ArticleThe journal of physical chemistry. B2013
5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed.
- Re-analysis of publicly available methylomes using signal detection yields new information.Scientific reports · 2023Article
- Single-molecule micromanipulation studies of methylated DNA.Biophysical journal · 2021Article
- Infrared nanospectroscopic mapping of a single metaphase chromosome.Nucleic acids research · 2019Article
- Genome-Wide Discriminatory Information Patterns of Cytosine DNA Methylation.International journal of molecular sciences · 2016Article
- Information Thermodynamics of Cytosine DNA Methylation.PloS one · 2016Article
- Theoretical modelling of epigenetically modified DNA sequences.F1000Research · 2015Article
- Crop epigenetics and the molecular hardware of genotype × environment interactions.Frontiers in plant science · 2015Review
- Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation.Epigenetics · 2014Article
- Arginine-phosphate salt bridges between histones and DNA: intermolecular actuators that control nucleosome architecture.The Journal of chemical physics · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile "opening" mode and two shear "sliding" and "tearing" modes in the orthogonal plane. The stacking interactions of the methyl groups globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. Additionally, the indirect effects of the methyl groups on possible base-pair steps neighboring CG:CG are observed to be of comparable importance to their direct effects on CG:CG. The results have implications for the epigenetic control of DNA mechanics.
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Registered trials
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