title: DNA Bending through Roll Angles Is Independent of Adjacent Base Pairs.
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.
authors: Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States.
authors: Justin
authors: J
authors: Spiriti
authors: Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States.
authors: Arjan
authors: A
authors: van der Vaart
keywords: DNA bending; cooperativity; free energy; molecular dynamics; simulation