Synthesis and application of a novel, crystalline phosphoramidite monomer with thiol terminus, suitable for the synthesis of DNA conjugates

Article abstract of DOI:10.1016/S0968-0896(00)00339-4

A new, crystalline 5′-thiol modifier phosphoramidite monomer (3), suitable for DNA synthesis, has been prepared. This monomer has been built into an oligonucleotide using the standard protocol. After cleavage, purification and removal of the trityl group

Full text of DOI:10.1016/S0968-0896(00)00339-4

Bioorganic & Medicinal Chemistry 9 (2001) 1241±1247
Synthesis and Application of a Novel, Crystalline
Phosphoramidite Monomer with Thiol Terminus,
Suitable for the Synthesis of DNA Conjugates
Zoltan Kupihar,a Zoltan Schmel,b Zoltan Kele,a
Botond Penkea and Lajos Kovacsa,*
a
Â
Â
Department of Medicinal Chemistry, Dom ter 8, University of Szeged, H-6720 Szeged, Hungary
bDepartment of Pharmaceutical Analysis, Somogyi B. u. 4, University of Szeged, H-6720 Szeged, Hungary
Received 7 September 2000; accepted 14 December 2000
AbstractÐA new, crystalline 50-thiol modi®er phosphoramidite monomer (3), suitable for DNA synthesis, has been prepared. This
monomer has been built into an oligonucleotide using the standard protocol. After cleavage, puri®cation and removal of the trityl
group with Ag+, a free 50-thiol terminal oligonucleotide (15) has been obtained which was subsequently coupled to a cysteine
derivative via a disul®de bridge to a€ord conjugate 16. # 2001 Elsevier Science Ltd. All rights reserved.
Introduction
morpholinophosphite (MMP),2 2-cyanoethyl-N,N-di-
isopropyl-phosphoramidite5 H-phosphonate1
or
Conjugates of synthetic nucleic acids are indispensible
tools of modern molecular biology. These conjugates
can be simple organic compounds (¯uorescent dyes,
biotin) and/or biopolymers (peptides, proteins). The
synthesis of these conjugates implies the formation of a
suitable functional group on the nucleic acid for cou-
pling. This can be performed both in solution, when the
corresponding nucleic acid is modi®ed either chemically
or enzymatically, and on solid phase, when the desired
protected functional group is coupled to the terminus
during oligonucleotide synthesis.
derivative. A high eciency in incorporating these
modi®ers is due to the enhanced reactivity of P(III)
compounds. The common drawback of these mono-
mers, except the trityl protected propyl chain and
MMP-containing compound, is that they can only be
synthesized as oils, which makes further use less con-
venient. On the other hand, the use of the propyl chain-
containing compound is restricted as the short spacer
arm may result in low eciency in further use of the DNA
conjugates of peptides and proteins.6
In our experience, almost quantitative coupling can be
achieved with the most widely applied and commercially
available monomer 15 (Fig. 1) if it is freshly prepared
and puri®ed while the older monomer (synthesized some
months before) results in less ecient coupling. This is
due to the dicult puri®cation and easier decomposi-
tion of oils, and, in addition, amidites are sensitive to
moisture, acidic environment and oxidation. Therefore,
our aim was to develop a stable, crystalline amidite
monomer and to demonstrate its utility in the preparation
of an oligonucleotide conjugate.
This latter method is applied most widely as it is easier
to carry out and o€ers less side reactions. Among many
others, a 50 terminal thiol group is one of the most
popular groups. Coupling to this group can be per-
formed by a reactive halogene-containing compound,
such as derivatives of iodoacetic acid or another (active)
thiol resulting in a thioether or disul®de, respectively.
For solid-phase oligonucleotide synthesis, several 50-
thiol modi®ers have been described previously.1À4 These
modi®ers are mostly a,o-thioalcohols containing three
or six carbon atoms. The thiol group of these com-
pounds is protected by trityl1,2 or the base sensitive 2-
(2,4-dinitrophenyl)ethyl (Dnpe)4 groups and the
hydroxyl function is converted to its methoxy-
Results and Discussion
Puri®cation of the modi®ed oligonucleotides is easier if
the 50-thiol is protected by trityl rather than by Dnpe
group because the former keeps its trityl group after
*Corresponding author. Tel.: +36-62-54-5145; fax: +36-62-54-5971;
e-mail: kupi@ovrisc.mdche.u-szeged.hu (Z. Kupihar), kovacs@ov-
risc.mdche.u-szeged.hu (L. Kovacs)
0968-0896/01/$ - see front matter # 2001 Elsevier Science Ltd. All rights reserved.
PII: S0968-0896(00)00339-4

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Z. Kupihar et al. / Bioorg. Med. Chem. 9 (2001) 1241±1247
1242
cleavage under standard condition with ammonia (this
latter is commonly referred to as the `trityl-on' method).
The use of amidites compared to H-phosphonates is a
more fortunate choice as subsequent oxidation after
coupling requires milder conditions, ruling out the
removal of trityl group, which can also take place under
harsh oxidation conditions.7 Therefore, we have applied
phosphoramidite monomer 1 (Fig. 1) as a lead structure
considering that incorporation of one or more amide
bonds might result in a crystalline substance.
identi®cation of the products easier on TLC. Thus,
amidite 2 has been obtained by coupling acid 4 and the
protected amine 6 with HOBT/HBTU (!7), subse-
quently desilylated with TBAF (!8) and followed by
phosphitylation using 2-cyanoethyl N,N-diisopropyl-
chlorophosphoramidite9 (!2, Scheme 1). Unfortu-
nately, although 1H, 13C and 31P NMR characterization
revealed the purity of compound 2, it remained oil after
several puri®cations by column chromatography fol-
lowed by trituration with di€erent solvents (light
petroleum, diethyl ether or EtOAc).
