Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.

ABSTRACT: We develop a robust coarse-grained model for single- and double-stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully repro

SUBMITTER: Chakraborty D 

PROVIDER: S-EPMC6423546 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature