₂] to

give nucleoside 25 (1.1 g, 53 % from 23) as white foam. R_f0.3

1-[3-O-Benzyl-5-O-(methylsulfonyl)-4-C-(methylsulfonyloxymethyl)-

α-L-erythro-pentofuranosyl]thymine (23): Nucleoside 22 (8.87 g,

17.2 mmol) was dissolved in a mixture of aqueous H₂SO₄(0.4 m,

300 cm³) and acetone (300 cm³) and refluxed for 14 h with stirring.

After cooling to room temp. the reaction mixture was evaporated

to approx. half the volume under reduced pressure and cooled to

–20 °C, which resulted in the precipitation of nucleoside 23. The

white precipitate was filtered and washed thoroughly with H₂O af-

fording nucleoside 23 (9.0 g, 98%) as a white solid material. R_f0.51

1

(MeOH/CH₂Cl₂,10:90, v/v). H NMR (CDCl₃): δ = 10.99 (br. s, 1

H, NH), 7.86 (d, J = 1.1 Hz, 1 H, 6-H), 7.43–7.32 (m, 5 H), 6.11

(d, J = 3.4 Hz, 1 H, 1Ј-H), 5.20 [d, J = 11.9 Hz, 1 H, CH₂Ph(a)],

5.11 (br. s, 1 H, 2Ј-H), 4.86 (d, J = 12.0 Hz, 1 H), 4.61 (d, J =

11.9 Hz, 1 H), 4.44 (d, J = 4.2 Hz, 1 H, 3Ј-H), 4.43 (d, J = 10.8 Hz,

1 H), 4.37 [d, J = 12.0 Hz, 1 H, CH₂Ph(b)], 4.27 (d, J = 10.8 Hz,

1 H), 3.08 (s, 3 H, SO₂CH₃), 2.89 (s, 3 H, SO₂CH₃), 1.95 (s, 1 H,

2Ј-OH), 1.83 (s, 3 H, 5-CH₃) ppm. ¹³C NMR (CDCl₃): δ = 166.1

(C-4), 150.4 (C-2), 139.4 (C-6), 136.7, 128.5, 128.3, 128.0, 108.5 (C-

5), 87.1 (C-1Ј), 82.3 (C-4Ј), 77.8 (C-3Ј), 72.0 (CH₂Ph), 69.3 (C-2Ј),

68.5 and 67.8 (C-5Ј and C-5ЈЈ), 37.8 and 37.3 (2×SO₂CH₃), 11.8

(5-CH₃) ppm. ESI-MS: m/z 535.1 ([MH]⁺, calcd. 535.1).

C₂₀H₂₆N₂O₁₁S₂·0.25H₂O: calcd. C 44.56, H 4.95, N 5.20; found C

44.43, H, 4.75, N 5.55.

1

(MeOH/CH₂Cl₂, 10:90, v/v). H NMR (CDCl₃): δ = 9.10 (br. s, 1

H, NH), 7.36 (d, J = 1.1 Hz, 1 H, 6-H), 7.32–7.29 (m, 3 H), 7.14–

7.11 (m, 2 H), 5.63 (s, 1 H, 1Ј-H), 4.68 (d, J = 11.5 Hz, 1 H, 5Ј-

Ha), 4.64 (d, J = 11.5 Hz, 1 H, 5Ј-Hb), 4.42 [d, J = 11.0 Hz, 1 H,

CH₂Ph(a)], 4.30 [d, J = 11.0 Hz, 1 H, CH₂Ph(b)], 4.08 (d, J =

1.7 Hz, 1 H, 3Ј-H), 3.91 (d, J = 1.7 Hz, 1 H, 2Ј-H), 3.22 (d, J =

10.6 Hz, 1 H, 5ЈЈ-Ha), 3.18 (d, J = 10.6 Hz, 1 H, 5ЈЈ-Hb), 3.08 (s,

3 H, SO₂CH₃), 1.80 (br. s, 1 H, NH), 1.62 (d, J = 1.1 Hz, 3 H, 5-

CH₃) ppm. ¹³C NMR (CDCl₃): δ =163.8 (C-4), 150.2 (C-2), 136.4,

135.8, 128.5, 128.3, 127.9, 108.3 (C-5), 90.9 (C-1Ј), 86.9 (C-4Ј), 80.9

(C-3Ј), 72.7 (CH₂Ph), 65.4 (C-5Ј), 59.2 (C-2Ј), 50.5 (C-5ЈЈ), 37.7

(SO₂CH₃), 12.1 (5-CH₃) ppm. ESI-MS: m/z 438.1 ([MH]⁺,

C₁₉H₂₄N₃O₇S⁺calcd. 438.1).

1-[2-C-Azido-3-O-benzyl-2-deoxy-5-O-(methylsulfonyl)-4-C-(meth-

ylsulfonyloxymethyl)-α-L-threo-pentofuranosyl]thymine (24): Nucle-

(1R,3R,4R,7R)-1-(Benzoyloxymethyl)-7-benzyloxy-3-(thymin-1-yl)-

2-oxa-5-azabicyclo[2.2.1]heptane (26): To a solution of nucleoside

25 (1.27 g, 2.90 mmol) in anhydrous DMF (300 cm³) was added

sodium benzoate (4.2 g, 29.0 mmol) and 15-crown-5 (2.18 cm³,

14.5 mmol). The reaction mixture was stirred at 120 °C for 30 h,

cooled to room temp. and H₂O (600 cm³) was added. Extraction

was performed with a mixture of EtOAc and n-heptane (1:1, v/v,

5×300 cm³). The combined organic phase was washed with satu-

rated aq. NaHCO₃(2×200 cm³), dried (Na₂SO₄) and the solvents

evaporated to dryness under reduced pressure. An analytical sam-

ple was purified by DVDC [3–5% (v/v) MeOH in EtOAc] to give

nucleoside 26 as a yellow viscous oil. R_f0.52 (MeOH/CH₂Cl₂,

10:90, v/v). ¹H NMR (CDCl₃): δ = 9.23 (br. s, 1 H, NH), 8.02 (dd,

J = 1.4 and 8.4 Hz, 2 H, Bz) 7.59 (tt, J = 1.4 and 7.5 Hz, 1 H, Bz),

7.46–7.41 (m, 3 H, 6-H and Bz), 7.25–7.23 (m, 3 H, Bn), 7.12–7.08

(m, 2 H, Bn), 5.70 (s, 1 H, 1Ј-H), 4.85 (d, J = 12.3 Hz, 1 H, 5Ј-

Ha), 4.76 (d, J = 12.3 Hz, 1 H, 5Ј-Hb), 4.47 [d, J = 11.2 Hz, 1 H,

CH₂Ph(a)], 4.25 [d, J = 11.2 Hz, 1 H, CH₂Ph(b)], 4.11 (br. s, 1 H,

3Ј-H), 3.71 (br. s, 1 H, 2Ј-H), 3.32 (d, J = 10.7 Hz, 1 H, 5ЈЈ-Ha),

3.19 (d, J = 10.7 Hz, 1 H, 5ЈЈ-Hb), 1.57 (s, 3 H, 5-CH₃) ppm. ¹³C

NMR (CDCl₃): δ =165.9 (C-4), 150.0 (C-2), 136.7, 135.9, 133.4,

129.6, 128.5, 128.4, 128.2, 128.0, 108.1 (C-5), 87.3 (C-1Ј), 79.3 (C-

3Ј), 72.8 (CH₂Ph), 60.7 (C-5Ј), 59.2 (C-2Ј), 50.9 (C-5ЈЈ), 12.1 (5-

CH₃) ppm; the signals for COPh and C4Ј could not be identified.

ESI-MS: m/z 464.2 ([MH]⁺, C₂₅H₂₆N₃O₆calcd. 464.2). The major

part of this product was used in the next step without purification

by DCVC.

oside 23 (5.11 g, 9.57 mmol) was dissolved in anhydrous CH₂Cl₂

(300 cm³) and cooled to –78 °C. Anhydrous pyridine (7.70 cm³,

95.6 mmol) and DMAP (4.67 g, 38.2 mmol) were added, followed

by the dropwise addition of trifluoromethanesulfonic anhydride

(1.77 cm³, 10.5 mmol) over a period of 15 min. The stirred reaction

mixture was warmed to 0 °C. After 6 h, additional trifluorome-

thanesulfonic anhydride (0.40 cm³, 2.38 mmol) was added. The re-

action was stirred for another hour and ice-cold saturated aq.

NaHCO₃(50 cm³) was added. The organic phase was separated

and washed successively with saturated aq. NaHCO₃(2×100 cm³),

aqueous HCl (1 m, 3 × 100 cm³) and saturated aq. NaHCO₃

(2×100 cm³). The organic phase was dried with Na₂SO₄and the

solvents evaporated to dryness in vacuo. The residue was purified

by DCVC [60–90% (v/v) EtOAc in n-heptane] to give an intermedi-

ate residue (5.1 g) as a light yellow foam. R_f0.4 (MeOH/CH₂Cl₂,

5:95, v/v. ESI-MS: m/z 665.0). The yellow foam (5.1 g) was dis-

solved in anhydrous DMF (90 cm³) and NaN₃(550 mg, 8.46 mmol)

was added and the reaction mixture stirred for 18 h. H₂O (200 cm³)

was added and the aqueous phase was extracted with a mixture of

EtOAc and light petroleum (1:1, v/v, 5×100 cm³). The combined

organic phase was washed successively with saturated aq. NaHCO₃

(100 cm³) and brine (100 cm³), dried (Na₂SO₄) and the solvents

evaporated to dryness under reduced pressure. The residue was

purified by DCVC [60–80% (v/v) EtOAc in n-heptane] to give azide

24 (3.5 g) as white foam. R_f0.65 (MeOH/CH₂Cl₂,10:90, v/v). NMR

spectroscopic data revealed the compound to be contaminated with

traces of DMF. ¹H NMR ([D₆]DMSO): δ = 11.51 (br. s, 1 H, NH),

7.65 (s, 1 H, 6-H), 7.44–7.31 (m, 5 H), 6.06 (d, J = 8.2 Hz, 1 H, 1Ј- (1R,3R,4R,7R)-7-Benzyloxy-1-(hydroxymethyl)-3-(thymin-1-yl)-2-

H), 4.83 (t, J = 8.2 Hz, 1 H, 2Ј-H), 4.77 [d, J = 11.4 Hz, 1 H,

CH₂Ph(a)], 4.70 [d, J = 11.4 Hz, 1 H, CH₂Ph(b)], 4.55 (d, J =

oxa-5-azabicyclo[2.2.1]heptane (27): The yellow viscous oil 26

(Ϸ2.0 g) was dissolved in saturated methanolic NH₃(100 cm³) at

2310

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Eur. J. Org. Chem. 2005, 2297–2321

XNA (xylo Nucleic Acid): A Summary and New Derivatives

FULL PAPER

5 °C, where upon the mixture was warmed to room temp. and

stirred for 18 h. The reaction mixture was evaporated in vacuo,

reaction mixture was stirred for further 11 h. EtOAc (20 cm³) was

added and the organic phase was washed successively with satd.

and purified by DVDC [8–10% (v/v) MeOH in CH₂Cl₂] to give aq. NaHCO₃(3×15 cm³) and brine (15 cm³). The aqueous phase

nucleoside 27 (0.5 g, 48 % from 25) as a white foam. R_f0.23

was extracted with EtOAc (15 cm³) and the combined organic

(MeOH/CH₂Cl₂, 10:90, v/v). ¹H NMR ([D₆]DMSO): δ = 11.17 (br. phase was dried (Na₂SO₄) and filtered. The filtrate was evaporated

s, 1 H, NH), 7.42 (d, J = 1.3 Hz, 1 H, H-6), 7.31–7.24 (m, 3 H),

7.18–7.14 (m, 2 H), 5.47 (s, 1 H, 1Ј-H), 4.99 (br. s, 1 H, NH), 4.46

[d, J = 11.5 Hz, 1 H, CH₂Ph(a)], 4.28 [d, J = 11.5 Hz, 1 H,

CH₂Ph(b)], 3.92 (d, J = 1.7 Hz, 1 H, 3Ј-H), 3.90 (d, J = 11.7 Hz,

1 H, 5Ј-Ha), 3.80 (d, J = 11.7 Hz, 1 H, 5Ј-Hb), 3.59 (d, J = 1.7 Hz,

1 H, 2Ј-H), 3.06 (d, J = 10.1 Hz, 1 H, 5ЈЈ-Ha), 2.77 (d, J = 10.1 Hz,

to dryness under reduced pressure and the residue was subjected

to DCVC [4–7% MeOH in CH₂Cl₂, containing 0.5% pyridine, v/

v/v] to give nucleoside 30 (178 mg, 94%) as white solid material.

1

R_f0.62 (MeOH/CH₂Cl₂, 10:90, v/v). H NMR ([D₆]DMSO, major

rotamer): δ = 11.28 (br. s, 1 H, NH), 7.48–7.23 (m, 10 H), 6.95–

6.90 (m, 4 H), 5.97 (d, J = 2.9 Hz, 1 H, 3Ј-OH), 5.66 (s, 1 H, 1Ј-

1 H, 5ЈЈ-Hb), 1.45 (d, J = 1.1 Hz, 3 H, 5-CH₃) ppm. ¹³C NMR H), 4.70 (br. s, 1 H, 2Ј-H), 4.25 (t, J = 2.5 Hz, 1 H, 3Ј-H), 3.75 (s,

([D₆]DMSO): δ = 163.9 (C-4), 150.2 (C-2), 137.6, 136.9, 128.2,

6 H, 2×OCH₃), 3.69 (d, J = 11.5 Hz, 1 H, 5Ј-Ha), 3.64 (d, J =

127.5, 127.4, 106.1 (C-5), 89.8 (C-1Ј and C-4Ј), 81.1 (C-3Ј), 71.4 11.5 Hz, 1 H, 5Ј-Hb), 3.60 (d, J = 10.6 Hz, 1 H, 5ЈЈ-Ha), 3.37 (d,

(CH₂Ph), 58.9 and 57.8 (C-2Ј and C-5Ј), 50.2 (C-5ЈЈ), 12.1 (5-CH₃) J = 10.6 Hz, 1 H, 5ЈЈ-Hb), 1.70 (s, 3 H, 5-CH₃) ppm. ¹³C NMR

ppm. ESI-MS: m/z 360.2 ([MH]⁺, C₁₈H₂₂N₃O₅calcd. 360.2).

([D₆]DMSO, major rotamer): δ = 163.9 (C-4), 158.1, 154.0 (q, ²J_C,F

37.4, COCF₃), 149.8 (C-2), 144.4, 135.1, 134.9, 134.8, 129.7, 127.8,

126.1, 115.6 (q, J_C,F= 287.6 Hz, CF₃), 113.2, 106.0 (C-5), 89.0

(1R,3R,4R,7R)-7-Benzyloxy-1-(hydroxymethyl)-3-(thymin-1-yl)-5-

(trifluoroacetyl)-2-oxa-5-azabicyclo[2.2.1]heptane (28): To a solu-

tion of nucleoside 27 (0.5 g, 1.39 mmol) in anhydrous MeOH

(10 cm³) was added DMAP (340 mg, 2.78 mmol) and ethyl trifluo-

roacetate (0.99 cm³, 8.35 mmol). The resulting mixture was stirred

for 16 h at room temp. The reaction mixture was evaporated to

dryness in vacuo. The residue was purified by DVDC [80–100% (v/

v) EtOAc in n-heptane] to give nucleoside 28 (0.59 g, 93%) as a

white solid material. ¹H and ¹³C NMR showed two conformations

of the amide (rotamers) in 1:2 ratio. R_f0.48 (MeOH/CH₂Cl₂, 10:90,

1

(C-4Ј), 87.9 (C-1Ј), 85.8 (CAr₃), 72.6 (C-3Ј), 62.3 (C-2Ј), 60.2 (C-

5Ј), 54.9 (2× OCH₃), 53.4 (C-5ЈЈ), 12.4 (5-CH₃) ppm. ESI-MS:

–

m/z 666.2 ([M – H]^–, C₃₄H₃₁F₃N₃O₈calcd. 666.2).

(1R,3R,4R,7R)-7-[2-Cyanoethoxy(diisopropylamino)phosphanyloxy]-1-

(4,4Ј-dimethoxytrityloxymethyl)-3-(thymin-1-yl)-5-(trifluoroacetyl)-2-

oxa-5-azabicyclo[2.2.1]heptane (31): Nucleoside 30 (211 mg,

0.32 mmol) was co-evaporated with anhydrous acetonitrile

(2×3 cm³) under reduced pressure, dissolved in anhydrous CH₂Cl₂

(2 cm³) and diisopropylethylamine (0.33 cm³, 1.90 mmol) and 2-cy-

anoethyl N,N-diisopropylphosphoramidochloridite (0.21 cm³,

0.95 mmol) were added. The mixture was stirred at room temp. for

8 h. MeOH (0.15 cm³) and then EtOAc (20 cm³) were added and

washing was performed with satd. aq. NaHCO₃(2×10 cm³). The

combined aqueous phase was extracted with EtOAc (10 cm³) and

the combined organic phase was dried (Na₂SO₄), filtered and the

solvent evaporated to dryness in vacuo. The residue was purified

by flash column chromatography [50% EtOAc in CH₂Cl₂, contain-

ing 1% Et₃N, v/v/v] to give nucleoside 31 (246 mg, 90%) as a white

foam. R_f0.46, 0.55 (MeOH/CH₂Cl₂, 5:95, v/v). ³¹P NMR

(500 MHz, CDCl₃): δ = 154.5, 153.7, 152.3, 152.0 ppm. ESI-MS:

m/z 866.2 ([M – H]^–, C₄₃H₄₈F₃N₅O₉P⁺calcd. 866.3).

