Radial compression property of ds-DNA molecules studied by a mesoscale model

¹  Shanghai Institute of Applied Physics, Chinese Academy of Sciences - P.O. Box 800-204, Shanghai 201800, China
²  Theoretical Physics Center for Science Facilities (TPCSF), CAS - 19(B) Yuquan Road, Beijing 100049, China

Corresponding author: fanghaiping@sinap.ac.cn

Received: 10 November 2009
Accepted: 4 February 2010

Abstract

The elastic properties of double-stranded DNA (ds-DNA) molecules are believed to play an important role in their biological functions. By using a mesoscale model, we construct a simple cylinder-DNA-surface system to explore the radial elastic property of a ds-DNA molecule through a Langevin-dynamics-based computer simulation. The numerical predictions of the radial elastic property are favorable with the recent experimental results. The analysis of the hydrogen bonds and base stacking interaction shows that local conformation transition occurs through the breaking of local hydrogen bonds, and this transition minimizes the inner strain aggregated during compression. This behavior provides an alternative method for studying the local property of ds-DNA, which is expected to be helpful in better understanding the local interaction between ds-DNA and protein, and the mechanics of the short-segment DNA molecule.