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Mathematical and biological modelling of RNA secondary structure and its effects on gene expression.

Hughes, T. A. and McElwaine, J. N. (2006) 'Mathematical and biological modelling of RNA secondary structure and its effects on gene expression.', Computational and mathematical methods in medicine., 7 (1). pp. 37-43.

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.

Item Type:Article
Keywords:UTR, RNA folding, Dynamic programming, Translational regulation.
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Status:Peer-reviewed
Publisher Web site:http://dx.doi.org/10.1080/10273660600906416
Publisher statement:© 2006 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Date accepted:23 June 2006
Date deposited:17 September 2015
Date of first online publication:March 2006
Date first made open access:No date available

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