Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes

Bergues-Pupo, A. ; Arias-Gonzalez, J. ; Morón, M.C. (Universidad de Zaragoza) ; Fiasconaro, A. (Universidad de Zaragoza) ; Falo, F. (Universidad de Zaragoza)

Resumen: 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 K+ 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.

Idioma: Inglés

DOI: 10.1093/nar/gkv690

Año: 2015

Publicado en: Nucleic Acids Research 43, 15 (2015), 7638-7647
ISSN: 0305-1048

Factor impacto JCR: 9.202 (2015)

Categ. JCR: BIOCHEMISTRY & MOLECULAR BIOLOGY rank: 18 / 289 = 0.062 (2015) - Q1 - T1

Factor impacto SCIMAGO: 7.358 - Genetics (Q1)

Financiación: info:eu-repo/grantAgreement/ES/DGA/E19
Financiación: info:eu-repo/grantAgreement/ES/MINECO/FIS2011-25167
Financiación: info:eu-repo/grantAgreement/ES/MINECO/FIS2014-55867-P
Financiación: info:eu-repo/grantAgreement/ES/MINECO/MAT2013-49455-EXP

Tipo y forma: Article (Published version)

Área (Departamento): Área Física Materia Condensada (Dpto. Física Materia Condensa.)