1

v/v). H NMR (CDCl₃, major rotamer): δ = 8.68 (br. s, 1 H, NH),

7.30–7.27 (m, 4 H), 7.17–7.10 (m, 2 H), 5.58 (br. s, 1 H, 1Ј-H), 4.81

(br. s, 1 H, 2Ј-H), 4.55 [d, J = 11.2 Hz, 1 H, CH₂Ph(a)], 4.38 [d, J

= 11.2 Hz, 1 H, CH₂Ph(b)], 4.22–4.11 (m, 2 H, 5Ј-H), 3.95 (d, J =

2.0 Hz, 1 H, 3Ј-H), 3.78 (d, J = 12.3 Hz, 1 H, 5ЈЈ-Ha), 3.59 (d, J =

12.3 Hz, 1 H 5ЈЈ-Hb), 2.32 (br. s, 1 H, 5Ј-OH), 1.61 (d, J = 1.1 Hz,

3 H, 5-CH₃) ppm. ¹³C NMR (CDCl₃, major rotamer): δ = 163.5

(C-4), 155.5 (q, ²J_C,F= 38.2 Hz, COCF₃), 149.6 (C-2), 136.0, 135.2

1

(C-6), 128.9, 128.6, 128.0, 115.5 (q, J_C,F286.9, CF₃), 108.5 (C-5),

89.2 (C-4Ј), 88.3 (C-1Ј), 79.8 (C-3Ј), 73.5 (CH₂Ph), 60.8 (C-2Ј), 58.7

(C-5Ј), 52.7 (C-5ЈЈ), 12.2 (5-CH₃) ppm. ESI-MS: m/z 454.1 ([M –

H]^–, calcd. 454.1). C₂₀H₂₀F₃N₃O₆: calcd. C 52.75, H 4.43, N 9.23;

found C 52.38, H 4.39, N 8.88.

(1R,3R,4R,7R)-7-Hydroxy-1-(hydroxymethyl)-3-(thymin-1-yl)-5-(tri-

fluoroacetyl)-2-oxa-5-azabicyclo[2.2.1]heptane (29): To a solution of

nucleoside 28 (494 mg, 1.08 mmol) in MeOH (125 cm³) was added

Pd/C (740 mg, 10% Pd on carbon) and the reaction was stirred

under H₂for 2 h. The reaction mixture was filtered through a plug

of celite affording nucleoside 29 (382 mg, 96%) as a white solid

material. R_f0.41 (MeOH/CH₂Cl₂, 10:90, v/v). ¹H NMR ([D₆]

DMSO, major rotamer): δ = 11.25 (br. s, 1 H, NH), 7.53 (d, J =

1.3 Hz, 1 H, 6-H), 5.98 (br. s, 1 H, 3Ј-OH), 5.59 (s, 1 H, 1Ј-H), 5.14

(t, J = 5.7 Hz, 1 H, 5Ј-OH), 4.65 (br. s, 1 H, 2Ј-H), 4.18 (t, J =

2.4 Hz, 1 H, 3Ј-H), 3.92–3.84 (m, 2 H, 5Ј-H), 3.68 (d, J = 11.9 Hz,

1 H, 5ЈЈ-Ha), 3.42 (d, J = 11.9 Hz, 1 H, 5ЈЈ-Hb), 1.76 (s, 3 H, 5-

CH₃) ppm. ¹³C NMR ([D₆]DMSO, major rotamer): δ = 164.1 (C-

1-[2-O-Acetyl-3-O-benzyl-5-O-(methylsulfonyl)-4-C-(methylsulfonyl-

oxymethyl)-α-L-threo-pentofuranosyl]-3-(benzyloxymethyl)thymine

(32): Nucleoside 15 (5.02 g, 8.71 mmol) was dissolved in anhydrous

CH₂Cl₂(25 cm³) at 0 °C with stirring. BOMCl (7.28 cm³,

52.3 mmol) was added dropwise over a period of 5 min followed

by addition of DIPEA (7.58 cm³, 43.6 mmol) and the reaction mix-

ture was warmed to room temp. and stirred for 44 h. The reaction

mixture was diluted with CH₂Cl₂(200 cm³), washed successively

with satd. aq. NaHCO₃(2×150 cm³) and half saturated aq. NH₄Cl

(2×100 cm³). The organic phase was dried (Na₂SO₄) and the sol-

vents evaporated to dryness in vacuo. The residue was purified by

DCVC [70–90% (v/v) EtOAc in n-heptane] to give nucleoside 32

(5.19 g, 86%) as a white foam, while 0.36 g (6%) of starting mate-

rial 15 was recovered by elution with EtOAc. R_f0.55 (MeOH/

CH₂Cl₂, 5:95, v/v). ¹H NMR (CDCl₃): δ = 7.41–7.28 (m, 11 H),

6.31 (d, J = 2.9 Hz, 1 H, 1Ј-H), 5.49 (d, J = 9.9 Hz, 1 H, BOM),

5.45 (d, J = 9.9 Hz, 1 H, BOM), 5.32 (dd, J = 2.2 and 2.9 Hz, 1

2

4), 154.2 (q, J_C,F= 37.4 Hz, COCF₃), 150.0 (C-2), 136.8 (C-6),

1

115.8 (q, J_C,F= 287.3 Hz, CF₃), 106.1 (C-5), 89.2 (C-4Ј), 87.9 (C-

1Ј), 72.3 (C-3Ј), 60.8 (C-2Ј), 57.2 (C-5Ј), 53.2 (C-5ЈЈ), 12.5 (5-CH₃)

ppm. ESI-MS: m/z 364.1 ([M – H]^–; C₁₃H₁₃F₃N₃O₆calcd. 364.1).

–

(1R,3R,4R,7R)-1-(4,4Ј-Dimethoxytrityloxymethyl)-7-hydroxy-3-(thy- H, 2Ј-H), 4.79 (d, J = 11.2 Hz), 4.71–4.64 (m, 3 H), 4.57 (d, J =

min-1-yl)-5-(trifluoroacetyl)-2-oxa-5-azabicyclo[2.2.1]heptane (30): 11.2 Hz), 4.41 (d, J = 11.4 Hz), 4.35 (d, J = 10.7 Hz), 4.25 (d, J =

To a stirred solution of nucleoside 29 (104 mg, 0.28 mmol) in anhy-

drous pyridine (1.7 cm³) at room temp. was added dimethoxytrityl

chloride (145 mg, 0.43 mmol). After stirring for 7 h additional 4,4Ј-

dimethoxytrityl chloride (19 mg, 0.06 mmol) was added, and the

10.7 Hz), 4.22 (d, J = 2.2 Hz, 1 H, 3Ј-H), 3.02 (s, 6 H, 2×SO₂CH₃),

2.20 (s, 3 H, COCH₃), 1.82 (s, 3 H, 5-CH₃) ppm. ¹³C NMR

(CDCl₃): δ = 169.6, 162.9, 150.9, 137.8, 135.8, 133.7, 128.7, 128.6,

128.4, 128.2, 127.6, 111.6, 88.8, 85.1, 81.1, 79.7, 73.0, 72.1, 70.6,

Eur. J. Org. Chem. 2005, 2297–2321

www.eurjoc.org

2311

J. Wengel et al.

FULL PAPER

66.8, 64.9, 37.8, 37.7, 20.7, 13.0 ppm. FAB-MS: m/z 697.1 1-[2-C-Azido-3-O-benzyl-2-deoxy-5-O-(methylsulfonyl)-4-C-(meth-

([MH]⁺, C₃₀H₃₇N₂O₁₃S₂calcd. 697.2).

ylsulfonyloxymethyl)-α-L-threo-pentofuranosyl]-3-(benzyloxymeth-

+

yl)thymine (37): To a solution of nucleoside 36 (5.11 g, 6.49 mmol)

in anhydrous DMF (100 cm³) was added NaN₃(465 mg,

7.14 mmol). The reaction mixture was stirred at room temp. for

18 h. H₂O (200 cm³) was added and the aqueous phase was ex-

tracted with a mixture of EtOAc and light petroleum (1:1, v/v,

5×100 cm³). The combined organic phase was washed successively

with satd. aq. NaHCO₃(100 cm³) and brine (100 cm³), dried

(Na₂SO₄) and the solvents evaporated to dryness under reduced

pressure. The residue was purified by DCVC [65–75% (v/v) EtOAc

in n-heptane] to give azide 37 (3.66 g, 83%) as a white foam. R_f

1-[3-O-Benzyl-5-O-(methylsulfonyl)-4-C-(methylsulfonyloxymethyl)-

α-L-threo-pentofuranosyl]-3-(benzyloxymethyl)thymine (33): A solu-

tion of nucleoside 32 (5.2 g, 7.46 mmol) in saturated methanolic

NH₃(250 cm³) was stirred in an ice-bath for 15 min, then warmed

to room temp. and subsequently evaporated to dryness under re-

duced pressure. The residue was purified by column chromatog-

raphy [1% (v/v) MeOH in CH₂Cl₂] to give nucleoside 33 (4.6 g,

94 %) as a white foam. R_f0.50 (MeOH/CH₂Cl₂, 5:95, v/v). ¹H

NMR (CDCl₃): δ = 7.43–7.26 (m, 11 H), 5.78 (d, J = 4.4 Hz, 1 H,

1Ј-H), 5.43 and 5.42 (2s, 1 H each, BOM), 4.75–4.20 (m, 11 H),

3.04 (s, 3 H, SO₂CH₃), 2.99 (s, 3 H, SO₂CH₃), 1.91 (s, 3 H, 5-CH₃)

ppm. ¹³C NMR (CDCl₃): δ = 163.0, 151.8, 137.7, 136.4, 133.7,

128.6, 128.5, 128.4, 128.2, 128.1, 127.7, 127.6, 126.9, 110.9, 91.6,

84.6, 83.1, 80.1, 72.9, 72.3, 70.5, 67.1, 37.6, 37.5, 12.9 ppm. ESI-

0.62 (acetone/benzene, 20:80, v/v). IR (nujol): ν

= 2114 cm^–1.

˜

max

¹H NMR (CDCl₃): δ = 7.42–7.23 (m, 11 H), 5.94 (d, J = 6.1 Hz, 1

H, 1Ј-H), 5. 49 (d, J = 9.7 Hz, 1 H, BOM), 5.47 (d, J = 9.7 Hz, 1

H, BOM), 4.75–4.63 (m, 4 H), 4.53 (d, J = 11.0 Hz), 4.38 (t, J =

6.1 Hz, 1 H, 2Ј-H), 4.35 (d, J = 11.0 Hz), 4.23 (d, J = 11.0 Hz),

4.19 (d, J = 6.1 Hz, 1 H, 3Ј-H), 4.17 (d, J = 11.2 Hz), 3.06 (s, 3 H,

SO₂CH₃), 2.98 (s, 3 H, SO₂CH₃), 1.93 (s, 3 H, 5-CH₃) ppm. ¹³C

NMR (CDCl₃): δ =162.8, 150.9, 137.6, 135.7, 133.6, 128.8, 128.3,

128.2, 127.6, 111.7, 87.7, 83.4, 81.9, 74.0, 72.2, 70.6, 67.6, 67.4,

67.2, 37.7, 37.4, 12.9 ppm. FAB-MS: m/z 679.8 ([M]⁺,

+

MS: m/z 637.1 ([M – H₂O + H]⁺, C₂₈H₃₃N₂O₁₁S₂calcd. 637.2).

1-[3-O-Benzyl-5-O-(methylsulfonyl)-4-C-(methylsulfonyloxymethyl)-

α-L-erythro-pentofuranosyl]-3-(benzyloxymethyl)thymine (35): Nu-

cleoside 33 (46 mg, 0.07 mmol) was dissolved in CH₂Cl₂(3 cm³)

and cooled to 0 °C. Pyridine (56 μL, 0.7 mmol) and DMAP (34 mg,

0.28 mmol) were added followed by the dropwise addition of tri-

fluoromethanesulfonic anhydride (23 μL, 0.14 mmol) over a period

of 2 min. After 4 h ice-cold satd. aq. NaHCO₃(1.0 cm³) was added.

The organic phase was separated and washed with satd. aq.

NaHCO₃(2×1 cm³), dried (Na₂SO₄) and the solvent evaporated

to dryness in vacuo. The residue was purified by DCVC [55–75%

(v/v) EtOAc in n-heptane] to give nucleoside 35 (33 mg, 72%) as a

white foam. R_f0.55 (MeOH/CH₂Cl₂, 5:95, v/v). ¹H NMR (CDCl₃):

δ = 7.59 (br. s, 1 H), 7.44–7.21 (m, 10 H), 6.12 (d, J = 2.9 Hz), 5.41

(s, 2 H), 4.92 (d, J = 11.7 Hz), 4.66 (s, 2 H), 4.64 (s, 2 H), 4.41–

4.20 (m, 5 H), 3.15 (br. s, 1 H), 3.06 (s, 3 H), 3.03 (s, 3 H), 1.90 (s,

3 H) ppm. ¹³C NMR (CDCl₃): δ = 163.9, 151.3, 138.2, 137.2, 136.6,

129.2, 128.6, 128.0, 109.3, 85.9, 81.9, 79.8, 74.1, 72.4, 70.6, 69.6,

68.9, 68.4, 38.2, 37.9, 13.2 ppm. ESI-MS: m/z 655.2 ([MH]⁺,

+

C₂₈H₃₃N₅O₁₁S₂calcd. 679.2).

(1R,3R,4R,7R)-7-Benzyloxy-3-[3-(benzyloxymethyl)thymin-1-yl]-1-

(methylsulfonyloxymethyl)-2-oxa-5-azabicyclo[2.2.1]heptane (38):

To a solution of triphenylphosphane (386 mg, 1.47 mmol) in anhy-

drous pyridine (50 cm³) was added nucleoside 37 (505 mg,

0.74 mmol) and the resulting mixture was stirred at room temp.

for 20 h. Concentrated aqueous NH₃(50 cm³) was added and the

reaction mixture was stirred for additional 24 h. Extraction was

performed with CH₂Cl₂(3 ×70 cm³) and the combined organic

phase was successively washed with satd. aq. NaHCO₃(2×50 cm³)

and satd. aq. NaCl (50 cm³), dried (Na₂SO₄) and the solvents evap-

orated to dryness in vacuo. The residue was purified by DCVC [3–

6% (v/v) MeOH in CH₂Cl₂] to give nucleoside 38 (410 mg, 99%)

as a white foam. R_f0.43 (MeOH/CH₂Cl₂, 10:90, v/v). ¹H NMR

(CDCl₃): δ = 7.39–7.25 (m, 9 H), 7.10–7.06 (m, 2 H), 5.58 (s, 1 H,

1Ј-H), 5.49 (d, J = 9.6 Hz, 1 H, BOM), 5.44 (d, J = 9.6 Hz, 1 H,

BOM), 4.70 (s, 2 H, BOM), 4.67 (d, J = 11.5 Hz, 1 H, 5Ј-Ha), 4.62

(d, J = 11.5 Hz, 1 H, 5Ј-Hb), 4.40 [d, J = 11.2 Hz, 1 H, CH₂Ph(a)],

4.25 [d, J = 11.2 Hz, 1 H, CH₂Ph(b)], 4.08 (d, J = 1.7 Hz, 1 H, 3Ј-

H), 3.92 (d, J = 1.7 Hz, 1 H, 2Ј-H), 3.20 (d, J = 10.6 Hz, 1 H, 5ЈЈ-

Ha), 3.16 (d, J = 10.6 Hz, 1 H, 5ЈЈ-Hb), 3.07 (s, 3 H, SO₂CH₃),

1.70 (br. s, 1 H, NH), 1.66 (d, J = 1.3 Hz, 3 H, 1 H, 5-CH₃) ppm.

¹³C NMR (CDCl₃): δ =163.2 (C-4), 150.6 (C-2), 137.8, 135.8, 135.1

(C-6), 128.5, 128.4, 128.3, 128.1, 127.8, 127.5, 127.5, 107.6 (C-5),

91.3 (C-1Ј), 86.8 (C-4Ј), 80.9 (C-3Ј), 72.8 (CH₂Ph), 72.1 and 70.1

(BOM), 65.4 (C-5Ј), 59.2 (C-2Ј), 50.5 (C-5ЈЈ), 37.7 (SO₂CH₃), 12.9

(5-CH₃) ppm. FAB-MS: m/z 558.2 ([MH]⁺, C₂₇H₃₂N₃O₈S⁺calcd.

558.2).

+

C₂₈H₃₅N₂O₁₂S₂calcd. 655.2).

