On a barrier height problem for RNA branching
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Publication:6430403
DOI10.4310/JOC.2023.V14.N4.A5arXiv2303.12227MaRDI QIDQ6430403FDOQ6430403
Authors: Christine E. Heitsch, Chi N. Y. Huynh, Greg Johnston 
Publication date: 21 March 2023
Abstract: 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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