ArticleJournal of chemical theory and computation2017
Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Conformational landscape of 2-aminopurine-substituted RNA oligonucleotides from machine-learning-driven enhanced sampling.Physical chemistry chemical physics : PCCP · 2026Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations.Journal of chemical theory and computation · 2022Article
- Phospholipid Scrambling by G Protein-Coupled Receptors.Annual review of biophysics · 2022Review
- Estimating the dimensionality of the manifold underlying multi-electrode neural recordings.PLoS computational biology · 2021Article
- Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.Journal of the American Chemical Society · 2021Article
- Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis.Biophysical journal · 2019Article
- Barnaba: software for analysis of nucleic acid structures and trajectories.RNA (New York, N.Y.) · 2019Article
- Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.Journal of chemical theory and computation · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics.The Journal of chemical physics · 2018Article
- Estimating the intrinsic dimension of datasets by a minimal neighborhood information.Scientific reports · 2017Article
- Physics-based all-atom modeling of RNA energetics and structure.Wiley interdisciplinary reviews. RNA · 2017Review
- StreAM-[Formula: see text]: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs.Algorithms for molecular biology : AMB · 2017Article
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Authors and funding
7 authors.
Funding
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.
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