Backbone modifications of aromatic peptide nucleic acid (APNA) monomers and their hybridization properties with DNA and RNA

Article abstract of DOI:10.1021/jo001650o

Aromatic peptide nucleic acid (APNA) monomers containing N-(2-aminobenzyl)-glycine, N-(2-aminobenzyl)-(R)- or -(S)-alanine, and N-(2-aminobenzyl)-β-alanine moieties as part of their backbone were synthesized. These novel analogues were incorporated as a single "point mutation" in PNA hexamers, and their physicochemical properties were investigated by UV thermal denaturation and CD experiments. Destabilization in triplex formation between the PNA-APNA chimeras and complementary DNA or RNA oligomers was observed, as compared to the PNA control. The APNA monomer composed of the N-(2-aminobenzyl)-glycine backbone led to the smallest decrease in the thermal stability of the triplexes formed with DNA and RNA, while maintaining selectivity for base-pairing recognition. Since the PNA-APNA chimeras are more lipophilic than the corresponding PNA homopolymers, these oligomers may also exhibit better cell membrane permeability properties.

Full text of DOI:10.1021/jo001650o

3372
J . Org. Chem. 2001, 66, 3372-3379
Ba ck bon e Mod ifica tion s of Ar om a tic P ep tid e Nu cleic Acid (AP NA)
Mon om er s a n d Th eir Hybr id iza tion P r op er ties w ith DNA a n d RNA
Lee D. Fader,† Michael Boyd,§ and Youla S. Tsantrizos*,†,‡
Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada, and
Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Laval, Quebec H7S 2G5, Canada
ytsantrizos@lav.boehringer-ingelheim.com
Received November 22, 2000
Aromatic peptide nucleic acid (APNA) monomers containing N-(2-aminobenzyl)-glycine, N-(2-
aminobenzyl)-(R)- or -(S)-alanine, and N-(2-aminobenzyl)-â-alanine moieties as part of their
backbone were synthesized. These novel analogues were incorporated as a single “point mutation”
in PNA hexamers, and their physicochemical properties were investigated by UV thermal
denaturation and CD experiments. Destabilization in triplex formation between the PNA-APNA
chimeras and complementary DNA or RNA oligomers was observed, as compared to the PNA control.
The APNA monomer composed of the N-(2-aminobenzyl)-glycine backbone led to the smallest
decrease in the thermal stability of the triplexes formed with DNA and RNA, while maintaining
selectivity for base-pairing recognition. Since the PNA-APNA chimeras are more lipophilic than
the corresponding PNA homopolymers, these oligomers may also exhibit better cell membrane
permeability properties.
In tr od u ction
Over the past 20 years, the preparation and properties
of modified oligonucleotides (ODNs) have been exten-
sively investigated, as their potential as therapeutic
agents is increasingly recognized.1 Peptide nucleic acids
(PNAs) are DNA analogues having the phosphodiester/
deoxyribose backbone completely replaced by N-(2-ami-
noethyl)-glycine units to which the nucleobases are
attached via acetate linkers.2 These molecules have
emerged as a unique class of oligonucleotide mimics with
ever-increasing potential as antisense/antigene agents
and as biomedical diagnostic tools. PNAs bind to DNA
and RNA in a sequence specific manner and with
remarkably higher thermal stability relative to all other
synthetic or natural analogues of ODNs.3 Moreover,
PNAs are stable toward degradation by both protease and
nuclease enzymes, thus possessing many of the critical
requirements for oligomers used in antisense/antigene
drug development.4
by their poor cell membrane permeability. In an effort
to overcome this limitation, PNA conjugates of nuclear
internalizing peptides were recently explored. For ex-
ample, biotinylated PNA conjugates linked to the mono-
clonal antibody OX26 were shown to undergo in vivo
receptor-mediated transcytosis through the blood-brain
barrier, thus effectively transporting the PNA oligomers
into brain cells.6 PNAs have also been transported into
cells as unmodified PNA-DNA duplexes encapsulated
into cationic lipid micelles. This latter approach has been
used to effectively inhibit telomerase activity in DU145
prostate-derived tumor cells.7 Although such studies are
encouraging, a more direct approach involves modifica-
tions of the PNA structure so as to increase their inherent
cell membrane permeability without significantly com-
promising their superior hybridization properties or
stability against enzymatic degradation.
Although the microinjection of PNA oligomers into cells
has been shown to induce transcription and translation
arrest,5 their therapeutic utility is seriously compromised
* Tel: (450) 682-4640. Fax: (450) 682-4189.
† McGill University.
‡ Boehringer Ingelheim (Canada) Ltd..
§ Current address: Department of Medicinal Chemistry, Merck
Frosst Canada Inc.
(1) (a) Uhlmann, E.; Peyman, A. Chem. Rev. 1990, 90, 543. (b) De
Mesmaeker, A.; Ha¨ner, R.; Martin, P.; Moser, H. E. Acc. Chem. Res.
1995 28, 366. (c) Peptide Nucleic Acids: Protocols and Applications;
Nielsen, P. E., Egholm, M., Eds.; Horizon Scientific Press: Wy-
mondham, U.K., 1999.
(2) (a) Nielsen, P. E.; Egholm, M.; Berg, R. H.; Buchardt, O. Science
1991 254, 1497. (b) Egholm, M.; Buchardt, O.; Nielsen, P. E.; Berg, R.
H. J . Am. Chem. Soc. 1992, 114, 1895.
(5) Hanvey, J . C.; Peffer, N. J .; Bisi, J . E.; Thomson, S. A.; Cadilla,
R.; J osey, J . A.; Ricca, D. J .; Hassman, C. F.; Bonham, M. A.; Au, K.
G.; Carter, S. G.; Bruckenstein, D. A.; Boyd, A. L.; Noble, S. A.; Babiss,
L. E. Science 1992, 258, 1481.
(3) Egholm, M.; Buchardt, O.; Christensen, L.; Behrens, C.; Freier,
S. M.; Driver, D. A.; Berg, R. H.; Kim, S. K.; Norde´n, B.; Neilsen, P. E.
Nature 1993, 365, 566.
(4) Demidov, V. V.; Potaman, V. N.; Frank-Kamenetskii, M. D.;
Egholm, M.; Buchard, O.; So¨nnichsen, S. H.; Nielsen, P. E. Biochem.
Pharmacol. 1994, 48(6), 1310.
(6) (a) Bickel, U.; Yoshikawa, T.; Landaw, E. M.; Faull, K. F.;
Pardridge, W. M. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 2618. (b)
Pardridge, W. M.; Boado, R. J .; Kang, Y.-S. Proc. Natl. Acad. Sci. U.S.A.
1995, 92, 5592.
(7) Hamilton, S. E.; Simmons, C. G.; Kathiriya, I. S.; Corey, D. R.
Chem. Biol. 1999, 6, 343.
10.1021/jo001650o CCC: $20.00 © 2001 American Chemical Society
Published on Web 04/26/2001

Aromatic Peptide Nucleic Acid Monomers
J . Org. Chem., Vol. 66, No. 10, 2001 3373
In 1997, we reported the design and synthesis of the
first peptide nucleic acid analogue having an aromatic
moiety as an integral part of its backbone, which we
termed aromatic peptide nucleic acids (APNA).8 The
synthesis of a thymine derivative of (S)-2-hydroxy-4-(2-
aminophenyl)butanoic acid was achieved in high enan-
tiomeric purity and was shown to be a useful building
block for the production of this novel class of APNA
oligomers (1). At approximately the same time, oligo-
nucleotide analogues having an N-phenylacetamide back-
bone,9 as well as acyclic oligomers composed of 2-amino-
1-phenyl-1,3-propanediol phosphoramidite monomers,10
were described in the literature. All of these reports
suggested that the introduction of an aromatic substitu-
ent in the backbone of a modified oligonucleotide does
not seriously hamper the formation of a duplex or triplex
structure with DNA or RNA.
merase enzymes as base-base hydrogen bonding.16 Thus,
in addition to applications in antisense/antigene chemo-
therapy, APNA chimeras of natural ODNs or synthetic
analogues could also be of potential value as enzyme
inhibitors of virally encoded DNA or RNA processing
enzymes.
