Evaluation of elastic properties of atomistic DNA models

¹ Institute de Biologie Physico-Chimique

^* To whom correspondence should be addressed. E-mail: alexey{at}ibpc.fr.

Submitted on June 14, 2006
Revised on September 12, 2006
Accepted on 13 September 2006

	Abstract

A number of intriguing aspects in dynamics of double helical DNA is related with the coupling between its macroscopic and microscopic states. A link between the elastic properties of long DNA chains and their atom level dynamics can be established by comparing the worm-like chain model of polymer DNA with the conformational ensembles produced by molecular dynamics simulations. This problem is complicated by the complexity of the DNA structure, the small size of DNA fragments, and relatively short trajectory durations accessible in computer simulations of microscopic DNA dynamics. A careful studies of all these aspects has been performed by using longer DNA fragments and increased durations of MD trajectories as compared to earlier such investigations. A special attention is paid to the necessary conditions and criteria of time convergence, and the possibility to increase the sampling by using constrained DNA models and simplified simulation conditions. It is found that dynamics of 25-mer duplexes with regular sequences agrees well with the WLC theory and that accurate evaluation of DNA elastic parameters requires at least 2 turns of the double helix and about 20 ns duration of trajectories. Bond length and bond angle constraints affect the estimates within numerical errors. In contrast, simplified treatment of solvation can strongly change the observed elastic parameters of DNA. The elastic parameters evaluated for AT- and GC- alternating duplexes reasonably agree with experimental data and suggest that the torsional and stretching elasticities of the double helix vary with the base pair sequence much stronger than the bending stiffness.

Key Words: Bending elasticity of DNA, DNA dynamics, MD simulations of DNA, Stretching elasticity of DNA, Torsion elasticity of DNA, Worm-like chain DNA behavior

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