1-[3-O-Benzyl-5-O-(methylsulfonyl)-4-C-(methylsulfonyloxymethyl)-

2-O-(trifluoromethylsulfonyl)-α-L-erythro-pentofuranosyl]-3-(benzyl-

oxymethyl)thymine (36): Nucleoside 35 (19.0 g, 29.0 mmol) was dis-

solved in CH₂Cl₂(1000 cm³) and the resulting mixture was cooled

to 0 °C. Pyridine (23.4 cm³, 290.8 mmol) and DMAP (14.2 g,

116.3 mmol) were added followed by the dropwise addition of tri-

fluoromethanesulfonic anhydride (9.78 cm³, 58.2 mmol) over a

period of 15 min. After 4 h ice-cold satd. aq. NaHCO₃was added.

The organic phase was separated and washed successively with

satd. aq. NaHCO₃(2×300 cm³), 1 m aqueous HCl (3×300 cm³)

and satd. aq. NaHCO₃(2×300 cm³), dried (Na₂SO₄) and the sol-

vents evaporated to dryness in vacuo. The residue was purified by

DCVC [60–75% (v/v) EtOAc in n-heptane] to give triflated nucleo-

side 36 (16.0 g, 70%) as a white foam. R_f0.65 (MeOH/CH₂Cl₂,

1

5:95, v/v). H NMR (CDCl₃): δ = 7.57–7.26 (m, 11 H), 6.25 (d, J (1R,3R,4R,7R)-7-Benzyloxy-1-(benzoyloxymethyl)-3-[3-(benzyloxy-

= 2.6 Hz, 1 H, 1Ј-H), 5.46 (dd, J = 2.8 and 3.8 Hz, 2Ј-H), 5.42 (d,

J = 9.8 Hz, 1 H, BOM), 5.39 (d, J = 9.8 Hz, 1 H, BOM), 4.80 [d,

methyl)thymin-1-yl]-2-oxa-5-azabicyclo[2.2.1]heptane (39): To a

solution of nucleoside 38 (6.17 g, 11.1 mmol) in anhydrous DMF

J = 11.2 Hz, 1 H, CH₂Ph(a)], 4.61–4.54 (m, 4 H), 4.47 [d, J = (300 cm³) were added sodium benzoate (4.05 g, 28.6 mmol) and 15-

11.2 Hz, 1 H, CH₂Ph(b)], 4.26 (d, J = 11.0 Hz), 4.21 (d, J =

12.2 Hz), 3.97 (d, J = 11.0 Hz), 2.96 (s, 3 H, SO₂CH₃), 2.91 (s, 3

crown-5 (0.63 g, 0.8 cm³) and the resulting mixture was stirred at

120 °C for 24 h. The reaction mixture was cooled to room temp.

H, SO₂CH₃), 1.97 (d, J = 1.3 Hz, 3 H, 5-CH₃) ppm. ¹³C NMR and H₂O (600 cm³) was added. Extraction was performed with a

(CDCl₃): δ =162.8 (C-4), 150.6 (C-2), 137.5, 135.2, 133.7, 129.1, mixture of EtOAc and n-heptane (1:1, v/v, 5×300 cm³) and the

1

128.9, 128.8, 128.2, 127.7, 118.0 (q, J_C,F= 421.0 Hz, CF₃), 110.9

combined organic phase was washed with satd. aq. NaHCO₃

(C-5), 83.5 (C-1Ј), 82.4 (C-2Ј), 82.0 (C-4Ј), 77.1 (C-3Ј), 74.7 (BOM), (2×200 cm³), dried (Na₂SO₄) and the solvents evaporated to dry-

72.1 (CH₂Ph), 70.3 (BOM), 67.8 and 67.7 (C-5Ј and C-5ЈЈ), 37.9 ness under reduced pressure. The residue was purified by DCVC

(SO₂CH₃), 37.6 (SO₂CH₃), 12.7 (5-CH₃) ppm. ESI-MS: m/z 787.1 [3–5% (v/v) MeOH in EtOAc] to give nucleoside 39 (5.94 g, 92%)

([MH]⁺, C₂₉H₃₄F₃N₂O₁₄S₃calcd. 787.1).

as a white foam. R_f0.63 (MeOH/CH₂Cl₂, 10:90, v/v). ¹H NMR

+

2312

www.eurjoc.org

Eur. J. Org. Chem. 2005, 2297–2321

XNA (xylo Nucleic Acid): A Summary and New Derivatives

FULL PAPER

(CDCl₃, 400 MHz): δ = 8.02 (dd, J = 1.2 and 8.4 Hz, 2 H, Bz), (1R,3R,4R,7R)-7-Hydroxy-1-(hydroxymethyl)-3-(thymin-1-yl)-5-(tri-

7.59 (tt, J = 1.2 and 7.5 Hz, 1 H, Bz), 7.45–7.36 (m, 6 H), 7.32 (t, fluoroacetyl)-2-oxa-5-azabicyclo[2.2.1]heptane (29): Compound 41

J = 7.5 Hz, 1 H, Bz), 7.24–7.18 (m, 3 H), 7.05–7.01 (m, 2 H), 5.59

(s, 1 H, 1Ј-H), 5.50 (d, J = 9.7 Hz, 1 H, BOM), 5.46 (d, J = 9.7 Hz,

1 H, BOM), 4.84 (d, J = 12.3 Hz, 1 H, 5Ј-Ha), 4.75 (d, J = 12.3 Hz,

(1.21 g, 2.1 mmol) was dissolved in anhydrous CH₂Cl₂(30 cm³) and

stirred at –78 °C where upon BCl₃(4.6 cm³, 1 m in CH₂Cl₂) was

added dropwise. The reaction mixture was slowly warmed to room

1 H, 5Ј-Hb), 4.72 (s, 2 H, BOM), 4.39 [d, J = 11.2 Hz, 1 H, temp. over a period of 2 h, cold MeOH (2 cm³) was added dropwise

CH₂Ph(a)], 4.25 [d, J = 11.2 Hz, 1 H, CH₂Ph(b)], 4.11 (d, J =

followed by addition of NaHCO₃(1.06 g) and the resulting mixture

1.7 Hz, 1 H, 3Ј-H), 3.90 (d, J = 1.7 Hz, 1 H, 2Ј-H), 3.24 (d, J = was evaporated to dryness under reduced pressure. The residue was

10.4 Hz, 1 H, 5ЈЈ-Ha), 3.19 (d, J = 10.4 Hz, 1 H, 5ЈЈ-Hb), 1.60 (br. purified by DCVC [9–10% (v/v) MeOH in CH₂Cl₂] to give a mix-

s, 1 H, NH), 1.56 (d, J = 0.9 Hz, 3 H, 5-CH₃) ppm. ¹³C NMR ture of 29 and 42 as a white solid material. The mixture was stirred

(CDCl₃, 100.6 MHz): δ = 165.9 (COPh), 163.3 (C-4), 150.7 (C-2),

in H₂O (250 cm³) for 24 h, then concentrated to dryness under re-

137.9 (BOM), 136.0, 135.5, 133.3, 129.6, 129.3, 128.4, 128.4, 128.2,

duced pressure affording 29 (699 mg, 91%) as a white solid mate-

128.1, 127.8, 127.5, 107.4 (C-5), 91.2 (C-1Ј), 87.3 (C-4Ј), 81.2 (C- rial. Analytical data were identical to that listed above.

3Ј), 72.7 (CH₂Ph), 72.1 and 70.1 (BOM), 60.9 (C-5Ј), 59.2 (C-2Ј),

4-C-Hydroxymethyl-1,2-O-isopropylidene-α-D

-xylofuranose (43):^[35]

51.1 (C-5ЈЈ), 12.8 (5-CH₃) ppm. ESI-MS: m/z 584.3 ([MH]⁺,

C₃₃H₃₄N₃O₇calcd. 584.2).

Palladium hydroxide (20% on carbon, 10.0 g) was added to a solu-

tion of 3-O-benzyl-4-C-(hydroxymethyl)-1,2-O-isopropylidene-α-d-

xylofuranose (13, 18.0 g) in methanol (100 cm³). Ammonium for-

mate (20.0 g) was added and the resulting mixture was refluxed for

16 h. The catalyst was removed by filteration through a short pad

of silica gel and washed thoroughly with a hot mixture of CHCl₃

and MeOH (5:1, v/v, 250 cm³). The filterate was concentrated to

dryness under reduced pressure to yield furanoside 43 as a white

solid material (11.4 g, 89 %). R_f0.19 (MeOH/CH₂Cl₂, 10:90, v/

v).¹H NMR ([D₆]DMSO): δ = 5.84 (d, J = 4.0 Hz, 1-H), 5.30 (d,

J = 5.2 Hz, 1 H, 3-OH), 4.65 (dd, J = 5.5 Hz and 5.9, OH), 4.51

(d, J = 4.2 Hz, 1 H, 2-H), 4.37 (dd, J = 5.3 Hz and 5.7, OH), 4.12

(d, J = 5.5 Hz, 1 H, 3-H), 3.55–3.39 (m, 4 H, 5-H and 5Ј-H), 1.45

and 1.24 [2s, 3 H each, CH₃(isopropylidene)] ppm. ¹³C NMR ([D₆]

DMSO): δ = 111.3 [OC(CH₃)₂O], 104.0 (C-1), 90.2 (C-4), 88.3 (C-

2), 75.7 (C-3), 61.1 (C-5 and C-5Ј), 27.1 and 26.6 [CH₃(isopropylid-

ene)] ppm. MALDI-HRMS: m/z 243.0834 ([M + Na]⁺,

C₉H₁₆O₆Na⁺calcd. 243.0839).

+

(1R,3R,4R,7R)-7-Benzyloxy-3-[3-(benzyloxymethyl)thymin-1-yl]-1-

(hydroxymethyl)-2-oxa-5-azabicyclo[2.2.1]heptane (40): Nucleoside

39 (1.75 g, 3.0 mmol) was dissolved in saturated methanolic NH₃

(150 cm³) at 5 °C, warmed to room temp. and stirred for 20 h. The

reaction mixture was evaporated in vacuo, and purified by DCVC

[8–10% (v/v) MeOH in EtOAc] to give nucleoside 40 (1.34, 93%)

as a white foam. R_f0.42 (MeOH/CH₂Cl₂, 10:90, v/v). ¹H NMR

(C₅D₅N): δ = 7.76 (d, J = 1.1 Hz, 1 H, 6-H), 7.52–7.49 (m, 2 H),

7.35–7.21 (m, 8 H), 6.98 (br. s, 1 H, NH), 6.10 (s, 1 H, 1Ј-H), 5.74

(d, J = 9.5 Hz, 1 H, BOM), 5.72 (d, J = 9.5 Hz, 1 H, BOM), 4.96

(br. s, 1 H, 5Ј-OH), 4.91 (s, 2 H, BOM), 4.55 [d, J = 11.4 Hz, 1 H,

CH₂Ph(a)], 4.50–4.41 (m, 2 H, 5Ј-H), 4.40 [d, J = 11.4 Hz, 1 H,

CH₂Ph(b)], 4.35 (d, J = 1.8 Hz, 1 H, 3Ј-H), 4.22 (d, J = 1.8 Hz, 1

H, 2Ј-H), 3.66 (d, J = 10.3 Hz, 1 H, 5ЈЈ-Ha), 3.40 (d, J = 10.3 Hz,

1 H, 5ЈЈ-Hb), 1.73 (d, J = 1.1 Hz, 3 H, 5-CH₃) ppm. ¹³C NMR

(C₅D₅N): δ = 163.9 (C-4), 151.6 (C-2), 139.3, 138.1, 136.8, 128.9,

128.8, 128.4, 128.3, 128.1, 128.0, 107.1 (C-5), 91.9 and 91.4 (C-1Ј

and C-4Ј), 82.3 (C-3Ј), 72.8 (CH₂Ph), 72.4 and 70.9 (BOM), 60.4

(C-2Ј), 59.1 (C-5Ј), 51.7 (C-5ЈЈ), 13.4 (5-CH₃) ppm. ESI-MS: m/z

5-O-(tert-Butyldiphenylsilyl)-4-C-(hydroxymethyl)-1,2-O-isopro-

pylidene-α-D-xylofuranose (44): tert-Butyldiphenylsilyl chloride

(3.96 g, 14.4 mmol) was added dropwise to a stirred suspension of

diol 43 (3.52 g, 16 mmol) in a mixture of CH₂Cl₂(20 cm³) and tri-

ethylamine (10 cm³). The reaction mixture was stirred for 12 h at

room temp. Additional amount of tert-butyldiphenylsilyl chloride

(880 mg, 3.2 mmol) was added and the resulting mixture was

stirred for another 24 h. The reaction mixture was diluted with

CH₂Cl₂(200 cm³) and washing was performed with saturated aq.

NaHCO₃(2×100 cm³). The organic phase was dried (Na₂SO₄), fil-

tered, concentrated and purified by column chromatography [35–

40% (v/v), EtOAc in light petroleum] to give furanose 44 as a white

solid material (6.82 g, 93%). R_f0.35 (EtOAc/light petroleum, 40:60,

v/v). ¹H NMR ([D₆]DMSO): δ = 7.75–7.69 (m, 4 H), 7.43–7.40 (m,

6 H), 5.90 (d, J = 4.4 Hz, 1 H, 1-H), 5.43 (d, J = 5.2 Hz, 1 H, 3-

OH), 4.82 (dd, J = 5.1 Hz and 5.3, 5Ј-OH), 4.58 (dd, J = 1.6 Hz

and 4.3, 2-H), 4.20 (dd, J = 1.3 Hz and 5.0, 3-H), 3.72 (s, 2 H, 5-

H), 3.64 (dd, J = 5.3 and 10.7 Hz, 1 H, 5Ј-Ha), 3.53 (dd, J = 5.4

and 10.7 Hz, 1 H, 5Ј-Hb), 1.48 and 1.26 [2s, 3 H each, CH₃(isopro-

pylidene)], 0.99 [s, 9 H, C(CH₃)₃] ppm. ¹³C NMR ([D₆]DMSO): δ

= 135.2, 135.1, 133.1, 133.0, 129.7, 127.8, 111.5 [OC(CH₃)₂O],

104.2 (C-1), 90.3 (C-4), 88.4 (C-2), 75.7 (C-3), 63.6 (C-5), 61.1 (C-

5Ј), 27.1 and 26.7 [CH₃(isopropylidene)], 26.5 [C(CH₃)₃], 18.8

[SiC(CH₃)₃] ppm. MALDI-HRMS: m/z 481.2001 ([M + Na]⁺,

C₂₅H₃₄O₆SiNa⁺calcd. 481.2017).

480.2 ([MH]⁺, C₂₆H₃₀N₃O₆calcd. 480.2).

+

(1R,3R,4R,7R)-7-Benzyloxy-3-[3-(benzyloxymethyl)thymin-1-yl]-1-

(hydroxymethyl)-5-(trifluoroacetyl)-2-oxa-5-azabicyclo[2.2.1]hep-

tane (41): To a solution of nucleoside 40 (1.3 g, 2.71 mmol) in anhy-

drous MeOH (20 cm³) were added DMAP (662 mg, 5.42 mmol)

and ethyl trifluoroacetate (1.93 cm³, 16.3 mmol). The reaction was

stirred for 3 h at room temp., additional DMAP (166 mg,

1.36 mmol) and ethyl trifluoroacetate (0.32 cm³, 2.71 mmol) were

added, the reaction mixture was stirred for another 1 h and then

evaporated to dryness in vacuo. The residue was purified by DCVC

[70–100% (v/v) EtOAc in n-heptane] to give nucleoside 41 (1.21 g,

78%) as a white foam. ¹H and ¹³C NMR showed it to be a mixture

1

rotamers in the ratio 2:3. R_f0.62 (MeOH/CH₂Cl₂, 10:90, v/v). H

NMR (CDCl₃, major rotamer): δ = 7.40–7.27 (m, 9 H), 7.11–7.05

(m, 2 H), 5.61 (s, 1 H, 1Ј-H), 5.51 (d, J = 9.5 Hz, 1 H, BOM), 5.44

(d, J = 9.5 Hz, 1 H, BOM), 4.81 (br. s, 1 H, 2Ј-H), 4.72 (s, 2 H,

BOM), 4.50 [d, J = 11.2 Hz, 1 H, CH₂Ph(a)], 4.33 [d, J = 11.2 Hz,

1 H, CH₂Ph(b)], 4.20–4.09 (m, 2 H, 5Ј-H), 3.98 (d, J = 1.8 Hz, 1

H, 3Ј-H), 3.75 (d, J = 12.1 Hz, 1 H, 5ЈЈ-Ha), 3.58 (d, J = 12.1 Hz,

1 H, 5ЈЈ-Hb), 2.19 (br. s, 1 H, 5Ј-OH), 1.71 (s, 3 H, 5-CH₃) ppm.

¹³C NMR (CDCl₃, major rotamer): δ = 163.2 (C-4), 155.3 (q, ²J_C,F

= 37.7 Hz, COCF₃), 150.3 (C-2), 137.7, 135.4, 134.9, 128.7, 128.6,

128.5, 128.1, 128.0, 127.7, 127.6, 127.5, 115.5 (q, ¹J_C,F287.0, CF₃),

4-C-(Benzoyloxymethyl)-5-O-(tert-butyldiphenylsilyl)-1,2-O-isopro-

107.8 (C-5), 89.3 and 88.2 (C-1Ј and C-4Ј), 79.7 (C-3Ј), 73.5 pylidene-α-D

-xylofuranose (45): Benzoyl chloride (2.1 cm³,

(CH₂Ph), 72.1 and 70.1 (BOM), 58.7 and 58.4 (C-2Ј and C-5Ј), 52.6 18.1 mmol) was added dropwise to a stirred solution of furanose

(C-5ЈЈ), 12.9 (5-CH₃) ppm. ESI-MS: m/z 576.2 ([MH]⁺,

C₂₈H₂₉F₃N₃O₇calcd. 576.2).