Our ongoing research in the area of peptide nucleic
acids has recently led to the development of a new class
of APNA monomers (3a -c), which we incorporated into
the solid-phase synthesis of APNA-PNA chimeras. We
developed an efficient synthetic protocol that is amenable
to the parallel or combinatorial preparation of numerous
APNA building blocks with a high degree of structural
diversity. As in the case of the original PNA analogues,
the nucleobases are attached to the backbone via an
acetate linker, therefore conserving the three-bond dis-
tance between the base and the backbone of the oligomer.
However, since these molecules incorporate aromatic
rings directly into the backbone of each monomer unit,
they are fundamentally different from the PNAs, having
at least three bonds of the backbone coplanar. Although
the optimum distance between nucleobases along the
backbone of PNAs corresponds to six σ bonds, oligonucle-
otides having a distance of seven σ bonds between units
have also been shown to form stable duplexes with
natural ODNs.17 Thus, one of our goals is to identify the
optimum length and backbone substitution required in
order to achieve maximum stability of the complexes
formed between the APNAs and natural oligonucleotides,
via either Watson-Crick or Ho¨ogsteen base pairing. In
this paper, we report our synthetic protocol for the
preparation of APNA monomers having the general
structure 3 and the relative hybridization properties of
four key analogues (3a -c).
More recently, PNA-APNA chimeras of the general
structure 2 were investigated by our group and shown
to form stable duplex structures with complementary
DNA and RNA strands.11 In addition, both APNA ana-
logues 1 and 2 were designed in order to investigate
possible π-stacking or dipole-quadrupole interactions
along the backbone of the APNA oligomers and the
possible stabilizing effect on a duplex or triplex struc-
ture.12,13 Although it is widely believed that the major
stabilizing forces of double and triple helices are the
π-stacking interactions between adjacent base pairs,14 the
study of such interactions within the backbone of oligo-
nucleotide analogues is completely unprecedented and
therefore may be of considerable interest.15 Furthermore,
Kool and co-workers have recently demonstrated that
DNA shape complemetarity may play as important a role
in recognition and catalysis associated with DNA poly-
Resu lts a n d Discu ssion
Syn th esis of AP NA Mon om er s. Our initial efforts
in the structure optimization of the APNA monomers
focused on establishing the optimum backbone space
between adjacent nucleobases in a Lys-PNA2-APNA-
PNA3-Ac chimera. Synthesis of the required APNA
monomers was initiated with reductive alkylation of the
appropriate amino esters with commercially available
2-nitrobenzaldehyde using sodium triacetoxyborohydride
as the reducing agent (Scheme 1).18 Following workup of
(8) Tsantrizos, Y. S.; Lunetta, J . F.; Boyd, M.; Fader, L. D.; Wilson,
M.-C. J . Org. Chem. 1997 62, 5451.
(9) Waldner, A.; De Mesmaeker, A.; Wendeborn, S. Bioorg. Med.
Chem. Lett. 1996, 6, 2363.
(10) Rana, V. S.; Kumar, V. A.; Ganesh, K. N. Bioorg. Med. Chem.
Lett. 1997, 7, 2837.
(11) (a) Tsantrizos, Y. S.; Lunetta, J . F.; Fader, L. D.; Boyd, M.;
Mancuso, J . 81st Canadian Society for Chemistry Conference and
Exhibition, Wistler, BC, May, 1998. (b) Fader, L. D.; Tsantrizos, Y. S.
Unpublished data.
(15) During the course of this work, phosphonate analogues of PNAs
containing aromatic rings within the backbone were proposed; however,
no details on the synthesis or physicochemical properties of these
compounds were disclosed. Efimov, V. A.; Buryakova, A. A.; Choob,
M. V.; Chakhmakhcheva, O. G. Nucleosides Nucleotides 1999, 18, 1393.
(16) (a) Morales, J . C.; Kool, E. T. Nat. Struct. Biol. 1998, 5, 950.
(b) Guckian, K. M.; Krugh, T. R.; Kool, E. T. Nat. Struct. Biol. 1998, 5,
954.
(17) J ones, A. S.; MacCoss, M.; Walker, R. T. Biochim. Biophys. Acta
1973, 365, 365.
(18) (a) Abdel-Magid, A. F.; Carson, K. G.; Harris, B. D.; Maryanoff,
C. A.; Shah, R. D. J . Org. Chem. 1996, 61, 3849. (b) Abdel-Magid, A.
F.; Maryanoff, C. A.; Carson, K. G. Tetrahedron Lett. 1990, 31, 5595.
(12) Dougherty, D. A. Science 1996, 271, 163.
(13) (a) Levitt, M.; Perutz, M. F. J . Mol. Biol. 1988, 201, 751. (b)
Adams, H.; Harris, K. D.m.; Hembury, G. A.; Hunter, C. A.; Living-
stone, D.; McCabe, J . F. Chem. Commun. 1996, 2531. (c) Adams, H.;
Carver, F. J .; Hunter, C. A.; Osborne, N. J . Chem. Commun. 1996,
2529.
(14) (a) Sowers, L. C.; Shaw, B. R.; Sedwick, W. D. Biochem. Biophys.
Res. Commun. 1987, 148, 790 and references therein. (b) Delcourt, S.
G.; Blake, R. D. J . Biol. Chem. 1991, 266, 15160. (c) Zimmerman, S.
C. In Biorganic Chemistry Frontiers; Dugas, H., Ed.; Springer-Verlag:
New York, 1991; Vol. 2, p 33. (d) Schweitzer, B. A.; Kool, E. T. J . Am.
Chem. Soc. 1995, 117, 1863.

3374 J . Org. Chem., Vol. 66, No. 10, 2001
Fader et al.
Sch em e 1. Syn th esis of AP NA Mon om er s 6a -c
Sch em e 2. Syn th esis of Cbz-P r otected AP NA-Cy
Mon om er 12
Sch em e 3. Syn th esis of P NA-Th 6 (17)
each reaction mixture, the secondary amines 4a , 4b, and
(R)-4c or (S)-4c were precipitated as the corresponding
HCl salts, in good yield and high purity as determined
by NMR. The amines were then coupled to thymidyl-1-
acetic acid,19 using O-(7-azabenzotriazol-1-yl)-1,1,3,3-
tetramethyluronium hexafluorophosphate (HATU) as the
coupling reagent, to give the desired tertiary amides in
good to excellent yields (60% for the (R)- or (S)-alanine,
85% and 93% for the glycine and â-alanine analogues,
respectively). In all cases, the products were isolated after
trituration of the reaction mixture with ethyl acetate/
hexane giving the pure thymine derivatives 5a -c. The
subsequent catalytic hydrogenation of the nitro moiety
was carried out using palladium on charcoal with tri-
ethylammonium formate, leading to the isolation of the
aniline intermediates 6a -c in nearly quantitative yields
and excellent purity. [None of the synthetic steps shown
in Scheme 1 require purification of the products by
chromatography.]
APNA monomers containing cytosine were synthesized
following a slightly modified protocol (Scheme 2). Ami-
nobenzyl alcohol 7 was first converted to the allyl
carbamate derivative 8,20 and the hydroxy moiety was
subsequently converted to the bromide to obtain com-
pound 9. Displacement of the bromide with glycine
methyl ester gave intermediate 10 in high yield, which
was then coupled with the Cbz-protected cytosine in the
presence of HATU under basic conditions. Deprotection
of the aniline moiety of 11 was efficiently achieved using
Bu3SnH and catalytic amounts of Pd(Ph3)4,21 giving the
required methyl ester of the APNA cytosine monomer 12
in >80% yield after chromatography (Scheme 2).
PNA oligomers were synthesized having a single APNA
substitution in the middle of a hexamer strand. The
thymine PNA monomers were prepared using a modified
literature procedure (Scheme 3).22 Ethylenediamine was
mono-Boc protected by reaction with limiting amounts
of di-tert-butyl dicarbonate to give pure compound 13 in
>98% yield. Compound 13 was further reacted with a
limiting amount of ethyl bromoacetate in the presence
of K2CO3, giving the PNA backbone 14 in 96% yield.22
Excess amine 13 was required in this reaction in order
to avoid dialkylation; however, the unreacted starting
material was usually recovered quantitatively. Thymidyl-
1-acetic acid was then coupled to secondary amine 14,
giving fully protected thymine monomer 15, which was
hydrolyzed to the free carboxylic acid 16. Compound 16
was used as such in the automated, solid-phase synthesis
of the PNA homothymine hexamer 17, as well as the
Syn th esis of AP NA-P NA Hexa m er s. To evaluate the
hybridization properties of these novel monomers 3a -c,
(19) Dueholm, K. L.; Egholm, M.; Behrens, C.; Christensen, L.;
Hansen, H. F.; Vulpius, T.; Petersen, K. H.; Berg, R. H.; Nielsen, P.
