ArticleNature communications2014
On the absence of intrahelical DNA dynamics on the μs to ms timescale.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Chemical Composition and Backbone Modifications Define Deformability of Nucleic Acid Nanoparticles.ACS nano · 2025Article
- GID4 recognition of Pro/N-degron peptides: Conformational selection and induced fit.Biophysical journal · 2025Article
- Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications.NAR genomics and bioinformatics · 2024Article
- Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy.International journal of molecular sciences · 2024Article
- van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.Journal of chemical theory and computation · 2024Article
- Mechanical codes of chemical-scale specificity in DNA motifs.Chemical science · 2023Article
- Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.Journal of chemical theory and computation · 2023Article
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations.Journal of chemical information and modeling · 2023Article
- Bubble Relaxation Dynamics in Homopolymer DNA Sequences.Molecules (Basel, Switzerland) · 2023Article
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA.The journal of physical chemistry letters · 2022Article
- Article
- Searching for Low Probability Opening Events in a DNA Sliding Clamp.Life (Basel, Switzerland) · 2022Article
- Insights into the binding mode of AS1411 aptamer to nucleolin.Frontiers in molecular biosciences · 2022Article
- Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?Biophysical reviews · 2021Review
- Recombinant laccase rPOXA 1B real-time, accelerated and molecular dynamics stability study.BMC biotechnology · 2021Article
- Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations.Nucleic acids research · 2021Article
- Ancillary Ligand in Ternary CuThe journal of physical chemistry. B · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
DNA helices display a rich tapestry of motion on both short (<100 ns) and long (>1 ms) timescales. However, with the exception of mismatched or damaged DNA, experimental measures indicate that motions in the 1 μs to 1 ms range are effectively absent, which is often attributed to difficulties in measuring motions in this time range. We hypothesized that these motions have not been measured because there is effectively no motion on this timescale, as this provides a means to distinguish faithful Watson-Crick base-paired DNA from damaged DNA. The absence of motion on this timescale would present a 'static' DNA sequence-specific structure that matches the encounter timescales of proteins, thereby facilitating recognition. Here we report long-timescale (~10-44 μs) molecular dynamics simulations of a B-DNA duplex structure that addresses this hypothesis using both an 'Anton' machine and large ensembles of AMBER GPU simulations.
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