44 (7.9 g, 17.2 mmol) in a mixture of pyridine (20 cm³) and CH₂Cl₂

+

(50 cm³), at 0 °C and the resulting mixture was stirred for 12 h at

Eur. J. Org. Chem. 2005, 2297–2321

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2313

J. Wengel et al.

FULL PAPER

room temp. Methanol (0.5 cm³) was added and the resulting mix-

ture was stirred for another 30 min. The reaction mixture was evap-

orated to dryness under reduced pressure and the residue was dis-

solved in CH₂Cl₂(200 cm³) and washed with saturated aq.

NaHCO₃(2×100 cm³). The organic phase was dried (Na₂SO₄), fil-

tered, concentrated to dryness and purified by column chromatog-

raphy [30% (v/v) EtOAc in light petroleum] to give furanose 45 as a

white solid material (8.35 g, 86%). R_f0.29 (EtOAc/light petroleum,

7.67 (m, 4 H), 7.61–7.21 (m, 17 H), 7.13–7.08 (m, 2 H), 6.10 (br. s,

1 H, 1-H), 5.16 (dd, J = 1.3 and 3.1 Hz, 1 H, 2-H), 4.47 (d, J =

3.0 Hz, 1 H, 3-H), 4.36 (d, J = 11.3 Hz, 1 H, 5Ј-Ha), 4.31 (d, J =

11.3 Hz, 1 H, 5Ј-Hb), 4.11 (d, J = 11.5 Hz, 1 H, 5-Ha), 4.03 (d, J

= 11.6 Hz, 1 H, 5-Hb), 1.93 and 1.74 (2s, 3 H each, COCH₃), 1.08

and 0.91 [2s, 9 H each, 2 × C(CH₃)₃] ppm. ¹³C NMR (CDCl₃,

major isomer): δ = 169.5 and 169.2 (2×COCH₃), 165.9 (COC₆H₅),

135.9, 135.8, 135.7, 133.3, 133.2, 133.1, 132.8, 131.7, 130.2, 130.1,

129.9, 129.8, 129.7, 128.4, 127.9, 127.8, 98.5 (C-1), 89.1 (C-4), 82.3

(C-2), 77.3 (C-3), 64.9 and 63.6 (C-5 and C-5Ј), 26.9 and 26.8

[C(CH₃)₃], 21.2 and 20.4 (2×COCH₃), 19.3 and 19.2 [2×SiC(CH₃)

1

25:75, v/v). H NMR (CDCl₃): δ = 7.89–7.86 (m, 2 H), 7.70–7.61

(m, 4 H), 7.53 (m, 1 H), 7.51–7.25 (m, 8 H), 6.06 (d, J = 3.8 Hz, 1

H, 1-H), 4.69 (d, J = 3.8 Hz, 1 H, 2-H), 4.56 (d, J = 11.6 Hz, 1 H,

5Ј-Ha), 4.38 (d, J = 11.6 Hz, 1 H, 5Ј-Hb), 4.37 (d, J = 5.1 Hz, 1

H, 3-H), 4.09 (d, J = 10.8 Hz, 1 H, 5-Ha), 3.95 (d, J = 10.5 Hz, 1

H, 5-Hb), 3.70 (d, J = 5.4 Hz, 1 H, 3-OH), 1.56 and 1.33 [2s, 3 H

each, CH₃(isopropylidene)], 1.07 [s, 9 H, C(CH₃)₃] ppm. ¹³C NMR

₃] p p m . M A L D I - H R M S : m / z 8 6 7 . 3 3 8 8 ( [ M + N a ] ⁺

,

C₄₉H₅₆O₉Si₂Na⁺calcd. 867.3355). ¹H NMR (CDCl₃, minor iso-

mer): δ = 7.81–7.73 (m, 6 H), 7.69–7.65 (m, 2 H), 7.61–7.58 (m, 2

H), 7.53 (m, 1 H), 7.47–7.29 (m, 12 H), 7.26–7.21 (m, 2 H), 6.41

(CDCl₃): δ =166.1 (COC₆H₅), 135.8, 135.7, 135.6, 133.1, 132.0, (d, J = 4.9 Hz, 1 H, 1-H), 5.83 (dd, J = 4.9 and 9.2 Hz, 1 H, 2-H),

131.9, 130.2, 129.9, 129.8, 128.4, 128.1, 128.0, 112.9 [OC(CH₃)₂O], 4.71 (d, J = 9.2 Hz, 1 H, 3-H), 4.29 (d, J = 12.1 Hz, 1 H, 5Ј-Ha),

105.7 (C-1), 88.2 (C-4), 87.6 (C-2), 78.6 (C-3), 64.8 and 64.3 (C-5 4.04 (d, J = 10.7 Hz, 1 H, 5-Ha), 3.85 (d, J = 12.1 Hz, 1 H, 5Ј-

and C-5Ј), 27.0 [CH₃(isopropylidene)], 26.9 [C(CH₃)₃], 26.3 [CH₃(i-

sopropylidene)], 19.2 [SiC(CH₃)₃] ppm. MALDI-HRMS: m/z

585.2251 ([M + Na]⁺, C₃₂H₃₈O₇SiNa⁺calcd. 585.2279).

Hb), 3.74 (d, J = 10.8 Hz, 1 H, 5-Hb), 1.69 and 1.49 (2s, 3 H each,

2×COCH₃), 1.17 and 1.02 [2s, 9 H each, 2×C(CH₃)₃] ppm.¹³C

NMR (CDCl₃, minor isomer): δ = 169.8 and 169.4 (2×COCH₃),

165.7 (COC₆H₅), 136.1, 135.9, 135.8, 135.7, 135.6, 133.7, 133.1,

133.0, 132.5, 131.6, 130.2, 130.1, 130.0, 129.9, 129.8, 129.7, 128.4,

128.2, 128.0, 127.9, 127.8, 127.7, 127.6, 92.6 (C-1), 84.3 (C-4), 76.3

(C-2), 73.2 (C-3), 63.6 and 63.5 (C-5 and C-5Ј), 27.0 and 26.8

[2 × C(CH₃)₃], 20.7 and 19.9 (2 × COCH₃), 19.3 and 19.2

[2×SiC(CH₃)₃] ppm. MALDI-HRMS: m/z 867.3396 ([M + Na]⁺,

C₄₉H₅₆O₉Si₂Na⁺calcd. 867.3355).

4-C-(Benzoyloxymethyl)-3,5-di-O-(tert-butyldiphenylsilyl)-1,2-O-iso-

propylidene-α-D-xylofuranose (46): To a stirred solution of furanose

45 (12.0 g, 21.3 mmol) in a anhydrous DMF (25 cm³) was added

DMAP (244 mg, 2 mmol), imidazole (4.36 g, 64 mmol) and tert-

butyldiphenylsilyl chloride (6.48 g, 23.3 mmol) and the resulting

mixture was stirred 12 h at room temp. The reaction mixture was

partitioned between 5 % aqueous KHSO₄(250 cm³) and EtOAc

(250 cm³). Layers were separated and the aqueous layer was ex-

tracted with EtOAc (100 cm³). The combined organic phase was

dried (Na₂SO₄), filtered and concentrated to dryness under reduced

pressure. The residue obtained was purified by column chromatog-

raphy [5–6% (v/v) EtOAc in light petroleum] to give compound

1-[2-O-Acetyl-4-C-(benzoyloxymethyl)-3,5-di-O-(tert-butyldiphenyl-

silyl)-β-D-xylofuranosyl]thymine (48a): N,O-Bis(trimethylsilyl)acet-

amide (6.0 cm³, 24.3 mmol) was added to a suspension of furanose

47 (7.2 g, 8.5 mmol) and thymine (1.33 g, 10.5 mmol) in anhydrous

acetonitrile (100 cm³). The reaction mixture was refluxed for 1 h

whereupon the clear solution was cooled to room temp. TMS-trifl-

46 as a white solid material (16.0 g, 93%). R_f0.56 (EtOAc/light

1

petroleum, 25:75, v/v). H NMR (CDCl₃): δ = 7.77–7.73 (m, 4 H), ate (2.1 cm³, 11.6 mmol) was added dropwise and the resulting mix-

7.68–7.59 (m, 4 H), 7.54–7.49 (m, 3 H), 7.42–7.24 (m, 12 H), 7.19–

ture was refluxed for 12 h. The reaction mixture was then cooled

7.14 (m, 2 H), 6.01 (d, J = 4.4 Hz, 1 H, 1-H), 4.63 (dd, J = 2.2 Hz to room temp. and CH₂Cl₂(200 cm³) was added. Washing was per-

and 4.4, 2-H), 4.53 (d, J = 2.1 Hz, 1 H, 3-H), 4.35 (d, J = 11.1 Hz, formed with saturated aq. NaHCO₃(2×100 cm³) and the organic

1 H, 5Ј-Ha), 4.18 (d, J = 11.5 Hz, 1 H, 5Ј-Hb), 4.00 (d, J = 10.7 Hz,

1 H, 5-Ha), 3.84 (d, J = 11.0 Hz, 1 H, 5-Hb), 1.39 and 1.18 [2s, 3 dryness under reduced pressure. The residue was purified by col-

H each, CH₃(isopropylidene)], 1.07 and 0.98 [2s, 9 H each, umn chromatography [40–50% (v/v) EtOAc in light petroleum] to

phase was dried (Na₂SO₄), filtered and the solvents evaporated to

2×C(CH₃)₃] ppm. ¹³C NMR (CDCl₃): δ =165.9 (COC₆H₅), 136.0, give nucleoside 48a as a white solid material (7.06 g, 91%). R_f0.27

135.9, 135.8, 135.7, 134.9, 133.1, 133.0, 132.9, 132.5, 130.0, 129.9,

(EtOAc/light petroleum, 40:60, v/v). ¹H NMR (CDCl₃): δ = 8.32

129.8, 129.7, 128.3, 127.9, 127.8, 112.8 [OC(CH₃)₂O], 104.7 (C-1),

(br. s, 1 H, NH), 7.76–7.71 (m, 4 H),7.68–7.65 (m, 2 H), 7.61 (m,

89.0 (C-4), 87.7 (C-2), 78.8 (C-3), 64.5 and 63.5 (C-5 and C-5Ј), 1 H), 7.58–7.48 (m, 7 H), 7.47–7.32 (m, 7 H), 7.28–7.26 (m, 2 H),

27.3 and 26.8 [CH₃(isopropylidene)], 27.1, 27.0 and 26.7 [C- 7.23–7.11 (m, 3 H), 6.01 (d, J = 5.9 Hz, 1 H, 1Ј-H), 5.45 (dd, J =

(CH₃)₃], 19.4 and 19.3 [SiC(CH₃)₃] ppm. MALDI-HRMS: m/z 5.5 and 5.6 Hz, 1 H, 2Ј-H), 4.54 (d, J = 5.9 Hz, 1 H, 3Ј-H), 4.38

823.3434 ([M + Na]⁺, C₄₈H₅₆O₇Si₂Na⁺calcd. 823.3457).

(d, J = 11.5 Hz, 1 H, 5ЈЈ-Ha), 4.20 (d, J = 11.7 Hz, 1 H, 5ЈЈ-Hb),

4.19 (d, J = 11.4 Hz, 1 H, 5Ј-Ha), 3.90 (d, J = 11.7 Hz, 1 H, 5Ј-

Hb), 1.63 (s, 3 H, COCH₃), 1.57 (d, J = 1.1 Hz, 3 H, 5-CH₃), 1.13

and 0.94 [2s, 9 H each, 2×C(CH₃)₃] ppm. ¹³C NMR (CDCl₃): δ

=169.8 (COCH₃), 165.7 (COC₆H₅), 163.7 (C-4), 150.6 (C-2), 135.9,

135.8, 135.6, 135.5, 133.3, 132.9, 132.6, 132.5, 131.0, 130.4, 130.1,

130.0, 129.8, 129.4, 128.5, 128.1, 128.0, 127.8, 111.4 (C-5), 86.1 (C-

4Ј), 85.3 (C-1Ј), 79.9 (C-2Ј), 75.4 (C-3Ј), 64.5 and 63.3 (C-5Ј and

C-5ЈЈ), 27.1 and 27.0 [2×C(CH₃)₃], 20.3 (COCH₃), 19.5 and 19.2

[2×SiC(CH₃)₃], 12.1 (5-CH₃) ppm. MALDI-HRMS: m/z 933.3530

([M + Na]⁺, C₅₂H₅₈N₂O₉Si₂Na⁺calcd. 933.3573).

1,2-Di-O-acetyl-4-C-(benzoyloxymethyl)-3,5-di-O-(tert-butyldiphen-

ylsilyl)-α,β-D

-xylofuranose (47): Concd. H₂SO₄(0.12 cm³, 2.4 μmol)

was added, dropwise, to a stirred solution of furanose 46 (15.0 g,

18.7 mmol) in a mixture of acetic acid (160 cm³) and acetic anhy-

dride (16.0 cm³, 170.1 mmol). After stirring for 4 h at room temp.

the reaction mixture was poured carefully in an ice-water mixture

(1000 cm³) and stirred for another 30 min. Brine (250 cm³) was

added and extraction was performed with EtOAc (2 ×500 cm³).

The organic phase was dried (Na₂SO₄), filtered, concentrated to

dryness under reduced pressure and coevoporated successively with

absolute ethanol (2×100 cm³) and toluene (2×20 cm³). The resi-

due was purified by column chromatography [15–20% (v/v) EtOAc

in light petroleum] to give the anomeric mixture 47 as a white foam

(13.8 g, 87%). R_f0.41, 0.44 (EtOAc/light petroleum, 25:75, v/v). ¹H

9-[2-O-Acetyl-4-C-(benzoyloxymethyl)-3,5-di-O-(tert-butyldiphenyl-

silyl)-β-D

-xylofuranosyl]-6-N-benzoyladenine (48b): SnCl₄(2.2 cm³,

18.8 mmol) was added to a suspension of furanose 47 (3.03 g,

3.58 mmol) and 6-N-benzoyladenine (1.62 g, 6.77 mmol) in anhy-

NMR (CDCl₃, major isomer): δ = 7.82 (d, J = 7.4 Hz, 2 H), 7.75– drous acetonitrile (30 cm³). The reaction mixture was refluxed for

2314

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XNA (xylo Nucleic Acid): A Summary and New Derivatives

FULL PAPER

36 h, then cooled to room temp. and saturated aq. NaHCO₃

(100 cm³) was added slowly. Extraction was performed with

CH₂Cl₂(2×100 cm³), and the combined organic phase was washed

with brine (2×100 cm³), dried (Na₂SO₄) and the solvents evapo-

rated to dryness under reduced pressure. The residue was purified

by column chromatography [30–35% (v/v) EtOAc in light petro-

leum] to give nucleoside 48b as a white solid material (2.43 g, 66%).

129.5, 129.0, 128.7, 128.0, 124.2, 87.8 and 87.6 (C-1Ј and C-4Ј),

81.7 (C-2Ј), 77.1 (C-3Ј), 64.2 and 63.1 (C-5Ј and C-5ЈЈ), 20.7

(COCH₃) ppm. MALDI-HRMS: m/z 570.1585 ([M + Na]⁺,

C₂₇H₂₅N₅O₈Na⁺calcd. 570.1595).

1-[2-O-Acetyl-4-C-(benzoyloxymethyl)-5-O-(4,4Ј-dimethoxytrityl)-

β-D-xylofuranosyl]thymine (50a): A solution of nucleoside 49a

(350 mg, 0.81 mmol) and dimethoxytrityl chloride (328 mg,

0.97 mmol) in anhydrous pyridine (2 cm³) was stirred for 12 h at

room temp., CH₂Cl₂(100 cm³) was added and the resulting mixture

was washed with saturated aq. NaHCO₃(2×50 cm³). The organic

phase was dried (Na₂SO₄), filtered and concentrated to dryness

under reduced pressure and the residue was coevoporated with tol-

uene (2×2.0 cm³). The residue was purified by column chromatog-

raphy [65–70% (v/v) EtOAc in light petroleum] to give nucleoside

50a as a white solid material (482 mg, 81 %). R_f0.3 (MeOH/

1

R_f0.41 (EtOAc/light petroleum, 50:50, v/v). H NMR (CDCl₃): δ

= 9.09 (s, 1 H, NH), 8.74 (s, 1 H, 8-H), 8.30 (s, 1 H, 2-H), 8.03 (d,

J = 7.7 Hz, 2 H), 7.80 (d, J = 7.5 Hz, 2 H), 7.68 (d, J = 6.7 Hz, 4

H), 7.63–7.58 (m, 2 H), 7.55–7.50 (m, 4 H), 7.46–7.42 (m, 6 H),

7.38–7.30 (m, 5 H), 7.26–7.15 (m, 5 H), 6.14 (d, J = 5.1 Hz, 1 H,

1Ј-H), 5.88 (dd, J = 5.4 and 5.6 Hz, 1 H, 2Ј-H), 4.70 (d, J = 5.9 Hz,

1 H, 3Ј-H), 4.58 (d, J = 11.4 Hz, 1 H, 5ЈЈ-Ha), 4.36 (d, J = 11.6 Hz,

1 H, 5Ј-Ha), 4.25 (d, J = 11.4 Hz, 1 H, 5ЈЈ-Hb), 4.02 (d, J =

11.5 Hz, 1 H, 5Ј-Hb), 1.60 (s, 3 H, COCH₃), 1.11 and 0.92 (2s, 9

H each, 2×C(CH₃)₃) ppm. ¹³C NMR (CDCl₃): δ =169.4 (COCH₃),

165.7 and 164.6 (2×COC₆H₅), 152.9, 151.6, 149.5, 141.4, 135.9,

135.7, 135.6, 135.5, 133.9, 133.2, 132.8, 132.7, 132.5, 130.9, 130.4,

130.1, 130.0, 129.8, 129.5, 128.9, 128.5, 128.0, 127.9, 127.8, 127.7,

122.8, 87.1 (C-4Ј), 85.3 (C-1Ј), 80.4 (C-2Ј), 75.7 (C-3Ј), 64.7 and

63.4 (C-5Ј and C-5ЈЈ), 27.1 and 27.0 [2×C(CH₃)₃], 20.2 (COCH₃),

19.4 and 19.2 [2 × SiC(CH₃)₃] ppm. MALDI-HRMS: m/z

1047.7639 ([M + Na]⁺, C₅₉H₆₁N₅O₈Si₂Na⁺calcd. 1047.3051).

