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DNA Bending through Roll Angles Is Independent of Adjacent Base Pairs
Justin Spiriti1, Arjan van der Vaart1
1Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States.
Abstract:
We have studied DNA bending for a wide range of DNA sequences by two-dimensional adaptive umbrella sampling simulations on adjacent roll angles. Calculated free energy surfaces are largely additive and can be well approximated by the sum of the one-dimensional free energy surfaces. Cooperativity between adjacent roll angles was found to be negligible: less than 1.0 kcal/mol and a small fraction of the overall bending energy. Our calculations validate the assumptions underlying many popular coarse-grained models for DNA bending, and demonstrate their theoretical validity for investigating DNA bending.
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