Stretched DNA Investigated Using Molecular-Dynamics and Quantum-Mechanical Calculations

We combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our combined quantum-mechanical/molecular-mechanical approach demonstrates that molecular-mechanical force fields are able to des...

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Bibliographic Details
Published in:Biophysical journal 2010-01, Vol.98 (1), p.101-110
Main Authors: Řezáč, Jan, Hobza, Pavel, Harris, Sarah A.
Format: Article
Language:English
Subjects:
Computer Simulation
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - ultrastructure
Elastic Modulus
Kinetics
Models, Chemical
Models, Molecular
Nucleic Acid
Nucleic Acid Conformation
Quantum physics
Quantum Theory
Simulation
Stress, Mechanical
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Summary:We combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our combined quantum-mechanical/molecular-mechanical approach demonstrates that molecular-mechanical force fields are able to describe both the backbone and base-base interactions within the highly distorted nucleic acid structures produced by stretching the DNA from the 5′ ends, which include conformations containing disassociated basepairs, just as well as these force fields describe relaxed DNA conformations. The molecular-dynamics simulations indicate that the force-induced melting pathway is sequence-dependent and is influenced by the availability of noncanonical hydrogen-bond interactions that can assist the disassociation of the DNA basepairs. The biological implications of these results are discussed.
ISSN:0006-3495
1542-0086
DOI:10.1016/j.bpj.2009.08.062