ArticleBiophysical journal2008
The pathway of oligomeric DNA melting investigated by molecular dynamics simulations.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Molecular Interpretation of Temperature-Induced DNA Melting Monitored through Base Dipole Moment Changes as a Surrogate of the Hypochromic Shift.The journal of physical chemistry letters · 2026Article
- Fitting coarse-grained models to macroscopic experimental data via automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Construction of aMolecular therapy. Nucleic acids · 2024Article
- Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.Journal of the American Chemical Society · 2021Article
- Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy.Frontiers in molecular biosciences · 2021Review
- Asymmetric base-pair opening drives helicase unwinding dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Free-energy landscape and characteristic forces for the initiation of DNA unzipping.Biophysical journal · 2015Article
- Melting dynamics of short dsDNA chains in saline solutions.SpringerPlus · 2015Article
- Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics.The journal of physical chemistry. B · 2014Article
- Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs.Journal of computer-aided molecular design · 2014Article
- DNA-directed base pair opening.Molecules (Basel, Switzerland) · 2012Review
- Effect of temperature on DNA double helix: An insight from molecular dynamics simulation.Journal of biosciences · 2012Article
- Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations.Nucleic acids research · 2011Article
- THE MELTING MECHANISM OF DNA TETHERED TO A SURFACE.International journal of numerical analysis and modeling · 2009Article
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Authors and funding
2 authors.
Funding
Abstract
Details of the reaction coordinate for DNA melting are fundamental to much of biology and biotechnology. Recently, it has been shown experimentally that there are at least three states involved. To clarify the reaction mechanism of the melting transition of DNA, we perform 100-ns molecular dynamics simulations of a homo-oligomeric, 12-basepair DNA duplex, d(A(12)).d(T(12)), with explicit salt water at 400 K. Analysis of the trajectory reveals the various biochemically important processes that occur on different timescales. Peeling (including fraying from the ends), searching for Watson-Crick complements, and dissociation are recognizable processes. However, we find that basepair searching for Watson-Crick complements along a strand is not mechanistically tied to or directly accessible from the dissociation steps of strand melting. A three-step melting mechanism is proposed where the untwisting of the duplex is determined to be the major component of the reaction coordinate at the barrier. Though the observations are limited to the characteristics of the system being studied, they provide important insight into the mechanism of melting of other more biologically relevant forms of DNA, which will certainly differ in details from those here.
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