ArticleNucleic acids research2008
Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats.Journal of chemical information and modeling · 2025Article
- emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level.Journal of molecular biology · 2022Article
- Insight into the sequence-specific elements leading to increased DNA bending and ligase-mediated circularization propensity by antitumor trabectedin.Journal of computer-aided molecular design · 2021Article
- Structural Landscape of the Transition from an ssDNA Dumbbell Plus Its Complementary Hairpin to a dsDNA Microcircle Via a Kissing Loop Intermediate.Molecules (Basel, Switzerland) · 2021Article
- Traveling Salesman Finds Random Walk: A Curve Reconstruction Algorithm for Supercoiled DNA.Biophysical journal · 2020Article
- Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts.Journal of computer-aided molecular design · 2020Article
- BIOPHYSICS MEETS GENE THERAPY: HOW EXPLORING SUPERCOILING-DEPENDENT STRUCTURAL CHANGES IN DNA LED TO THE DEVELOPMENT OF MINIVECTOR DNA.Technology and innovation · 2019Article
- Strong deformations of DNA: Effect on the persistence length.The European physical journal. E, Soft matter · 2018Article
- Probing hyper-negatively supercoiled mini-circles with nucleases and DNA binding proteins.PloS one · 2018Article
- Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles.Nucleic acids research · 2017Article
- The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity.Biophysical reviews · 2016Review
- Article
- DNA minicircles clarify the specific role of DNA structure on retroviral integration.Nucleic acids research · 2016Article
- Assessing the Current State of Amber Force Field Modifications for DNA.Journal of chemical theory and computation · 2016Article
- Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics.Nucleic acids research · 2016Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
- Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA.Biophysical journal · 2015Article
- Structural diversity of supercoiled DNA.Nature communications · 2015Article
- Close encounters with DNA.Journal of physics. Condensed matter : an Institute of Physics journal · 2014Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have investigated the effects of duplex length, sequence, salt concentration and superhelical density on the conformation of DNA nanocircles containing up to 178 base pairs using atomistic molecular dynamics simulation. These calculations reveal that the partitioning of twist and writhe is governed by a delicate balance of competing energetic terms. We have identified conditions which favour circular, positively or negatively writhed and denatured DNA conformations. Our simulations show that AT-rich DNA is more prone to denaturation when subjected to torsional stress than the corresponding GC containing circles. In contrast to the behaviour expected for a simple elastic rod, there is a distinct asymmetry in the behaviour of over and under-wound DNA nanocircles. The most biologically relevant negatively writhed state is more elusive than the corresponding positively writhed conformation, and is only observed for larger circles under conditions of high electrostatic screening. The simulation results have been summarised by plotting a phase diagram describing the various conformational states of nanocircles over the range of circle sizes and experimental conditions explored during the study. The changes in DNA structure that accompany supercoiling suggest a number of mechanisms whereby changes in DNA topology in vivo might be used to influence gene expression.
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