Crowding on DNA in Protein Search for Targets

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dc.citation.firstpage2502
dc.citation.issueNumber13
dc.citation.journalTitleThe Journal of Physical Chemistry Letters
dc.citation.lastpage2506
dc.citation.volumeNumber7
dc.contributor.authorShvets, Alexey A.
dc.contributor.authorKolomeisky, Anatoly B.
dc.contributor.orgCenter for Theoretical Biological Physics
dc.date.accessioned2016-09-19T21:20:39Z
dc.date.available2016-09-19T21:20:39Z
dc.date.issued2016
dc.description.abstractProteins searching and recognizing specific sites on DNA is required for initiating all major biological processes. While the details of the protein search for targets on DNA in purified in vitro systems are reasonably well understood, the situation in real cells is much less clear. The presence of other types of molecules on DNA should prevent reaching the targets, but experiments show that, surprisingly, the molecular crowding on DNA influences the search dynamics much less than expected. We develop a theoretical method that allowed us to clarify the mechanisms of the protein search on DNA in the presence of crowding. It is found that the dimensionality of the search trajectories specifies whether the crowding will affect the target finding. For 3D search pathways it is minimal, while the strongest effect is for 1D search pathways when the crowding particle can block the search. In addition, for 1D search we determined that the critical parameter is a mobility of crowding agents: highly mobile molecules do not affect the search dynamics, while the slow particles can significantly slow down the process. Physical-chemical explanations of the observed phenomena are presented. Our theoretical predictions thus explain the experimental observations, and they are also supported by extensive numerical simulations.
dc.identifier.citationShvets, Alexey A. and Kolomeisky, Anatoly B.. "Crowding on DNA in Protein Search for Targets." <i>The Journal of Physical Chemistry Letters,</i> 7, no. 13 (2016) American Chemical Society: 2502-2506. http://dx.doi.org/10.1021/acs.jpclett.6b00905.
dc.identifier.doihttp://dx.doi.org/10.1021/acs.jpclett.6b00905
dc.identifier.urihttps://hdl.handle.net/1911/91580
dc.language.isoeng
dc.publisherAmerican Chemical Society
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society.
dc.titleCrowding on DNA in Protein Search for Targets
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpost-print
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