The ®rst compound of choice has been a substance
containing one amide bond (2, Fig. 1). The synthesis of
this compound has been attempted ®rst by coupling
acid 48 (Scheme 1) to 3-aminopropanol (5). In order to
avoid coupling on the unprotected hydroxyl group of
3-aminopropanol, the less reactive DCC has been used
as a coupling agent. Unfortunately, the resulting DCU
could not be removed quantitatively even by repeated
column chromatography. Therefore, we have performed
the coupling reaction applying the TBDPS protecting
group that has been stable during coupling and later
upon Fmoc deprotection and its removal with TBAF
has not a€ected the S-trityl group, and made the
Therefore, we have considered the incorporation of
further amide bonds into the spacer arm in order to
improve its crystallization propensity. Thus, an addi-
tional Gly-Gly moiety has been built into the former
amidite (3, Fig. 1). The multistep synthesis of this com-
pound is illustrated in Scheme 2. Fmoc-Gly-Gly-OH (9)
has been coupled to protected amine 6 to give com-
pound 10, then, after removal of the Fmoc group with
diethylamine, acid 4 has been coupled to amine 11
applying HOBT/HBTU (!12). After desilylation
with TBAF (!13), subsequent phosphitylation using
2-cyanoethyl N,N-diisopropylchlorophosphoramidite
and puri®cation by column chromatography followed
by trituration with cold diethyl ether, the desired ami-
dite monomer 3 has been obtained as a crystalline sub-
stance. It is noteworthy that phosphoramidites are
sensitive to acids, nucleophilic attack and oxidation
therefore their mass spectrometric characterization is
Figure 1. Phosphoramidite monomers with thiol terminus, amenable
for the synthesis of DNA conjugates.
Scheme 1. Reagents and conditions: (a) TBDPS-Cl, DCM, TEA, rt,
1 h, then aq HCl; (b) HOBT, HBTU, DIPEA, DCM, rt, 1 h; (c)
TBAF, THF, rt, 6 h; (d) 2-cyanoethyl N,N-diisopropylchloropho-
sphoramidite, DIPEA, abs DCM, rt, 1 h.
Scheme 2. Reagents and conditions: (a) HOBT, HBTU, DIPEA,
THF, rt, 3 h; (b) diethylamine, DCM, rt, 16 h; (c) HOBT, HBTU,
DIPEA, DCM, rt, 3 h; (d) TBAF, THF, rt, 6 h; (e) 2-cyanoethyl N,N-
diisopropylchlorophosphoramidite, DIPEA, abs DCM, rt, 1 h.

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Z. Kupihar et al. / Bioorg. Med. Chem. 9 (2001) 1241±1247
1243
Scheme 3. Reagents and conditions: (a) (1) standard phosphoramidite
coupling with CPG-bound 50-HO-T6 oligomer; (2) deprotection with
aq cc. NH3, 50 ꢀC, 16 h; (b) (1) AgNO3, 0.1 M TEAA, pH 7.0, 30 min;
(2) DTT, 0.1 M TEAA, pH 7.0, 1 h; (c) N-Boc-l-Cys(Npys)-OH, 0.1
M TEAA, pH 7.0, rt, 16 h.
Figure 3. Nano-ESI mass spectrum of conjugate 14. Calcd Mr 2330.5
(monoisotopic).
the general protocol with the only di€erence being at the
oxidation step. There are contradictory data in the litera-
ture as if iodine removes the S-trityl group,2,7 therefore a
tBuOOH/THF/water solution, applied successfully in the
phosphorylation of peptides,11 has been used for oxida-
tion instead of iodine. Subsequent cleavage with aqu-
eous NH3 and puri®cation after synthesis has been
carried out in the usual manner. According to LC±MS
analyses, only 1±2% of homoT hexamer lacking the
linker residue has been found. The HPLC pro®le and
nano-ESI mass spectrum of oligonucleotide 14, puri®ed
on a Poly-PakTM cartridge according to a modi®ed
procedure, are presented in Figs 2 and 3. Removal of
the trityl group (!15) was carried out by AgNO3 fol-
lowed by DTT treatment.2 According to HPLC and MS
analyses, this method can be applied with the same e-
ciency as for the previously used monomer 1.
In order to test the new monomer, the free thiol-con-
taining oligonucleotide 15 has been coupled to a pro-
tected cysteine. To form this asymmetric disul®de
bridge, the 3-nitro-2-pyridinesulfenyl (S-Npys) acti-
vated12 cysteine derivative N-Boc-l-Cys(Npys)-OH has
been used. According to LC±MS analysis, the oligonu-
cleotide has been converted to the corresponding di-
sul®de 16 quantitatively.
Figure 2. HPLC chromatogram of puri®ed oligonucleotide 14.
troublesome. Their analysis is further hampered by the
presence of (substituted) trityl groups, common protec-
tive groups in oligonucleotide chemistry, which a€ord
very intensive signals in the mass spectrum. These di-
culties have been successfully eliminated by the applica-
tion of our recently developed nanoelectrospray
methodology employing lithium chloride in acetonitrile
solution.10 We have extensively applied this novel
method during the course of the synthesis.
Conclusion
We have described the synthesis and application of a
novel, crystalline 50-thiol modi®er phosporamidite
monomer (3) for oligonucleotide synthesis. Although
the multistep synthesis described herein is a lengthy one,
compared to that of the generally used monomer (1), it
employs standard steps with good yields and the
Next, amidite monomer 3 has been coupled to a homo-
thymidine hexamer (Scheme 3, !14) using an auto-
matic DNA synthesizer. As the monomer is highly
soluble in acetonitrile, its coupling was very similar to

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Z. Kupihar et al. / Bioorg. Med. Chem. 9 (2001) 1241±1247
1244
following use of the compound is more convenient.
