According to the classical Watson–Crick model of Bform
double helix DNA, the base pairs are co-planar,
i.e., they appear to be on the same plane. In reality the
Watson–Crick base pairs in nucleic acid structures are
not absolutely co-planar. The Watson–Crick helix in
B-form DNA (very regular) came from the model building
based on X-ray diffraction data and from the DNA
fibers consisting of parallel oriented DNA molecules.
The crystal structure of 12 base-pairs DNA (dodecamer)
looks mostly like Watson–Crick B-form helix, but there
are some irregularities in comparison with the Watson–
Crick model. In particular, in the single crystal structure
of DNA oligomers, there is some propeller twists within
base pairs [34]. The A–T pairs can show a higher degree
of propeller twisting than the G–C pairs: the angle between
the planes of two paired bases constitutes 12
for A–T and 7 for G–C base pairs. The propeller twist
in the base pairs makes stacking into a dinucleotide step
more awkward than in the case of plane base pairs; it
enhances the stacking of the bases on the strand and
increases the stability of the helix. In particular, it provides
a stereochemical locking effect, which can make
steps with highly propeller twisted base pairs rigid. This
result provides a key to understanding the flexibility of
DNA.
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