A Pyrimidopyrimidine Janus-AT nucleoside with improved base-pairing properties to both A and T within a DNA duplex: The stabilizing effect of a second endocyclic ring nitrogen

Article abstract of DOI:10.1002/chem.201303867

Janus bases are heterocyclic nucleic acid base analogs that present two different faces able to simultaneously hydrogen bond to nucleosides that form Watson-Crick base pairs. The synthesis of a Janus-AT nucleotide analogue, ^NJ_AT, that has an additional endocyclic ring nitrogen and is thus more capable of efficiently discriminating T/A over G/C bases when base-pairing in a standard duplex-DNA context is described. Conversion to a phosphoramidite ultimately afforded incorporation into an oligonucleotide. In contrast to the first generation of carbocyclic Janus heterocycles, it remains in its unprotonated state at physiological pH and, therefore, forms very stable Watson-Crick base pairs with either A or T bases. Biophysical and computational methods indicate that ^NJ_AT is an improved candidate for sequence-specific genome targeting. N-Game for DNA recognition: The synthesis and oligonucleotide incorporation of an optimized, soluble Janus-AT base ( ^NJ_AT) that efficiently discriminates T/A over G/C bases, while retaining a nonprotonated state at physiological pH, is reported. ^NJ_AT was characterized in a duplex-DNA context with a set of biophysical and computational methods, all pointing out that this new base is a very good candidate for sequence-specific genome targeting (see figure). Copyright

Full text of DOI:10.1002/chem.201303867

DOI: 10.1002/chem.201303867
Communication
&
DNA Recognition
A Pyrimidopyrimidine Janus-AT Nucleoside with Improved
Base-Pairing Properties to both A and T within a DNA Duplex:
The Stabilizing Effect of a Second Endocyclic Ring Nitrogen
Eric Largy, Wenbo Liu, Abid Hasan, and David M. Perrin*[a]
counterbalance the energetic cost of disrupting the double
Abstract: Janus bases are heterocyclic nucleic acid base
analogs that present two different faces able to simultane-
ously hydrogen bond to nucleosides that form Watson–
Crick base pairs. The synthesis of a Janus-AT nucleotide
helix. Nevertheless, the displaced strand remains unpaired and
is therefore poised to eject the inserted strand to recapture its
position within the DNA duplex. This may explain the general
thermodynamic instability of D-loops. To potentially overcome
this thermodynamic ambiguity, Lehn and co-workers proposed
the concept of Janus bases that would simultaneously hydro-
gen bond to bases on both strands by forming pseudo-
Watson–Crick base pairs simultaneously with each base.[5] This
concept was explored by several groups with oligonucleotides
containing either singly-embedded Janus bases or tracts of
Janus bases.[5] These examples provide important insight into
the potential for such recognition. Yet, until recently, Janus
bases that recognize a Watson–Crick base pair and not mis-
matched bases, have not been thoroughly investigated. Rea-
sons for this are unclear, but may reflect synthetic challenges
in creating and characterizing heterocycles with an inherent
propensity for self-association and aggregation. Towards these
ends, we recently synthesized and characterized a Janus nu-
cleotide analogue, JAT, capable of associating with A and T nu-
cleotides, preferentially to G and C.[6] This first report detailed
the synthesis of a pyrimidopyridine that base pairs with both A
and T (Scheme 1). However, an oligonucleotide containing
a single JAT gave unusually wide UV melting transitions in pres-
ence of complementary DNA, particularly when juxtaposed
across from A. This complicated the evaluation of the modified
base and raised questions as to the extent of fully competent
base pairing. Although both CD melting and extensive in silico
N
analogue, JAT, that has an additional endocyclic ring nitro-
gen and is thus more capable of efficiently discriminating
T/A over G/C bases when base-pairing in a standard
duplex-DNA context is described. Conversion to a phos-
phoramidite ultimately afforded incorporation into an oli-
gonucleotide. In contrast to the first generation of carbo-
cyclic Janus heterocycles, it remains in its unprotonated
state at physiological pH and, therefore, forms very stable
Watson–Crick base pairs with either A or T bases. Biophys-
N
ical and computational methods indicate that JAT is an
improved candidate for sequence-specific genome target-
ing.
