ArticleNucleic acids research2007
Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition.Nucleic acids research · 2025Article
- Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.Journal of chemical theory and computation · 2024Article
- Plasmonic hot spots reveal local conformational transitions induced by DNA double-strand breaks.Scientific reports · 2022Article
- Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer.ACS omega · 2020Article
- Kinetics of the B-A transition of DNA: analysis of potential contributions to a reaction barrier.European biophysics journal : EBJ · 2018Article
- Effect of Methylation on Local Mechanics and Hydration Structure of DNA.Biophysical journal · 2018Article
- Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.BMC biophysics · 2018Article
- Article
- The "sugar" coarse-grained DNA model.Journal of molecular modeling · 2017Article
- Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions.International journal of molecular sciences · 2016Article
- Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex.Journal of the American Chemical Society · 2016Article
- Article
- Single-Walled Carbon Nanotubes Modulate the B- to A-DNA Transition.The journal of physical chemistry. C, Nanomaterials and interfaces · 2014Article
- Conformational preferences of DNA in reduced dielectric environments.The journal of physical chemistry. B · 2014Article
- Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods.Journal of chemical theory and computation · 2014Article
- Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.PloS one · 2013Article
- Mapping L1 ligase ribozyme conformational switch.Journal of molecular biology · 2012Article
- Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures.Methods (San Diego, Calif.) · 2012Review
- Condensation prevails over B-A transition in the structure of DNA at low humidity.Biophysical journal · 2011Article
- An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods.Journal of chemical theory and computation · 2010Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We explore here the possibility of determining theoretically the free energy change associated with large conformational transitions in DNA, like the solvent-induced B<-->A conformational change. We find that a combination of targeted molecular dynamics (tMD) and the weighted histogram analysis method (WHAM) can be used to trace this transition in both water and ethanol/water mixture. The pathway of the transition in the A-->B direction mirrors the B-->A pathway, and is dominated by two processes that occur somewhat independently: local changes in sugar puckering and global rearrangements (particularly twist and roll) in the structure. The B-->A transition is found to be a quasi-harmonic process, which follows closely the first spontaneous deformation mode of B-DNA, showing that a physiologically-relevant deformation is in coded in the flexibility pattern of DNA.
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