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

0342611 - ÚOCHB 2011 RIV US eng J - Journal Article
Řezáč, Jan - Hobza, Pavel - Harris, S. A.
Stretched DNA Investigated Using Molecular-Dynamics and Quantum-Mechanical Calculations.
Biophysical Journal. Roč. 98, č. 1 (2010), s. 101-110. ISSN 0006-3495. E-ISSN 1542-0086
R&D Projects: GA MŠMT LC512
Institutional research plan: CEZ:AV0Z40550506
Keywords : mechanical properties of DNA * DNA melting * molecular dynamics
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 4.218, year: 2010

We combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our 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 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.
Permanent Link: http://hdl.handle.net/11104/0185302