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 concentrati...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 NaC1 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.展开更多
基金Project supported by the National Natural Science Foundation of China(Grant Nos.20876083 and 20736003)Specialized Research Fund for the Doctorial Program of Higher Education of China(Grant No.2007003009)
文摘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 NaC1 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.