NMR purity control revealed that the new compound is
stable for more than half a year without detectable trace
of decomposition or oxidation if stored at À20 ꢀC under
refers to the fraction with distillation range 40±60 ꢀC.
Organic solutions were dried using magnesium sulfate
and evaporated in Buchi rotary evaporators. TLC: Kie-
selgel 60F
(Merck), visualization: UV light and nin-
254
t
argon. Furthermore, BuOOH-mediated oxidation, pre-
hydrin solution for amines, IN3 solution for S(II) and
P(III) compounds. Column chromatography: Kieselgel
60 (0.063±0.200 mm, Merck). Amidites (1±3) were pur-
i®ed on Merck TLC silica gel 60H (mean particle size
15 mm) absorbent.18,19 Mp: Electrothermal IA 8103
apparatus. Elemental analysis: Perkin-Elmer CHNS
analyzer model 2400; no attempt was made to analyze
syrupy substances. NMR: Bruker Avance DRX 500
spectrometer (1H: 500.13 MHz; 13C: 125.76 MHz, 31P:
202.50 MHz), CDCl3 or DMSO-d6 solutions, d (ppm), J
(Hz). Spectral patterns: s, singlet; d, doublet; dd, double
doublet; t, triplet; m, multiplet; br, broad. For the 2D
experiments (HMQC, HMBC, COSY), the standard
viously employed in peptide phosphorylation, has been
succesfully applied to the P(III)!P(V) transformation
in the solid phase oligonucleotide synthesis in the pres-
ence of a thioether group. The applicability of amidite 3
was prove by incorporating it into DNA which was then
coupled, via a disul®de bridge, to a cysteine derivative to
yield a cysteine±DNA conjugate.
Experimental
General
Bruker
software
packages
(INV4GSSW,
INV4GSLRNDSW, COSYGS) were applied. Mass
spectrometry: Finnigan MAT TSQ 7000, electrospray
(ESI) or nanoelectrospray20 for analysis of oligonucleo-
tides (14±16), phosphoramidites (1±3) and highly apolar
compounds (7, 8, 10, 12). Calculated molecular weights
for oligonucleotides 14±16 are given for the most inten-
sive monoisotopic peak.
The following abbreviations are employed: controlled
pore glass support (CPG); N,N-diisopropylethylamine
(DIPEA); dichloromethane (DCM); N,N0-dicyclohexyl-
urea (DCU); 1,4-dithio-dl-threitol (DTT); 2-(1H-ben-
zotriazol-1-yl)-1,1,3,3-tetramethyluronium
hexa-
¯uorophosphate (HBTU); N-hydroxybenzotriazole
(HOBT); triethylamine (TEA); triethylammonium ace-
tate (TEAA); tetrabutylammonium ¯uoride (TBAF);
tert-butildiphenylsilyl chloride (TBDPS-Cl). The 50-O-
dimethoxytrityl-protected thymidine phosphoramidite
monomer for oligonucleotide synthesis was obtained
from ChemGenes Corporation (Ashland, MA, USA).
Other chemicals were purchased from Aldrich, Fluka or
Bachem. 2-Cyanoethyl N,N-diisopropylchlorophos-
phoramidite was prepared using the procedure of Sinha
et al.9 Amidite 15 was synthesized by direct tritylation of
6-mercaptohexanol13 followed by phosphitylation.9
Acids 4 and 9 have been prepared ®rst by Biilman and
Due8 and Carpino and Han,15 respectively, without
characterization except the mp and elementary analysis.
Oligonucleotide conjugate 14 was synthesized on an
Expedite 8909 nucleic acid synthesizer on a 1 mmol scale.
Cleavage of the oligonucleotide from the CPG-support
was performed by cc. aq NH3 for 16 h at 50 ꢀC. The
crude cleavage mixture was puri®ed on 50mg Poly-
PakTM (Glen Research, Sterling, VA, USA) cartridge
using a slightly modi®ed eluent pro®le (1) washing with
acetonitrile (5 mL), (2) conditioning with 1.0M TEAA
(5 mL), (3) sample application, (4) washing with 3% (w/
v) aq NH3 (5 mL) then with deionized water (10mL), (5)
elution with 30% (v/v) aq acetonitrile16 and lyophilized.
The quantity of the resulting oligonucleotide was deter-
mined by using UV absorbance at 260nm, its purity was
checked by HPLC and characterized by nano-ESI mass
spectrometry. Puri®cation, detritylation and conjuga-
tion of oligonucleotides were performed in aq 0.1 M
TEAA bu€er (pH 7.0). HPLC chromatography was
performed on a HP1050 instrument with the following
conditions: Rutin RP column C18, 300 A, 250Â4 mm
(supplier: BST Ltd., Budapest, Hungary); detection at
260nm; ¯ow rate: 1.0mL/min; eluents, A: 0.1 M aq
TEAA (pH 7.0), B: 0.1 M aq TEAA (pH 7.0)±acetoni-
trile 2:8; gradient: 10±50% B in A in 40 min. Anhydrous
solvents were prepared as described.17 Light petroleum
S-Trityl-2-mercaptoacetic acid (4). Trityl chloride
(6.13 g, 22 mmol, 1.1 equiv) was dissolved in toluene
(50mL), then TEA (3.07 mL, 22 mmol, 1.1 equiv) and
2-mercaptoacetic acid (1.40mL, 20mmol) were added at
rt. After 3 h, the reaction mixture was evaporated, dis-
solved in DCM (100 mL) and extracted with water
(2Â100 mL). The organic phase was dried and con-
centrated in vacuo, the residue was crystallized from
toluene to a€ord the product as white neeꢀdles (4.95 g,
74%). Mp 163±164 ꢀC (lit.8 mp. 162.5±163 C); Rf 0.43
(DCM:MeOH 9:1); (found: C, 75.1; H, 5.2; S, 9.4. Calcd
for C21H18O2S: C, 75.4; H, 5.4; S, 9.6); dH (500 MHz,
DMSO-d6) 2.89 (2 H, s, CH2), 7.22±7.26 (3 H, m, arom.