E.; Buchardt, O. J . Org. Chem. 1994, 59, 5767.
(20) Corey, E. J .; Suggs, J . W. J . Org. Chem. 1973, 38, 3223.
(21) Dangles, O.; Guibe´, F.; Balavoine, G.; Lavielle, S.; Marquet, A.
J . Org. Chem. 1987, 52, 4984.
(22) In previously reported procedures for the preparation of
compound 14, a 1:1 molar ratio of Boc-protected ethylenediamine to
ethyl bromoacetate was used. In our hands, this method lead to
uncontrollable dialkylation as a major side reaction. Aldrian-Herrada,
G.; Rabie´, A.; Wintersteiger, R.; Brugidou, J . J . Peptide Sci. 1998, 4,
266.

Aromatic Peptide Nucleic Acid Monomers
J . Org. Chem., Vol. 66, No. 10, 2001 3375
Sch em e 4. Syn th esis of AP NA-P NA Dim er s
synthesis of the PNA-APNA chimeras 20-24, following
a slightly modified protocol from that originally developed
23
by Nielsen and co-workers.
The solid-phase peptide synthesis was carried out on
a methylbenzhydrylamine (MBHA) resin using 2-(1H-
benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluo-
rophosphate (HBTU) as the coupling reagent in the
presence of diethylcyclohexylamine (DECA) and in a
solvent mixture of pyridine/DMF. After each step, unre-
acted free amino residues were capped by treatment of
the resin with Ac2O in the presence of pyridine. Capping
of the N-terminus of the hexapeptide is essential in order
to avoid intramolecular N-acyl transfer of the last acetyl-
nucleobase moiety.23b The Boc protecting group was
hydrolyzed by treatment of the peptide with 25% TFA
in dichloromethane, and the progress of both the coupling
and deprotection steps was monitored using the Kaiser
test.24 A lysine residue was included at the C-terminus
of each peptide in order to prevent aggregation of the
polymer-bound oligomer during its synthesis on the solid
support.2b Cleavage from the resin was achieved by
treatment of the polymer-bound peptide with trifluro-
methanesulfonic acid (TFMSA) in TFA. The crude pep-
tides were first precipitated from the TFA solution by
diluting the mixture with anhydrous diethyl ether (20-
fold dilution) and then purified by preparative C18
reversed-phase HPLC.
The ortho-substituted anilines (e.g., 3a -c) were found
to react sluggishly during peptide synthesis and under
the above conditions, even when an excess of free acid
monomer and coupling reagents were used. Furthermore,
free aniline moieties cannot be detected using the Kaiser
test. Therefore, a different method for monitoring the
coupling cycles of each APNA unit had to be explored.
We decided to incorporate all of the APNA monomers into
the synthetic scheme as the APNA-PNA dimers 19a -d .
These were easily synthesized in solution by the coupling
of monomers 6a -c and 12 with the PNA monomer 16
using HATU/DIPEA (Scheme 4). The ester moieties of
intermediates 18a -d were hydrolyzed to give the free
acids 19a -d , which were used directly in the solid-phase
synthesis of the Lys-PNA2-APNA-PNA3-Ac hexamers
(20-24) following the same protocol as in the PNA
control (Scheme 5). After cleavage of the hexamers from
the solid support, HPLC analysis of the crude material
indicated the presence of the desired PNA-APNA chime-
ras in >65% of the total sample. However, oligomers 20-
24 were isolated in approximately 30-50% yield after
HPLC purification.
Sch em e 5. P NA-AP NA Ch im er a s
Hybr id iza tion Stu d ies of AP NA-P NA Hexa m er s.
To gain some insight into the physicochemical properties
of each APNA monomer, we compared the hybridization
properties of hexamers 20-24 with poly(rA) and poly-
(dA) to those of the control PNA-T6 (17). In all cases, the
stability of triplex formation was evaluated by UV-
thermal melting (Tm) experiments at nearly physiological
conditions (pH ) 7.1, 150mM NaCl, 10mM NaH2PO4,
1mM EDTA). Hexamers were mixed in a 2:1 ratio (T2/A)
based on the expectation that each PNA strand (or
APNA-PNA chimera) would bind to the DNA or RNA
strand to form PNA2/DNA or PNA2/RNA triplexes.25 The
circular dichroism (CD) spectrum of the complex formed
between the Lys-PNA2-APNA-PNA3-Ac chimera 20 and
poly(rA) at a 2:1 molar ratio was very similar to that
observed for the triplex of the control PNA-T6 (17) with
poly(rA).25 Similar CD spectra were also observed for the
complexes formed between the PNA-T6 and poly(dA), as
well as chimera 20 and poly(dA), strongly suggesting that
the incorporation of a single monomer of structure 3a into
the PNA homopolymer did not alter the known hybrid-
ization characteristics of these oligomers.25 The melting
(23) (a) Christensen, L.; Fitzpatrick, R.; Gildea, B.; Petersen, K. H.;
Hansen, H. F.; Koch, T.; Egholm, M.; Buchardt, O.; Nielsen, P. E.;
Coull, J .; Berg, R. H. J . Peptide Sci. 1995, 1(3), 175. (b) Christensen,
L.; Fitzpatrick, R.; Gildea, B.; Petersen, K. H.; Hansen, H. F.; Koch,
T.; Egholm, M.; Buchardt, O.; Nielsen, P. E. J . Peptide Sci. 1995, 1(3),
185. c) Koch, T.; Hansen, H. F.; Andersen, P.; Larsen, T.; Batz, H. G.;
Otteson, K.; Orum, H. J . Peptide Res. 1997, 49(1), 80.
(24) Sarin, V. K.; Kent, S. B. H.; Tam, J . P.; Merrifield, R. B. Anal.
Biochem. 1981, 117, 147.
(25) Kim, S. K.; Nielsen, P. E.; Egholm, M.; Buchardt, O.; Berg, R.
H.; Norden, B. J . Am. Chem. Soc. 1993, 115, 6477.

3376 J . Org. Chem., Vol. 66, No. 10, 2001
Fader et al.
Ta ble 1. Resu lts of Th er m a l Den a tu r a tion Exp er im en tsa
for Com p lexes of Hexa m er s 17 a n d 20-24 w ith p oly(r A)
a n d p oly(d A)
genetic information is through activation of RNase H and
degradation of the target RNA molecules.29
Once the APNA monomer derived from glycine (3a )
was identified as the most promising lead structure in
this series, it was important to confirm that the decrease
in the melting temperatures observed with chimera 20
(∆Tm ) -15 and -11 °C for hybridization with poly(rA)
and poly(dA), respectively), as compared to the PNA
control, was not due to lack of base-pairing between the
APNA thymine residue and its complementary adenosine
residue.30 Thus, we prepared hexamer 24 containing a
cytosine residue at the APNA position and studied the
stability of the triplexes formed with poly(rA) and poly-
(dA). A far greater destabilizing effect was observed due
to the presence of a cytosine-adenosine mismatch than
that resulting by the incorporation of an APNA unit
having a complementary base (Table 1), strongly sug-
gesting that the APNA unit of hexamer 20 is indeed
participating in Watson-Crick or Ho¨ogsteen base-pairing
with the complementary nucleobase of poly(rA) and poly-
(dA).
In summary, we have described the synthesis of a new
class of aromatic peptide nucleic acid monomers with
potential biomedical applications. The synthetic meth-
odology developed can provide APNA monomers rapidly
and in high yields and purity. Furthermore, our synthetic
scheme is amenable to combinatorial or parallel synthesis
of larger libraries of APNA analogues. Incorporation of
these monomers into the automated, solid-phase synthe-
sis of APNA-PNA chimeras allows for rapid evaluation
of their hybridization properties, as well as modulation
of the physicochemical properties of the resulting oligo-
mers. Further optimization of the chemical structure and
hybridization properties of novel APNA-PNA chimeras
and investigation of their ability to penetrate cell mem-
branes in vivo is currently in progress.