1

CH₂Cl₂, 5:95, v/v). H NMR (CDCl₃): δ = 8.96 (s, 1 H, NH), 7.87

(d, J = 7.1 Hz, 2 H), 7.56 (m, 1 H), 7.47–7.22 (m, 12 H), 6.83–6.79

(m, 4 H), 6.04 (d, J = 4.6 Hz, 1 H, 1Ј-H), 5.44 (dd, J = 4.2 and

4.3 Hz, 1 H, 2Ј-H), 4.61 (d, J = 11.6 Hz, 1 H, 5ЈЈ-Ha), 4.42–4.38

(m, 2 H, 3Ј-H and 5ЈЈ-Hb), 3.76 (s, 3 H, OCH₃), 3.75 (s, 3 H,

OCH₃), 3.69 (d, J = 7.4 Hz, 1 H, 3Ј-OH), 3.62 (d, J = 9.5 Hz, 1 H,

5Ј-Ha), 3.50 (d, J = 9.5 Hz, 1 H, 5Ј-Hb), 2.12 (s, 3 H, COCH₃),

1.62 (s, 3 H, 5-CH₃) ppm. ¹³C NMR (CDCl₃): δ =170.7 (COCH₃),

166.1 (COC₆H₅), 163.7 (C-4), 158.9, 150.5 (C-2), 144.1, 137.1,

135.0, 134.9, 133.4, 130.2, 129.9, 129.4, 128.5, 128.2, 127.2, 113.4,

111.9 (C-5), 88.4 (C-1Ј), 87.6 and 86.7 (C-4Ј and CAr₃), 82.1 (C-

2Ј), 76.7 (C-3Ј), 64.1 and 62.0 (C-5Ј and C-5ЈЈ), 55.3 (2×OCH₃),

20.8 (COCH₃), 12.1 (5-CH₃) ppm. MALDI-HRMS: m/z 759.2536

([M + Na]⁺, C₄₁H₄₀N₂O₁₁Na⁺calcd. 759.2524).

1-[2-O-Acetyl-4-C-(benzoyloxymethyl)-β-D-xylofuranosyl]thymine

(49a): A solution of nucleoside 48a (2.73 g, 3.0 mmol) and tetrabu-

tylammonium fluoride (3.5 cm³, 3.5 mmol, 1.0 m solution in THF)

in THF (5 cm³) was stirred for 2 h at room temp. Toluene (10 cm³)

was added and the mixture was then concentrated to approx. one

third of the orginal volume under reduced pressure. The concen-

trated mixture was purified by column chromatography [4–5% (v/

v) MeOH in CH₂Cl₂] to give nucleoside 49a as a white solid mate-

9-[2-O-Acetyl-4-C-(benzoyloxymethyl)-5-O-(4,4Ј-dimethoxytrityl)-

β-D-xylofuranosyl]-6-N-benzoyladenine (50b): Tritylation of nucleo-

1

side 49b (364 mg, 0.66 mmol) was carried out with DMTCl

(270 mg, 0.80 mmol) in the presence of pyridine (5.0 cm³) as de-

scribed above for 50a. After the ususal work-up procedure, the resi-

due obtained was purified by column chromatography [2% MeOH

in CH₂Cl₂, containing 0.5% Et₃N (v/v/v)] to afford nucleoside 50b

as a white solid material (497 mg, 88%). R_f0.28 (EtOAc/light pe-

troleum, 75:25, v/v). ¹H NMR (CDCl₃): δ = 9.09 (s, 1 H, NH), 8.63

(s, 1 H, 8-H), 8.06 (s, 1 H, 2-H), 8.02 (d, J = 7.2 Hz, 2 H), 8.00–

7.82 (m, 2 H), 7.61–7.49 (m, 5 H), 7.47–7.26 (m, 8 H), 7.19–7.16

(m, 2 H), 6.76–6.68 (m, 4 H), 6.09 (d, J = 2.0 Hz, 1 H, 1Ј-H), 5.46

(d, J = 1.9 Hz, 1 H, 2Ј-H), 4.97 (d, J = 11.4 Hz, 1 H, 5ЈЈ-Ha), 4.54

(d, J = 11.5 Hz, 1 H, 5ЈЈ-Hb), 4.48 (d, J = 11.0 Hz, 1 H, 3Ј-H),

3.73 and 3.72 (2s, 3 H each, 2×OCH₃), 3.63 (d, J = 9.6 Hz, 1 H,

5Ј-Ha), 3.58 (d, J = 9.4 Hz, 1 H, 5Ј-Hb), 2.16 (s, 3 H, COCH₃)

ppm. ¹³C NMR (CDCl₃): δ =170.3 (COCH₃), 166.3 and 164.4

(2×COC₆H₅), 158.5, 152.0, 150.3, 149.7, 144.6, 143.1, 135.7, 135.6,

133.5, 133.4, 133.1, 131.0, 130.2, 130.0, 129.6, 129.0, 128.9, 128.5,

127.9, 127.8, 126.8, 124.0, 113.1, 90.3 and 89.8 (C-1Ј and C-4Ј),

86.6 (C-2Ј), 85.6 (CAr₃), 76.8 (C-3Ј), 62.3 and 60.7 (C-5Ј and C-

5ЈЈ), 55.2 (OCH₃), 20.8 (COCH₃) ppm. ESI-HRMS: m/z 850.3083

rial (1.21 g, 93%). R_f0.28 (MeOH/CH₂Cl₂, 10:90, v/v). H NMR

(CDCl₃): δ = 9.56 (br. s, 1 H, NH), 8.05 (d, J = 7.1 Hz, 2 H), 7.58

(m, 1 H), 7.56–7.43 (m, 3 H), 5.89 (d, J = 5.6 Hz, 1 H, 1Ј-H), 5.45

(dd, J = 5.1 and 5.3 Hz, 1 H, 2Ј-H), 4.74 (br. s, 1 H, OH), 4.55 (d,

J = 11.8 Hz, 1 H, 5ЈЈ-Ha), 4.44 (d, J = 4.4 Hz, 1 H, 3Ј-H), 4.36 (d,

J = 11.9 Hz, 1 H, 5ЈЈ-Hb), 4.00 (d, J = 11.9 Hz, 1 H, 5Ј-Ha), 3.92

(d, J = 12.1 Hz, 1 H, 5Ј-Hb), 3.52 (br. s, 1 H, OH), 2.10 (s, 3 H,

COCH₃), 1.91 (s, 3 H, 5-CH₃) ppm. ¹³C NMR (CDCl₃): δ =171.3

(COCH₃), 166.4 (COC₆H₅), 164.1 (C-4), 150.8 (C-2), 137.8, 133.6,

129.8, 129.4, 128.7, 111.9 (C-5), 88.9 (C-1Ј), 86.6 (C-4Ј), 82.2 (C-

2Ј), 76.9 (C-3Ј), 64.5 and 62.7 (C-5Ј and C-5ЈЈ), 20.8 (COCH₃), 12.6

(5-CH₃) ppm. MALDI-HRMS: m/z 457.1197 ([M + Na]⁺,

C₂₀H₂₂N₂O₉Na⁺calcd. 457.1218).

9-[2-O-Acetyl-4-C-(benzoyloxymethyl)-β-D-xylofuranosyl]-6-N-ben-

zoyladenine (49b): Tetrabutylammonium fluoride (1.75 cm³,

1.75 mmol, 1.0 m solution in THF) was added to a solution of fu-

ranoside 48b (1.78 g, 1.74 mmol) in THF (25 cm³). The reaction

mixture was stirred for 1 h at room temp. Toluene (25 cm³) was

added and the mixture concentrated to approx. one third of the

original volume under reduced pressure. The concentrated mixture

was purified by column chromatography [2–3 %(v/v) MeOH in

CH₂Cl₂) affording nucleoside 49b as a white solid material (497 mg,

52%). R_f0.42 (MeOH/CH₂Cl₂, 10:90, v/v). ¹H NMR (CDCl₃): δ =

9.21 (s, 1 H, NH), 8.70 (s, 1 H, 8-H), 8.02 (s, 1 H, 2-H), 7.97 (d, J

([M + H]⁺, C₄₈H₄₄N₅O₁₀calcd. 850.3387).

+

1-{2-O-Acetyl-4-C-(benzoyloxymethyl)-3-O-[2-cyanoethoxy(diiso-

propylamino)phosphanyl]-5-O-(4,4Ј-dimethoxytrityl)-β-

D-xylofuranos-

yl}thymine (51a): 2-Cyanoethyl N,N-diisopropylphosphor-

= 7.1 Hz, 2 H), 7.96–7.92 (m, 2 H), 7.54–7.49 (m, 2 H), 7.44–7.36 amidochloridite (170 mg, 0.72 mmol) was added dropwise to a

(m, 4 H), 5.91 (d, J = 5.5 Hz, 1 H, 1Ј-H), 5.84 (dd, J = 5.3 and

5.6 Hz, 1 H, 2Ј-H), 5.55 (br. s, 1 H, OH), 5.37 (d, J = 10.8 Hz, 1

H, OH), 4.53–4.45 (m, 2 H, 3Ј-H and 5ЈЈ-Ha), 4.35 (d, J = 11.7 Hz,

1 H, 5ЈЈ-Hb), 3.95–3.92 (m, 2 H, 5Ј-H), 2.00 (s, 3 H, COCH₃) ppm.

¹³C NMR (CDCl₃): δ =170.2 (COCH₃), 166.3 and 164.7

(2×COC₆H₅), 152.2, 150.5, 150.4, 142.8, 133.6, 133.4, 133.1, 129.8,

stirred solution of the nucleoside 50a (440 mg, 0.6 mmol) and diiso-

propylethylamine (1.0 cm³) in anhydrous CH₂Cl₂(5.0 cm³). After

stirring the resulting mixture was 12 h at room temp., the reaction

mixture was diluted with EtOAc (50 cm³). Washing was performed

with saturated aq. NaHCO₃(2×25 cm³). The separated organic

phase was dried (Na₂SO₄), filtered and concentrated under reduced

Eur. J. Org. Chem. 2005, 2297–2321

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2315

J. Wengel et al.

FULL PAPER

pressure. The residue obtained was purified by column chromatog-

raphy [45–60% EtOAc in n-hexane, containing 0.5% Et₃N (v/v/v)]

to give amidite 51a as a white foam (462 mg, 83%). R_f0.46 and

0.40 (MeOH/CH₂Cl₂, 5:95, v/v). ³¹P NMR (CDCl₃): δ = 154.1,

153.6 ppm. MALDI-HRMS: m/z 959.3622 ([M + Na]⁺,

C₅₀H₅₇N₄O₁₂Na⁺calcd. 959.3602).

129.9, 129.8, 129.7, 129.6, 127.9, 127.8, 127.7, 127.6, 112.9

[OC(CH₃)₂O], 104.4 (C-1), 90.6 (C-4), 88.3 (C-2), 80.3 (C-3), 65.8

(C-5), 59.4 (C-5Ј), 55.1 and 54.5 [CH₂(piperazinyl)], 46.1 (NCH₃),

28.1 and 28.0 [CH₃(isopropylidene)], 27.2 and 27.0 [C(CH₃)₃], 19.5

and 19.1 [2×SiC(CH₃)₃] ppm. MALDI-HRMS: m/z 802.4082 ([M

+ Na]⁺, C₄₆H₆₂N₂O₅Si₂Na⁺calcd. 802.4090).

9-{2-O-Acetyl-4-C-(benzoyloxymethyl)-3-O-[2-cyanoethoxy(di-

3,5-Di-O-(tert-butyldiphenylsilyl)-1,2-O-isopropylidene-4-C-piperaz-

isopropylamino)phosphanyl]-5-O-(4,4Ј-dimethoxytrityl)-β-

D

-xylo-

inylmethyl-α-D-xylofuranose (53b): Conversion into triflate of fu-

furanosyl}-6-N-benzoyladenine.(51b): Reaction of compound 50b

(462 mg, 0.54 mmol) with 2-cyanoethyl N,N-diisopropylphos-

phoramidochloridite (141 mg, 0.60 mmol) in the presence of diiso-

propylethylamine (1.0 cm³) and anhydrous CH₂Cl₂(5.0 cm³) fol-

lowed by workup procedure (as described above for compound 51a)

and column chromatography [50% EtOAc in n-hexane containing

0.5% Et₃N (v/v/v)] afforded phosphoramidite 51b as a white foam

(490 mg, 86%). R_f0.23 and 0.31 (EtOAc/petroleum ether, 75:25, v/

v). ³¹P NMR (CDCl₃): δ = 154.3, 152.3 ppm.

ranose 52 (8.58 g, 12.3 mmol) in a mixture of pyridine (15 cm³) and

CH₂Cl₂(100 cm³) with triflic anhydride (5.21 g, 18.5 mmol) was

carried out as described above for 53a. The crude residue obtained

was dissolved in THF (34 cm³), piperazine (10.5 g, 121.9 mmol)

was added and the resulting mixture was stirred at room temp.

for 12 h. The reaction mixture was concentrated to dryness under

reduced pressure and the residue was coevoporated with toluene

(2×25 cm³). The residue was purified by column chromatography

[10% (v/v) MeOH in CH₂Cl₂] to give furanose 53b as a pale yellow

solid material(8.6 g, 91%). R_f0.35 (MeOH/CH₂Cl₂, 10:90, v/v). ¹H

NMR (CDCl₃): δ = 7.69–7.55 (m, 8 H), 7.37–7.28 (m, 7 H), 7.27–

7.18 (m, 5 H), 6.00 (d, J = 5.0 Hz, 1 H, 1-H), 4.92 (dd, J = 4.5 and

4.6 Hz, 1 H, 2-H), 4.39 (d, J = 4.0 Hz, 1 H, 3-H), 3.78 (d, J =

10.7 Hz, 1 H, 5-Ha), 3.51 (d, J = 10.7 Hz, 1 H, 5-Hb), 2.52–1.93

[m, 11 H, 5Ј-H, NH and CH₂(piperazinyl)], 1.28 and 1.22 [2s, 3 H

each, CH₃(isopropylidene)], 1.02 and 1.01 [2s, 9 H each, 2×C(CH₃)

₃] ppm. ¹³C NMR (CDCl₃): δ = 136.4, 136.3, 136.0, 135.7, 133.4

133.3, 133.1, 133.0, 129.9, 129.8, 129.7, 128.0, 127.9, 127.8,

127.7,127.6, 113.0 (OC(CH₃)₂O), 104.5 (C-1), 90.5 (C-4), 88.3 (C-

2), 80.2 (C-3), 65.7 (C-5), 59.9 (C-5Ј), 55.5 and 45.6 [CH₂(piperaz-

inyl)], 28.1 and 28.0 [CH₃(isopropylidene)], 27.2 and 27.0 [C-

(CH₃)₃], 19.5 and 19.1 [SiC(CH₃)₃] ppm. MALDI-HRMS: m/z

787.3904 ([M + Na]⁺, C₄₅H₆₀N₂O₅Si₂Na⁺calcd. 787.3933).