CH), 7.30±7.36 (12 H, m, arom. CH), 12.74 (1 H, br s,
COOH); dC (125 MHz, DMSO-d6) 34.8 (CH2), 66.4
(Cq), 127.0, 128.2, 129.1 (arom. CHs); 144.0 (arom. Cq);
170.3 (COOH) m/z (ESI (EtOH)): 333.1 ((MÀH)À,
84%), 667.1 ((2MÀH)À, 100%).
O-tert-Butyldiphenylsilyl-3-aminopropanol hydrochloride
(6). 3-Aminopropanol (5, 3.80mL, 50.0mmol, 2.5
equiv) was dissolved in DCM (50mL), then TBDPS-Cl
(5.20mL, 20mmol) in DCM (10mL) was added drop-
wise during 15 min at 0 ꢀC then TEA (4.20mL,
30mmol) was added. After stirring at rt for 1 h, the
reaction mixture was extracted with 10% (w/v) aq
NaHSO4 (2Â50mL) and satd aq NaHCO 3 (2Â50mL).
The organic phase was concentrated in vacuo, the resi-
due was dissolved in methanol (100 mL), the pH of the
solution was adjusted to 6 with 1 M aq HCl and evap-
orated to dryness followed by repeated co-evaporation
with acetonitrile (2Â50mL). The residue was crystal-
lized from DCM/diethyl ether to a€ord the product as
white needles (6.02 g, 86%). Mp 165±166 ꢀC (subl. from
130 ꢀC); Rf 0.63 (DCM:MeOH:TEA 70:30:5); (Found:
C, 64.95; H, 7.9; N, 4.1. Calcd for C19H28ClNOSi: C,
65.2; H, 8.1; N, 4.0%); dH (500 MHz, CDCl3) 1.03 [9H,

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Z. Kupihar et al. / Bioorg. Med. Chem. 9 (2001) 1241±1247
1245
s, C(CH3)3), 2.01 (2 H, m, CH2CH2CH2), 3.20(2 H, t,
J=7.5, NCH2), 3.74 (2 H, t, J=5.5, CH2O), 7.39 (6 H,
m, arom. CH), 7.63 (4 H, m, arom. CH) 8.39 (3 H, br s,
NH+3 ); dC (125 MHz, CDCl3) 19.8 (C(CH3)3), 27.6
(CH3), 30.9 (CH2CH2CH2), 38.7 (NCH2), 61.9 (CH2O),
128.5, 130.5, 136.2 (arom. CHs); 133.7 (arom. Cq); m/z
(ESI (aq MeOH)): 314 ((M+H)+, 100%). The free
amine has been mentioned by Kende and Mendoza21
but not described in detail.
DIPEA (0.52 g, 3 mmol, 1.5 equiv) and 2-cyanoethyl N,N-
diisopropylchlorophosphoramidite (0.67 mL, 3 mmol, 1.5
equiv) were added. After 1 h stirring MeOH (0.1 mL,
2.5 mmol), then after 5 min DCM (40mL) were added
and the mixture was extracted with satd. aq NaHCO3
(2Â50mL), dried and concentrated. The residue was
puri®ed by column chromatography using a light pet-
roleum:DCM:TEA 95:5:10±70:30:10 eluent to give the
phosphoramidite 2 (0.65 g, 55%) as a colorless oil. Rf
0.36 (light petroleum:DCM:TEA 75:25:10); dH
(500 MHz, CDCl3) 1.16 (12 H, m, 4ÂCH3), 1.66 (2 H,
m, CH2CH2CH2), 2.57 (2 H, t, J=6.4, CH2CN), 3.09 (4
H, m, SCH2+NCH2CH2), 3.52±3.65 (4 H, m,
CH2CH2CH2O+2ÂCH), 3.70±3.85 (2 H, m,
CH2CH2CN), 6.22 (1 H, br s, NH), 7.23 (3 H, m, arom.
CH), 7.29 (6 H, m, arom. CH), 7.40(6 H, m, arom.
N-(S-Trityl-2-mercaptoacetyl)-O-tert-butyldiphenylsilyl-
3-aminopropanol (7). Acid 4 (2.68 g, 8 mmol, 2 equiv),
HOBT (1.22 g, 8 mmol, 2 equiv) and HBTU (3.03 g,
8 mmol, 2 equiv) were dissolved in DCM (30mL),
hydrochloride 6 (1.40g, 4 mmol) and DIPEA (2.10mL,
12 mmol, 3 equiv) in DCM (20mL) were added drop-
wise at rt. The resulting solution was stirred at rt for 1 h.
The reaction mixture was extracted with 10% (w/v) aq
3
CH); dC (125 MHz, CDCl3) 20.7 (d, JC,P=6.8,
CH2CN), 25.0(d, JC,P=7.0, CH3), 30.9 (d, JC,P=6.9,
3
3
NaHSO4 (2Â50mL) and 10% (w/v) aq Na CO3
CH2CH2CH2), 36.5 (SCH2), 37.5 (NCH2), 43.5 (d, 2JC,P
2
2
(2Â50mL), then the organic layer was dried and con-
centrated. The crude product was puri®ed by column
chromatography using DCM as eluent and crystallized
from methanol to give a white powder (2.21 g, 88%).
