title: Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes.
abstract: Cations are known to mediate diverse interactions in nucleic acids duplexes but they are critical in the arrangement of four-stranded structures. Here, we use all-atom molecular dynamics simulations with explicit solvent to analyse the mechanical unfolding of representative intramolecular G-quadruplex structures: a parallel, a hybrid and an antiparallel DNA and a parallel RNA, in the presence of stabilising cations. We confirm the stability of these conformations in the presence of [Formula: see text] central ions and observe distortions from the tetrad topology in their absence. Force-induced unfolding dynamics is then investigated. We show that the unfolding events in the force-extension curves are concomitant to the loss of coordination between the central ions and the guanines of the G-quadruplex. We found lower ruptures forces for the parallel configuration with respect to the antiparallel one, while the behaviour of the force pattern of the parallel RNA appears similar to the parallel DNA. We anticipate that our results will be essential to interpret the fine structure rupture profiles in stretching assays at high resolution and will shed light on the mechanochemical activity of G-quadruplex-binding machinery.
authors.affiliation: Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor, 50018 Zaragoza, Spain Departamento de Física, Universidad de Oriente, 90500 Santiago de Cuba, Cuba.
authors.forename: Ana Elisa
authors.initials: AE
authors.lastname: Bergues-Pupo
authors.affiliation: Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Cantoblanco, 28049 Madrid, Spain CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología, Madrid, Spain'
authors.forename: J Ricardo
authors.initials: JR
authors.lastname: Arias-Gonzalez
authors.affiliation: Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain.
authors.forename: María Carmen
authors.initials: MC
authors.lastname: Morón
authors.affiliation: School of Mathematical Sciences, Queen Mary University of London - Mile End Road, London E1 4NS, UK A.Fiasconaro@qmul.ac.uk.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Fiasconaro
authors.affiliation: Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor, 50018 Zaragoza, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Falo
mesh_terms: D002412:Cations; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011188:Potassium / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D016615:Telomere / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D002412:Cations; D012313:RNA; D004247:DNA; D011188:Potassium