ArticleNucleic acids research2014
Analyzing ion distributions around DNA.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 116 citations in OpenAlex.
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- Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer-promoter communication.The Journal of chemical physics · 2024Article
- Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.Journal of chemical theory and computation · 2024Article
- What tunes guanine ionization potential in a nucleosome? An all-in-one systematic QM/MM assessment.Biophysical journal · 2024Article
- Alternate conformational trajectories in ribosome translocation.PLoS computational biology · 2024Article
- DNA simulation benchmarks revealed with the accumulation of high-resolution structures.Biophysical reviews · 2024Review
- Deciphering Sequence-Specific DNA Binding by H-NS Using Molecular Simulation.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The pseudotorsional space of RNA.RNA (New York, N.Y.) · 2023Article
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations.The journal of physical chemistry. B · 2022Article
- Structure and Dynamics of dsDNA in Cell-like Environments.Entropy (Basel, Switzerland) · 2022Review
- Spatial and Temporal Resolution of the Oxygen-Independent Photoinduced DNA Interstrand Cross-Linking by a Nitroimidazole Derivative.Journal of chemical information and modeling · 2022Article
- Twisting DNA by salt.Nucleic acids research · 2022Article
- Twist-diameter coupling drives DNA twist changes with salt and temperature.Science advances · 2022Article
- Rolling circle RNA synthesis catalyzed by RNA.eLife · 2022Article
- Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.PLoS computational biology · 2022Article
- Implementation of a cylindrical distribution function for the analysis of anisotropic molecular dynamics simulations.PloS one · 2022Article
- Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of SpermidineFrontiers in chemistry · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.