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

doi:10.1088/1674-1056/19/8/088701

Abstract 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.

Keywords: molecular dynamics simulation nucleic acid conformational transition electrolyte

Received: 05 October 2009
Revised: 23 December 2009
Accepted manuscript online:

PACS:	87.15.H-	(Dynamics of biomolecules)
	87.14.G-	(Nucleic acids)
	87.15.A-	(Theory, modeling, and computer simulation)
	87.15.B-	(Structure of biomolecules)
	87.15.Cc	(Folding: thermodynamics, statistical mechanics, models, and pathways)
	87.15.N-	(Properties of solutions of macromolecules)

Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 20876083 and 20736003) and Specialized Research Fund for the Doctorial Program of Higher Education of China (Grant No. 2007003009).

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Shintaro Fujimoto(藤本晋太郎) and Yu Yang-Xin(于养信) Effect of electrolyte concentration on DNA A–B conformational transition：An unrestrained molecular dynamics simulation study 2010 Chin. Phys. B 19 088701

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

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