Mathematical and Biological Modelling of RNA Secondary Structure and Its Effects on Gene Expression

Hughes, T.A.; McElwaine, J.N.

Abstract

Secondary structures within the 5′ untranslated regions of messenger RNAs can have profound effects on the efficiency of translation of their messages and thereby on gene expression. Consequently they can act as important regulatory motifs in both physiological and pathological settings. Current approaches to predicting the secondary structure of these RNA sequences find the structure with the global-minimum free energy. However, since RNA folds progressively from the 5′ end when synthesised or released from the translational machinery, this may not be the most probable structure. We discuss secondary structure prediction based on local-minimisation of free energy with thermodynamic fluctuations as nucleotides are added to the 3′ end and show that these can result in different secondary structures. We also discuss approaches for studying the extent of the translational inhibition specified by structures within the 5′ untranslated region.

Citation

Hughes, T., & McElwaine, J. (2006). Mathematical and Biological Modelling of RNA Secondary Structure and Its Effects on Gene Expression. Computational and mathematical methods in medicine, 7(1), 37-43. https://doi.org/10.1080/10273660600906416

• Journal Article Type: Article
• Acceptance Date: Jun 23, 2006
• Publication Date: Mar 1, 2006
• Deposit Date: May 23, 2013
• Publicly Available Date: Sep 17, 2015
• Journal: Computational and Mathematical Methods in Medicine
• Print ISSN: 1748-670X
• Electronic ISSN: 1748-6718
• Publisher: Taylor and Francis
• Peer Reviewed: Peer Reviewed
• Volume: 7
• Issue: 1
• Pages: 37-43
• DOI: https://doi.org/10.1080/10273660600906416
• Keywords: UTR, RNA folding, Dynamic programming, Translational regulation.
• Public URL: https://durham-repository.worktribe.com/output/1454861