DNA represents a therapeutic target, because it programs bio-
logical processes at the earliest step of gene expression.
Hꢀlꢁne and co-workers[1] and Moser and Dervan[2] were the
first to report the potential of an antigene strategy. Based on
their seminal work, sequence-specific recognition of DNA has
been extensively studied over the years, whereby DNA is rec-
ognized in a sequence-specific manner by oligonucleotides,
peptides, and minor groove-binding ligands.[3] Oligonucleo-
tides are attractive, because they have an inherent base-pair-
ing capability that enables them to target potentially any se-
quence, usually by triplex formation by Hoogsteen or reverse
Hoogsteen base pairing.[4] However, the number of hydrogen
bonds contained within a Hoogsteen base pair is limited to
two. Moreover, target sequences are limited largely to polypu-
rine tracts. Alternatively, D-loop formation involves the invasion
of a complementary strand with concomitant strand displace-
ment; such might thus be preferred, because D-loop formation
involves the formation of comparatively more stable Watson–
Crick base pairs (particularly, G–C), the formation of which
[a] Dr. E. Largy,+ W. Liu,+ A. Hasan, Prof. D. M. Perrin
Department of Chemistry, University of British Columbia
2036 Main Mall, Vancouver, BC, V6T-1Z1 (Canada)
E-mail: dperrin@chem.ubc.ca
Scheme 1. JAT and NJAT structure, partial numbering, and putative hydrogen
bonding with A and T (dashed lines). Janus-AT bases display two faces
adapted to different hydrogen-bonding patterns (DAD and ADA; D=proton
donor, A=proton acceptor). Purple stays for the potential protonation site
(N9). The canonical ribose has been substituted with a carbocycle (C6’ in-
stead of O4’). Shown is the antiparallel base pairing with bases in anti-con-
formation.
[+] These authors contributed equally to this work.
Supporting information for this article is available on the WWW under
http://dx.doi.org/10.1002/chem.201303867.
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modeling suggested that Watson–Crick-like base pairs to both
A and T were achievable, we hypothesized that the anomalous
behavior observed in standard Tm analysis may have been due
to partial protonation of N9 (Scheme 1, purple) at physiological
pH (pKa was calculated to be ca. 7.5), leading to a dynamically
equilibrating mixture of standard base-pairing interactions
with the free base and pseudo-base-pairing interactions with
a cationic (protonated) form (not shown).
Because further synthetic elaborations of heterocycles capa-
ble of acting as Janus-AT nucleosides are needed to probe un-
natural base-pairing interactions, we expanded this work to in-
clude a second-generation Janus-AT nucleotide, in which the
inclusion of an endocyclic nitrogen would render the heterocy-
cle considerably less basic, thereby minimizing the potential
for protonation to a cationic species capable of mispairing.
N
Therefore, the optimized structure, referred to as JAT, differs by
substitution of the C7ÀH group by a nitrogen atom to signifi-
cantly lower the pKa of the conjugate acid of N9, as suggested
by empirical calculation (Scheme 1, orange).[7,8] This would
more closely mimic the structure of a diaminopurine to pro-
vide an additional hydrogen bond. Finally, we substituted the
canonical deoxyribose with a cyclopentane analogue to pre-
clude potential depurination-like elimination, enhance associa-
tion DNA, and increase nuclease stability.[9] With these aims in
mind, synthetic design necessitated a new synthetic approach
that has never been elaborated for this Janus-AT nucleoside
analogue. Hereafter, we refer to the T-face and A-face by analo-
gy with their base-pairing behavior (the T-face binds to A, and
vice versa) as we report preliminary biophysical data, whereby
we conclude that this new heterocycle has improved proper-
ties in terms of recognizing either a complementary A or T.