Mp 117±118 ꢀC; Rf 0.77 (DCM:MeOH 9:1); (found: C,
76.4; H, 7.1; N, 2.3; S, 5.1. Calcd for C40H43NO2SSi: C,
76.3; H, 6.9; N, 2.2; S, 5.2%); dH (500 MHz, CDCl3)
1.03 (9H, s, C(CH3)3), 1.58 (2 H, m, CH2CH2CH2), 3.05
(2 H, s, SCH2), 3.11 (2 H, m, NCH2), 3.60(2 H, t,
J=5.7 Hz, CH2O), 6.02 (1 H, br s, NH), 7.21 (3 H, m,
arom. CH), 7.27 (6 H, m, arom. CH), 7.34 (4 H, m,
arom. CH), 7.39 (8 H, m, arom. CH), 7.62 (4 H, m,
arom. CH); dC (125 MHz, CDCl3) 19.9 (C(CH3)3), 27.6
(CH3), 32.4 (CH2CH2CH2), 36.7 (SCH2), 37.8 (NCH2),
62.4 (CH2O), 68.4 (Ph3C), 127.7, 128.4, 128.8, 130.2
130.4, 136.2 (arom. CHs), 134.3, 144.8 (arom. Cqs),
168.5 (CONH); m/z (nano-ESI (toluene)): 630
((M+H)+, 3%), 243 (Tr+, 100).
12.3, CH), 58.8 (d, JC,P=19.4, CH2CH2CN), 61.8 (d,
2JC,P=17.5, CH2CH2CH2O), 68.5 (Ph3C), 118.0(CN),
127.5, 128.5, 129.9 (arom. CHs), 144.5 (arom. Cq), 168.3
(CONH); dP (200 MHz, CDCl3, H-decoupling) 149.01;
m/z (nano-ESI (MeCN/LiCl)): 614 ((M+Na)+, 5%),
598 ((M+Li)+, 100), 243 (Tr+, 5).
N-9-Fluorenylmethoxycarbonyl-glycyl-glycine (9). Gly-
cyl-glycine (6.60g, 50mmol, 1.25 equiv) and Na CO3
2
(15.0g, 142 mmol) were dissolved in dioxane:water 2:1
(450mL), then Fmoc chloride (10.35 g, 40mmol) in
dioxane (200 mL) was added dropwise over 1 h.14 The
reaction mixture was stirred overnight at rt, then it was
evaporated. The resulting solid was triturated with 10%
aq NaHSO4 (400 mL), ®ltered, washed with water and
dried. The residue was crystallized from EtOAc and
light petroleum to give the product (9) as a white pow-
der (10.91 g, 77%). Mp 178±179 ꢀC (lit.15 mp. 176±
177 ꢀC (MeCN)); Rf 0.52 (BuOH:AcOH:H2O 4:1:1);
(found: C, 64.35; H, 4.9; N, 7.7. Calcd for C19H18N2O5:
C, 64.4; H, 5.1; N, 7.9%); dH (500 MHz, DMSO-d6)
3.73 (2 H, d, J=4.9, NHCH2), 3.83 (2 H, d, J=4.6,
NHCH2), 4.25 (1 H, t, J=5.9, CH2CH), 4.32 (2 H, d,
J=6.1, CH2CH), 7.33 (2 H, m, arom. CH), 7.41 (2 H,
m, arom. CH), 7.64 (1 H, br s, NH), 7.73 (2 H, m, arom.
CH), 7.87 (2 H, m, arom. CH), 8.21 (1 H, br s, NH),
12.68 (1 H, br s, COOH); dC (125 MHz, DMSO-d6)
40.7, 43.4 (2ÂCH2CO), 46.7 (CHCH2), 65.9 (CHCH2),
120.2, 125.4, 127.2, 127.7 (arom. CHs), 140.8, 143.9
(arom. Cqs), 156.6 (OCONH), 169.7 (CH2CONH);
171.3 (COOH) m/z (ESI (aq MeOH)): 355.2
((M+H)+), 100%, 377.1 ((M+Na)+, 26%), 709.1
((2M+H)+, 23%).
N-(S-Trityl-2-mercaptoacetyl)-3-aminopropanol (8). Com-
pound 7 (2.00 g, 3.2 mmol) dissolved in THF (10 mL)
was allowed to react with 1 M TBAF (in THF, 6.4 mL,
6.4 mmol, 2 equiv) for 6 h at rt. The reaction mixture
was concentrated in vacuo and puri®ed by column
chromatography (1±4% (v/v) MeOH in DCM). The
collected fractions were concentrated and the residue
was crystallized from EtOAc and light petroleum to give
the alcohol 8 as a white powder (0.98 g, 78%). Mp 128±
129 ꢀC; Rf 0.42 (DCM:MeOH 9:1); (found: C, 73.5; H,
6.2; N, 3.65; S, 8.3. Calcd for C24H25NO2S: C, 73.6; H,
6.4; N, 3.6; S, 8.2%); dH (500 MHz, CDCl3) 1.51 (2 H,
m, CH2CH2CH2), 2.87 (1 H, t, J=6.0, OH), 3.10 (2 H,
m, NCH2), 3.15 (2 H, s, SCH2), 3.45 (2 H, m, CH2O),
6.28 (1 H, br s, NH), 7.23 (3 H, m, arom. CH), 7.29 (6
H, m, arom. CH), 7.41 (6 H, m, arom. CH); dC (125
MHz, CDCl3) 32.7 (CH2CH2CH2), 36.4 (SCH2), 37.0
(NCH2), 59.7 (CH2O), 68.7 (Ph3C), 127.8, 128.9, 130.1
(arom. CHs), 144.7 (arom. Cq), 170.0 (CONH); m/z
(nano-ESI (MeOH/LiCl)) 398 ((M+Li)+, 100%), 243
(Tr+, 90).
