2005/07/31 by Wilfred Ndifon · 1 citation
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Evolution and Genetic Dynamics #RNA Research and Splicing #RNA and protein synthesis mechanisms #nlin.AO #q-bio.BM
paper · pdf · doi:10.1016/j.biosystems.2005.08.004
23 pages, 4 figures, 2 tables, to be published in BioSystems (Note: updated 2 references)
arxiv created 2005/08/14 · openalex publication_date 2005/09/20 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base pairs engage in local stacking interactions that determine the probabilities (or fitnesses) of possible SRs. Meanwhile, selection operates at the level of SRs; an autonomous stochastic process periodically (i.e., from one time step to another) selects a subset of possible SRs for realization based on the fitnesses of the SRs. Using examples based on selected natural and synthetic RNAs, the model is shown to qualitatively reproduce characteristic (nonlinear) RNA folding dynamics such as the attainment by RNAs of alternative stable states. Possible applications of the model to the analysis of properties of fitness landscapes, and of the RNA sequence to structure mapping are discussed.