title: Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.
abstract: Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time or spatial resolution. Here we use state-of-the-art computational techniques, namely, atomistic molecular dynamics and Markov state models, to provide insight into the rapid dynamics of short RNA oligonucleotides, to elucidate the kinetics of stacking interactions. Analysis of multiple microsecond-long simulations indicates that the main relaxation modes of such molecules can consist of transitions between alternative folded states, rather than between random coils and native structures. After properly removing structures that are artificially stabilized by known inaccuracies of the current RNA AMBER force field, the kinetic properties predicted are consistent with the time scales of previously reported relaxation experiments.
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies , 265 Via Bonomea, I-34136 Trieste, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Pinamonti
authors.affiliation: Department of Chemistry, University of Rochester , Rochester, New York 14627, United States.
authors.forename: Jianbo
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Department of Chemistry, University of Rochester , Rochester, New York 14627, United States.
authors.forename: David E
authors.initials: DE
authors.lastname: Condon
authors.affiliation: Department for Mathematics and Computer Science, Freie Universität , Arnimallee 6, Berlin 14195, Germany.
authors.forename: Fabian
authors.identifier: http://orcid.org/0000-0002-1478-1827
authors.initials: F
authors.lastname: Paul
authors.affiliation: Department for Mathematics and Computer Science, Freie Universität , Arnimallee 6, Berlin 14195, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Noè
authors.affiliation: Department of Chemistry, University of Rochester , Rochester, New York 14627, United States.
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies , 265 Via Bonomea, I-34136 Trieste, Italy.
authors.forename: Giovanni
authors.identifier: http://orcid.org/0000-0001-9216-5782
authors.initials: G
authors.lastname: Bussi
mesh_terms: D007700:Kinetics; D008390:Markov Chains; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry* / Q000378:metabolism*; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D013696:Temperature
chemical_list: D009841:Oligonucleotides; D012313:RNA