A computational study of nucleosomal DNA flexibility

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dc.contributorVirginia Techen
dc.contributor.authorRuscio, Jory Z.en
dc.contributor.authorOnufriev, Alexey V.en
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentPhysicsen
dc.date.accessed2014-02-05en
dc.date.accessioned2014-02-26T19:10:03Zen
dc.date.available2014-02-26T19:10:03Zen
dc.date.issued2006-12-01en
dc.description.abstractMolecular dynamics simulations of the nucleosome core particle and its isolated DNA free in solution are reported. The simulations are based on the implicit solvent methodology and provide insights into the nature of large-scale structural fuctuations and flexibility of the nucleosomal DNA. In addition to the kinked regions previously identified in the x-ray structure of the nucleosome, the simulations support the existence of a biochemically identified distorted region of the DNA. Comparison of computed relative free energies shows that formation of the kinks is associated with little, if any, energy cost relative to a smooth, ideal conformation of the DNA superhelix. Isolated nucleosomal DNA is found to be considerably more flexible than expected for a 147 bp stretch of DNA based on its canonical persistence length of 500 A. Notably, the significant bending of the DNA observed in our simulations occurs without breaking of Watson-Crick bonds. The computed relative stability of bent conformations is sensitive to the ionic strength of the solution in the physiological range; the sensitivity suggests possible experiments that might provide further insights into the structural origins of the unusual flexibility of the DNA.en
dc.description.sponsorshipNational Institutes of Health GM076121en
dc.description.sponsorshipASPIRES seed grant from Virginia Techen
dc.identifier.citationRuscio, Jory Z.; Onufriev, Alexey, "A computational study of nucleosomal DNA flexibility," Biophysical Journal 91(11), 4121-4132 (2006); doi: 10.1529/biophysj.106.082099en
dc.identifier.doihttps://doi.org/10.1529/biophysj.106.082099en
dc.identifier.issn0006-3495en
dc.identifier.urihttp://hdl.handle.net/10919/25764en
dc.identifier.urlhttp://www.sciencedirect.com/science/article/pii/S0006349506721282en
dc.language.isoen_USen
dc.publisherCELL PRESSen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectGeneralized born modelen
dc.subjectMolecular-dynamics simulationsen
dc.subjectNucleic-acidsen
dc.subjectProteinsen
dc.subjectMechanismsen
dc.subjectCoreen
dc.subjectTranscriptionen
dc.subjectChromatinen
dc.subjectCyclizationen
dc.subjectDistortionen
dc.titleA computational study of nucleosomal DNA flexibilityen
dc.title.serialBiophysical Journalen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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