Tm (°C)
compound
complex with poly(rA)
complex with poly(dA)
17
20
21
22
23
24
64
50
26
30
39
17
56
44
<5
26
30
<5
a
Melting temperatures of triplexes were determined on a Cary
3 UV-vis spectrophotometer.31 All Tm solutions were 150 mM in
NaCl, 10 mM in NaH2PO4, 1 mM in EDTA, and the pH was
adjusted to 7.1. The solutions were heated to 90 °C for 10 min,
then cooled slowly to 4 °C and stored at that temperature for at
least 1 h. The melting curves were recorded by heating the
solutions from 5 to 90 °C in steps of 0.5 °C/min.
temperatures (Tm) of the complexes studies are sum-
marized in Table 1. The PNA-T6 control strand (17) gave
Tm values of 65 and 56 °C when hybridized to poly(rA)
and poly(dA), respectively (Table 1), consistent with those
reported previously for triplexes of PNAs with natural
oligonucleotides.2b,25,26 Destabilization was observed upon
insertion of one APNA unit into the hexamer, resulting
in a significant decrease in the Tm values observed for
the complexes formed between the Lys-PNA2-APNA-
PNA3-Ac chimeras and poly(rA) or poly(dA) as compared
to those of the control (Table 1). Increasing the backbone
distance between adjacent nucleobases as in the case of
the â-alanine APNA analogue (chimera 21) had the most
detrimental effect in the stability of the complex formed
with poly(rA) [hybridization was not observed between
21 and poly(dA)], whereas the glycine APNA analogue
(chimera 20) corresponded to the most favorable back-
bone modification in this series of compounds (Table 1).
In addition, a pronounced hysteresis of the melting
behavior of the triplexes was observed with all of the
PNA-APNA chimeras with either poly(rA) or poly(dA),
indicating a very slow rate of triplex formation, typical
of PNAs.27
Exp er im en ta l Section
Gen er a l Meth od s. Solvents were purchased from Fischer
Scientific and purified as follows. THF was distilled from
sodium/benzophenone ketyl; CH2Cl2 was distilled from P2O5
or CaH2; DMF was treated with KOH overnight at room
temperature and then vacuum distilled from CaO or BaO and
stored over activated 4 Å molecular sieves; MeCN was distilled
from CaH2; and pyridine was distilled from CaH2. HPLC
solvents were HPLC grade and were filtered through 0.45 µm
filters (Supelco, Bellefonte, PA) prior to use. HATU was
purchased from PerSeptive Biosystems Ltd., and MBHA resin
was purchased from Nova Biochem Ltd. All other starting
materials and reagents were purchased from Sigma/Aldrich
Canada and were used without further purification, except for
DIPEA and Et3N, which were refluxed over CaH2 and then
distilled and stored over activated 4 Å molecular sieves. Thin-
layer chromatography was carried out on aluminum-backed
silica gel 60 F254 plates (EM Science, Germany) using the
solvent systems indicated. Reversed phase thin-layer chroma-
tography was carried out on glass-backed RP-18 F254s plates
(EM Science, Germany) using the solvent systems indicated.
Deuterated NMR solvents were purchased from Isotec Inc.
(Miamisburg, OH). NMR spectra were obtained at ambient
Backbone substitutions at CR of the amino acid moiety
in the APNA backbone was also detrimental, although
methyl substitution of the R configuration (chimera 23)
was slightly better than the S (chimera 22). The desta-
bilizing effects observed due to backbone substitution of
the APNA analogues are far more significant than those
previously reported for CR-substituted analogues of
PNAs. However, a direct comparison with previous
studies of substituted PNAs cannot be made, since our
investigation was focused on the formation of triplexes,
whereas previous reports examined the effects of back-
bone substitutions in the formation of duplexes.28 In all
cases, the known selectivity of PNAs for recognition of
RNA over DNA was also observed with the PNA-APNA
chimeras (Table 1).26 This is particularly important for
DNA-PNA chimeras and their applications in antisense
technology, since a key approach to halting the flow of
(29) Seitz, O. Angew. Chem., Int. Ed. 1999, 38, 3466.
(30) Hyrup, B.; Egholm, M.; Nielsen, P. E.; Wittung, P.; Norde´n,
B.; Buchardt, O. J . Am. Chem. Soc. 1994, 116, 7964.
(31) (a) A variability of (1 °C was observed in the Tm values
measured for different samples of the same oligomers; this may be
due to some variability in the purity of the commercial poly(rA) and
poly(dA) samples. (b) At a slower heating rate of 0.2 °C/min, all Tm
values measured were on the average 2-4 °C lower, as would be
expected.
(26) Lagriffoule, P.; Wittung, P.; Eriksson, M.; J ensen, K. K.;
Norden, B.; Buchardt, O.; Nielsen, P. E. Chem. Eur. J . 1997, 3, 912.
(27) (a) Egholm, M.; Christensen, L.; Dueholm, K. L.; Buchardt, O.;
Coull, J .; Nielsen, P. E. Nucleic Acids Res. 1995, 23, 217. (b) Lesnik,
E. A.; Risen, L. M.; Driver, D. A.; Griffith, M. C.; Sprankle, K.; Freier,
S. M. Nucleic Acids Res. 1997, 25, 568.
(28) Haaima, G,; Lohse, A.; Buchardt, O.; Nielsen, P. E. Angew.
Chem., Int. Ed. Engl. 1996, 35, 1939.

Aromatic Peptide Nucleic Acid Monomers
J . Org. Chem., Vol. 66, No. 10, 2001 3377
temperature unless otherwise indicated. 1H and 13C NMR
chemical shifts are quoted in ppm and are referenced to the
internal deuterated solvent. Mixtures of rotamers were often
observed by NMR; in those cases the ratio is indicated and
the signals are denoted as major (ma) and minor (mi). Some
NMR spectra were also recorded at high temperatures in order
to confirm the presence of rotamers. All 1H NMR spectra were
recorded on a Varian Mercury (400 MHz) or a Unity Inova
(300 MHz) spectrometer. 13C NMR spectra were recorded on
a J EOL (67.5 MHz) or a Varian Mercury spectrometer (100
MHz).
to use a DCC/pentafluorophenol preactivation protocol; how-
ever, this procedure gave a lower yield of 5a (∼70%). Com-
pound 5a : TLC Rf (EtOAc) ) 0.288; 1H NMR (300 MHz,
DMSO-d6, mixture of rotamers in 1:1 ratio) δ 1.74 and 1.75
(s, 3H), 3.62 and 3.69 (s, 3H), 4.05 and 4.36 (s, 2H), 4.58 and
4.83 (s, 2H), 4.64 and 5.06 (s, 2H), 7.39-7.44 (m, 1.5H), 7.53
(dt, 0.5H, J ) 7.0 and 1.2 Hz), 7.58-7.62 (m, 1H), 7.70 and
7.80 (dt, 1H, J ) 7.0 and 1.2 Hz), 8.05 and 8.16 (dd, 1H, J )
7.0 and 1.2 Hz), 11.28 and 11.31 (s, 1H), coalescence of each
pair of rotamer resonances was achieved at ∼90 °C; 13C NMR
(67.5 MHz, DMSO-d6, 120 °C) δ 12.0, 48.6, 49.4, 52.4, 109.0,
125.2, 129.1, 129.6, 132.3, 134.2, 142.2, 149.1, 151.5, 164.6,
169.0, 169.6; FAB+ MS (glycerol) m/z 391 (M + H)+.
