ArticleBiophysical journal2011
A multiscale dynamic model of DNA supercoil relaxation by topoisomerase IB.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Programmable electric tweezers.Science advances · 2026Article
- Two-phase dynamics of DNA supercoiling based on DNA polymer physics.Biophysical journal · 2022Article
- WASP: a software package for correctly characterizing the topological development of ribbon structures.Scientific reports · 2021Article
- Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome.Biophysical journal · 2020Article
- A Mathematical Model for Vibration Behavior Analysis of DNA and Using a Resonant Frequency of DNA for Genome Engineering.Scientific reports · 2020Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
- Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation.Nucleic acids research · 2015Article
- Slowdown of Interhelical Motions Induces a Glass Transition in RNA.Biophysical journal · 2015Article
- Role of microscopic flexibility in tightly curved DNA.The journal of physical chemistry. B · 2014Article
- Variola type IB DNA topoisomerase: DNA binding and supercoil unwinding using engineered DNA minicircles.Biochemistry · 2014Article
- Gold(III) macrocycles: nucleotide-specific unconventional catalytic inhibitors of human topoisomerase I.Journal of the American Chemical Society · 2014Article
- Theoretical frameworks for multiscale modeling and simulation.Current opinion in structural biology · 2014Review
- Sophisticated modeling uncovers atomic DNA structure in bacteriophage φ29 cavity.Biophysical journal · 2013Article
- Structural ensemble and dynamics of toroidal-like DNA shapes in bacteriophage ϕ29 exit cavity.Biophysical journal · 2013Article
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5 authors.
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Abstract
In this study, we report what we believe to be the first multiscale simulation of the dynamic relaxation of DNA supercoils by human topoisomerase IB (topo IB). We leverage our previous molecular dynamics calculations of the free energy landscape describing the interaction between a short DNA fragment and topo IB. Herein, this landscape is used to prescribe boundary conditions for a computational, elastodynamic continuum rod model of a long length of supercoiled DNA. The rod model, which accounts for the nonlinear bending, twisting, and electrostatic interaction of the (negatively charged) DNA backbone, is extended to include the hydrodynamic drag induced by the surrounding physiological buffer. Simulations for a 200-bp-long DNA supercoil in complex with topo IB reveal a relaxation timescale of ∼0.1-1.0 μs. The relaxation follows a sequence of cascading reductions in the supercoil linking number (Lk), twist (Tw), and writhe (Wr) that follow companion cascading reductions in the supercoil elastic and electrostatic energies. The novel (to our knowledge) multiscale modeling method may enable simulations of the entire experimental setup that measures DNA supercoiling and relaxation via single molecule magnetic trapping.
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