N
Figure 1. Geometries of the N-methylated JAT-A and NJAT-T base pairs ob-
tained by BP86/TZ2P DFT calculations. Carbon in grey, hydrogen in white, ni-
trogen in blue, oxygen in red, and computed hydrogen bonds as purple
dashes. Bases are quasi co-planar, with acceptor-/donor-group distance con-
sistent with Watson–Crick hydrogen bonding.
N
mary amines. The potential of base pairing by JAT with T or A
is thus supported by 1) the compatibility of electrostatic po-
tentials for hydrogen bonding; 2) the electron-density localiza-
tion; 3) the deformation of the NÀH and C=O bonds involved
in hydrogen bonding; 4) the stabilization observed for the
complexes; and 5) the quasi co-planarity of the bases. To test
N
To gauge the capability of the JAT for base pairing with A or
N
T, we conducted BP86/TZ2P DFT geometry optimization on the
these in silico predictions, we tackled the synthesis of the JAT
nucleotide and its corresponding phosphoramidite that ena-
N-methylated structures of A, T, and NJAT bases,[10] and their cor-
N
N
N
responding base pairs.[6,11] The JAT-A and JAT-T complex geo-
metries feature quasi co-planar bases (10–158 between the
planes defined by the interacting cycles, Figure 1), and electron
densities before and after binding appear compatible with hy-
drogen bonding (Figures S1 and S2 in the Supporting Informa-
tion). Interestingly, the intramolecular N10ÀH···O6 hydrogen
bled its incorporation into a JAT-modified oligonucleotide.
Janus-type nucleotides typically have very low solubility in
organic solvents, which can impede the solid-phase synthesis
of modified oligonucleotides.[12] Moreover, JAT heterocycles
proved refractory to standard acylation or phthaloylation
under several conditions (data not shown) that otherwise
would have afforded a protected heterocycle with increased
solubility that would undergo normal deprotection with am-
monia. In light of this, we opted for the synthesis of a sulfone-
masked Janus-AT heterocycle that ultimately provided a phos-
phoramidite of much greater solubility, owing to a disrupted
hydrogen-bonding pattern, hence avoiding self-aggregation
(see below). The other advantage of such a target compound
is that upon global deprotection following solid-phase oligo-
nucleotide synthesis, the sulfone is converted to the desired
exocylic amine by nucleophilic displacement.[6] Initially, we in-
vestigated the feasibility of a “west/east” disconnection analo-
gous to the one we used for the JAT nucleotide, that is, in
which the T-face is elaborated first followed by closure of the
A-face (Scheme S1 in the Supporting Information). The key in-
termediate 3 was prepared by condensation of carbamate
1 with the carbocyclic deoxyribose analogue 2, by following
a protocol that we and others reported previously.[9b,12] Un-
N
bond observed for the isolated JAT is disrupted upon binding
with A and, to a lesser extent, T, consistent with the change in
electron density as a consequence of intermolecular hydrogen
bonding. Hydrogen bond donor/acceptor-atom distances
(Table S1 in the Supporting Information), as well as the bind-
ing-induced deformations of the NÀH and C=O bonds involved
in hydrogen bonding only (Tables S2 and S3 in the Supporting
Information), are consistent with extant hydrogen-bonding in-
teractions. Notably, donor/acceptor distances of the A-face, but
not of the T-face, are globally shorter than previously found for
JAT, which is likely due to the inclusion of the ring nitrogen of
this heterocycle. Finally, the complexes lie in the same energy
range as an AT base pair, suggesting efficient hydrogen bond-
ing (Table S4 in the Supporting Information). Notably, G or C
N
bases cannot form co-planar complexes with either face of JAT,
most likely because of important electronic repulsion due to
electron-rich oxygen atoms and steric constraints due to pri-
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can thus be prepared in a robust
manner, ensuring its availability
and compatibility with standard
oligonucleotide solid-phase syn-
thesis. MALDI-TOF analysis (see
the Supporting Information)
gave proof to its successful in-
corporation along with intended
addition of the amine instead of
the benzylsulfone.
