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Temperature dependence of circular DNA topological states
Circular double stranded DNA has different topological states which are
defined by their linking numbers. Equilibrium distribution of linking numbers
can be obtained by closing a linear DNA into a circle by ligase. Using Monte
Carlo simulation, we predict the temperature dependence of the linking number
distribution of small circular DNAs. Our predictions are based on flexible
defect excitations resulted from local melting or unstacking of DNA base pairs.
We found that the reduced bending rigidity alone can lead to measurable changes
of the variance of linking number distribution of short circular DNAs. If the
defect is accompanied by local unwinding, the effect becomes much more
prominent. The predictions can be easily investigated in experiments, providing
a new method to study the micromechanics of sharply bent DNAs and the thermal
stability of specific DNA sequences. Furthermore, the predictions are directly
applicable to the studies of binding of DNA distorting proteins that can
locally reduce DNA rigidity, form DNA kinks, or introduce local unwinding.Comment: 15 pages in preprint format, 4 figure
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