Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution

Abstract

Unrestrained molecular dynamics (MD) simulations have been carried out to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA conformational transitions in aqueous RbCl solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbCl concentration on the dynamics of the A→B conformational transition in the DNA duplex d(CGCGAATTCGCG)2. Canonical A- and B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was monitored for 3.0 ns and the distances between the C5′ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simulations. In addition, increasing the RbCl concentration in aqueous solution hindered the A→B conformational transition and the transition in aqueous RbCl solution was faster than that in aqueous NaCl solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A→B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The rubidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help explain the effect of RbCl concentration on the dynamics of the A→B conformational transition.