Syn th esis of Com p ou n d s 5b a n d 5c. Analogues 5b and
5c were synthesized using the same procedure as that
described for compound 5a . Compound 5b: yield 93%; TLC Rf
(EtOAc) ) 0.226; 1H NMR (400 MHz, DMSO-d6, mixture of
rotomers in 1:1.7 ratio) δ 1.14 (mi) and 1.15 (ma) (t, 3H, J )
7.0 Hz), 1.73 (bs, 3H), 2.55 (mi) and 2.71 (ma) (t, 2H, J ) 8.1
Hz), 3.45 (mi) and 3.62 (ma) (t, 2H, J ) 8.1 Hz), 3.99 (mi) and
4.01 (ma) (q, 2H, J ) 7.8 Hz), 4.45 (mi) and 4.75 (ma) (s, 2H),
4.81 (ma) and 5.01 (mi) (s, 2H), 7.31-7.37 (m, 1.6H), 7.44 (d,
0.4H, J ) 7.6 Hz), 7.53 (ma) and 7.60 (mi) (t, 1H, J ) 7.2 Hz),
7.69 (ma) and 7.81 (mi) (t, 1H, J ) 7.6 Hz), 8.06 (ma) and
8.17 (mi) (d, 1H, J ) 8.0 Hz), 11.25 (bs, 1H); 13C NMR (75
MHz, DMSO-d6) δ 12.4, 12.5, 14.5, 32.5, 33.2, 34.2, 35.4, 43.2,
43.4, 46.7, 48.6, 48.7, 49.0, 49.7, 60.6, 60.7, 108.5, 108.6, 125.4,
125.9, 128.0, 128.3, 128.7, 129.1, 133.2, 133.3, 134.3, 135.0,
142.7, 148.2, 148.6, 151.7, 151.9, 165.3, 168.4, 171.6, 171.8;
FAB+ MS (glycerol) m/z 419 (M + H)+. Compounds (R)-5c and
(S)-5c: yields for both compounds ∼80%; TLC Rf (EtOAc) )
0.350; 1H NMR (300 MHz, DMSO-d6, 120 °C) δ 1.37 (d, 3H, J
) 7.2 Hz), 1.79 (d, 3H, J ) 1.2 Hz), 3.64 (s, 3H), 4.48-4.87
(overlapping broad signals, 4H), 5.05 (d, 1H, J ) 18 Hz),
6.67.28 (d, 1H, J ) 1.2 Hz), 7.53-7.59 (m, 2H), 7.73 (bd, 1H,
J ) 5.4 Hz), 8.06 (d, 1H, J ) 8.1 Hz), 10.70 (bs, 1H); 13C NMR
(67.5 MHz, DMSO-d6, 130 °C) δ 11.9, 15.3, 46.5, 49.1, 52.4,
55.7, 108.9, 125.1, 129.0, 129.5, 133.0, 134.0, 142.3, 148.7,
151.5, 164.6, 167.0, 171.5; FAB+ MS (glycerol) m/z 405 (M +
H)+.
Syn th esis of Meth yl N-(2-Nitr oben zyl)glycin a te (4a ).
2-Nitrobenzaldehyde (5.70 g, 38 mmol), methyl glycinate
hydrochloride (4.30 g, 34 mmol), and triethylamine (5.0 mL,
38 mmol) were dissolved in dry CH2Cl2 (160 mL). This mixture
was stirred under N2 for 30 min, and then NaBH(OAc)3 was
added. The reaction was stirred for 5 h and then quenched by
the addition of H2O (30 mL), and the aqueous layer was
discarded. The crude product was extracted into 0.1 M HCl
(100 mL), and the water layer was back-extracted with CH2-
Cl2 (2 × 300 mL). The pH was adjusted to 4 by dropwise
addition of NaOH (1 M), and the product was extracted into
CH2Cl2 (4 × 500 mL). The combined organic layers were dried
over anhydrous MgSO4 and concentrated to dryness, giving
the title compound as an orange oil in 68% yield and in high
purity. For more convenient storage and handling of the
material, compound 4a was converted quantitatively to its
hydrochloride salt by dissolution of the oil in 1:1 Et2O/EtOAc
(60 mL) followed by addition of HCl (1.5 equiv, 2 M HCl in
Et2O). The white precipitate was collected by filtration and
1
dried in vacuo: TLC Rf (60% hex in EtOAc) 0.246; H NMR
(300 MHz, CDCl3) δ 2.41 (bs, 1H), 3.43 (s, 2H), 3.69 (s, 3H),
4.07 (s, 2H), 7.40 (dt, 1H, J ) 8.0 and 1.4 Hz), 7.53-7.62 (m,
2H), 7.93 (d, 1H, J ) 8.0 Hz); 13C NMR (75 MHz, CDCl3) δ
50.27, 50.36, 51.94, 124.91, 128.23, 131.06, 133.31, 135.12,
149.17, 172.70. HCl salt of 4a : 1H NMR (300 MHz, CD3OD) δ
3.86 (s, 3H), 4.14 (s, 2H), 4.58 (s, 2H), 7.74-7.89 (m, 3H), 8.29
(dd, 1H, J ) 8.4 and 1.0 Hz); FAB+ HRMS (glycerol/KCl) m/z
found 225.0875 (M + H)+, calcd for (C10H13N2O4)+ 225.0876.
Syn th esis of 4b a n d 4c. These analogues were synthesized
using the same procedure as that described for 4a . Amine 4b:
yield 70%; TLC Rf (free amine, 1:1 hex/EtOAc) ) 0.182; 1H
NMR (300 MHz, CDCl3) δ 1.25, (t, 3H, J ) 6.9 Hz), 3.02 (t,
2H, J ) 5.9 Hz), 3.36, (t, 2H, J ) 6.4 Hz), 4.17, (q, 2H, J ) 7.0
Hz), 4.37, (s, 1H), 7.63, (dt, 1H, J ) 7.6 and 1.2 Hz), 7.76 (dt,
1H, J ) 7.6 and 1.8 Hz), 8.01 (dd, 1H, J ) 6.4 and 1.2 Hz),
8.16 (dd, 1H, J ) 7.0 and 1.2 Hz); 13C NMR (100 MHz, DMSO-
d6) δ 14.7, 30.8, 43.3, 47.6, 61.2, 125.9, 127.9, 131.3, 134.0,
134.9, 149.0, 170.6; FAB+ HRMS (glycerol) m/z found 253.1188
(M + H)+, calcd for (C12H17N2O4)+ 253.1188. Amine (R)-4c and
(S)-4c: yields in both cases 70-75%; 1H NMR (400 MHz,
CDCl3) δ 1.30 (d, 3H, J ) 6.9 Hz), 3.25 (q, 1H, J ) 6.9 Hz),
3.68 (s, 3H), 3.95 (d, 1H, J ) 15 Hz), 4.07 (d, 1H, J ) 15 Hz),
7.39, (dt, 1H, J ) 8.6 and 1.6 Hz), 7.55 (dt, 1H, J ) 7.8 and
1.2 Hz), 7.60 (dd, 1H, J ) 7.8 and 1.2 Hz), 7.92 (dd, 1H, J )
7.8 and 1.2 Hz); 13C NMR (100 MHz, CDCl3) δ 19.3, 49.1, 52.1,
56.6, 125.0, 128.3, 131.3, 133.4, 135.3, 149.3, 176.0; FAB+
HRMS (glycerol/KCl) m/z found 239.1032 (M + H)+, calcd for
(C11H15N2O4)+ 239.1032.
Syn th esis of Meth yl N-(2-Nitr oben zyl)-N-(th ym in -1-
yla cetyl)glycin a te (5a ). Thymidyl acetic acid (1.50 g, 8.1
mmol) and HATU (3.09 g, 8.1 mmol) were dissolved in
anhydrous DMF (20 mL) under N2 and cooled to 0 °C. To this
solution, DIPEA (1.5 mL, 8.6 mmol) was added, and the
reaction mixture was stirred for 10 min at 0 °C. Compound
4a (1.69 g, 7.5 mmol) was than added as a solution in
anhydrous DMF (10 mL), and the reaction was allowed to
warm up to room temperature and stir overnight. The reaction
mixture was then concentrated to ∼5 mL, and EtOAc (50 mL)
was added. This solution was washed with water (3 × 15 mL),
and the organic layer was concentrated to about 10 mL and
cooled to 0 °C. The precipitate formed was collected by
filtration and washed once with 10% hexanes in EtOAc giving
2.50 g of compound 5a (85% yield) in high purity. For large-
scale synthesis of 5a (i.e. >20 g) it was far more cost-effective
Syn th esis of Meth yl N-(2-Am in oben zyl)-N-(th ym in -1-
yla cetyl)glycin a te (6a ). Compound 5a (434 mg, 1.1 mmol)
was dissolved in anhydrous DMF (3 mL), and Pd-C (65 mg)
was added. Triethylamine (0.6 mL, 4.3 mmol) and formic acid
(0.13 mL, 3.3 mmol) were added, and the reaction mixture was
stirred at room temperature for 4 h. EtOH (10 mL) was added,
and the mixture was filtered through Celite and concentrated
to dryness. The resulting white solid was dried in vacuo to
giving 388 mg (97% yield) of compound 6a , which was
1
determined to be pure by H NMR: TLC Rf (EtOAc) ) 0.213;
1H NMR (400 MHz, DMSO-d6, mixture of rotamers in 1:1.5
ratio) δ 1.75 (mi) and 1.76 (ma) (d, 3H, J ) 1.2 Hz), 3.59 (mi)
and 3.62 (ma) (s, 3H), 3.97 (mi) and 4.20 (ma) (s, 2H), 4.37
(ma) and 4.50 (mi) (s, 2H), 4.56 (ma) and 4.61 (mi) (s, 2H),
5.01 (mi) and 5.06 (ma) (bs, 2H), 6.47 (dt, 0.6H, J ) 6.3 and
1.2 Hz), 6.60 (m, 0.9H, J ) 7.0 and 1.2 Hz), 6.69 (dd, 0.5H, J
) 7.6 and 1.2 Hz), 6.96-7.01 (m, 2H), 7.35 (ma) and 7.40 (mi)
(d, 1H, J ) 1.2 Hz), 11.29 (mi) and 11.32 (ma) (bs, 1H); 13C
NMR (67.5 MHz, DMSO-d6, 130 °C) δ 12.0, 48.0, 48.6, 52.2,
109.0, 116.3, 117.2, 119.5, 129.0, 130.0, 142.3, 147.1, 151.5,
164.6, 168.7, 169.6; FAB+ HRMS (glycerol) m/z found 361.1512
(M + H)+, calcd for (C17H21N4O5)+ 361.1511.
Syn th esis of Com p ou n d s 6b a n d 6c. These analogues
were synthesized using the same procedure as for compound
1
6a . Aniline 6b: yield 80%; TLC Rf (EtOAc) ) 0.130; H NMR
(300 MHz, DMSO-d6, mixture of rotamers in 1:2.3 ratio) δ 1.14
(mi) and 1.18 (ma) (t, 3H, J ) 7.1 Hz), 1.74 (mi) and 1.75 (ma)
(bs, 3H), 2.49 (mi) and 2.69 (ma) (t, 2H, J ) 7.5 Hz), 3.42 (mi)
and 3.48 (ma) (t, 2H, J ) 7.5 Hz), 4.00 (mi) and 4.07 (ma) (q,
2H, J ) 7.1 Hz), 4.37 (ma) and 4.42 (mi) (s, 2H), 4.49 (mi) and
4.67 (ma) (s, 2H), 4.99 (mi) and 5.05 (ma) (s, 2H), 6.49 (t, 0.6H,
J ) 6.9 Hz), 6.57-6.61 (m, 1H), 6.67 (d, 0.4 H, J ) 7.8 Hz),
6.90-7.03 (m, 2H), 7.39 (mi) and 7.41 (ma) (bs, 1H), 11.28 (bs,
1H); 13C NMR (100 MHz, DMSO-d6) δ 11.9, 14.0, 32.1, 32.20,
40.91, 42.3, 44.7, 46.5, 48.1, 48.2, 60.0, 60.2, 107.9, 108.0, 114.7,

3378 J . Org. Chem., Vol. 66, No. 10, 2001
Fader et al.
115.3, 115.7, 116.6, 119.0, 119.3, 126.2, 127.9, 128.4, 129.8,
142.3, 142.4, 146.0, 146.6, 151.1, 164.5, 167.3, 171.0, 171.1;
FAB+ HRMS (glycerol) m/z found 389.1825 (M + H)+, calcd
for (C19H25N4O5)+ 389.1826. Aniline (R)-6c and (S)-6c: yield
7.03 (m, 1H), 7.10-7.12 (m, 1H), 7.22-7.39 (m, 7H), 7.53 (bs,
1H), 7.70 (bd, 1H, J ) 6.9 Hz), 8.04 (bd, 1H, J ) 6.9 Hz), 8.34
(bs, 1H); ES+ MS m/z 564 (M + H)+; ES- MS m/z 562 (M -
H)-.
1
80%; Rf (EtOAc) ) 0.40; H NMR (300 MHz, DMSO-d6, 120
Syn th esis of AP NA Cytosin e Mon om er 12. Allyl car-
bamate 11 (164 mg, 0.3 mmol) was dissolved in DCM (6 mL)
and H2O (100 µL), and Bu3SnH (81 µL, 0.3 mmol) followed by
Pd(PPh3)4 (16 mg, 5mol %) were added. After 15 min the
reaction mixture was concentrated to an oil, which was then
purified by flash column chromatography using a solvent
gradient of 0-5% MeOH in CHCl3 as the eluent. Pure aniline
12 was isolated as a glassy solid (140 mg, 91%): 1H NMR (300
MHz, CDCl3, mixture of rotamers in 1:1.3 ratio) δ 3.58 (mi)
and 3.62 (ma) (s, 3H), 3.96 (mi) and 4.23 (ma) (s, 2H), 4.37
(ma) and 4.51 (mi) (s, 2H), 4.70 (ma) and 4.77 (mi) (s, 2H),
5.01 (mi) and 5.02 (ma) (s, 2H), 5.17 (mi) and 5.18 (ma) (s,
2H), 6.47 (ddd, 0.6H, J ) 7.2 and 1.2 Hz), 6.56-6.60 (m, 0.9H),
6.69 (d, 0.5H, J ) 7.6 Hz), 6.95-7.03 (m, 3H), 7.33-7.40 (m,
5H), 7.94-7.99 (m, 1H), 10.74 (bs, 1H); ES+ MS m/z 480 (M +
H)+; ES- MS m/z 478 (M - H)-.
Syn th esis of [AP NA(gly)-Th ]-[P NA-Th ] P r otected Dim er
(18a ). Free acid 16 (830 mg, 2.2 mmol), aniline 6a (773 mg,
2.2 mmol), and HATU (828 mg, 2.2 mmol) were placed in a
flask under N2, and anhydrous DMF (5 mL) was added. The
mixture was cooled to 0 °C, and a solution of DIPEA (0.11 mL,
10% solution in anhydrous DMF, 4.3 mmol) was added
dropwise. The reaction mixture was allowed to warm up to
room temperature and stir for 6 h before quenching with H2O
(15 mL). A mixture of 10% MeOH in CHCl3 (50 mL) was added,
and the organic layer was washed with 5% NaHCO3 (2 × 15
mL) and brine (1 × 15 mL), dried over anhydrous MgSO4, and
concentrated to dryness. The crude product was purified by
flash column chromatography, using a solvent gradient of
0-8% MeOH in CHCl3 as the eluent to give 1.56 g (79% yield)
of pure dimer 18a : TLC Rf (8% MeOH in CHCl3) ) 0.211; 1H
NMR (300 MHz, DMSO-d6) δ 1.36-1.38 (bs, 9H), 1.74 (bs, 6H),
3.06-3.44 (m, 4H), 3.59-3.62 (bs, 3H), 3.97-4.68 (m, 8H),
6.74-7.68 (m, 6H), 9.55-9.86 (m, 1H), 11.29-11.33 (m, 2H);
FAB+ HRMS (glycerol/KCl) m/z found 765.260910 (M + K)+,
calcd for (C32H40N8O11K)+ 765.261013.
Syn th esis of Dim er s 18b-d . Dimers 18b, 18c, and 18d
were synthesized using the same procedure as for dimer 18a .
