ArticleBiophysical journal2005
The B- to A-DNA transition and the reorganization of solvent at the DNA surface.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.Journal of chemical theory and computation · 2024Article
- C-B-A Test of DNA Force Fields.ACS omega · 2023Article
- Structure-Activity Relationships in Nucleic-Acid-Templated Vectors Based on Peptidic Dynamic Covalent Polymers.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- The structural plasticity of nucleic acid duplexes revealed by WAXS and MD.Science advances · 2021Article
- Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer.ACS omega · 2020Article
- A New Look into the Mode of Action of Metal-Based Anticancer Drugs.Molecules (Basel, Switzerland) · 2020Article
- Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0].Living journal of computational molecular science · 2019Article
- Dehydrated DNA in B-form: ionic liquids in rescue.Nucleic acids research · 2018Article
- Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.BMC biophysics · 2018Article
- Conformational preferences of DNA in reduced dielectric environments.The journal of physical chemistry. B · 2014Article
- Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.The journal of physical chemistry. B · 2014Article
- Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs.Nucleic acids research · 2014Article
- Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.PloS one · 2013Article
- Biological physics in México: Review and new challenges.Journal of biological physics · 2011Article
- Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA.Biophysical journal · 2008Article
- Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations.Nucleic acids research · 2008Article
- Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water.Nucleic acids research · 2007Article
- A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution.Nucleic acids research · 2005Article
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1 author.
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Abstract
DNA geometry depends on relative humidity. Using the CHARMM22 force field to push B-DNA to A-DNA, a molecular dynamics simulation of a mixed-sequence 24-basepair DNA double-stranded oligomer, starting from B-DNA, was carried out to explore both the mechanism of the transition and the evolution of hydration patterns on the surface of DNA. Over the 11-ns trajectory, the transition recapitulates the slide-first, roll-later mechanism, is opposed by DNA electrostatics, and is favored by an increasing amount of condensed sodium ions. Hydration was characterized by counting the hydrogen bonds between water and DNA, and by the number of water bridges linking two DNA atoms. The number of hydrogen bonds between water and DNA remains constant during the transition, but there is a 40% increase in the number of water bridges, in agreement with the principle of economy of hydration. Water bridges emerge as delicate sensors of both structure and dynamics of DNA. Both local flexibility and the frustration of the water network on the surface of DNA probably account for the low populations and short residence times of the bridges, and for the lubricant role of water in ligand-DNA interactions.
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