N
The capability of JAT to asso-
ciate with A and T preferentially
over G and C in a double-strand-
ed (ds) DNA context was as-
sessed by UV melting experi-
ments. The melting curves dis-
played very clear single transi-
tions for all four complementary
sequences (Figure 2), supporting
our initial hypothesis that lower-
ing the pKa of a hypothetical
conjugate acid at N9 would lead
Scheme 2. a) Compound 2 (1 equiv), dry NEt3 (2 equiv), absolute ethanol, reflux, 55%; b) compound 4 (1.2 equiv),
NEt3 (2 equiv), iPrOH, reflux, 61%; c) m-CPBA (3 equiv), MeOH, CHCl3, 72%; d) dimethyltryptamine (DMT)-Cl
(1.1 equiv), DIPEA (1.1 equiv), 1,4-dioxane, 51%; e) 2-cyanoethyl N,N-diisopropylchlorophosphoramidite (1.1 equiv),
DIPEA (1.1 equiv), dry CH2Cl2, molecular sieves (4 ꢃ), 60%.
to more consistent and well-be-
N
fortunately, the T-face cyclization of 3 did not occur upon heat-
ing at reflux despite the use of a variety of conditions includ-
ing acid, base, and nucleophilic catalysts, such as triethanol-
amine (TEA) and 1,4-diazabicyclo[2.2.2]octane (DABCO; data
not shown). We hypothesized that this could be due to the
steric hindrance of the thiomethyl group in the b position of
the enone, as was described in literature.[13] Consequently, we
attempted A-face cyclization by reacting 3 with 4, the latter
being easily obtained in high yield from thiourea and benzyl-
bromide.[14] Interestingly, when 3 and 4 were combined at
reflux in presence of triethylamine as a mild base, much to our
delight, the bicyclic intermediate 5 was obtained directly. This
critical step allowed us to construct the bicyclic compound in
an original, convergent, and rapid manner. It was then straight-
forward to oxidize 5 with meta-chloroperoxybenzoic acid (m-
CPBA) to obtain the sulfone-masked compound 6 (Scheme 2).
However, attempted elaboration of the phosphoramidite in
pyridine[9b] led to the rapid and untoward formation of a here-
tofore unknown Zincke salt 10 through facile displacement of
the sulfone by pyridine (Scheme S2 in the Supporting Informa-
tion).[15] Alternative solvent/base systems were screened, and
fortunately, we identified 1,4-dioxane/N,N-diisopropylethyl-
amine (DIPEA) to be highly suitable for accessing the protected
nucleotide 7, which was converted to phosphoramidite 8.[9b]
Overall, 15 steps were required, of which eleven are on the
longest linear path with an overall yield of 4.1% (see the Sup-
porting Information for detailed methods and 1H/13C NMR
spectra). Compound 8 was used for solid-phase oligonucleo-
tide synthesis to prepare the sequence 5’-GAGCGATG-NJAT-
GTAGCCAG-3’. Hereafter, all oligonucleotides have the se-
quence 5’-GAGCGATG-Y-GTAGCCAG-3’ (“strand I”) or the com-
plementary 5’-CTGGCTAC-X-CATCGCTC-3’ (“strand II”), in which
X is either A, T, C, G, or the NJAT and Y is A, T, C or G, and are
haved base-pairing interaction. As was expected, the JAT base
clearly prefers binding to T and A (Tm =58.4 and 57.98C, re-
spectively, close to the melting temperature of the canonical
A-T: 58.38C) compared to G and C (54.9 and 53.18C). The large
differences in stability between recognition of T versus C
(5.38C) or between A and G (3.08C), as was usually observed
with non-modified mismatches,[16] validates our design and
N
suggests that JAT oligonucleotides might be able to bind very
preferentially to either A- and T-tracts. Circular dichroism (CD)
analysis was then used to verify that the modified oligonucleo-
tide forms a B-DNA duplex with cDNA. All spectra were charac-
terized by two extremes consistent with a standard B-DNA
helix (maximum/minimum 280/250 nm; Figure S3 in the Sup-
porting Information),[17] which suggests that both strands un-
dergo disassociation following a cooperative two-state model
N
Figure 2. Dissociated fraction of JAT-Y (Y=A, T, G, C) oligonucleotides (1 mm
strand concentration) as a function of temperature in sodium cacodylate
N
named “X–Y”. A soluble, sulfone-masked, JAT phosphoramidite
(20 mm), NaCl (100 mm), and EDTA (0.5 mm) adjusted at pH 7.0.
