Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations.

ABSTRACT: We present a coarse-grained (CG) model of a rodlike higher-order quadruplex with explicit monovalent salts, which was developed from radial distribution functions of an underlying reference atomistic molecular dynamics simulation using inverse Monte Carlo technique. This work improves our previous CG model and extends its applicability beyond the minimal salt conditions, allowing its use at variable ionic strengths. The strategies necessary for the model development are clearly explained and discussed. The effects of the number of stacked quadruplexes and varied salt concentration on the elasticity of the rodlike higher-order quadruplex structures are analyzed. The CG model reproduces the deformations of the terminal parts in agreement with experimental observations without introducing any

SUBMITTER: Rebic M 

PROVIDER: S-EPMC6641151 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature