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Stretching and twisting of the DNA duplexes in coarse-grained dynamical models

Szymon Niewieczerzał and Marek Cieplak

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Three coarse-grained molecular dynamics models of the double-stranded DNA are proposed and compared in the context of single molecule mechanical manipulation such as twisting and various schemes of stretching—unzipping, shearing, two-strand stretching and stretching of only one strand. The models differ in the number of effective beads (between two and five) representing each nucleotide. They all show similar behaviour, but the bigger the resolution, the more details in the force patterns. The models incorporate the effective Lennard-Jones potentials in the couplings between two strands and harmonic potentials to describe the structure of a single strand. The force patterns are shown to depend on the sequence studied. In particular, both shearing and unzipping for an all-AT sequence lead to lower forces than for an all-CG sequence. The unzipping patterns and the corresponding scenario diagrams for the contact rupture events are found to reflect the sequential information if the temperature is moderate and initial transients are discarded. The derived torque–force phase diagram is found to be qualitatively consistent with experiments and all-atom simulations.


PACS

87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways

87.14.G- Nucleic acids

87.15.B- Structure of biomolecules

87.15.K- Molecular interactions; membrane-protein interactions

87.15.H- Dynamics of biomolecules

Subjects

Biological physics

Dates

Issue 47 (25 November 2009)

Received 30 April 2009, in final form 25 June 2009

Published 5 November 2009



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