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Why double-stranded RNA resists condensation

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dc.contributor.authorTolokh, Igor S.en
dc.contributor.authorPabit, Suzette A.en
dc.contributor.authorKatz, Andrea M.en
dc.contributor.authorChen, Yujieen
dc.contributor.authorDrozdetski, Aleksander V.en
dc.contributor.authorBaker, Nathanen
dc.contributor.authorPollack, Loisen
dc.contributor.authorOnufriev, Alexey V.en
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentPhysicsen
dc.date.accessioned2019-04-12T14:55:18Zen
dc.date.available2019-04-12T14:55:18Zen
dc.date.issued2014-09-15en
dc.description.abstractThe addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different double helical form. Here, we combine experiment and atomistic simulations to propose a mechanism that explains the variations in condensation of short (25 base-pairs) nucleic acid (NA) duplexes, from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA: RNA hybrid, to A-like RNA. Circular dichroism measurements suggest that duplex helical geometry is not the fundamental property that ultimately determines the observed differences in condensation. Instead, these differences are governed by the spatial variation of cobalt hexammine (CoHex) binding to NA. There are two major NA-CoHex binding modes-internal and external-distinguished by the proximity of bound CoHex to the helical axis. We find a significant difference, up to 5-fold, in the fraction of ions bound to the external surfaces of the different NA constructs studied. NA condensation propensity is determined by the fraction of CoHex ions in the external binding mode.en
dc.description.notesNIH [R01 GM099450]; NSF [CNS-0960081]; HokieSpeed supercomputer at Virginia Tech. Source of open access funding: NIH [R01 GM099450]; NSF [CNS-0960081].en
dc.description.sponsorshipNIH [R01 GM099450]; NSF [CNS-0960081]; HokieSpeed supercomputer at Virginia Techen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gku756en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.issue16en
dc.identifier.pmid25123663en
dc.identifier.urihttp://hdl.handle.net/10919/88951en
dc.identifier.volume42en
dc.language.isoen_USen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectmolecular-dynamics simulationsen
dc.subjectdna condensationen
dc.subjectmultivalent cationsen
dc.subjectpoisson-boltzmannen
dc.subjectnucleic-acidsen
dc.subjectoriented dnaen
dc.subjectforce-fielden
dc.subjectsodium-ionsen
dc.subjectbindingen
dc.subjectcounterionsen
dc.titleWhy double-stranded RNA resists condensationen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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