Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

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dc.citation.firstpage258105en_US
dc.citation.issueNumber25en_US
dc.citation.journalTitlePhysical Review Lettersen_US
dc.citation.volumeNumber114en_US
dc.contributor.authorHayes, Ryan L.en_US
dc.contributor.authorNoel, Jeffrey K.en_US
dc.contributor.authorMandic, Anaen_US
dc.contributor.authorWhitford, Paul C.en_US
dc.contributor.authorSanbonmatsu, Karissa Y.en_US
dc.contributor.authorMohanty, Udayanen_US
dc.contributor.authorOnuchic, José N.en_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2016-06-10T18:07:39Zen_US
dc.date.available2016-06-10T18:07:39Zen_US
dc.date.issued2015en_US
dc.description.abstractRNA is highly sensitive to the ionic environment and typically requires Mg2+ to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg2+ ions explicitly to account for ion-ion correlations neglected by mean-field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, nonlimiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg2+ associated with the RNA, Γ2+, because Γ2+ is directly related to the Mg2+-RNA interaction free energy. The excellent agreement with experiment demonstrates that the model captures the ionic dependence of the RNA free energy landscape.en_US
dc.identifier.citationHayes, Ryan L., Noel, Jeffrey K., Mandic, Ana, et al.. "Generalized Manning Condensation Model Captures the RNA Ion Atmosphere." <i>Physical Review Letters,</i> 114, no. 25 (2015) American Physical Society: 258105. http://dx.doi.org/10.1103/PhysRevLett.114.258105.en_US
dc.identifier.doihttp://dx.doi.org/10.1103/PhysRevLett.114.258105en_US
dc.identifier.urihttps://hdl.handle.net/1911/90489en_US
dc.language.isoengen_US
dc.publisherAmerican Physical Societyen_US
dc.rightsArticle is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.en_US
dc.titleGeneralized Manning Condensation Model Captures the RNA Ion Atmosphereen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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