# The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models

Source: [The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models](<https://www.sota2.com/research/paper/68fa398d1e209131ce8c3903>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-24T23:35:14.478Z

Authors: Giovanni Pinamonti, Fabian Paul, Frank No\\'e, Alex Rodriguez, Giovanni Bussi

Published: 2018-11-29T13:54:48.000Z

## Abstract

The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA fraying and its sequence and direction dependence. In particular, we first introduce a method for determining biomolecular dynamics employing core-set Markov state models constructed using an advanced clustering technique. The method is validated on previously reported simulations. We then use the method to analyze extensive trajectories for four different RNA model duplexes. Results obtained using D. E. Shaw research and AMBER force fields are compared and discussed in detail, and show a non-trivial interplay between the stability of intermediate states and the overall fraying kinetics.

## Recorded benchmark results

A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage.

## Original sources and implementation

[Original paper](<https://arxiv.org/abs/1811.12144>)

[PDF](<https://arxiv.org/pdf/1811.12144.pdf>)