The Multiscale Future of RNA Modeling

Šulc, Petr

doi:10.1016/j.bpj.2020.08.026

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“…one where each step increases the number of edges from the final tree by at least one. The edges incident on a leaf are the crucial first steps in such a path, and indeed the stability of RNA hairpins is a critical component of biological function [4] and modeling accuracy [28]. Hence, a suitable model for hairpin rearrangements [29] may be an important component of a higher resolution barrier height analysis.…”

Section: Introductionmentioning

confidence: 99%

On a barrier height problem for RNA branching

Heitsch¹,

Huynh²,

Johnston³

2023

Journal of Combinatorics

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The branching of an RNA molecule is an important structural characteristic yet difficult to predict correctly, especially for longer sequences. Using plane trees as a combinatorial model for RNA folding, we consider the thermodynamic cost, known as the barrier height, of transitioning between branching configurations. Using branching skew as a coarse energy approximation, we characterize various types of paths in the discrete configuration landscape. In particular, we give sufficient conditions for a path to have both minimal length and minimal branching skew. The proofs offer some biological insights, notably the potential importance of both hairpin stability and domain architecture to higher resolution RNA barrier height analyses.

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Section: Introductionmentioning

confidence: 99%