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Computational and Mathematical Methods in Medicine
Volume 7, Issue 1, Pages 37-43

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

1Pathology and Tumour Biology Section, Level 4 Leeds Institute for Molecular Medicine, St James's University Hospital, Leeds University, Leeds LS9 7TF, UK
2Department of Applied Maths and Theoretical Physics, Centre for Mathematical Sciences, Cambridge University, Wilberforce Road, Cambridge CB3 0WA, UK

Received 26 May 2006; Revised 12 June 2006; Accepted 23 June 2006

Copyright © 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.


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.