ArticlePhysical review letters2011
Molecular origins of DNA flexibility: sequence effects on conformational and mechanical properties.
Article in Physical review letters, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed, 58 citations in OpenAlex.
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- Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation.RSC advances · 2024Article
- The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.Nucleic acids research · 2024Article
- Article
- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for biology · 2023Article
- Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids.The journal of physical chemistry. B · 2023Article
- Cooperative DNA looping by PRC2 complexes.Nucleic acids research · 2021Article
- Nucleosomes effectively shield DNA from radiation damage in living cells.Nucleic acids research · 2020Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins.Scientific reports · 2018Article
- Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA.Nucleic acids research · 2016Article
- Atomic force microscopy study of DNA flexibility on short length scales: smooth bending versus kinking.Nucleic acids research · 2014Article
- Modeling DNA thermodynamics under torsional stress.Biophysical journal · 2014Article
- Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis.PloS one · 2014Article
- Mechanical properties of DNA-like polymers.Nucleic acids research · 2013Article
- An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization.The Journal of chemical physics · 2013Article
- Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching.Chemical reviews · 2013Review
- Pack it up, pack it in: unraveling H-NS mediated genome packaging.Biophysical journal · 2013Article
- DNA methylation regulated nucleosome dynamics.Scientific reports · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
A central question in biophysics is whether DNA sequence affects its mechanical properties, which are thought to influence nucleosome positioning and gene expression. Previous attempts to answer this question have been hindered by an inability to resolve DNA structure and dynamics at the base-pair level. Here we use a model to measure the effects of sequence on the stability of DNA under bending. Sequence is shown to influence DNA's flexibility and its ability to form kinks, which arise when certain motifs slide past others to form non-native contacts. A mechanism for nucleosome positioning is proposed in which sequence influences DNA-histone binding by altering the local base-pair-level structure when subject to the curvature necessary for binding.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.