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Figure 3.
Figure 3. Waters in the CpG dinucleotides of B-DNA and E-DNA.
a, Stereo view of waters (gold spheres) hydrogen bonded (broken
lines) to the guanine at the CpG steps in d(GGCGCC)[2] as B-DNA,
and in d(GGCGm5CC)[2] and d(GGCGBr5CC)[2] as E-DNA. The waters
are overlaid relative to the guanine N7 nitrogen of an average
structure built from three unique CpG steps found in each
conformation (the C4 carbon of the cytosine base is colored
black). b, Mechanism for the spontaneous deamination of cytosine
to uracil24. The nucleophilic attack of a water molecule at the
C4 carbon forms a hemiaminal intermediate. Release of ammonia
results in a tautomer, which subsequently rearranges to uracil.
c, Model of the hemiaminal intermediate in B-DNA and E-DNA. The
hemiaminal intermediate at the CpG step was modeled by adding a
hydroxyl group to the C4 carbon (colored black) of the cytosine
base, followed by geometry optimization using the AMBER25 force
field as implemented in the program InsightII (Biosym/MSI). The
starting positions of the waters and the starting cytosine base
are shown as transparent overlays.
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