ArticleBiophysical journal2010
Stretched DNA investigated using molecular-dynamics and quantum-mechanical calculations.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- DNA Origami-Templated Aptamer Chiral Structures Realize Cellular Enantioselectivity.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Article
- The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA.Nucleic acids research · 2020Article
- Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics.Journal of the Royal Society, Interface · 2014Article
- Direct observation of single DNA structural alterations at low forces with surface-enhanced Raman scattering.Biophysical journal · 2013Article
- Noncovalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers.The journal of physical chemistry. A · 2010Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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