B-DNA structure and function
As mentioned above, the structure of B-DNA is strongly
dependent on its sequence. Thus, some sequences which
can melt readily (e.g. TATA) can be strategically placed to
open the DNA helix for initiation of transcription. Other
sequences that are more rigid (or flexible) can serve as sites
for protein binding and formation of specific complexes. In
bacteria as well as eukaryotes, sequences upstream of
transcription start sites contain regions which are more
rigid and will melt more readily. In addition to the three
different helical conformations of DNA, there are numerous
other DNA structures, such as DNA curvature,
cruciforms, triple-stranded DNA, tetraplex DNA and
parallel-stranded DNA, that can be formed under various
conditions. Thus there is much more to DNA structure
than merely the Watson–Crick B-DNA conformation.
Summary
Whether a DNA sequence will be in the A-, B-or Z-DNA
conformation depends on at least three conditions. The
first is the ionic or hydration environment, which can
facilitate conversion between different helical forms. ADNA
is favoured by low hydration, whereas Z-DNA can
be favoured by high salt. The second condition is the DNA
sequence: A-DNA is favoured by certain stretches of
purines (or pyrimidines), whereas Z-DNA can be most
readily formed by alternating purine–pyrimidine steps.
The third condition is the presence of proteins that can
bind to DNA in one helical conformation and force the
DNA to adopt a different conformation, such as proteins
which bind to B-DNA and can drive it to either A-or Zforms.
In living cells, most of the DNA is in a mixture of Aand
B-DNA conformations, with a few small regions
capable of forming Z-DNA.