N-(N0-9-Fluorenylmethoxycarbonyl-glycyl-glycyl)-O-tert-
butyldiphenylsilyl-3-aminopropanol (10)
Fmoc-Gly-Gly-OH (9, 4.25 g, 12 mmol, 1.5 equiv),
HOBT (1.84 g, 12 mmol, 1.5 equiv) and HBTU (4.55 g,
12 mmol, 1.5 equiv) were dissolved in THF (100 mL)
then hydrochloride 6 (2.80g, 8 mmol) and DIPEA
(3.48 mL, 20mmol, 2.5 equiv) in THF (30mL) were
added dropwise at rt. After 3 h at rt, the reaction mix-
ture was evaporated, the residue was dissolved in
O-(N-(S-Trityl-2-mercaptoacetyl)-3-aminopropyl)-O0-2-
cyanoethyl-N 0,N 0-diisopropylphosphoramidite (2). Alcohol
8 (0.78 g, 2 mmol) was dissolved in abs DCM (10mL),

Â
Z. Kupihar et al. / Bioorg. Med. Chem. 9 (2001) 1241±1247
1246
EtOAc (100 mL) and extracted with 10% (w/v) aq
Na2CO3 (3Â100 mL) and 10% (w/v) aq NaHSO4
(2Â100 mL). The organic phase was dried, concentrated
and the residue was crystallized from methanol to a€ord
the product as white crystals (4.57 g, 88%). Mp 70±71 ꢀC;
Rf 0.53 (DCM-MeOH 9:1); (found C, 70.2; H, 6.45; N,
6.4. Calc. for C38H43N3O5Si: C, 70.25; H, 6.7; N, 6.5%);
C44H49N3O4SSi: C, 71.0; H, 6.65; N, 5.65; S, 4.3%); dH
(500 MHz, CDCl3) 1.06 (9 H, s, C(CH3)3), 1.72 (2 H, m,
CH2CH2CH2), 3.13 (2 H, s, SCH2), 3.36 (2 H, m,
NCH2CH2), 3.56 (2 H, d, J=5.2, NHCH2CO), 3.72 (4
H, m, CH2O+NHCH2CO), 6.17 (1 H, t, J=5.1, NH),
6.41 (1 H, t, J=5.1, NH), 6.49 (1 H, t, J=5.4, NH), 7.21
(3 H, m, arom. CH), 7.27 (6 H, m, arom. CH), 7.40(12
H, m, arom. CH), 7.64 (4 H, m, arom. CH); dC
(125 MHz, CDCl3) 19.9 (C(CH3)3), 27.6 (CH3), 32.2
(CH2CH2CH2), 36.3 (SCH2), 38.2 (NCH2CH2), 43.5,
44.1 (2 Â CH2CONH), 62.9 (CH2O), 68.5 (Ph3C), 127.7,
128.5, 128.9, 130.2, 130.5, 136.2 (arom. CHs), 134.1,
144.6 (arom. Cqs); 168.7, 169.1, 169.6 (3ÂCONHs); m/z
(nano-ESI (MeCN)) 766 ((M+Na)+, 100%), 243 (Tr+,
95).
d
H (500 MHz, CDCl3) 1.06 (9 H, s, C(CH3)3), 1.74 (2 H,
m, CH2CH2CH2), 3.38 (2 H, m, NCH2CH2), 3.73 (2 H,
t, J=5.6, CH2O), 3.79 (2 H, d, J=4.9, NHCH2CO),
3.85 (2 H, d, J=5.0, NHCH2CO), 4.20(1 H, t, J=6.8,
CH2CH), 4.41 (2 H, d, J=6.8, CH2CH), 5.56 (1 H, br s,
NH), 6.21 (1 H, br s, NH), 6.73 (1 H, t, J=5.0, NH),
7.29 (2 H, m, arom. CH), 7.40(8 H, m, arom. CH), 7.56
(2 H, m, arom. CH), 7.64 (4 H, m, arom. CH), 7.74 (2
H, m, arom. CH); dC (125 MHz, CDCl3) 19.9
(C(CH3)3), 27.6 (CH3), 32.1 (CH2CH2CH2), 38.3
(NCH2CH2), 43.5, 45.1 (2ÂCH2CONH), 47.8 (CH),
N-(S-Trityl-2-mercaptoacetyl-glycyl-glycyl)-3-aminopro-
panol (13). The solution of compound 12 (2.00 g,
2.7 mmol) in THF (20mL) and 1 M TBAF (in THF,
5.4 mL, 5.4 mmol, 2 equiv) were allowed to react at rt
for 6 h, then the reaction mixture was concentrated and
puri®ed by column chromatography (0±20% (v/v)
MeOH in DCM). The collected fractions were evapo-
rated and the resulting white foam was crystallized from
toluene/DCM to a€ord the alcohol 13 as a white solid
(1.05 g, 77%). Mp 139±140 ꢀC (sinters from 115 ꢀC); Rf
0.24 (DCM:MeOH 9:1); (Found C, 66.3; H, 6.0; N, 8.5;
S, 6.35. Calc. for C28H31N3O4S: C, 66.5; H, 6.2; N, 8.3;
S, 6.3%); dH (500 MHz, CDCl3) 1.65 (2 H, m,
CH2CH2CH2), 3.15 (2 H, s, SCH2), 3.30(1 H, br s,
OH), 3.35 (2 H, m, NCH2CH2), 3.56 (2 H, d, J=5.4,
NHCH2CO), 3.59 (2 H, m, CH2CH2O), 3.85 (2 H, d,
J=5.8, NHCH2CO), 6.69 (1 H, t, J=5.3, NH), 6.86 (1
H, t, J=5.8, NH), 6.95 (1 H, t, J=5.6, NH), 7.23 (3 H,
m, arom. CH), 7.29 (6 H, m, arom. CH), 7.42 (6 H, m,
arom. CH); dC (125 MHz, CDCl3) 32.3 (CH2CH2CH2),
63.0(CH O), 67.8 (CHCH2), 120.7, 125.7, 127.8, 128.4,
2
128.5, 130.6, 136.2 (arom. CHs), 134.1, 142.0, 144.4
(arom. Cqs), 157.4 (OCONH), 168.8, 169.9
(2ÂCH2CONH); m/z (nano-ESI (toluene)) 672
((M+Na)+, 100%), 650 ((M+H)+, 2).
