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MedChemComm
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DOI: 10.1039/C6MD00536E
ARTICLE
Table 3 Chemical shifts and line width of imino protons
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chemical shifts of N3 (ppm)
nucleobase
line width (half height width, Hz)
monomera
11.30
PNA1-4:DNA2 duplexb
Δδc
2.14
2.32
2.21
2.19
T
13.44
14.20
14.11
14.06
20
36
25
22
FU
11.88
ClU
BrU
11.90
11.87
a chemical shifts of the N3 imino proton of PNA monomers in DMSO-d6. b chemical shifts of the N3 imino proton of the duplexes of PNA-
DNA2. 1H NMR spectra were recorded at 5 °C with 512 scans using a water suppression WATEGATE program with d19 of 40 μs. The
oligonucleotide was dissolved in a a solution of 100 mM NaCl, 10 mM Na2HPO4, and 0.2 mM EDTA, Ph 7.0 in 10% D2O. c Δδ = δoligo
-
δmonomer
.
imino proton. The chemical shift and the line width of the N3 nucleobase of 5-XU-PNA oligomers, in combination with the
imino proton are listed in Table 3.
release of 5-XU from 5-XU-PNA, is in progress.
In PNA monomers, the chemical shifts of N3 imino proton in
This work was supported by the Foundation and Advanced
DMSO-d6 were observed to be 11.27, 11.88, 11.90 and 11.87 Research Project of CQ CSTC (2013jjB0011), Fund Project for
ppm, respectively (Supporting Information). The imino protons Transformation of Scientific and Technological Achievements
of 5-XUs are more acidic than the corresponding imino proton from the Ministry of Science and Technology
of T. Similarly, significant downfield shifts in the N3 resonance (2014KXWQT071242) and Animal Disease Prevention and Food
of 0.62-0.76 ppm in the XU:A relative to the T:A were observed Safety Key Laboratory of Sichuan Province.
in NMR studies of PNA-DNA duplexes (table 3, column3). The
Notes and references
difference chemical shift of N3 imino proton between 5-XU and
T is attributed to the difference electronic effect of the
halogen atom versus methyl. The 5-halo substituent of XU is
electron withdrawing whereas the T methyl group is electron
donating. The electron withdrawing properties of all three
halogens result in low electron density of the pyrimidine ring,
and increase the acidity of N3 protons. The increased acidity of
N3 protons of 5-XU would be expected to strengthen the
hydrogen bond between N3-H and adenine. Moreover, upon
substitution of T with 5-XUs, the N3 chemical shifts in duplexes
move further downfield (table 3, column4). The NMR
measurements indicate that the strength order of the
hydrogen bond is FU:A > ClU:A > BrU:A > T:A. This is consistent
with the results of UV melting studies.
1
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2
3
4
5
6
7
On the other hand, the N3 imino proton line widths for
duplexes containing 5-XU:A were slightly broader than the
corresponding T:A duplex (table 3, column5). Previous studies
have suggested that the broadening of the ClU:A imino proton
in DNA duplex might result from proton exchange from within
the intact base pair.13a Therefore, the observed broadening of
the XU:A imino proton is not directly related to the duplex
stability.
8
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In conclusion, we have synthesized the monomers of
peptide nucleic acid containing 5-XU using Fmoc protection
strategy for the first time. PNA carrying 5-XU forms a duplex
with complementary DNA or RNA with higher affinity than that
of unmodified PNA. The XU:A base pair is more stable than the
T:A base pair in PNA:DNA or PNA:RNA duplex. Based on the
significant roles of 5-XU in the pharmaceutical applications, we
can envision that 5-XU-PNA might be useful as a potent anti-
tumor agent. Further work that includes the cellular delivery of
5-XU-PNA and the antisense effect of the functionalized
4 | MedChemComm., 2016, 00, 1-3
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