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when melted as a decrease of band intensities together with
an isosbestic point around 260 nm where observed. Taken as
N
a whole, results of biophysical experiments suggest that JAT is
capable of associating with T and A with no noticeable secon-
dary-structure perturbation. This observation differs slightly
from the previously reported pyrimidopyridine JAT heterocycle,
for which melting analysis suggested poorer base pairing to A.
Equally important is that NJAT-G/C base pairs lead to a significant
destabilization of the dsDNA due to their mismatched nature,
and can thus be easily discriminated against.
In an effort to acquire more structural insights, notably
around the modified base-pair position in the duplex, we per-
N
N
formed molecular-dynamics calculation on the JAT-A and JAT-T
duplexes and compared the results with their canonical coun-
terparts. Stochastic simulations were thus conducted in an
AMBER force field with implicit water solvation at constant
temperature (300 K) on a 2 ns timescale (Figures S4 and S5,
Table S5 in the Supporting Information).[18] When comparing
modified duplexes to their canonical counterpart, dihedral
angles along the phosphate backbone and the pseudo N-gly-
cosidic bond are mostly unchanged (Figure 3 and Table S6 in
the Supporting Information), the only significant variation
being observed for d (Dd=18 and 298 for JAT-A vs. T-A and JAT-
T vs. A-T, respectively). This is consistent with what has been
monitored for the first-generation JAT and is believed to arise
from the use of a carbocyclic deoxyribose analogue instead of
the standard deoxyribose. Indeed, the carbocyclic deoxyribose
N
Figure 4. NJAT-T and JAT-A base pairing (hydrogen bonds depicted as purple
dashes) in average structures from molecular-dynamics results. Other atoms
are not shown for clarity.
T-face is largely positioned in the groove, which resulted in
a slightly more solvent-accessible surface area (SASA) than
when pairing with T (208.0 vs. 205.6 ꢃ).
N
analogue displays a nonstandard puckering (P=758 for JAT-A
N
and 578 for JAT-T, respectively), which correspond respectively
to C4’-exo/O4’-endo (0T4) and C4’-exo (4E) conformations (Fig-
ure S6 in the Supporting Information). The N-glycosidic torsion
Hydrogen-bond lengths and angles are analogous to the
non-modified sequences, and very little if any base pairing dis-
ruption was observed over the course of the 2 ns simulation
N
N
angle c (À1268 and À1328 for JAT-A and for JAT-T, respective-
ly) is very similar to the non-modified sequence containing all
deoxyribose linkages, that is, in a classical anti base conforma-
tion (Figure S7 in the Supporting Information). Notably, the
N
(Figure 4 and Table S7 in the Supporting Information). JAT
base-pairing isostery with natural bases was verified by using
a set of virtual parameters, defined by Olson and co-workers
(Table S6 in the Supporting Information).[19] The only significant
discrepancy with the canonical base pair is the small desym-
metrization observed for the interphosphate distances, likely
due to the modification in phosphate torsion angles, most no-
tably around the pseudo-sugar C3’ÀC4’ (see above). Overall,
N
anti-conformation implies that when JAT associates with A, the
N
the JAT nucleotide induces little to no distortion of the base
pair nor of the whole duplex, compared to its canonical coun-
terparts, consistent with DFT, CD, and UV melting (Figure S8 in
the Supporting Information).
