Towards more realistic dynamical models for DNA secondary structure

Abstract

We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate perpendicular to the sequence axis. We show, through molecular dynamics simulations, that the model has the correct behaviour at the denaturation transition.

accepted for publication in Chemical Physics Letters

References in corpus (1)

• Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation

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• Theoretical and Experimental Investigations of DNA Open States
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• Theoretical investigation of finite size effects at DNA melting
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