3,5-Di-O-(tert-butyldiphenylsilyl)-4-C-(hydroxymethyl)-1,2-O-iso-

propylidene-α-D-xylofuranose (52): A solution of furanose 46

(10.3 g 12.9 mmol) in saturated methanolic ammonia (200 cm³) was

stirred for 24 h at room temp. The solution was evaporated to dry-

ness under reduced pressure and the residue was coevaporated with

toluene (2 × 10 mL). The residue was purified by column

chromatography [15% (v/v) EtOAc in light petroleum] to give fu-

ranoside 52 as a white solid material (8.1 g, 90%). R_f0.60 (EtOAc/

1

light petroleum, 25:75, v/v). H NMR (CDCl₃): δ = 7.75–7.63 (m,

6 H), 7.59–7.56 (m, 2 H), 7.45–7.39 (m, 4 H), 7.36–7.24 (m, 8 H),

5.97 (d, J = 4.8 Hz, 1 H, 1-H), 4.78 (dd, J = 3.2 and 4.5 Hz, 1 H,

2-H), 4.43 (d, J = 3.1 Hz, 1 H, 3-H), 3.86 (d, J = 11.1 Hz, 1 H, 5-

Ha), 3.64 (d, J = 11.1 Hz, 1 H, 5-Hb), 3.37 (dd, J = 5.8 and

11.8 Hz, 1 H, 5Ј-Ha), 3.19 (dd, J = 7.7 and 11.8 Hz, 1 H, 5Ј-Hb),

1.77 (dd, J = 5.9 and 7.6 Hz, 1 H, 5Ј-OH), 1.32 and 1.22 [2s, 3 H 3,5-Di-O-(tert-butyldiphenylsilyl)-1,2-O-isopropylidene-4-C-(N-tri-

each, CH₃(isopropylidene)], 1.09 and 1.03 [2s, 9 H each, 2×C(CH₃)

₃] ppm. ¹³C NMR (CDCl₃): δ = 136.1, 136.0, 135.9, 135.7, 133.1,

133.0, 132.9, 130.0, 129.9, 129.8, 127.9, 127.8, 127.7, 112.9

fluoroacetylpiperazinyl)methyl-α-D-xylofuranose (53c): Trifluoro-

acetic anhydride (2.34 cm³, 16.3 mmol) was added to a stirred solu-

tion of furanose 53b (6.36 g, 8.3 mmol) in a mixture of Et₃N

[OC(CH₃)₂O], 104.4 (C-1), 90.3 (C-4), 88.5 (C-2), 78.7 (C-3), 65.2 (1.2 cm³) and CH₂Cl₂(40 cm³) and the resulting mixture was

(C-5), 62.9 (C-5Ј), 27.6 and 27.5 [CH₃(isopropylidene)], 27.1 and

27.0 [C(CH₃)₃], 19.4 and 19.2 [SiC(CH₃)₃] ppm. MALDI-HRMS:

m/z 719.3156 ([M + Na]⁺, C₄₁H₅₂O₆Si₂Na⁺calcd. 719.3195).

stirred for 4 h at room temp. The reaction mixture was concen-

trated to dryness under reduced pressure and the residue was coev-

oparated with toluene (2×10 cm³). The residue was purified by col-

umn chromatography [50% (v/v) EtOAc in light petroleum] to give

furanose 53c as a white solid (6.23 g, 87%). R_f0.43 (EtOAc/light

3,5-Di-O-(tert-butyldiphenylsilyl)-1,2-O-isopropylidene-4-C-(N-meth-

ylpiperazinyl)methyl-α-D-xylofuranose (53a): To a stirred solution

1

petroleum, 25:75, v/v). H NMR (CDCl₃): δ = 7.69–7.54 (m, 8 H),

of furanose 52 (2.76 g, 3.96 mmol) in a mixture of pyridine (5 cm³)

and CH₂Cl₂(30 cm³), was added dropwise triflic anhydride (1.7 g,

6.03 mmol) at –30 °C over 30 min and the resulting mixture was

stirred 12 h at room temp. The reaction mixture was washed with

saturated. aq. NaHCO₃(2×50 cm³), dried (Na₂SO₄), filtered and

the solvents evaporated to dryness under reduced pressure. The res-

idue was coevaporated with toluene (2×25 cm³) and then dissolved

in THF (22 cm³). N-methylpiperazine (3.9 g, 38.9 mmol) was added

to the stirred solution and the resulting mixture was stirred at room

temp. for 12 h. The reaction mixture was concentrated to dryness

under reduced pressure and the residue was coevoporated with tol-

uene (2×10 cm³). The residue was purified by column chromatog-

raphy [1% (v/v) MeOH in CH₂Cl₂] to give furanose 53a as a pale

7.37–7.17 (m, 12 H), 6.01 (d, J = 4.8 Hz, 1 H, 1-H), 4.95 (dd, J =

4.3 and 4.7 Hz, 1 H, 2-H), 4.38 (d, J = 4.1 Hz, 1 H, 3-H), 3.78 (d,

J = 11.0 Hz, 1 H, 5-Ha), 3.48 (d, J = 10.8 Hz, 1 H, 5-Hb), 3.22–

3.07 [m, 4 H, CH₂(piperazinyl)], 2.32–1.95 [m, 6 H, 5Ј-H and

CH₂(piperazinyl)], 1.29 and 1.24 [2s, 3 H each, CH₃(isopropylid-

ene)], 1.03 and 1.02 [2s, 9 H each, 2×C(CH₃)₃] ppm. ¹³C NMR

2

(CDCl₃): δ = 157.8 (q, J_C,F= 38.9 Hz, COCF₃), 136.4, 136.2,

136.0, 135.7, 133.3, 133.2, 132.9, 130.1, 130.0, 129.9, 129.8, 127.9,

1

127.8, 127.7, 116.4 (q, J_C,F= 288.0 Hz, CF₃), 113.1, 104.5, 90.4,

88.2, 80.2, 65.5, 58.8, 54.3, 53.7, 45.6, 43.2, 28.1, 28.0, 27.2, 27.0,

19.5, 19.1 ppm. MALDI-HRMS: m/z 883.3745 ([M + Na]⁺,

C₄₇H₅₉F₃N₂O₆Si₂Na⁺calcd. 883.3761).

yellow solid (2.86 g, 93%). R_f0.73 (MeOH/CH₂Cl₂, 10:90, v/v). ¹H 1,2-O-Isopropylidene-4-C-(N-methylpiperazinyl)methyl-α-

D-xylofur-

NMR (CDCl₃): δ = 7.69–7.56 (m, 8 H), 7.34–7.17 (m, 12 H), 6.00 anose (54a): Tetrabutylammonium fluoride (7.6 cm³, 7.6 mmol,

(d, J = 4.8 Hz, 1 H, 1-H), 4.92 (dd, J = 4.4 and 4.6 Hz, 1 H, 2-H),

4.40 (d, J = 3.8 Hz, 1 H, 3-H), 3.78 (d, J = 10.9 Hz, 1 H, 5-Ha),

3.52 (d, J = 10.9 Hz, 1 H, 5-Hb), 2.48–1.95 [m, 13 H, 5Ј-H, NCH₃

1.0 m solution in THF) was added to a solution of furanose 53a

(2.82 g, 3.62 mmol) in THF (20 cm³) and the resulting mixture was

stirred for 12 h at room temp. The reaction mixture was concen-

and CH₂(piperazinyl)], 1.27 and 1.21 [2s, 3 H each, CH₃(isopropyli- trated to dryness under reduced pressure and the residue was coev-

dene)], 1.02 and 1.01 [2s, 9 H each, 2×C(CH₃)₃] ppm. ¹³C NMR oporated with toluene (2×10 cm³). The residue was purified by

(CDCl₃): δ =136.4, 136.3, 135.9, 135.7, 133.4, 133.3, 133.1, 133.0, column chromatography [11% (v/v) MeOH in CH₂Cl₂] to give fu-

2316

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Eur. J. Org. Chem. 2005, 2297–2321

XNA (xylo Nucleic Acid): A Summary and New Derivatives

ranose 54a as a pale yellow solid material (960 mg, 88%) which

FULL PAPER

54b (2.80 g) with benzoyl chloride (2.57 cm³, 22.1 mmol) in a mix-

was crystallized from a 1:9 mixture of methanol and toluene. R_f

ture of pyridine (8 cm³) and CH₂Cl₂(20 cm³) was carried out as

1

0.36 (MeOH/CH₂Cl₂, 15:85, v/v). H NMR (CDCl₃): δ = 5.93 (d, described above for compound 55a. The crude residue obtained

J = 4.0 Hz, 1 H, 1-H), 4.60 (d, J = 4.1 Hz, 1 H, 2-H), 4.28 (s, 1 H, after work-up procedure was purified by column chromatography

3-H), 3.85 (s, 2 H, 5-H), 2.87 (d, J = 14.0 Hz, 1 H, 5Ј-Ha), 2.78– [20% (v/v) EtOAc in light petroleum] to give furanose 55b as a

2.74 [m, 3 H, 5Ј-Hb and CH₂(piperazinyl)], 2.66 [br. s, 2 H, CH₂(pi-

perazinyl)], 2.43 [br. s, 4 H, CH₂(piperazinyl)], 2.27 (s, 3 H, NCH₃),

1.56 and 1.31 [2s, 3 H each, CH₃(isopropylidene)] ppm. ¹³C NMR

white solid material (3.84 g, 84 % from 53c). R_f0.53 (MeOH/

CH₂Cl₂, 5:95, v/v). H NMR (CDCl₃): δ = 7.85 (d, J = 7.7 Hz, 4

H), 7.51–7.27 (m, 6 H), 6.02 (d, J = 4.5 Hz, 1 H), 5.60 (br. s, 1 H),

1

(CDCl₃): δ = 112.4 [OC(CH₃)₂O], 105.3 (C-1), 88.3 (C-4), 87.6 (C- 4.81 (m, 1 H), 4.63 (d, J = 11.5 Hz, 1 H), 4.33 (d, J = 11.4 Hz, 1

2), 79.2 (C-3), 66.2 (C-5), and 63.8 (C-5Ј), 55.4 and 55.2 [CH₂(pip-

H), 3.58–3.50 (m, 4 H), 2.87–2.74 (m, 4 H), 2.60–2.53 (m, 2 H),

erazinyl)], 46.0 (NCH₃), 27.0 and 26.2 [CH₃(isopropylidene)] ppm.

1.61 (s, 3 H), 1.32 (s, 3 H) ppm. ¹³C NMR (CDCl₃): δ = 165.9,

MALDI-HRMS: m/z 325.1736 ([M + Na]⁺, C₁₄H₂₆N₂O₅Na⁺165.5, 155.5 (d, J = 35.8 Hz), 133.8, 133.5, 133.4, 130.2, 129.8,

calcd. 325.1734).

129.6, 129.5, 128.9, 128.7 128.6, 128.5, 116.5 (d, J = 287.9 Hz),

113.9, 105.2, 88.3, 86.2, 79.6, 64.7, 60.3, 54.7, 54.2, 46.0 (d, J =

3.0 Hz), 43.6, 27.5, 26.9 ppm. MALDI-HRMS: m/z 615.1917 ([M

+ Na]⁺, C₂₉H₃₁F₃N₂O₈Na⁺calcd. 615.1925).

1,2-O-Isopropylidene-4-C-(N-trifluoroacetylpiperazinyl)methyl-α-D-

xylofuranose (54b): Tetrabutylammonium fluoride (17.7 cm³,

17.7 mmol, 1.0 m solution in THF) was added to a solution of fu-

ranose 53c (6.1 g, 7.1 mmol) in THF (50 cm³). The reaction mix-

ture was stirred for 12 h at room temp., concentrated to dryness

under reduced pressure and the residue was coevoporated with tol-

uene (2×15 cm³). The residue obtained was purified by column

chromatography [6% (v/v) MeOH in CH₂Cl₂] affording furanose

18b as a white solid material (2.56 g). R_f0.36 (MeOH/CH₂Cl₂,

10:90, v/v); NMR spectroscopic data revealed the compound to be

1,2-Di-O-acetyl-3,5-di-O-benzoyl-4-C-(N-methylpiperazinyl)methyl-

α,β-D-xylofuranose (56a): A solution of furanose 55a (2.5 g,

4.9 mmol) in 80% aqueous trifluoroacetic acid (25 cm³) was stirred

at room temp. for 3 h.The reaction mixture was concentrated to

dryness under reduced pressure and the residue was coevaporated

successively with absolute ethanol (2×20 cm³), toluene (2×10 cm³)

and pyridine (2×5 cm³). The yellow viscous oil obtained was dis-

solved in pyridine (10 cm³), acetic anhydride (4.62 cm³, 49 mmol)

was added dropwise, and the resulting mixture was stirred for 12 h

at room temp. The reaction mixture was concentrated to dryness

and the residue was dissolved in CH₂Cl₂(50 cm³) and washing was

performed with saturated aq. NaHCO₃(2×50 cm³). The organic

phase was dried (Na₂SO₄), filtered, concentrated to dryness under

reduced pressure. The residue was purified by column chromatog-

raphy [5% (v/v) MeOH in CH₂Cl₂] to give furanose 56a (1:1 mix-

ture of anomers, 2.46 g, 93%) as a white solid material. R_f0.60

(MeOH/CH₂Cl₂, 15:85, v/v). ¹H NMR (CDCl₃): δ = 7.86–7.80 (m,

8 H), 7.77–7.16 (m, 12 H), 6.41 [d, J = 4.6 Hz, 1 H, 1-H(A)], 6.16

[d, J = 2.1 Hz, 1 H, 1-H(B)], 5.84 [d, J = 4.0 Hz, 1 H, 3-H(B)], 5.79

[d, J = 8.6 Hz, 1 H, 3-H(A)], 5.65 [dd, J = 4.7 and 8.7 Hz, 1 H, 2-

H(A)], 5.54 [dd, J = 2.1 and 3.9 Hz, 1 H, 2-H(B)], 4.49–4.37 (m, 4

H, 5-H), 2.89–2.10 [m, 20 H, 5Ј-H and CH₂(piperazinyl)], 2.13 and

2.10 (2s, 3 H each, NCH₃), 2.02 and 1.91 (2s, 6 H each, 4×COCH₃)

ppm. ¹³C NMR (CDCl₃): δ =170.0, 169.8, 169.5, 165.9, 165.8,

165.4, 133.7, 133.6, 133.2, 133.1, 129.9, 129.8, 129.6, 129.5, 128.9,

128.7, 128.6, 128.5, 128.4, 98.6, 92.5, 88.9, 85.1, 81.2, 78.0, 76.4,

74.5, 64.5, 64.4, 63.1, 60.8, 55.5, 55.3, 54.9, 54.7, 46.1, 46.0, 21.2,

21.1, 20.9, 20.6 ppm. MALDI-HRMS: m/z 577.2165 ([M + Na]⁺,

C₂₉H₃₄N₂O₉Na⁺calcd. 577.2157).

1

contaminated with traces of tetrabutylammonium salts. H NMR

(CDCl₃): δ = 5.84 (d, J = 4.3 Hz, 1 H, 1-H), 4.48 (dd, J = 1.0 and

4.3 Hz, 1 H, 2-H), 4.05 (s, 1 H, 3-H), 3.77 (d, J = 12.0 Hz, 1 H, 5-

Ha), 3.73 (d, J = 12.3 Hz, 1 H, 5-Hb), 3.53–3.46 [m, 4 H, CH₂(pip-

erazinyl)], 2.77–2.68 [m, 2 H, CH₂(piperazinyl)], 2.64 (d, J =

14.0 Hz, 1 H, 5Ј-Ha), 2.57 (d, J = 14.1 Hz, 1 H, 5Ј-Hb), 2.50–2.39

[m, 2 H, CH₂(piperazinyl)], 1.43 and 1.19 [2s, 3 H each, CH₃(iso-

propylidene ppm. ¹³C NMR (CDCl₃): δ =155.7 (q, J = 37.8 Hz),

116.5 (q, J = 287.9 Hz), 112.6, 105.3, 89.6, 87.9, 79.9, 65.0, 61.6,

54.7, 54.3, 45.9 (d, J = 2.7 Hz), 43.5, 27.1, 26.3 ppm. MALDI-

HRMS: m/z 407.1391 ([M + Na]⁺, C₁₅H₂₃F₃N₂O₆Na⁺calcd.

407.1400).

3,5-Di-O-benzoyl-1,2-O-isopropylidene-4-C-(N-methylpiperazinyl)-

methyl-α-D

-xylofuranose (55a): Benzoyl chloride (1.98 cm³,

17.0 mmol) was added dropwise to a stirred solution of furanose

54a (1.71 g, 5.65 mmol) in a mixture of pyridine (6 cm³) and

CH₂Cl₂(15 cm³) and the resulting mixture was stirred 12 h at room

temp. The reaction mixture was evaporated to dryness under re-

duced pressure and the residue was dissolved in CH₂Cl₂(100 cm³)

and washed with saturated aq. NaHCO₃(2×50 cm³). The organic

phase was dried (Na₂SO₄), filtered, concentrated and coevaporated

with toluene (2×5 cm³). The residue obtained was purified by col-

umn chromatography [5% (v/v) MeOH in CH₂Cl₂] to give the fu-

ranose 55a (2.51 g, 87%) as a white solid material. R_f0.52 (MeOH/

CH₂Cl₂, 15:85, v/v). ¹H NMR (CDCl₃): δ = 7.83–7.79 (m, 4 H),

7.43 (d, J = 7.4 Hz), 7.39 (d, J = 7.5 Hz), 7.32–7.21 (m, 4 H), 6.02

(d, J = 4.4 Hz, 1 H, 1-H), 5.57 (d, J = 2.0 Hz, 1 H, 3-H), 4.78 (dd,

J = 1.9 Hz and 4.4, 2-H), 4.63 (d, J = 11.5 Hz, 1 H, 5-Ha), 4.35

(d, J = 11.7 Hz, 1 H, 5-Hb), 2.78–2.35 [m, 10 H, 5Ј-H and CH₂(pip-

erazinyl)], 2.18 (s, 3 H, NCH₃), 1.64 and 1.32 [2s, 3 H each, CH₃-

(isopropylidene)] ppm. ¹³C NMR (CDCl₃): δ = 166.0 and 165.5

(2×COC₆H₅), 133.6, 133.3, 129.8, 129.6, 129.5, 129.1, 128.6, 128.5,

113.9 [OC(CH₃)₂O], 105.1 (C-1), 88.2 (C-4), 86.5 (C-2), 79.9 (C-

3), 65.4 (C-5), 60.8 (C-5Ј), 55.2 and 54.8 [CH₂(piperazinyl)], 46.0

(NCH₃), 27.6 and 27.1 [CH₃(isopropylidene)] ppm. MALDI-

HRMS: m/z 533.2261 ([M + Na]⁺, C₂₈H₃₄N₂O₇Na⁺calcd.