N
In conclusion, this new JAT has been fittingly designed to
base pair preferentially with T and A, and mismatch with G and
C, as was theoretically verified by DFT by using N-methylated
bases as model. Notably, our previous data suggested a new
hypothesis based on the potential basicity of the pyrimidopyri-
dine JAT heterocycle. Hence, we used synthesis to test the issue
of potential protonation of the A-face by introducing a second
N
ring nitrogen to create the pyrimidopyrimidine JAT herein. To
Figure 3. Backbone dihedral angles a, b, g, d, e, and z, relative orientation of
the bases versus the sugar (analogue) c, and atom numbering of the JAT
nucleotide (average structure from the 2 ns molecular dynamics simulation,
when pairing with T; strand II is not shown). NJAT stacks with the neighboring
guanines in a canonical fashion (see also Figure S7 in the Supporting Infor-
mation for more details).
mitigate the extremely low solubility of the phosphoramidite-
NJAT that proved refractory to incorporation into oligonucleo-
tides, we developed a synthetic strategy that involved the cre-
ation of a sulfone-masked precursor that we used successfully
for the carbocyclic JAT nucleoside. Nevertheless, the introduc-
N
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[3] a) M. P. Knauert, P. M. Glazer, Hum. Mol. Genet. 2001, 10, 2243–2251;
b) P. B. Dervan, A. T. Poulin-kerstien, E. J. Fechter, B. S. Edelson, Top. Curr.
Chem. 2005, 253, 1–31.
[4] N. T. Thuong, C. Hꢀlꢁne, Angew. Chem. 1993, 105, 697–723; Angew.
Chem. Int. Ed. Engl. 1993, 32, 666–690.
[5] a) N. Branda, G. Kurz, J. M. Lehn, Chem. Commun. 1996, 2443–2444;
b) D. Chen, M. Meena, S. K. Sharma, L. W. McLaughlin, J. Am. Chem. Soc.
2004, 126, 70–71; c) H. Chen, Meena, L. W. McLaughlin, J. Am. Chem.
Soc. 2008, 130, 13190–13191; d) D. Shin, Y. Tor, J. Am. Chem. Soc. 2011,
133, 6926–6929.
tion of the sulphone required considerable synthetic iteration
including the provision of a nucleophilic benzylthiourea that
would displace the thiomethyl ether in a double ring closure
in situ to give the desired pyrimidopyrimidine nucleus in
a single step. Further elaboration to the phosphoramidite re-
quired skirting the formation of a Zincke salt, because the sul-
fone in this case proved to be quite delicate. Subsequently,
successful incorporation into a DNA oligonucleotide by solid-
phase synthesis was achieved and confirmed by MALDI-TOF
analysis. UV melting experiments showed that NJAT can indeed
discriminate T and A over G and C, whereas CD and MD experi-
ments confirmed that there is little to no secondary-structure
modification for the duplexes formed with complementary
[6] E. Largy, W. Liu, A. Hassan, D. M. Perrin, ChemBioChem 2013, 14, 2199–
2208.
[7] Two different empirical methods (see Ref. [8]) suggest that the pKa of
N9 drops from 6.21–6.78 to 3.81–3.99 when C7ÀH is substituted by N7.
[8] a) J. C. Shelley, A. Cholleti, L. L. Frye, J. R. Greenwood, M. R. Timlin, M.
Uchimaya, J. Comput.-Aided Mol. Des. 2007, 21, 681–691; b) J. R. Green-
wood, D. Calkins, A. P. Sullivan, J. C. Shelley, J. Comput.-Aided Mol. Des.
