ArticleJournal of the Royal Society, Interface2014
The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics.
Article in Journal of the Royal Society, Interface, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed.
- Article
- Force-induced melting and S-DNA pathways for DNA overstretching exhibit distinct kinetics.Nucleic acids research · 2025Article
- Optical manipulation: advances for biophotonics in the 21st century.Journal of biomedical optics · 2021Review
- Nanomechanics of Diaminopurine-Substituted DNA.Biophysical journal · 2019Article
- 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
- Single-molecule studies of high-mobility group B architectural DNA bending proteins.Biophysical reviews · 2017Review
- An AT-barrier mechanically controls DNA reannealing under tension.Nucleic acids research · 2016Article
- Equilibrium and kinetics of DNA overstretching modeled with a quartic energy landscape.Biophysical journal · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The overstretching transition in torsionally unconstrained DNA is studied by means of atomistic molecular dynamics simulations. The free-energy profile as a function of the length of the molecule is determined through the umbrella sampling technique providing both a thermodynamic and a structural characterization of the transition pathway. The zero-force free-energy profile is monotonic but, in accordance with recent experimental evidence, becomes two-state at high forces. A number of experimental results are satisfactorily predicted: (i) the entropic and enthalpic contributions to the free-energy difference between the basic (B) state and the extended (S) state; (ii) the longitudinal extension of the transition state and (iii) the enthalpic contribution to the transition barrier. A structural explanation of the experimental finding that overstretching is a cooperative reaction characterized by elementary units of approximately 22 base pairs is found in the average distance between adenine/thymine-rich regions along the molecule. The overstretched DNA adopts a highly dynamical and structurally disordered double-stranded conformation which is characterized by residual base pairing, formation of non-native intra-strand hydrogen bonds and effective hydrophobic screening of apolar regions.
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