Dimer 18b: yield 71%; TLC Rf (12% MeOH in EtOAc) ) 0.121;
1H NMR (300 MHz, DMSO-d6) δ 1.09-1.19 (m, 3H), 1.35-
1.37 (m, 9H), 1.74 (bs, 6H), 2.41-2.71 (m, 2H), 3.00-3.52 (m,
6H), 3.93-4.73 (m, 10H), 6.74-7.66 (m, 7H), 9.57-9.90 (m,
1H), 11.27-11.30, (m, 2H); ES+ MS m/z 755 (M + H)+; ES-
MS m/z 753 (M - H)-. Dimer (R)-18c and (S)-18c: yield 70%;
1H NMR (300 MHz, DMSO-d6, 140 °C) δ 1.34 (d, 3H, J ) 7.2
Hz), 1.42 (s, 9H), 1.79 (m, 6H), 3.25 (q, 2H, J ) 6.3 Hz), 3.22-
3.55 (m, 2H), 3.60 (s, 3H), 4.22 (s, 2H), 4.44-4.68 (m, 7H), 6.32
(bs, 1H), 7.23-7.46 (m, 6H), 9.26 (bs, 1H), 10.63, (bs, 2H); ES+
MS m/z 764 (M + Na)+. Dimer 18d : yield 69%; TLC Rf (5%
MeOH in CHCl3) ) 0.19; 1H NMR (300 MHz, CDCl3) δ 1.35-
1.42 (m, 9H), 1.83-1.88 (m, 3H), 3.26-3.75 (m, 7H), 4.02-
4.79 (m, 10H), 5.19-5.43 (m, 2H), 6.97-8.47 (m, 13H), 8.81-
9.03 (m, 1H), 9.50-9.85 (m, 1H), 10.68 (bs, 1H); ES+ MS m/z
832 (M + H)+; ES- MS m/z 830 (M - H)-.
Syn th esis of [AP NA(gly)Th ]-[P NA-Th ] Fr ee Acid Dim er
19a . To a solution of ester 18a (1.97 g, 2.7 mmol) in THF (20
mL) was added aqueous LiOH (10 mL, 0.8M, 8.0 mmol), and
the reaction was stirred at room temperature for 45 min. The
mixture was then diluted with H2O (30 mL), cooled to 0 °C,
and acidified to pH 3 by the dropwise addition of aqueous HCl
(0.1 M). The solution was then extracted with 10% MeOH in
CHCl3 (3 × 100 mL), and the combined organic layers were
dried over anhydrous MgSO4 and concentrated to give dimer
19a as a white foam in 88% yield (1.70 g) and in high purity:
RP-TLC Rf (80% MeOH in H2O) ) 0.1; 1H NMR (300 MHz,
DMSO-d6, mixture of four rotamers) δ 1.34-1.36 (m, 9H),
1.71-1.75 (m, 6H), 3.02-3.48 (m, 4H), 3.82-4.69 (m, 10H),
5.19 (s, 2H), 5.31 (ma) and 5.35 (mi) (s, 2H), 6.70-7.70 (m,
6H), 9.57-9.68 (m, 1H), 10.66 (bs, 1H), 11.26-11.31 (m, 2H);
FAB+ HRMS (glycerol/NaCl) m/z found 735.2714 (M + Na)+,
calcd for (C32H40N8O11 + Na)+ 735.2712.
°C) δ 1.34 (d, 3H, J ) 6.9 Hz), 1.80 (bs, 3H), 3.60 (s, 3H), 4.41-
4.64 (m, 5H), 6.62 (dd, 1H, J ) 7.2 Hz), 6.72 (d, 1H, J ) 7.8
Hz), 7.01 (dd, 1H, J ) 7.5 Hz), 7.12 (d, 1H, 7.5 Hz), 7.25 (bs,
1H), 10.70 (s, 1H); FAB+ HRMS (glycerol) m/z found 375.1668
(M + H)+, calcd for (C18H23N4O5)+ 375.1667.
Syn th esis of Allyl Ca r ba m a te Der iva tive 8. 2-Ami-
nobenzyl alcohol (7, 1.04 g, 8.5 mmol) was dissolved in 1:1
DCM/pyridine (20 mL), and alloc-Cl (1.12 g, 9.3 mmol) was
added dropwise via syringe over a period of 15 min. After 1.5
h the reaction mixture was diluted with DCM (200 mL) and
extracted with H2O (100 mL). The organic layer was then dried
over anhydrous MgSO4 and concentrated to dryness. Flash
column chromatography, using 12% EtOAc in hexanes as the
eluent, provided 1.36 g of pure carbamate 8 (77% yield) as a
colorless oil: 1H NMR (300 MHz, CDCl3) δ 2.34 (bd, 1H, J )
11.7 Hz), 4.65 (ddd, 2H, J ) 5.1 and 1.8 Hz), 4.67 (s, 2H), 5.26
(dm, 1H, J ) 10.5 Hz), 5.36 (dm, 1H, J ) 17.1 Hz), 5.91-6.04
(m, 1H), 7.03 (ddd, 1H, J ) 7.0 and 1.2 Hz), 7.15 (dd, 1H, J )
7.0 and 1.2 Hz), 7.31 (ddd, 1H, J ) 8.2 and 1.8 Hz), 7.90 (bd,
1H, J ) 8.1 Hz), 7.97 (bs, 1H).
Syn th esis of Br om id e Der iva tive 9. Carbamate 8 (1.35
g, 3.7 mmol) was dissolved in anhydrous THF (50 mL). CBr4
(2.2 g, 6.5 mmol) followed by PPh3 (1.70 g, 6.5 mmol) were
added, and the reaction mixture was stirred at room temper-
ature for 2 h. Upon completion of the reaction, the solvent was
evaporated to dryness, and crude product was redissolved in
EtOAc (20 mL). The precipitated (OPPh3) was removed by
filtration, and the filtrate was concentrated to dryness. The
residue was the purified by flash column chromatography,
using 5% EtOAc in hexanes as the eluent, to give bromide 9
as a fluffy white solid (920 mg, 58% yield): 1H NMR (400 MHz,
CDCl3) δ 4.50 (s, 2H), 4.68 (dt, 2H, J ) 5.6 and 1.6 Hz), 5.27
(dm, 1H, J ) 10.8 Hz), 5.39 (dm, 1H, J ) 17.2 Hz), 5.95-6.05
(m, 1H), 6.88 (bs, 1H), 7.11 (ddd, 1H, J ) 7.1 and 1.2 Hz),
7.28 (dd, 1H, J ) 8.0 and 1.6 Hz), 7.34 (ddd, 1H, J ) 7.8 and
1.6 Hz), 7.83 (bd, 1H, J ) 7.2 Hz).
Syn th esis of Meth yla m in e In ter m ed ia te 10. To a solu-
tion of bromide 9 (268 mg, 1 mmol) in anhydrous DMF (3 mL)
were added HCl‚GlyOMe (500 mg, 3 mmol) and DIPEA (1.0
mL, 6.0 mmol). The reaction mixture was stirred overnight at
room temperature under N2. The crude product was then
partitioned between H2O (12 mL) and EtOAc (25 mL). The
organic layer was washed once with H2O (12 mL), dried over
anhydrous MgSO4, and evaporated to dryness. The residue was
purified by flash column chromatography, using 10% EtOAc
in hexanes as the eluent, to give 293 mg of pure amine 10
(92% yield) as a colorless oil: 1H NMR (400 MHz, CDCl3) δ
3.46 (s, 2H), 3.75 (s, 3H), 3.90 (s, 2H), 4.67 (ddd, 2H, J ) 6.0
and 0.8 Hz), 5.24 (dm, 1H, J ) 10.4 Hz), 5.38 (dm, 1H, J )
17.2 Hz), 5.94-6.04 (m, 1H), 7.03 (ddd, 1H, J ) 7.2 and 0.8
Hz), 7.18 (d, 1H, J ) 7.2 Hz), 7.31 (ddd, 1H, J ) 7.8 and 1.6
Hz), 7.94 (bd, 1H, J ) 8.0 Hz), 9.31 (bs, 1H); 13C NMR (67.5
MHz, CDCl3) δ 28.2, 50.1, 52.2, 65.5, 81.5, 117.6, 120.2, 122.6,
126.3, 128.6, 129.7, 133.0, 138.9, 153.8, 171.1.
Syn th esis of P r otected AP NA Cytosin e Mon om er 11.