2010, 24, 591–604; c) Calculator Plugins for structure property predic-
tion, Marvin 6.0.3, ChemAxon, Budapest (Hungary), 2013.
[9] a) J. Sꢄgi, A. Szemzꢅ, J. Szꢀcsi, L. Otvçs, Nucleic Acids Res. 1990, 18,
2133–2140; b) M. Ober, H. Mꢆller, C. Pieck, J. Gierlich, T. Carell, J. Am.
Chem. Soc. 2005, 127, 18143–18149.
N
DNA. Moreover, the sharp melting transitions observed for JAT,
unlike the broad ones of JAT, suggest that the partial protona-
tion of N9 was a likely issue, which we successfully addressed.
Taken as a whole, biophysical and computational results sug-
gest that NJAT can efficiently base pair with T and A with com-
parable stabilities and structures, whereas the robust synthetic
[10] Y. Yoshioka, Y. Kitagawa, Y. Takano, K. Yamaguchi, T. Nakamura, I. Saito, J.
Am. Chem. Soc. 1999, 121, 8712–8719.
[11] C. Fonseca Guerra, F. M. Bickelhaupt, J. G. Snijders, E. J. Baerends, Chem.
Eur. J. 1999, 5, 3581–3594.
N
pathway ensures the availability of a soluble JAT phosphorami-
N
dite for DNA incorporation. Therefore, JAT is a very promising
[12] A. Asadi, B. O. Patrick, D. M. Perrin, J. Org. Chem. 2007, 72, 466–475.
[13] a) Y. Kanda, H. Saito, T. Fukuyama, Tetrahedron Lett. 1992, 33, 5701–
5704; b) B.-R. Zhuang, G.-J. Hsu, K. Sung, Bioorg. Med. Chem. 2006, 14,
3399–3404; c) K. Sung, B.-R. Zhuang, P.-M. Huang, S.-W. Jhong, J. Org.
Chem. 2008, 73, 4027–4033.
candidate for sequence-specific gene targeting, and evaluation
N
of DNA and PNA JAT-tracts are currently under study.
[14] H. R. Bolliger, Helv. Chim. Acta 1951, 34, 916–917.
Acknowledgements
[15] a) T. Zincke, G. Heuser, W. Mçller, Justus Liebigs Ann. Chem. 1904, 333,
296–345; b) T. Zincke, G. Weißpfenning, Justus Liebigs Ann. Chem. 1913,
396, 103–131.
[16] A. Granzhan, E. Largy, N. Saettel, M. P. Teulade-Fichou, Chem. Eur. J.
2010, 16, 878–889.
The authors acknowledge Suzanne C. Perry (Proteomics Core
facility, UBC) for the MALDI-TOF analysis, Jane Cua for her kind
technical assistance, NSERC for funding this project, and the
Banting Postdoctoral Fellowship program for funding E.L.
ˇ
[17] J. Kypr, I. Kejnovskꢄ, D. Renciuk, M. Vorlꢇckovꢄ, Nucleic Acids Res. 2009,
37, 1713–1725.
[18] a) W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Fergu-
son, D. C. Spellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman, J. Am. Chem.
Soc. 1995, 117, 5179–5197; b) T. Gaillard, D. A. Case, J. Chem. Theory
Comput. 2011, 7, 3181–3198.
Keywords: base pairing
heterocycles · Janus bases
·
circular dichroism
·
DNA
·
[19] Y. Xin, W. K. Olson, Nucleic Acids Res. 2009, 37, D83–88.
[1] T. Le Doan, L. Perrouault, D. Praseuth, N. Habhoub, J.-l. Decout, N. T.
Thuong, J. Lhomme, C. Hꢀlꢁne, Nucleic Acids Res. 1987, 15, 7749–7760.
[2] H. Moser, P. Dervan, Science 1987, 238, 645–650.
Received: October 3, 2013
Published online on January 17, 2014
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