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Nucleic Acids Res. 2011 Mar;39(4):1220-30. doi: 10.1093/nar/gkq952. Epub 2010 Oct 23.

Geometrical correlations in the nucleosomal DNA conformation and the role of the covalent bonds rigidity.

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Department of Physics, Institute for Advanced Studies in Basic Sciences, Zanjan 45137-66731, Iran.


We develop a simple elastic model to study the conformation of DNA in the nucleosome core particle. In this model, the changes in the energy of the covalent bonds that connect the base pairs of each strand of the DNA double helix, as well as the lateral displacements and the rotation of adjacent base pairs are considered. We show that because of the rigidity of the covalent bonds in the sugar-phosphate backbones, the base pair parameters are highly correlated, especially, strong twist-roll-slide correlation in the conformation of the nucleosomal DNA is vividly observed in the calculated results. This simple model succeeds to account for the detailed features of the structure of the nucleosomal DNA, particularly, its more important base pair parameters, roll and slide, in good agreement with the experimental results.

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