Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

dc.contributor.authorDrozdetski, Aleksander V.en
dc.contributor.authorMukhopadhyay, Abhisheken
dc.contributor.authorOnufriev, Alexey V.en
dc.contributor.departmentCenter for Soft Matter and Biological Physicsen
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentPhysicsen
dc.date.accessioned2020-02-05T13:55:53Zen
dc.date.available2020-02-05T13:55:53Zen
dc.date.issued2019-11-29en
dc.description.abstractThe strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As the bending deformation increases beyond a certain (polymer-specific) point, the change in the convexity properties of the effective bending energy of the polymer makes the harmonic deformation energetically unfavorable: in this strong bending regime the energy of the polymer varies linearly with the average bending angle as the system follows the convex hull of the deformation energy function. For double-stranded DNA, the effective bending deformation energy becomes non-convex for bends greater than similar to 2 degrees per base-pair, equivalent to the curvature of a closed circular loop of similar to 160 base pairs. A simple equation is derived for the polymer loop energy that covers both the weak and strong bending regimes. The theory shows quantitative agreement with recent DNA cyclization experiments on short DNA fragments, while maintaining the expected agreement with experiment in the weak bending regime. Counter-intuitively, cyclization probability (j-factor) of very short DNA loops is predicted to increase with decreasing loop length; the j-factor reaches its minimum for loops of similar or equal to 45 base pairs. Atomistic simulations reveal that the attractive component of the short-range Lennard-Jones interaction between the backbone atoms can explain the underlying non-convexity of the DNA effective bending energy, leading to the linear bending regime. Applicability of the theory to protein-DNA complexes, including the nucleosome, is discussed.en
dc.description.notesThis work was supported in part by the National Institutes of Health (R21 GM131228) and the National Science Foundation (MCB-1715207).en
dc.description.sponsorshipNational Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [R21 GM131228]; National Science FoundationNational Science Foundation (NSF) [MCB-1715207]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3389/fphy.2019.00195en
dc.identifier.issn2296-424Xen
dc.identifier.other195en
dc.identifier.urihttp://hdl.handle.net/10919/96716en
dc.identifier.volume7en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectpolymer bendingen
dc.subjectDNAen
dc.subjectconvex hullen
dc.subjectdeformationen
dc.subjectcyclizationen
dc.subjectj-factoren
dc.titleStrongly Bent Double-Stranded DNA: Reconciling Theory and Experimenten
dc.title.serialFrontiers in Physicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen
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