- Pseudoknot
A pseudoknot is an RNA tertiary structure containing two
stem-loop structures in which the first stem's loop forms part of the second stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in1982 . Staple DW, Butcher SE. (2005). "Pseudoknots: RNA Structures with Diverse Functions". "PLoS Biology " 3(6). 2005 [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030213 Online Article]Open access publication] Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots.Prediction and identification
The
base pair ing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of pseudoknots in RNA sequences impossible to predict by the standard method ofdynamic programming , which uses a recursive scoring system to identify paired stems and consequently cannot detect non-nested base pairs under most circumstances, or by the newer method ofstochastic context-free grammar s. Thus popular secondary structure prediction methods like [http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html Mfold] and [http://www.daimi.au.dk/~compbio/rnafold/ Pfold] will not predict pseudoknot structures present in a query sequence; they will only identify the more stable of the two pseudoknot stems.It is possible to contrive situations in which dynamic programming-like methods can identify pseudoknots, but these methods are not general and are extremely inefficient. Rivas E, Eddy S. (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". "J Mol Biol" 285(5): 2053–2068.] The general problem of pseudoknot prediction has been shown to be
NP-complete . Lyngsø RB, Pedersen CN. (2000). "RNA pseudoknot prediction in energy-based models". "J Comput Biol" 7(3–4): 409–427.]Biological significance
Several important biological processes rely on RNA molecules that form pseudoknots. For example, the RNA component of human
telomerase contains a pseudoknot that is critical for activity.References
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