ArticleThe journal of physical chemistry. B2014
Conformational preferences of DNA in reduced dielectric environments.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Exploring the interactions of antihistamine with retinoic acid receptor beta (RARB) by molecular dynamics simulations and genome-wide meta-analysis.Journal of molecular graphics & modelling · 2023Pooled it
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- RBM45 Preferential Binding to mThe journal of physical chemistry. B · 2026Article
- Effects of Molecular Crowding on the Structure, Folding, and Stability of DNA.Sub-cellular biochemistry · 2025Review
- Evaluation of Pregabalin bioadhesive multilayered microemulsion IOP-lowering eye drops.Journal of controlled release : official journal of the Controlled Release Society · 2024Article
- AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics.Journal of chemical information and modeling · 2023Article
- Identification of key interactions between SARS-CoV-2 main protease and inhibitor drug candidates.Scientific reports · 2020Article
- Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil.Scientific reports · 2019Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.BMC biophysics · 2018Article
- Article
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016Review
- Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents.Protein science : a publication of the Protein Society · 2016Article
- Adenine versus guanine DNA adducts of aristolochic acids: role of the carcinogen-purine linkage in the differential global genomic repair propensity.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The effect of reduced dielectric environments on the conformational sampling of DNA was examined through molecular dynamics simulations. Different dielectric environments were used to model one aspect of cellular environments. Implicit solvent based on the Generalized Born methodology was used to reflect different dielectric environments in the simulations. The simulation results show a tendency of DNA structures to favor noncanonical A-like conformations rather than canonical A- and B-forms as a result of the reduced dielectric environments. The results suggest that the reduced dielectric response in cellular environments may be sufficient to enhance the sampling of A-like DNA structures compared to dilute solvent conditions.
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Registered trials
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