ArticleNucleic acids research2014
Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 72 citations in OpenAlex.
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- DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.Nucleic acids research · 2021Article
- 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
- Accurate modeling of DNA conformational flexibility by a multivariate Ising model.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Short-range template switching in great ape genomes explored using pair hidden Markov models.PLoS genetics · 2021Article
- Nucleosomal embedding reshapes the dynamics of abasic sites.Scientific reports · 2020Article
- Colibactin DNA-damage signature indicates mutational impact in colorectal cancer.Nature medicine · 2020Article
- Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.Nucleic acids research · 2020Article
- Bending of DNA duplexes with mutation motifs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- How methyl-sugar interactions determine DNA structure and flexibility.Nucleic acids research · 2019Article
- Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.Physical review letters · 2018Article
- Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography.Journal of biomolecular structure & dynamics · 2018Article
- Article
- Regulation of chromatin folding by conformational variations of nucleosome linker DNA.Nucleic acids research · 2017Article
- Conformational rearrangement of 1,2-d(GG) intrastrand cis-diammineplatinum crosslinked DNA is driven by counter-ion penetration within the minor groove of the modified site.Journal of molecular modeling · 2017Article
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric AnTn and asymmetric A2n tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and twisting relevant for looping. The symmetric tracts, in contrast, are more rigid than asymmetric tracts and the control, both locally and globally. Our results can reconcile the contradictory stiffness data on A-tracts and suggest symmetric A-tracts to be more efficient in nucleosome exclusion than the asymmetric ones. This would open a new possibility of gene expression manipulation using A-tracts.
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