The present results about the nonplanarity of the nucleic
acid bases and base pairs may have important consequences
for the realization of the particular structures
of these compounds in various molecular complexes.
The biological consequences of this nonplanarity may
be significant. Some interstrand NH2 group contacts in
B-form DNA crystal structures appear to be stabilized
by the NH2 group pyramidalization and the interstrand
bifurcated hydrogen bonds [1,2,27,28]. The geometry of
the NH2 group highly depends on the local environment
of the molecule. The flexibility offered by the NH2 group
is advantageous for the dimer, because the NH2 group
will most likely deform in such a way that the N–
HO bond is linear, creating an overall structure that
is bound by two linear hydrogen bonds by an induced
fit. In particular the amino group hydrogens can participate
in out-of-plane H-bonds, where the X–H bonds
are bent away from the molecular plane of bases. Besides
of that, the amino group nitrogen atom can serve
as a weak H-acceptor because of the partial sp3 hybridization
of the amino group nitrogen atoms. In other
words, there is a striking correlation between the conformational
flexibility of a dinucleotide step and the level of
propeller twist in the base pairs. The detailed discussion
of the role of the amino group nonplanarity in the different
kinds of unusual interactions and the potential biological
importance of interactions involving nonplanar
amino groups of bases were repeatedly stressed and
are given in the reviews of Sponer et al. [1,2].
R