ArticleThe journal of physical chemistry. B2011
Modeling DNA-bending in the nucleosome: role of AA periodicity.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
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- Centromeres drive and take a break.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Review
- Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses.Nucleic acids research · 2024Article
- The genetics and epigenetics of satellite centromeres.Genome research · 2022Article
- Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members.Nucleic acids research · 2020Article
- De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture.PLoS biology · 2018Article
- Simple and Complex Centromeric Satellites inGenetics · 2018Article
- Categorical spectral analysis of periodicity in nucleosomal DNA.Nucleic acids research · 2016Article
- The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy.The journal of physical chemistry. B · 2012Article
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4 authors.
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Abstract
This paper uses atomistic molecular mechanics within the framework of the JUMNA model to study the bending properties of DNA segments, with emphasis on understanding the role of the 10 bp periodicity associated with AA repeats that has been found to dominate in nucleosomal DNA. The calculations impose a bending potential on 18 bp segments that is consistent with nucleosome structures (i.e., radius of curvature of 4.1 nm), and then determine the energies of the minimum energy structures for different values of the rotational register (a measure of the direction of bending of the DNA) subject to forces derived from the Amber force field (parm99bsc0). The results show that sequences that contain the 10 bp repeats but are otherwise random have a narrow distribution of rotational register values that minimize the energy such that it is possible to combine several minimized structures to give the 147 bp nearly planar loop structure of the nucleosome. The rotational register values that lead to minimum bending energy with 10 bp AA repeats have a narrower minor groove, which points toward the histone interior at the positions of the AA repeats, which is a result that matches the experiments. The calculations also show that these sequences have a relatively flat potential energy landscape for bending to a 4.1 nm radius of curvature. Random sequences that do not have the 10 bp AA repeats have less stable bent structures, and a flat rotational register distribution, such that low energy nearly planar loops are less likely.
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