N-Glycyl-glycyl-O-tert-butyldiphenylsilyl-3-aminopropa-
nol (11). Compound 10 (3.90g, 6 mmol) and diethyla-
mine (6.23 mL, 60mmol, 10 equiv) in DCM (50mL)
were allowed to react for 16 h at rt, then the mixture was
evaporated and puri®ed by column chromatography.
The column was washed with DCM and 50% (v/v)
MeOH in DCM, then the product was eluted with
MeOH. Attempted crystallization from petroleum
ether, EtOAc or MeOH invariably resulted in a pale
yellow oil (1.74 g, 68%). Rf 0.25 (DCM:MeOH 7:3); dH
(500 MHz, CDCl3) 1.04 (9 H, s, C(CH3)3), 1.72 (2 H, m,
CH2CH2CH2), 3.35 (2 H, m, NCH2CH2), 3.52 (2 H, d,
J=6.1, NCH2CO), 3.70(2 H, t, J=5.7, CH2O), 3.82 (2
H, s, NCH2CO), 6.42 (1 H, t, J=5.3, NH), 7.41 (7 H,
m, arom. CH+NH), 7.62 (4 H, m, arom. CH) 7.74 (2
H, br s, NH2); dC (125 MHz, CDCl3) 19.9 (C(CH3)3),
27.6 (CH3), 32.3 (CH2CH2CH2), 38.1 (NCH2CH2),
43.5, 45.2 (2ÂCH2CONH), 62.9 (CH2O), 128.5, 130.5,
136.2 (arom. CHs), 134.2 (arom. Cq), 169.4, 173.7
(2ÂCH2CONH); m/z (ESI (aq MeOH)), 450
((M+Na)+, 5%), 428 ((M+H)+, 100).
36.3
(SCH2),
37.5
(NCH2CH2),
43.8,
44.5
(2ÂCH2CONH), 60.5 (CH2O), 68.7 (Ph3C), 127.8,
128.6, 130.2 (arom. CHs); 144.5 (arom. Cqs), 169.5,
170.0, 170.5 (3ÂCONH); m/z (ESI (MeOH)) 528
((M+Na)+, 40%), 506 ((M+H)+, 40), 243 (Tr+,
100).
O-(N-(S-Trityl-2-mercaptoacetyl-glycyl-glycyl)-3-amino-
propyl)-O 0 -2-cyanoethyl-N0,N0 -diisopropylphosphorami-
dite (3). Alcohol 13 (0.80 g, 1.6 mmol) was dissolved in
abs. DCM (10mL), then DIPEA (0.42 mL, 2.4 mmol,
1.5 equiv) and 2-cyanoethyl N,N-diisopropylchloropho-
sphoramidite (0.54 mL, 2.4 mmol, 1.5 equiv) were added
dropwise under stirring. After 1 h, MeOH (0.10 mL,
2.5 mmol) was added and stirring was continued for 5
min, then the solution was diluted with DCM (40mL)
and the reaction mixture was extracted with satd aq
NaHCO3 (2Â50mL). The organic phase was dried,
concentrated and puri®ed by column chromatography
(10% (v/v) TEA in DCM). The collected fractions were
evaporated and the resulting colorless oil was dried by
repeated coevaporation with acetonitrile (2Â25 mL) to
leave a white foam that formed a white solid after tri-
turation with dry diethyl ether (0.59 g, 52%). Mp 116±
118 ꢀC (sinters from 100 ꢀC); Rf 0.21 (DCM:
EtOAc:TEA 45:45:10); (found C, 62.8; H, 6.7; N, 9.8; S,
4.5. Calc. for C37H48N5O5PS: C, 63.0; H, 6.85; N, 9.9; S,
N-(S-Trityl-2-mercaptoacetyl-glycyl-glycyl)-O-tert-butyl-
diphenylsilyl-3-aminopropanol (12). Acid
6.6 mmol, 2 equiv), HOBT (1.01 g, 6.6 mmol, 2 equiv),
HBTU (2.50g, 6.6 mmol, equiv) and DIPEA
4 (2.20g,
2
(1.15 mL, 6.6 mmol, 2 equiv) were dissolved in DCM
(100 mL), then the solution of amine 11 (1.40g,
3.3 mmol) in DCM (10mL) was added dropwise. After
stirring at rt for 3 h, the mixture was successively
extracted with 10% (w/v) aq NaHSO4 (100 mL) then
with 10% (w/v) aq NaHCO3 (2Â100 mL), the organic
phase was dried, concentrated and puri®ed by column
chromatography (0±10% (v/v) MeOH in DCM). The
collected fractions were evaporated and the resulting oil
was triturated and crystallized from MeOH to give the
product as a white powder (2.06 g, 84%). Mp 138±
139 ꢀC (sinters from 127 ꢀC); Rf 0.48 (DCM:MeOH 9:1);
(found C, 71.2; H, 6.7; N, 5.8; S, 4.2. Calcd for

Â
Z. Kupihar et al. / Bioorg. Med. Chem. 9 (2001) 1241±1247
1247
4.5%); dH (500 MHz, CDCl3) 1.18 (12 H, m, 4ÂCH3),
Acknowledgements
1.82 (2 H, m, CH2CH2CH2), 2.63 (2 H, t, J=6.2,
CH2CN), 3.17 (2 H, s, SCH2), 3.36 (2 H, m, NCH2CH2),
3.53±3.63 (4 H, m, NCH2CO+2ÂCH), 3.65±3.80(3 H,
m, CH2CH2CH2O+1=2 OCH2CH2CN), 3.83±3.90(3 H,
m, 1=2 OCH2CH2CN+NCH2CO), 6.51 (1 H, br s,
NH), 6.60(1 H, t, J=5.0, NH), 6.65 (1 H, t, J=5.3,
NH), 7.23 (3 H, m, arom. CH), 7.29 (6 H, m, arom.
