Pseudoknots Nucleic acid secondary structure

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an rna pseudoknot structure. example, rna component of human telomerase.


a pseudoknot nucleic acid secondary structure containing @ least 2 stem-loop structures in half of 1 stem intercalated between 2 halves of stem. pseudoknots fold knot-shaped three-dimensional conformations not true topological knots. base pairing in pseudoknots not nested; is, base pairs occur overlap 1 in sequence position. makes presence of general pseudoknots in nucleic acid sequences impossible predict standard method of dynamic programming, uses recursive scoring system identify paired stems , consequently cannot detect non-nested base pairs common algorithms. however, limited subclasses of pseudoknots can predicted using modified dynamic programs. newer structure prediction techniques such stochastic context-free grammars unable consider pseudoknots.


pseudoknots can form variety of structures catalytic activity , several important biological processes rely on rna molecules form pseudoknots. example, rna component of human telomerase contains pseudoknot critical activity. hepatitis delta virus ribozyme known example of catalytic rna pseudoknot in active site. though dna can form pseudoknots, not present in standard physiological conditions.








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