ArticleProceedings of the National Academy of Sciences of the United States of America2021
Accurate modeling of DNA conformational flexibility by a multivariate Ising model.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 50 citations in OpenAlex.
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa.Nucleic acids research · 2024Article
- MCM2-7 loading-dependent ORC release ensures genome-wide origin licensing.Nature communications · 2024Article
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- DNA simulation benchmarks revealed with the accumulation of high-resolution structures.Biophysical reviews · 2024Review
- 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
- Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit inbioRxiv : the preprint server for biology · 2024Article
- Direct observation of coordinated assembly of individual native centromeric nucleosomes.The EMBO journal · 2023Article
- The development of nucleic acids force fields: From an unchallenged past to a competitive future.Biophysical journal · 2023Review
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Direct observation of coordinated assembly of individual native centromeric nucleosomes.bioRxiv : the preprint server for biology · 2023Article
- Correlated motions in DNA: beyond base-pair step models of DNA flexibility.Nucleic acids research · 2023Article
- Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions.PLoS computational biology · 2022Article
- Twisting DNA by salt.Nucleic acids research · 2022Article
- Mutation and selection explain why many eukaryotic centromeric DNA sequences are often A + T rich.Nucleic acids research · 2022Article
- Homologous basic helix-loop-helix transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism.QRB discovery · 2022Article
- Abnormal methylation in theQRB discovery · 2022Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The sequence-dependent structure and deformability of DNA play a major role for binding of proteins and regulation of gene expression. So far, most efforts to model DNA flexibility are based on unimodal harmonic stiffness models at base-pair resolution. However, multimodal behavior due to distinct conformational substates also contributes significantly to the conformational flexibility of DNA. Moreover, these local substates are correlated to their nearest-neighbor substates. A description for DNA elasticity which includes both multimodality and nearest-neighbor coupling has remained a challenge, which we solve by combining our multivariate harmonic approximation with an Ising model for the substates. In a series of applications to DNA fluctuations and protein-DNA complexes, we demonstrate substantial improvements over the unimodal stiffness model. Furthermore, our multivariate Ising model reveals a mechanical destabilization for adenine (A)-tracts to undergo nucleosome formation. Our approach offers a wide range of applications to determine sequence-dependent deformation energies of DNA and to investigate indirect readout contributions to protein-DNA recognition.
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