title: Stability and cations coordination of DNA and RNA 14-mer G-quadruplexes: a multiscale computational approach.
abstract: Molecular dynamics simulations have been used to study the differences between two DNA and RNA 14-mer quadruplexes of analogous sequences. Their structures present a completely different fold: DNA forms a bimolecular quadruplex containing antiparallel strands and diagonal loops; RNA forms an intrastrand parallel quadruplex containing a G-tetrad and an hexad, which dimerizes by hexad stacking. We used a multiscale computational approach combining classical Molecular dynamics simulations and density functional theory calculations to elucidate the difference in stability of the 2-folds and their ability in coordinating cations. The presence of 2'-OH groups in the RNA promotes the formation of a large number of intramolecular hydrogen bonds that account for the difference in fold and stability of the two 14-mers. We observe that the adenines in the RNA quadruplex play a key role in conserving the geometry of the hexad. We predict the cation coordination mode of the two quadruplexes, not yet observed experimentally, and we offer a rationale for the corresponding binding energies involved.
authors.affiliation: Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy.
authors.forename: Bruno
authors.initials: B
authors.lastname: Pagano
authors.forename: Carlo A
authors.initials: CA
authors.lastname: Mattia
authors.forename: Luigi
authors.initials: L
authors.lastname: Cavallo
authors.forename: Seiichi
authors.initials: S
authors.lastname: Uesugi
authors.forename: Concetta
authors.initials: C
authors.lastname: Giancola
authors.forename: Franca
authors.initials: F
authors.lastname: Fraternali