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Asymmetry in RNA pseudoknots: observation and theory

Aalberts, Daniel P. and Hodas, Nathan O. (2005) Asymmetry in RNA pseudoknots: observation and theory. Nucleic Acids Research, 33 (7). pp. 2210-2214. ISSN 0305-1048.

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RNA can fold into a topological structure called a pseudoknot, composed of non-nested double-stranded stems connected by single-stranded loops. Our examination of the PseudoBase database of pseudoknotted RNA structures reveals asymmetries in the stem and loop lengths and provocative composition differences between the loops. By taking into account differences between major and minor grooves of the RNA double helix, we explain much of the asymmetry with a simple polymer physics model and statistical mechanical theory, with only one adjustable parameter.

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Additional Information:© The Author 2005. Published by Oxford University Press. All rights reserved The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact Received January 16, 2005. Revised March 5, 2005. Accepted March 25, 2005. The authors thank Jesse Dill for noticing the duplications in PseudoBase and assisting with Table 1. This work was supported by National Institutes of Health grant GM068485. Funding to pay the Open Access publication charges for this article was provided by Williams College. Conflict of interest statement. None declared.
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Deposited On:27 Sep 2005
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