On the absence of intra-helical DNA dynamics on the µs to ms timescale
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Summary
Long-timescale molecular dynamics simulations of a B-DNA duplex structure are demonstrated to show that intra-helical motion of DNA at the μs timescale, which has been attributed to technical difficulties in observing motion in this time range.
- Type
- article
- Published
- 2014-10-29
- Cited by
- 78
- References
- 61
- Access
- Open access
- OpenAlex
- https://openalex.org/W1989915883
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:18594763
Keywords
DNA, Molecular dynamics, Dynamics (music), Base pair, Physics
References
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- Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods
- High-resolution field-cycling NMR studies of a DNA octamer as a probe of phosphodiester dynamics and comparison with computer simulation.
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- A CRITICAL REVIEW
- Dynamics of Water and Ions near DNA: Comparison of Simulation to Time-Resolved Stokes-Shift Experiments
Cited by
- Multiscale modelling of DNA mechanics
- Physics of base-pairing dynamics in DNA
- Molecular Dynamics Study of Supercoiled DNA Minicircles Tightly Bent and Supercoiled DNA in Atomistic Resolution
- The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis
- Conquering 2-Aminopurine’s Deficiencies: Highly Emissive Isomorphic Guanosine Surrogate Faithfully Monitors Guanosine Conformation and Dynamics in DNA
- Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)
- Intercalation processes of copper complexes in DNA
- Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields
- Probing the influence of hypermodified residues within the tRNA3(Lys) anticodon stem loop interacting with the A-loop primer sequence from HIV-1.
- Multiscale simulation of DNA.
- PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS
- A human transcription factor in search mode
- Energetics of Base Flipping at a DNA Mismatch Site Confined at the Latch Constriction of α-Hemolysin
- Long-timescale dynamics of the Drew–Dickerson dodecamer
- MD and EPR studies of the structure and dynamics of the MTSL spin-labelled activation loop of the Aurora-A kinase
- Transitions of Double-Stranded DNA Between the A- and B-Forms
- DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations.
- Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations
- Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
- Assessing the Current State of Amber Force Field Modifications for DNA
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