CH), 7.42 (6 H, m, arom. CH); dC (125 MHz, CDCl3)
21.2 (d, 3JC,P 6.7, CH2CN), 25.3 (d, 3JC,P 7.0, CH3), 25.4
This research has been supported by grants OTKA No.
T 030135 and FKFP No. 0597/1999.
References
1. Sinha, N. D.; Cook, R. M. Nucleic Acids Res. 1988, 16,
2659.
2. Connolly, B. A.; Rider, P. Nucleic Acids Res. 1985, 13,
4485.
3. Sproat, B. S.; Beijer, B.; Rider, P.; Neuner, P. Nucleic Acids
Res. 1987, 15, 4837.
4. de la Torre, B. G.; Avino, A. M.; Escarceller, M.; Royo, M.;
Albericio, F.; Eritja, R. Nucleosides Nucleotides 1993, 12, 993.
5. Glen Research, 22825 Davis Drive, Sterling, VA 20164,
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MA 01721, USA. (http://www.chemgenes.com).
6. Hermanson, G. T. Bioconjugate techniques Academic: San
Diego, 1996 p 656.
3
3
(d, JC,P 6.8, CH3), 31.2 (d, JC,P 7.3, CH2CH2CH2),
36.4 (SCH2), 37.8 (NCH2CH2), 43.6, 44.3
2
2
(2ÂCH2CONH), 43.9 (d, JC,P 12.6, CH), 58.8 (d, JC,P
19.5, CH2CH2CN), 62.5 (d, 2JC,P 17.2, CH2CH2CH2O),
68.6 (Ph3C), 118.8 (CN), 127.8, 128.9, 130.2 (arom.
CHs), 144.6 (arom. Cq), 169.1, 169.3, 169.8 (3ÂCONH);
dP (200 MHz, CDCl3, H-decoupling) 148.96; m/z (nano-
ESI (MeCN/LiCl)) 744 ((M+K)+, 76%), 728
((M+Na)+, 100), 712 ((M+Li)+, 25), 243 (Tr+, 18).
Oligonucleotide 15. The solution of oligonucleotide 14
(50 nmol) in 0.1 M TEAA (100 mL) was allowed to react
with aq 0.1 M AgNO3 (5 mL, 500 nmol, 10 equiv) at rt
for 1 h. Aq 0.1 M DTT solution (7.5 mL, 750nmol, 15
equiv) was added and after 30min the precipitate was
centrifuged, the supernatant was removed, the pre-
cipitate was washed with 0.1 M TEAA (3Â50 mL). The
combined aq phases were extracted with EtOAc
(3Â200 mL) to remove excess DTT. The resulting aq
solution containing the oligonucleotide 15 was puri®ed
by HPLC, lyophilized and analysed by mass spectro-
7. Kamber, B. Helv. Chim. Acta 1971, 54, 398.
8. Biilman, E.; Due, N. V. Bull. Soc. Chim. Fr. 1924, 35, 384
(Chem. Abstr., 1924, 18, 2003).
9. Sinha, N. D.; Biernat, J.; Koster, H. Tetrahedron Lett.
1983, 24, 5843.
10. Kele, Z.; Kupihar, Z.; Kovacs, L.; Janaky, T.; Szabo, P. T.
J. Mass Spectrom. 1999, 34, 1317.
11. de Bont, H. B. A.; van Boom, J. H.; Liskamp, R. M. J.
Tetrahedron Lett. 1990, 31, 2497.
12. Drijfhout, J. W.; Perdijk, E. W.; Weijer, W. J.; Bloemho€,
W. Int. J. Pept. Protein Res. 1988, 32, 161.
13. Kupihar, Z.; Schmel, Z.; Kovacs, L. Molecules 2000, 5,
M144.
14. Kocienski, P. Protecting Groups; Georg Thieme Verlag:
Stuttgart, 1994; p 204.
metry. m/z (Nano-ESI (aq MeCN)) 694.5 ((MÀ3H)3À
,
50%), 520.6 ((MÀ4H)4À, 100), 416.2 ((MÀ5H)5À, 20),
C69H95N15O46SP6 requires 2087.4.
15. Carpino, L. A.; Han, G. Y. J. Org. Chem. 1972, 37, 3404.
16. Anon. User Guide to Poly-PakTM Puri®cation; Glen
Research: Sterling, 1997 p 7 (http://www.glenres.com/Poly-
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PolyPak.html/PolyPakBooklet97.pdf).
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20. Kele, Z.; Janaky, T.; Meszaros, T.; Feher, A.; Dudits, D.;
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21. Kende, A. S.; Mendoza, J. S. Tetrahedron Lett. 1991, 32,
1699.
Conjugation of N-Boc-L-Cys(Npys)-OH to oligonucleo-
tide 15 (oligonucleotide 16). The solution of oligonu-
cleotide 15 (30nmol) in 0.1 M TEAA (50 mL) was
allowed to react with N-Boc-l-Cys(Npys)-OH (90nmol,
3 equiv) in 0.1M TEAA (10 mL) at rt for 16 h. 3-Nitro-2-
thiopyridone was removed by ethereal extraction
(3Â100 mL). The resulting aq solution containing the
oligonucleotide 16 was puri®ed by HPLC, lyophilized
and analysed by mass spectrometry. m/z (Nano-ESI (aq
MeCN)) 2305.8 ((MÀH)À, 2%), 1152.5 ((MÀ2H)2À
,
80), 767.9 ((MÀ3H)3À, 100), 575.5 ((MÀ4H)4À, 10),
C77H109N16O50S2P6 requires 2307.4.