Amine 10 (328 mg, 1.2 mmol), CyCbzCH2CO2H (466 mg, 1.5
mmol) and HATU (583 mg, 1.5 mmol) were suspended in
anhydrous DMF (7 mL) under N2 at 0 °C. To the stirred
suspension was added DIPEA (0.54 mL, 3.1 mmol), and after
stirring at 0 °C for 10 min the reaction mixture was allowed
to warm up to room temperature and stir for an additional 8
h. The crude product was diluted with EtOAc (100 mL) and
washed with H2O (1 × 75 mL), 5% NaHCO3 (1 × 75 mL), and
H2O (1 × 75 mL). The organic layer was then dried over
anhydrous MgSO4 and concentrated to dryness. Pure monomer
11 was obtained after flash column chromatography, using
pure EtOAc as the eluent, as a white foam (642 mg, 72%
yield): 1H NMR (300 MHz, CDCl3, mixture of rotamers in 1:3.5
ratio) δ 3.69 (bs, 3H), 4.00 (mi) and 4.26 (ma) (bs, 2H), 4.59-
4.85 (m, 6H), 5.19-5.37 (m, 4H), 5.85-6.02 (m, 1H), 6.98-

Aromatic Peptide Nucleic Acid Monomers
J . Org. Chem., Vol. 66, No. 10, 2001 3379
Syn th esis of Dim er 19b a n d 19c. The free acids of dimers
19b and 19c were synthesized using the same procedure as
for 19a . Free acid 19b: yield 90%; 1H NMR (400 MHz, DMSO-
d6) 1.35 and 1.37 (m, 9H), 1.73 and 1.75 (m, 6H), 2.36-2.65
(m, 2H), 3.03-3.61 (m, 6H), 4.04-4.73 (m, 10H), 6.74-7.71
(m, 6H), 9.64-9.97 (m, 1H), 11.29-11.32, (m, 2H), 12.26 (br,
1H); ES+ MS m/z 727 (M + H)+; ES- MS m/z 725 (M - H)-.
Free acid (R)-19c and (S)-19c: yield 97%; 1H NMR (400 MHz,
DMSO-d6) δ 1.17-1.25 (m, 3H), 1.36-1.37 (m, 9H), 1.73 (br,
6H), 3.06-3.45 (m, 4H), 4.04-4.77 (m, 9H), 6.57-7.59 (m, 6H),
9.64-9.90 (m, 1H), 11.28-11.32 (m, 1H); FAB+ HRMS (glycerol/
KCl) m/z found 765.261013 (M + K)+, calcd for (C33H42N8O11
washed with TFA (2 × 1 min) and then subjected to a precooled
(0 °C) solution of TFMSA/thioanisole/TFA (1:1:8) and mixed
for 1 h while coming to room temperature. The resin was then
removed by filtration, and the filtrate was diluted with
anhydrous Et2O (20×). The resulting mixture was then
centrifuged to give a white pellet. The ethereal supernatant
was decanted off, fresh Et2O was added, and the pellet was
broken up and resuspended. After centrifugation the super-
natant was decanted off, and the pellet was dried in vacuo.
The oligomers were then purified by reversed-phase HPLC and
analyzed by mass spectrometry. HPLC conditions A: C18 Vydac
reversed-phase column (4.6 × 125 mm, 5 µm), flow rate 1.5
mL/min, linear gradient from 5% aqueous CH3CN to 100%
CH3CN (all solvents contained 0.06% TFA) in 35 min, UV
monitored at λ ) 260 nm, room temperature. HPLC conditions
B: HP Zorbax RX-C18 reversed-phase column (9.4 × 250 mm,
5 µm), flow rate 4.2 mL/min, linear gradient from 100% H2O
to 30% aqueous CH3CN (all solvents contained 0.06% TFA) in
55 min, UV monitored at λ ) 260 nm, at 55 °C.
Hexa m er 17. HPLC conditions A; retention time ) 8.1 min
(peak area 100%); ES+ MS m/z 1807 (M + H)+, 1830 (M +
Na)+; ES- MS m/z 1805 (M - H)-, 1828 (M + Na - H)-.
Hexa m er 20. HPLC conditions A; retention time ) 9.6 min
(peak area 100%); ES+ MS m/z 1846.6 (M + H)+; ES- MS m/z
1844.6 (M - H)-.
Hexa m er 21. HPLC conditions B; retention time ) 24.8
min (peak area 100%); ES+ MS m/z 1861 (M + H)+; ES- MS
m/z 1859 (M - H)-.
1
+ K)+ 765.260910. Free acid 19d : yield 88%; H NMR (300
MHz, DMSO-d6) δ 1.34-1.36 (m, 9H), 1.71-1.75 (m, 3H),
3.02-3.48 (m, 4H), 3.86-4.83 (m, 10H), 5.18 (s, 2H), 6.70-
7.92 (m, 13H), 9.54-9.85 (m, 1H), 10.79 (bs, 1H), 11.30 (m,
1H); ES+ MS m/z 846 (M + H)+; ES- MS m/z 844 (M - H)-.
Solid -P h a se Syn th esis of Oligom er s. Oligomers 17 and
20-24 (0.02-0.03 mmol) were synthesized on MBHA resin
with
a
loading capacity of 0.19-0.40 mmol/g, using the
following protocol.
(1) Der iva tiza tion of MBHA Resin (p er 100 m g of d r y
r esin ). The dry MBHA‚HCl resin was suspended in DCM (5
mL) for 24 h. The resin was washed with 5% DIPEA in DMF
(2 × 3 mL, 10 min each time). Boc-Lys(2-Cl-Cbz)-OH (5 equiv)
was cross-linked to the resin using HATU (4.8 equiv) as the
coupling agent in the presence of DIPEA (10 equiv) until a
negative kaizer test was observed (∼3 h). The resin was treated
with a mixture of Ac2O/pyridine/DCM (1:25:25 ratio, 3 mL)
for 10 min and then washed with DCM (2 × 30 s, 3 mL), DMF
(2 × 30 s, 3 mL) and DCM (2 × 30 s, 3 mL).
Hexa m er 22. HPLC conditions A; retention time ) 9.8 min
(peak area 100%); ES+ MS m/z 1861 (M + H)+; ES- MS m/z
1859 (M - H)-.
Hexa m er 23. HPLC conditions A; retention time ) 9.7 min
(peak area 100%); ES+ MS m/z 1861 (M + H)+; ES- MS m/z
1859 (M - H)-.
Hexa m er 24. HPLC conditions B; retention time ) 24.3
min (peak area 100%); ES+ MS m/z 1856 (M + Na)+; ES- MS
m/z 1854 (M + Na - H)-.
(2) Cou p lin g of Mon om er or Dim er F r a gm en ts (ch a in
elon ga tion ). The resin-bound, Boc-protected amino moiety
was treated with 35% TFA in DCM (3 mL for 2 min and 3 mL
for 40 min), followed by washing with DCM (4 × 30 s, 3 mL),
DMF (3 × 30 s, 3 mL), DCM (3 × 30 s, 3 mL), and DMF (3 ×
30 s, 3 mL). Deprotection was monitored by the Kaizer test
using a small aliquot of resin-bound peptide (∼1 mg). The free
acid was first preactivated by reacting with HBTU/DECA in
a 3:2.85:6 molar ratio (acid/HBTU/DECA) in a solvent mixture
of 1:1 DMF/pyridine for 1 min. This latter solution was then
transferred to the reaction vessel containing the resin to give
a final concentration 0.07 M with respect to the free acid. The
coupling was allowed to proceed until a negative kaiser test
was observed (∼0.5-4 h). The resin was washed with DMF (3
× 30 s, 3 mL), DCM (3 × 30 s, 3 mL), DMF (3 × 30 s, 3 mL),
and DCM (3 × 30 s, 3 mL). The resin was finally capped by
treating with Ac2O/pyridine/DCM (1:1:2, 3 mL) for 5 min and
washed with DCM (4 × 30 s, 3 mL), DMF (2 × 30 s, 3 mL),
and DCM (2 × 30 s, 3 mL).
Ack n ow led gm en t. We thank the Natural Sciences
and Engineering Research Council of Canada for finan-
cial support (grants to Y.S.T.) and the Walter C. Sumner
Foundation (1999-2000) and NSERC for Fellowships
to L.D.F. We are also grateful to Professor Masad J .
Damha (Chemistry Department, McGill Universitry) for
numerous valuable discussions.
Su p p or tin g In for m a tion Ava ila ble: Copies of 1H and 13C
NMR spectra for key compounds monomers 6a -c and 12 and
dimers 18a -d . This material is available free of charge via
the Internet at http://pubs.acs.org.
(3) Clea va ge of Oligom er s fr om th e Resin . The resin
was dried in vacuo for at least 12 h. The dry resin was then
J O001650O