ArticleBiophysical journal2009
A mesoscale model of DNA and its renaturation.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems.Nature communications · 2024Article
- Investigating the Hydrogen Bond-Induced Self-Assembly of Polysulfamides Using Molecular Simulations and Experiments.Macromolecules · 2023Article
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Anomalous Diffusion of Polyelectrolyte Segments on Supported Charged Lipid Bilayers.Entropy (Basel, Switzerland) · 2023Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields.Molecules (Basel, Switzerland) · 2022Article
- Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide.JACS Au · 2022Article
- Bottom-Up Coarse-Grained Modeling of DNA.Frontiers in molecular biosciences · 2021Review
- Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning.Biomolecules · 2020Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.Biophysical journal · 2019Article
- Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments.Biophysics and physicobiology · 2019Article
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.Journal of chemical theory and computation · 2018Article
- Diffusion of ring-shaped proteins along DNA: case study of sliding clamps.Nucleic acids research · 2018Article
- The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization.Journal of the American Chemical Society · 2018Article
- Interactions of HP1 Bound to H3K9me3 Dinucleosome by Molecular Simulations and Biochemical Assays.Biophysical journal · 2018Article
- In silico evidence for sequence-dependent nucleosome sliding.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes.Biophysical journal · 2017Article
- Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations.Scientific reports · 2016Article
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Authors and funding
3 authors.
Funding
Abstract
A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Hückel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs.
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