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Nucleic Acids Research 2005 33(7):2210-2214; doi:10.1093/nar/gki508
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Published online 14 April 2005

© 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 journals.permissions{at}oupjournals.org

Article

Asymmetry in RNA pseudoknots: observation and theory

Daniel P. Aalberts* and Nathan O. Hodas

Physics Department, Williams College Williamstown, MA 01267, USA

*To whom correspondence should be addressed. Tel: +1 413 597 3520; Fax: +1 413 597 4116; Email: aalberts{at}williams.edu

Received January 16, 2005. Revised March 5, 2005. Accepted March 25, 2005.

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.

Present address: Nathan O. Hodas, Physics Department, California Institute of Technology, Pasadena, CA 91125, USA


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