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Mesoscopic model for DNA G-quadruplex unfolding

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Mesoscopic model for DNA G-quadruplex unfolding

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dc.contributor.author Bergues-Pupo, A.E. es_ES
dc.contributor.author Gutiérrez, I. es_ES
dc.contributor.author Arias-Gonzalez, J. R. es_ES
dc.contributor.author Falo, F. es_ES
dc.contributor.author Fiasconaro, A. es_ES
dc.date.accessioned 2020-10-23T03:31:16Z
dc.date.available 2020-10-23T03:31:16Z
dc.date.issued 2017-09-18 es_ES
dc.identifier.issn 2045-2322 es_ES
dc.identifier.uri http://hdl.handle.net/10251/153036
dc.description.abstract [EN] Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been reported to date by all-atom simulations, which cannot dissect the major physical interactions responsible for their cohesion. Here, we propose a mesoscopic model to describe both the mechanical and thermal stability of DNA G-quadruplexes, where each nucleotide of the structure, as well as each central cation located at the inner channel, is mapped onto a single bead. In this framework we are able to simulate loading rates similar to the experimental ones, which are not reachable in simulations with atomistic resolution. In this regard, we present single-molecule force-induced unfolding experiments by a high-resolution optical tweezers on a DNA telomeric sequence capable of adopting a G-quadruplex conformation. Fitting the parameters of the model to the experiments we find a correct prediction of the rupture-force kinetics and a good agreement with previous near equilibrium measurements. Since G-quadruplex unfolding dynamics is halfway in complexity between secondary nucleic acids and tertiary protein structures, our model entails a nanoscale paradigm for non-equilibrium processes in the cell. es_ES
dc.description.sponsorship Work supported by the Spanish Ministry of Economy and Competitiveness (MINECO), grant No. FIS2014-55867, co-financed by FEDER funds. We also thank the support of the Aragon Government and Fondo Social Europeo to FENOL group. Work in J.R.A.-G. laboratory was supported by a grant from MINECO, No. MAT2015-71806-R). es_ES
dc.language Inglés es_ES
dc.publisher Nature Publishing Group es_ES
dc.relation Gobierno de Aragón/E19 es_ES
dc.relation MINECO/MAT2015-71806-R es_ES
dc.relation MINECO/FIS2014-55867 es_ES
dc.relation.ispartof Scientific Reports es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject DNA modeling es_ES
dc.subject G-quadruplex es_ES
dc.subject Mechano-chemistry es_ES
dc.subject Stochastic es_ES
dc.subject Non-equilibrium es_ES
dc.subject.classification FISICA APLICADA es_ES
dc.title Mesoscopic model for DNA G-quadruplex unfolding es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1038/s41598-017-10849-2 es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Física Aplicada - Departament de Física Aplicada es_ES
dc.description.bibliographicCitation Bergues-Pupo, A.; Gutiérrez, I.; Arias-Gonzalez, JR.; Falo, F.; Fiasconaro, A. (2017). Mesoscopic model for DNA G-quadruplex unfolding. Scientific Reports. 7:1-13. https://doi.org/10.1038/s41598-017-10849-2 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1038/s41598-017-10849-2 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 13 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 7 es_ES
dc.identifier.pmid 28924219 es_ES
dc.identifier.pmcid PMC5603602 es_ES
dc.relation.pasarela S\407989 es_ES
dc.contributor.funder Gobierno de Aragón es_ES
dc.contributor.funder European Social Fund es_ES
dc.contributor.funder European Regional Development Fund es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
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