ArticleNucleic acids research2018
Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism.
Article in Nucleic acids research, 2018. 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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Who cites it
19 citing papers in PubMed.
- DNA Mechanical Strain Steers Transcription Factor Recognition.Research square · 2026Article
- DNA based nanoscale optoelectronic devices enabled by THz driven piezo vibrotronic effect.Scientific reports · 2025Article
- The development of nucleic acids force fields: From an unchallenged past to a competitive future.Biophysical journal · 2023Review
- Prediction of hub genes and key pathways associated with the radiation response of human hematopoietic stem/progenitor cells using integrated bioinformatics methods.Scientific reports · 2023Article
- Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis.Nucleic acids research · 2022Article
- An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays.Nucleic acids research · 2022Article
- RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems.Biophysical journal · 2022Article
- Homologous basic helix-loop-helix transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism.QRB discovery · 2022Article
- Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors.Nucleic acids research · 2021Article
- Energetics of twisted DNA topologies.Biophysical journal · 2021Review
- A unified computational view of DNA duplex, triplex, quadruplex and their donor-acceptor interactions.Nucleic acids research · 2021Article
- Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Specifically bound BZIP transcription factors modulate DNA supercoiling transitions.Scientific reports · 2020Article
- Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.Chemical science · 2020Article
- The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA.Nucleic acids research · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- Article
- Characterizing the interplay between gene nucleotide composition bias and splicing.Genome biology · 2019Article
- Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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3 authors.
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Abstract
Torsional restraints on DNA change in time and space during the life of the cell and are an integral part of processes such as gene expression, DNA repair and packaging. The mechanical behavior of DNA under torsional stress has been studied on a mesoscopic scale, but little is known concerning its response at the level of individual base pairs and the effects of base pair composition. To answer this question, we have developed a geometrical restraint that can accurately control the total twist of a DNA segment during all-atom molecular dynamics simulations. By applying this restraint to four different DNA oligomers, we are able to show that DNA responds to both under- and overtwisting in a very heterogeneous manner. Certain base pair steps, in specific sequence environments, are able to absorb most of the torsional stress, leaving other steps close to their relaxed conformation. This heterogeneity also affects the local torsional modulus of DNA. These findings suggest that modifying torsional stress on DNA could act as a modulator for protein binding via the heterogeneous changes in local DNA structure.
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