Effect of electrolyte concentration on DNA A—B conformational transition:An unrestrained molecular dynamics simulation study

<正>The DNA conformational transition depends on both the DNA sequences and environment such as solvent as well as electrolyte in the solution.This paper uses the AMBER8 package to investigate the electrolyte concentration influence on the dynamics of the A→B conformational transition of DNA duplex d(CGCGAATTCGCG)_2.The results from the restrained molecular dynamics(MD) simulations indicate that the total energies of the systems for A-DNA are always higher than those for B-DNA,and that the A→B conformational transition in aqueous NaCl solution is a downhill process.The results from the unrestrained MD simulations,as judged by the average distance between the C5' atoms(average helical rise per ten base pair),show that the concentrated NaCl solution slows down the A→B conformational transition.This observation can be well understood by analyses of the difference between the counterion distributions around A-DNA and B-DNA.