ArticleNucleic acids research2010
A measure of bending in nucleic acids structures applied to A-tract DNA.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 57 citations in OpenAlex.
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- 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
- Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis.Molecules (Basel, Switzerland) · 2021Article
- The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition.The journal of physical chemistry. B · 2021Article
- The structural plasticity of nucleic acid duplexes revealed by WAXS and MD.Science advances · 2021Article
- Distinct Modes of Promoter Recognition by Two Iron Starvation σ Factors with Overlapping Promoter Specificities.Journal of bacteriology · 2019Article
- Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics.Nucleic acids research · 2017Article
- Parmbsc1: a refined force field for DNA simulations.Nature methods · 2016Article
- cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.Nucleic acids research · 2014Article
- Symmetric curvature descriptors for label-free analysis of DNA.Scientific reports · 2014Article
- Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.Nucleic acids research · 2014Article
- DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations.Biochemistry · 2013Article
- DNA bending propensity in the presence of base mismatches: implications for DNA repair.The journal of physical chemistry. B · 2013Article
- Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters.Journal of chemical theory and computation · 2013Article
- Analyzing and building nucleic acid structures with 3DNA.Journal of visualized experiments : JoVE · 2013Article
- Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.Journal of chemical theory and computation · 2013Article
- The ABCs of molecular dynamics simulations on B-DNA, circa 2012.Journal of biosciences · 2012Review
- Label-free, atomic force microscopy-based mapping of DNA intrinsic curvature for the nanoscale comparative analysis of bent duplexes.Nucleic acids research · 2012Article
- Article
- Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.Journal of chemical theory and computation · 2011Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
A method is proposed to measure global bending in DNA and RNA structures. It relies on a properly defined averaging of base-fixed coordinate frames, computes mean frames of suitably chosen groups of bases and uses these mean frames to evaluate bending. The method is applied to DNA A-tracts, known to induce considerable bend to the double helix. We performed atomistic molecular dynamics simulations of sequences containing the A(4)T(4) and T(4)A(4) tracts, in a single copy and in two copies phased with the helical repeat. Various temperature and salt conditions were investigated. Our simulations indicate bending by roughly 10 degrees per A(4)T(4) tract into the minor groove, and an essentially straight structure containing T(4)A(4), in agreement with electrophoretic mobility data. In contrast, we show that the published NMR structures of analogous sequences containing A(4)T(4) and T(4)A(4) tracts are significantly bent into the minor groove for both sequences, although bending is less pronounced for the T(4)A(4) containing sequence. The bending magnitudes obtained by frame averaging are confirmed by the analysis of superhelices composed of repeated tract monomers.
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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.