533.2258).

1,2-Di-O-acetyl-3,5-di-O-benzoyl-4-C-(N-trifluoroacetylpiperazinyl)-

methyl-α,β-D-xylofuranose (56b): Acetolysis of furanose 55b (2.59 g,

4.37 mmol) was carried out with 80% trifluoroacetic acid (25 cm³)

following the procedure as described above for 56a. The residue

obtained after work-up procedure was acylated with acetic anhy-

dride (4.15 cm³, 44 mmol) in the presence of pyridine (10 cm³) and

the crude product obtained was purified by column chromatog-

raphy [5% (v/v) MeOH in CH₂Cl₂] to give furanose 56b (1:1 mix-

ture of anomers, 2.46 g, 91%) as a white solid material. R_f0.60

1

(MeOH/CH₂Cl₂, 5:95, v/v). H NMR (CDCl₃): δ = 7.88–7.81 (m,

8 H), 7.50–7.40 (m, 4 H), 7.36–7.19 (m, 8 H), 6.41 [d, J = 4.3 Hz,

1 H, 1-H(A)], 6.16 [br. s, 1 H, 1-H(B)], 5.84 [d, J = 4.1 Hz, 1 H, 3-

H(B)], 5.80 [d, J = 8.8 Hz, 1 H, 3-H(A)], 5.67 [dd, J = 4.8 and

8.6 Hz, 1 H, 2-H(A)], 5.57 [m, 1 H, 2-H(B)], 4.55–4.43 (m, 4 H, 5-

H), 3.60–3.50 (m, 8 H), 3.00 (d, J = 14.4 Hz), 2.86–2.61 (m, 9 H),

2.49–2.44 (m, 2 H), 2.08 (s, 6 H), 2.07 (s, 6 H) ppm. ¹³C NMR

3,5-Di-O-benzoyl-1,2-O-isopropylidene-4-C-(N-trifluoroacetylpiper- (CDCl₃): δ = 170.0, 169.7, 169.5, 169.4, 166.0, 165.8, 165.5, 155.7

azinyl)methyl-α- -xylofuranose (55b): Dibenzoylation of furanose (d, J = 35.5 Hz), 155.2 (d, J = 35.9 Hz), 133.9, 133.8, 133.6, 133.4,

D

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J. Wengel et al.

FULL PAPER

133.3, 130.2, 129.9, 129.8, 129.6, 129.5, 129.4, 129.3, 128.6, 128.5,

116.5 (q, J 289.3), 98.5, 92.6, 88.6, 84.9, 81.0, 77.8, 76.1, 74.2, 64.1,

62.4, 60.5, 54.7, 54.5, 54.2, 54.1, 46.2, 46.0, 43.7, 43.5, 21.2, 21.1,

ness under reduced pressure. The residue was coevoporated with

toluene (2×10 cm³) and purified by column chromatography [7–

8 % (v/v) MeOH in CH₂Cl₂] to give unreacted nucleoside 57a

20.9, 20.5 ppm. MALDI-HRMS: m/z 659.1832 ([M + Na]⁺, (620 mg, 30%), while [10% (v/v) MeOH in CH₂Cl₂] afforded the

C₃₀H₃₁F₃N₂O₁₀Na⁺calcd. 659.1823).

desired nucleoside 58 (1.1 g, 57%) as a white solid material. R_f0.41

1

(MeOH/CH₂Cl₂, 15:85, v/v). H NMR (CDCl₃/CD₃OD, 2:1): δ =

1-[2-O-Acetyl-3,5-di-O-benzoyl-4-C-(N-methylpiperazinyl)methyl-β-

7.90–7.84 (m, 4 H), 7.56–7.27 (m, 7 H), 6.06 (d, J = 6.6 Hz, 1 H),

5.80 (d, J = 6.5 Hz, 1 H), 4.52 (dd, J = 6.5 and 6.6 Hz), 4.38 (s, 2

H), 4.04 (br. s, 1 H), 2.89–2.67 (m, 10 H), 2.35 (s, 3 H), 1.60 (s, 3

H) ppm. ¹³C NMR (CDCl₃/CD₃OD, 2:1): δ = 166.0, 164.4, 151.3,

135.0, 133.8, 133.7, 129.6, 129.3, 129.2, 128.7, 128.6, 128.5, 111.5,

86.8, 85.5, 79.0, 77.1, 64.4, 60.5, 55.0, 54.0, 45.0, 11.9 ppm.

MALDI-HRMS: m/z 601.2280 ([M + Na]⁺, C₃₀H₃₄N₄O₈Na⁺

calcd. 601.2269).

D-xylofuranosyl]thymine (57a): N,O-Bis(trimethylsilyl)acetamide

(3.1 cm³, 12.5 mmol) was added to a suspension of furanose 56a

(2.46 g, 4.57 mmol) and thymine (0.70 g, 5.55 mmol) in anhydrous

acetonitrile (30 cm³). The reaction mixture was refluxed for 1 h

whereupon the clear solution was cooled to room temp. TMS-tri-

flate (1.1 cm³, 6.1 mmol) was added dropwise and the resulting

mixture was refluxed for 3 h. The reaction mixture was then cooled

to room temp. and diluted with CH₂Cl₂(100 cm³), washed with

saturated aq. NaHCO₃(2×50 cm³). The combined organic phase

was dried (Na₂SO₄), filtered and the solvents evaporated to dryness

under reduced pressure. The resulting yellow oil was purified by

column chromatography [5% (v/v) MeOH in CH₂Cl₂] to give the

nucleoside 57a (2.15 g, 76 %) as a white solid material. R_f0.50

1-[2-O-tert-Butyldimethylsilyl-3,5-di-O-benzoyl-4-C-(N-methylpip-

erazinyl)methyl-β-D-xylofuranosyl]thymine (59): A solution of nu-

cleoside 58 (1.04 g, 1.80 mmol), DMAP (440 mg, 3.6 mmol), imida-

zole (0.73 g, 10.7 mmol) and tert-butyldimethylsilyl chloride

(0.82 g, 5.4 mmol) in anhydrous DMF (18 cm³) was stirred for 12 h

(MeOH/CH₂Cl₂, 15:85, v/v). ¹H NMR (CDCl₃): δ = 8.01–7.98 (m, at 36 °C. To the reaction mixture was added CH₂Cl₂(100 cm³) and

2 H), 7.88–7.84 (m, 2 H), 7.55 (m, 1 H), 7.49–7.42 (m, 3 H), 7.40–

7.26 (m, 2 H), 7.21 (d, J = 1.1 Hz, 1 H, 6-H), 6.29 (d, J = 8.2 Hz,

1 H, 1Ј-H), 6.08 (d, J = 8.1 Hz, 1 H, 3Ј-H), 5.86 (t, J = 8.1 Hz, 1

washing was performed with saturated aq. NaHCO₃(2×50 cm³).

The organic phase was dried (Na₂SO₄), filtered, concentrated to

dryness under reduced pressure and the residue was purified by

H, 2Ј-H), 4.43 (d, J = 12.2 Hz, 1 H, 5Ј-Ha), 4.23 (d, J = 12.2 Hz, column chromatography [6% (v/v) MeOH in CH₂Cl₂] to give the

1 H, 5Ј-Hb), 2.84–2.66 [m, 10 H, 5ЈЈ-H and CH₂(piperazinyl)], 2.40

nucleoside 59 (1.06 g, 86 %) as a white solid material. R_f0.56

(s, 3 H, NCH₃), 2.04 (s, 3 H, COCH₃), 1.46 (s, 3 H, 5-CH₃) ppm. (MeOH/CH₂Cl₂, 15:85, v/v). ¹H NMR (CDCl₃): δ = 7.92–7.89 (m,

¹³C NMR (CDCl₃): δ = 170.4 (COCH₃), 165.9 and 165.8 2 H), 7.82–7.79 (m, 2 H), 7.48 (m, 1 H), 7.41–7.33 (m, 3 H), 7.26–

(2×COC₆H₅), 163.6 (C-4), 151.2 (C-2), 134.2, 134.0, 133.8, 129.8,

7.21 (m, 2 H), 7.16 (br. s, 1 H, 6-H), 6.01 (d, J = 7.1 Hz, 1 H, 1Ј-

129.5, 129.3, 129.0, 128.7, 128.5, 112.4 (C-5), 84.6 (C-4Ј), 82.3 (C- H), 5.76 (d, J = 6.9 Hz, 1 H, 3Ј-H), 4.51 (dd, J = 7.0 and 7.1 Hz,

1Ј), 75.9 and 75.5 (C-2Ј and C-3Ј), 64.8 (C-5Ј), 60.4 (C-5ЈЈ), 55.5

and 54.5 [CH₂(piperazinyl)], 45.4 (NCH₃), 20.8(COCH₃), 12.0 (5-

CH₃) ppm. MALDI-HRMS: m/z 643.2373 ([M + Na]⁺,

C₃₂H₃₆N₄O₉Na⁺calcd. 643.2375).

1 H, 2Ј-H), 4.38 (d, J = 12.1 Hz, 1 H, 5Ј-Ha), 4.24 (d, J = 12.2 Hz,

1 H, 5Ј-Hb), 2.88–2.60 [m, 6 H, 5ЈЈ-H and CH₂(piperazinyl)], 2.42

[br. s, 4 H, CH₂(piperazinyl)], 2.18 (s, 3 H, NCH₃), 1.49 (s, 3 H, 5-

CH₃), 0.68 [s, 9 H, C(CH₃)₃], –0.15 (s, 6 H, 2×SiCH₃) ppm. ¹³C

NMR (CDCl₃): δ = 165.9 and 165.8 (2×COC₆H₅), 163.6 (C-4),

150.6 (C-2), 134.7, 133.8, 133.7, 129.7, 129.4, 128.9, 128.8, 128.7,

111.8 (C-5), 85.3 (C-1Ј), 84.8 (C-4Ј), 79.2 (C-3Ј), 77.9 (C-2Ј), 64.8

(C-5Ј), 60.8 (C-5ЈЈ), 55.5 and 55.1 [CH₂(piperazinyl)], 45.9 (NCH₃),

25.5 [C(CH₃)₃], 17.9 [SiC(CH₃)₃], 12.0 (5-CH₃), –4.6 and –4.9

(2 × SiCH₃) ppm. MALDI-HRMS: m/z 715.3131 ([M + Na]⁺,

C₃₆H₄₈N₄O₈SiNa⁺calcd. 715.3134).

1-[2-O-Acetyl-3,5-di-O-benzoyl-4-C-(N-trifluoroacetylpiperazinyl)-

methyl-β-D-xylofuranosyl]thymine (57b): N,O-Bis(trimethylsilyl)

acetamide (2.6 cm³, 10.3 mmol) was added to a suspension of fu-

ranose 56b (2.29 g, 3.69 mmol) and thymine (0.57 g, 4.52 mmol) in

anhydrous acetonitrile (30 cm³). The reaction mixture was refluxed

for 1 h whereupon the clear solution was cooled to room temp.

TMS-triflate (0.84 cm³, 4.66 mmol) was added dropwise and the

mixture was refluxed for 3 h. After work-up procedure, as described

above for 57a, the resulting yellow oil was purified by column

chromatography [2% (v/v) MeOH in CH₂Cl₂] to give the nucleoside

1-[2-O-tert-Butyldimethylsilyl-4-C-(N-methylpiperazinyl)methyl-β-

D

-xylofuranosyl]thymine (60): A solution of nucleoside 59 (1.03 g

1.51 mmol) in saturated methanolic ammonia (50 cm³) was stirred

57b (2.15 g, 83 %) as a white solid material. R_f0.44 (MeOH/

CH₂Cl₂, 10:90, v/v). H NMR (CDCl₃): δ = 9.08 (br. s, 1 H, NH), under reduced pressure. The residue was coevoporated with toluene

8.08–8.05 (m, 2 H), 7.96–7.93 (m, 2 H), 7.66–7.58 (m, 2 H), 7.56–

for 24 h at room temp. The solution was evaporated to dryness

1

(2×10 cm³) and purified by column chromatography [10–12% (v/

7.48 (m, 2 H), 7.40–7.35 (m, 2 H), 7.26 (d, J = 1.2 Hz, 1 H, 6-H),

v) MeOH in CH₂Cl₂] to give nucleoside 60 (610 mg, 83%) as a

6.38 (d, J = 8.3 Hz, 1 H, 1Ј-H), 6.16 (d, J = 8.1 Hz, 1 H, 3Ј-H), white solid material. R_f0.36 (MeOH/CH₂Cl₂, 15:85, v/v). ¹H NMR

5.97 (dd, J = 8.2 and 8.3 Hz, 1 H, 2Ј-H), 4.51 (d, J = 12.2 Hz, 1

H, 5Ј-Ha), 4.29 (d, J = 12.4 Hz, 1 H, 5Ј-Hb), 3.93–3.73 [m, 4 H,

CH₂(piperazinyl)], 2.95–2.82 [m, 5 H, 5ЈЈ-Ha and CH₂(piperazi-

nyl)], 2.78 (d, J = 14.5 Hz, 1 H, 5ЈЈ-Hb), 2.12 (s, 3 H, COCH₃),

1.55 (s, 3 H, 5-CH₃) ppm. ¹³C NMR (CDCl₃): δ = 170.4, 166.1,

(CDCl₃): δ = 7.21 (s, 1 H, 6-H), 5.41 (d, J = 5.6 Hz, 1 H, 1Ј-H),

4.44 (dd, J = 5.4 and 5.4 Hz, 1 H, 2Ј-H), 4.02 (d, J = 5.2 Hz, 1 H,

3Ј-H), 3.74 (s, 2 H, 5Ј-H), 2.60–2.53 [m, 6 H, 5ЈЈ-H and CH₂(piper-

azinyl)], 2.39 [br. s, 4 H, CH₂(piperazinyl)], 2.21 (s, 3 H, NCH₃),

1.86 (s, 3 H, 5-CH₃), 0.80 (s, 9 H, C(CH₃)₃), 0.16 and –0.06 (2s, 3

165.9, 163.4, 155.5 (q, J = 35.9 Hz), 151.0, 134.2, 134.1, 134.0, H each, 2×SiCH₃) ppm. ¹³C NMR (CDCl₃): δ =163.8 (C-4), 150.7

129.9, 129.8, 129.5, 129.4, 129.3, 129.1, 128.8, 128.7, 128.3, 116.6

(q, J = 288.5 Hz), 112.5, 84.4, 82.2, 75.8, 75.0, 64.6, 60.4, 55.2,

54.7, 46.4, 43.9, 20.8, 12.1 ppm. MALDI-HRMS: m/z 725.2035([M

+ Na]⁺, C₃₃H₃₃F₃N₄O₁₀Na⁺calcd. 725.2041).

(C-2), 138.5 (C-6), 111.4 (C-5), 92.4 (C-1Ј), 87.5 (C-4Ј), 80.6 and

80.2 (C-2Ј and C-3Ј), 65.6 (C-5Ј), 62.3 (C-5ЈЈ), 55.3 and 55.0

[CH₂(piperazinyl)], 45.9 (NCH₃), 25.7 [C(CH₃)₃], 18.0 [SiC(CH₃)₃],

12.5 (5-CH₃), –4.5 and –4.9 (2×SiCH₃) ppm. MALDI-HRMS: m/

z 507.2608 ([M + Na]⁺, C₂₂H₄₀N₄O₆SiNa⁺calcd. 507.2609).

