Asymmetry in RNA pseudoknots: observation and theory
Open Access
- 1 January 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 33 (7) , 2210-2214
- https://doi.org/10.1093/nar/gki508
Abstract
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.Keywords
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