Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

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dc.citation.firstpage258105
dc.citation.issueNumber25
dc.citation.journalTitlePhysical Review Letters
dc.citation.volumeNumber114
dc.contributor.authorHayes, Ryan L.
dc.contributor.authorNoel, Jeffrey K.
dc.contributor.authorMandic, Ana
dc.contributor.authorWhitford, Paul C.
dc.contributor.authorSanbonmatsu, Karissa Y.
dc.contributor.authorMohanty, Udayan
dc.contributor.authorOnuchic, José N.
dc.contributor.orgCenter for Theoretical Biological Physics
dc.date.accessioned2016-06-10T18:07:39Z
dc.date.available2016-06-10T18:07:39Z
dc.date.issued2015
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.
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.
dc.identifier.doihttp://dx.doi.org/10.1103/PhysRevLett.114.258105
dc.identifier.urihttps://hdl.handle.net/1911/90489
dc.language.isoeng
dc.publisherAmerican Physical Society
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.
dc.titleGeneralized Manning Condensation Model Captures the RNA Ion Atmosphere
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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