1-[3,5-Di-O-benzoyl-4-C-(N-methylpiperazinyl)methyl-β-D-xylofur-

anosyl]thymine (58): A solution of nucleoside 57a (2.08 g,

3.35 mmol) in 10% saturated methanolic ammonia (80 cm³) was

stirred for 1 h at room temp. The solution was evaporated to dry-

1-[2-O-tert-Butyldimethylsilyl-5-O-(4,4Ј-dimethoxytrityl)-4-C-(N-

methylpiperazinyl)methyl-β-D-xylofuranosyl]thymine (61): Dimeth-

oxytrityl chloride (485 mg, 1.43 mmol) was added in one portion

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XNA (xylo Nucleic Acid): A Summary and New Derivatives

FULL PAPER

to a stirred solution of the nucleoside 60 (578 mg, 1.19 mmol) in

anhydrous pyridine (10 cm³). The reaction mixture was stirred for

12 h at room temp., methanol (0.2 cm³) was added and stirring was

continued for another 15 min. The mixture was concentrated to

dryness under reduced pressure and the residue was dissolved in

CH₂Cl₂(20 cm³) and washed with saturated aq. NaHCO₃

(2×10 cm³). The separated organic phase was dried (Na₂SO₄), fil-

tered, concentrated to dryness under reduced pressure and coevap-

orated with toluene (2×2 cm³). The crude product obtained was

purified by column chromatography [2% MeOH in CH₂Cl₂, con-

taining 0.5% Et₃N (v/v/v)] to afford nucleoside 61 as a white solid

material (826 mg, 88%). R_f0.47 (MeOH/CH₂Cl₂, 15:85, v/v). ¹H

NMR (CDCl₃): δ = 7.41 (s, 1 H, 6-H), 7.32 (d, J = 7.0 Hz, 2 H),

7.21–7.13 (m, 7 H), 6.72 (d, J = 8.8 Hz, 4 H), 5.88 (d, J = 6.5 Hz,

1 H, 1Ј-H), 4.24 (dd, J = 6.2 and 6.3 Hz, 1 H, 2Ј-H), 4.00 (dd, J =

6.4 and 7.5 Hz, 1 H, 3Ј-H), 3.70 (s, 6 H, 2×OCH₃), 3.27 (d, J =

10.8 Hz, 1 H, 5Ј-Ha), 3.23 (d, J = 10.7 Hz, 1 H, 5Ј-Hb), 2.74 (d, J

= 8.5 Hz, 1 H, 3Ј-OH), 2.43–2.26 [m, 10 H, 5ЈЈ-H and CH₂(piperaz-

inyl)], 2.13 (s, 3 H, NCH₃), 1.30 (s, 3 H, 5-CH₃), 0.77 [s, 9 H,

C(CH₃)₃], 0.10 and –0.07 (2s, 3 H each, 2×SiCH₃) ppm. ¹³C NMR

(CDCl₃): δ = 163.8, 159.0, 150.6, 144.1, 136.2, 135.1, 135.0, 130.2,

130.1, 128.2, 128.1, 127.4, 113.5, 111.3, 88.0, 87.1, 86.0, 81.0, 80.2,

64.7, 61.5, 55.3, 54.9, 45.9, 25.7, 18.0, 11.8, –4.4, –4.8 ppm.

MALDI-HRMS: m/z 809.3901 ([M + Na]⁺, C₄₃H₅₈N₄O₈SiNa⁺

calcd. 809.3916).

concentrated to dryness to afford nucleoside 64 (769 mg, 71%) as a

white solid material. R_f0.16 (MeOH/CH₂Cl₂, 15:85, v/v). ¹H NMR

(CD₃OD): δ = 7.92 (s, 1 H, 6-H), 5.93 (d, J = 5.1 Hz, 1 H, 1Ј-H),

4.29–4.26 (m, 2 H, 2Ј-H and 3Ј-H), 3.75 (d, J = 11.8 Hz, 1 H, 5Ј-

Ha), 3.62 (d, J = 12.0 Hz, 1 H, 5Ј-Hb), 2.93–2.89 [m, 4 H, CH₂(pip-

erazinyl)], 2.72–2.62 [m, 4 H, CH₂(piperazinyl)], 2.55 (d, J =

14.1 Hz, 1 H, 5ЈЈ-Ha), 2.48 (d, J = 14.4 Hz, 1 H, 5ЈЈ-Hb), 1.89 (s,

3 H) ppm. ¹³C NMR (CD₃OD): δ = 166.4, 153.0, 138.5, 111.7,

88.7, 87.9, 79.9, 78.9, 64.8, 62.8, 56.3, 46.5, 12.5 ppm. MALDI-

HRMS: m/z 379.1582 ([M + Na]⁺, C₁₅H₂₄N₄O₆Na⁺calcd.

379.1588).

1-[4-C-(N-Trifluoroacetylpiperazinyl)methyl-β-D-xylofuranosyl]thy-

mine (65): To a suspension of nucleoside 64 (713 mg, 2.0 mmol) in

anhydrous methanol (25 cm³) was added DMAP (122 mg,

1.0 mmol) and ethyl trifluoroacetate (568 mg, 4.0 mmol). The reac-

tion mixture was stirred for 12 h at room temp. and then concen-

trated to dryness under reduced pressure. The residue obtained was

purified by column chromatography [6–8% (v/v) MeOH in CH₂Cl₂]

to afford nucleoside 65 as a white solid material (760 mg, 84%). R_f

1

0.21 (MeOH/CH₂Cl₂, 10:90, v/v); H NMR (CDCl₃): δ = 7.59 (s,

1 H), 5.67 (d, J = 5.7 Hz, 1 H), 4.24 (dd, J = 5.9 and 6.1 Hz, 1 H),

4.12 (d, J = 6.3 Hz, 1 H), 3.63–3.47 (m, 6 H), 2.54–2.44 (m, 6 H),

1.71 (s, 3 H) ppm. ¹³C NMR (CDCl₃): δ = 164.8, 155.6 (q, J =

35.5 Hz), 151.6, 137.3, 116.5 (q, J 287.8), 111.1, 88.2, 87.9, 79.5,

78.6, 64.4, 61.4, 54.8, 54.3, 45.9, 43.5, 12.4. MALDI-HRMS: m/z

1-{2-O-tert-Butyldimethylsilyl-3-O-[2-cyanoethoxy(diisopropyl- 475.1402 ([M + Na]⁺, C₁₇H₂₃F₃N₄O₇Na⁺calcd. 475.1411).

amino)phosphanyl]-5-O-(4,4Ј-dimethoxytrityl)-4-C-(N-methylpipera-

zinyl)methyl-β-D-xylofuranosyl}thymine (62): 2-Cyanoethyl N,N-di-

1-[5-O-4,4Ј-Dimethoxytrityl-4-C-(N-trifluoroacetylpiperazinyl)-

methyl-β-D-xylofuranosyl]thymine (66): To a solution of nucleoside

isopropylphosphoramido chloridite (125 mg, 0.53 mmol) was

added dropwise to a stirred solution of the nucleoside 61 (350 mg,

0.44 mmol) in a mixture of diisopropylethylamine (0.5 cm³) and an-

hydrous CH₂Cl₂(10 cm³) at room temp. After stirring the mixture

was for 6 h, the reaction mixture was diluted with CH₂Cl₂(20 cm³).

Washing was performed with saturated aq. NaHCO₃(2×10 cm³).

The separated organic phase was dried (Na₂SO₄), filtered and con-

centrated to dryness under reduced pressure. The residue obtained

was purified by column chromatography [70–90% EtOAc in n-hex-

ane, containing 0.5% Et₃N (v/v/v)] to give amidite 62 as a white

solid material (400 mg, 91%). R_f0.36 (EtOAc/light petroleum,

75:25, v/v). ³¹P NMR (CDCl₃): δ = 151.6, 150.0 ppm.

65 (724 mg, 1.6 mmol) in anhydrous pyridine (3 cm³) was added

dimethoxytrityl chloride (592 mg, 1.75 mmol) and the resulting

mixture was were stirred for 12 h at room temp. MeOH (0.1 cm³)

was added and stirring was continued for 20 min. The mixture was

concentrated to dryness under reduced pressure and the residue

was dissolved in CH₂Cl₂(25 cm³) and washed with saturated aq.

NaHCO₃(2 × 25 cm³). The separated organic phase was dried

(Na₂SO₄), filtered, concentrated to dryness under reduced pressure

and coevaporated with toluene (2×1.0 cm³). The crude product ob-

tained was purified by column chromatography [3–5% MeOH in

CH₂Cl₂, containing 0.5% Et₃N (v/v/v)] to afford nucleoside 66 as

a white solid material (1.07 g, 89 %). R_f0.33 (MeOH/CH₂Cl₂,

1

1-[4-C-(N-Methylpiperazinyl)methyl-β-

D

-xylofuranosyl]thymine

15:85, v/v). H NMR (CDCl₃): δ = 7.38 (d, J = 7.6 Hz, 2 H), 7.36

(63): A solution of nucleoside 57a (124 mg, 0.2 mmol) in saturated

methanolic ammonia (10 cm³) was stirred for 36 h at room temp.

The solution was evaporated to dryness under reduced pressure,

and the residue dissolved in distilled water (10 cm³) and washing

was performed with diethyl ether (3×10 cm³). The separated aque-

ous phase was concentrated to dryness to afford nucleoside 64

(s, 1 H, 6-H), 7.28–7.15 (m, 7 H), 6.76 (d, J = 8.8 Hz, 4 H), 5.94

(d, J = 4.5 Hz, 1 H, 1Ј-H), 4.44 (dd, J = 4.1 and 4.3 Hz, 1 H, 2Ј-

H), 4.22 (d, J = 4.4 Hz, 1 H, 3Ј-H), 3.69 (s, 6 H, 2×OCH₃), 3.51–

3.38 [m, 5 H, 5Ј-Ha and CH₂(piperazinyl)], 3.25 (d, J = 10.0 Hz, 1

H, 5Ј-Hb), 2.66–2.51 [m, 6 H, 5ЈЈ-H and CH₂(piperazinyl)], 1.30 (s,

3 H, 5-CH₃) ppm. ¹³C NMR (CDCl₃): δ = 164.3, 158.9, 158.8,

(48 mg, 65%) as a white solid material. R_f0.25 (MeOH/CH₂Cl₂, 155.5 (q, J = 35.8 Hz), 151.8, 144.4, 137.0, 135.3, 135.2, 130.3,

1

15:85, v/v). H NMR (CD₃OD): δ = 7.92 (s, 1 H, 6-H), 5.92 (d, J 130.2, 128.2, 128.1, 127.2, 127.1, 116.5 (q, J = 287.7 Hz), 113.4,

= 5.3 Hz, 1 H, 1Ј-H), 4.29–4.26 (m, 2 H, 2Ј-H and 3Ј-H), 3.75 (d, 110.3, 89.5, 89.3, 87.5, 80.3, 78.5, 63.9, 60.7, 55.3, 54.6, 54.2, 46.0

J = 11.9 Hz, 1 H, 5Ј-Ha), 3.61 (d, J = 11.1 Hz, 1 H, 5Ј-Hb), 2.66–

2.53 [m, 9 H, 5ЈЈ-Ha and CH₂(piperazinyl)], 2.49 (d, J = 14.0 Hz,

1 H, 5ЈЈ-Hb), 2.32 (s, 3 H, NCH₃), 1.89 (s, 3 H, 5-CH₃) ppm. ¹³C

NMR (CD₃OD): δ = 167.6, 153.0, 138.5, 111.7, 88.6, 87.8, 79.8,

78.8, 64.8, 62.0, 56.2, 55.4, 45.8, 12.5 ppm. MALDI-HRMS: m/z

393.1757 ([M + Na]⁺, C₁₆H₂₆N₄O₆Na⁺calcd. 393.1745).

(d, J = 20.3 Hz), 43.4, 12.1 ppm. MALDI-HRMS: m/z 777.2680

([M + Na]⁺, C₃₈H₄₁F₃N₄O₉Na⁺calcd. 777.2718).

1-[2-O-Acetyl-5-O-(4,4Ј-dimethoxytrityl)-4-C-(N-trifluoroacetylpip-

erazinyl)methyl-β-D-xylofuranosyl]thymine (67): Acetic anhydride

(44 mg, 0.44 mmol) dissolved in CH₃CN (0.5 cm³) was added drop-

wise to a stirred solution of nucleoside 66 (330 mg, 0.44 mmol) and

DMAP (21 mg, 0.17 mmol) in CH₃CN (5 cm³). The reaction mix-

ture was stirred for 3 h at room temp. MeOH (0.2 cm³) was added

and stirring was continued for another 30 min. CH₂Cl₂(25 cm³)

was added and the mixture was washed with saturated aq.

NaHCO₃(2 × 10 cm³). The separated organic phase was dried

(Na₂SO₄), filtered and concentrated to dryness under reduced pres-

1-(4-C-Piperazinylmethyl-β-D-xylofuranosyl)thymine (64): A solu-

tion of nucleoside 57b (2.11g, 3.0 mmol) in saturated methanolic

ammonia (100 cm³) was stirred for 36 h at room temp. The solution

was evaporated to dryness under reduced pressure and then parti-

tioned between distilled water (50 cm³) and diethyl ether (50 cm³).

The aqueous phase was washed with diethyl ether (2×50 cm³) and

Eur. J. Org. Chem. 2005, 2297–2321

www.eurjoc.org

2319

J. Wengel et al.

FULL PAPER

sure. The crude product obtained was purified by column

mentary strands (assuming identical extinction coefficients of stan-

chromatography [60–66 % EtOAc in light petroleum, containing dard and modified nucleotides). During melting experiemnts, the

absorbance was monitored at 260 nm while the temperature was

0.5% Et₃N (v/v/v)] to afford nucleoside 67 as a white solid material

(252 mg, 72 %). R_f0.40 (MeOH/CH₂Cl₂, 10:90, v/v). ¹H NMR raised at a rate of 1 °C per min. The melting temperatures (T_m

(CDCl₃): δ = 9.31 (br. s, 1 H, NH), 7.57 (d, J = 1.0 Hz, 1 H, 6-H), values) of the complexes were determined as the maximum of the

7.46–7.43 (m, 2 H), 7.34–7.24 (m, 7 H), 6.85 (d, J = 8.6 Hz, 4 H), first derivatives of the melting curves obtained.

6.16 (d, J = 7.4 Hz, 1 H, 1Ј-H), 5.73 (dd, J = 7.3 and 7.4 Hz, 1 H,

Supporting Information (see also footnote on the first page of this

2Ј-H), 4.47 (d, J = 7.2 Hz, 1 H, 3Ј-H), 3.79 (s, 6 H, 2×OCH₃),

article): (ESI). Copies of ¹³C NMR spectra of compounds 3 (β-

3.66–3.55 [m, 4 H, CH₂(piperazinyl)], 3.40 (d, J = 10.5 Hz, 1 H,

anomer), 5a, 9, 10, 15, 16, 20–23, 25, 27–29, 32, 33, 36–39, 41, 43–

5Ј-Ha), 3.33 (d, J = 10.5 Hz, 1 H, 5Ј-Hb), 2.70–2.53 [m, 4 H,

46, 47 (major isomer), 47 (minor isomer), 48a, 48b, 49a, 49b, 50a,

CH₂(piperazinyl)], 2.43 (s, 2 H, 5ЈЈ-H), 2.16 (s, 3 H, COCH₃), 1.37

50b, 52, 53a, 53b, 54a, 55a, 55b, 56a, 56b, 57a, 57b, 58–61, 66, 67

(s, 3 H, 5-CH₃) ppm. ¹³C NMR (CDCl₃): δ = 171.0, 163.8, 159.1,

and ³¹P NMR spectra of compounds 7, 12, 31, 51a, 51b, 62 and

68.

159.0, 155.4 (d, J = 35.3 Hz), 151.1, 143.7, 135.9, 134.8, 134.7,

130.3, 130.2, 128.3, 128.2, 127.5, 116.5 (d, J = 287.9 Hz), 113.5,

112.1, 88.2, 86.7, 82.8, 78.9, 76.7, 64.2, 60.4, 55.4, 54.8, 54.4, 46.1,

43.6, 20.9, 11.7 ppm. MALDI-HRMS: m/z 819.2811 ([M + Na]⁺,

Acknowledgments

C₄₀H₄₃F₃N₄O₁₀Na⁺calcd. 819.2824).

We thank the Danish National Research Foundation for financial

support, Ms Britta M. Dahl, University of Copenhagen, for oligo-

nucleotide syntheses and Dr. Michael Meldgaard, Exiqon A/S, for

MALDI-MS analyses. We are grateful to the Technical University

of Denmark for diffractometer access to A. D. B.

1-{2-O-Acetyl-3-O-[2-cyanoethoxy(diisopropylamino)phosphanyl]-5-

O-(4,4Ј-dimethoxytrityl)-4-C-(N-trifluoroacetylpiperazinyl)methyl-

β-D-xylofuranosyl}thymine (68): 2-Cyanoethyl N,N-diisopropyl-

phosphoramidochloridite (125 mg, 0.53 mmol) was added dropwise

to a stirred solution of the nucleoside 67 (350 mg, 0.44 mmol) in a

mixture of diisopropylethylamine (0.5 cm³) and anhydrous CH₂Cl₂

(10 cm³) at room temp. After stirring the resulting mixture was for

6 h, the reaction mixture was diluted with CH₂Cl₂(20 cm³). Wash-

ing was performed with saturated aq. NaHCO₃(2×10 cm³). The

separated organic phase was dried (Na₂SO₄), filtered and concen-

trated to dryness under reduced pressure. The residue obtained was

purified by column chromatography [70–90% EtOAc in n-hexane

containing 0.5% Et₃N (v/v/v)] to give amidite 68 as a white solid

material (400 mg, 91%). R_f0.51, 0.56 (MeOH/CH₂Cl₂, 10:90, v/v);

δ_p(CDCl₃) 154.6 and 152.9. MALDI-HRMS: m/z 1019.3859 ([M

+ Na]⁺, C₄₉H₆₀F₃N₆O₁₁PNa⁺calcd. 1019.3902).

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2320

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Eur. J. Org. Chem. 2005, 2297–2321

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2321

Article Doi

XNA ?(xylo nucleic acid): A summary and new derivatives

DOI: 10.1002/ejoc.200500023

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Article abstract of DOI:10.1002/ejoc.200500023

Full text of DOI:10.1002/ejoc.200500023

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