Simulation study on dynamics of A- to B-form transition in aqueous DNA solution: Effect of alkali metal counterions

Abstract

DNA and its conformational transition can be used to design nanometer-scale structures, nano-tweezers and nanomechanical devices. Experiments and molecular simulations have been used to study the concentration effect on the A-DNA→B-DNA conformational transition, but a systematical investigation on counterion effect on the dynamics of this transition has not been reported up to now. In present work, restrained and unrestrained molecular dynamics (MD) simulations have been performed to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA transitions in aqueous solutions with different alkali metal counterions. The DNA duplex d(CGCGAATTCGCG)2, coion Cl− and counterions Li+, Na+, K+, Rb+ and Cs+ as well as water molecule were considered using the PARM99 force field in the AMBER8 package. It was found that B-form DNA is more stable than A-form DNA in aqueous electrolyte solutions with different alkali metal counterions. Increasing KCl concentration in solution hinders the A-DNA→B-DNA transition and the transition times for different alkali metal counterions conform to neither the simple sequence related to naked ion size nor to hydrated diameter, but an apparently abnormal sequence of K+ < Rb+ < Cs+ < Na+ < Li+. This abnormal sequence can be well understood in terms of an electrostatic model based on the effective cation diameters and the modified mean-spherical approximation (MMSA). The present results provide valuable information for the design of DNA-based nanomaterials and nanodevices.