A New Twist Step-parameter Coupled to the Chirality of the Global Structure of DNA

Sunday, September 16, 2007 - 4:45pm - 5:00pm
EE/CS 3-180
Irwin Tobias (Rutgers, The State University Of New Jersey )
DNA twist step-parameters are in common use in the
community of structural biologists. If, for a molecule with a
closed axial curve, the writhing number, a measure of the
chiral distortion of the axial curve of the molecule from
planarity, is added to the sum over all steps of such twists,
the result has no particular significance. This is in marked
contrast to the properties of the value obtained . the
topological invariant, an integer called the linking number -
when the same writhe is added to the total twist we obtain by
using step twists defined in a way consistent with the twist
associated with supercoiling. Also of interest is the
difference in the values of these two step-parameters for DNA
in various environments. Thus, when the DNA is relaxed, and
not interacting with any proteins, we find, and understand why,
the two twists for each step are close in value. On the other
hand, when the DNA is interacting with a protein, with the
histones in chromatin, for example, there are certain steps for
which one observes significant differences. By considering
various model structures, we find instances in which we are
able to relate the magnitude of an observed difference in
twists for a particular step to the specific nature and
chirality of the structural distortion being imposed by the
protein on the DNA in the region of the step.
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