ArticleBiophysical journal2003
DNA basepair step deformability inferred from molecular dynamics simulations.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers.
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108 citing papers in PubMed.
- Inferring DNA Kinkability from Biased MD Simulations.Journal of chemical theory and computation · 2026Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- An electrostatic repulsion model of centromere organisation.bioRxiv : the preprint server for biology · 2025Article
- Nucleosome spacing can fine-tune higher-order chromatin assembly.Nature communications · 2025Article
- Adaptation of DNA to Protein Binding Revealed by Spectroscopy and Molecular Simulation.The journal of physical chemistry. B · 2025Article
- Laplace approximation of J factors for rigid base and rigid basepair models of DNA cyclization.Biophysical journal · 2025Article
- Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies.Nature communications · 2024Article
- A commentary on the ABC consortium and its impact on the development of mesoscopic models of DNA.Biophysical reviews · 2024Article
- Temperature-dependent elasticity of DNA, RNA, and hybrid double helices.Biophysical journal · 2024Article
- Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors.Structure (London, England : 1993) · 2024Article
- Correlated motions in DNA: beyond base-pair step models of DNA flexibility.Nucleic acids research · 2023Article
- DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ.Biochimica et biophysica acta. Gene regulatory mechanisms · 2023Article
- emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level.Journal of molecular biology · 2022Article
- Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration.Life (Basel, Switzerland) · 2022Article
- Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics.Nucleic acids research · 2022Article
- Article
- Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.PLoS computational biology · 2022Article
- Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?Biophysical reviews · 2021Review
- The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.PLoS computational biology · 2021Article
- Energetics of twisted DNA topologies.Biophysical journal · 2021Review
48 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers: d(GCCTATAAACGCCTATAA) and d(CTAGGTGGATGACTCATT). From an analysis of the structural fluctuations, the harmonic potential energy functions for all 10 unique steps with respect to the six step parameters have been evaluated. In the case of roll, three distinct groups of steps have been identified: the flexible pyrimidine-purine (YR) steps, intermediate purine-purine (RR), and stiff purine-pyrimidine (RY). The YR steps appear to be the most flexible in tilt and partially in twist. Increasing stiffness from YR through RR to RY was observed for rise, whereas shift and slide lack simple trends. A proposed measure of the relative importance of couplings identifies the slide-rise, twist-roll, and twist-slide couplings to play a major role. The force constants obtained are of similar magnitudes to those based on a crystallographic ensemble. However, the current data have a less complicated and less pronounced sequence dependence. A correlation analysis reveals concerted motions of neighboring steps and thus exposes limitations in the dinucleotide model. The comparison of DNA deformability from this and other studies with recent quantum-chemical stacking energy calculations suggests poor correlation between the stacking and flexibility.
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