Journal Article

Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

Marco Pasi and Richard Lavery

in Nucleic Acids Research

Volume 44, issue 11, pages 5450-5456
Published in print June 2016 | ISSN: 0305-1048
Published online April 2016 | e-ISSN: 1362-4962 | DOI: https://dx.doi.org/10.1093/nar/gkw293

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DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA–core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA–core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome.

Journal Article.  5000 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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