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[21] RNA pseudoknot: Structure, detection, and prediction

1989; Academic Press; Linguagem: Inglês

10.1016/0076-6879(89)80107-7

1557-7988

Cornelis W.A. Pleij, Ludo Van Den Bosch,

RNA Research and Splicing

RNA pseudoknots are structural elements of the RNA architecture. A basic feature of the secondary structure of RNA is the classical stem–loop structure. Pseudoknots arise on base pairing of the single stranded loops enclosed by these stems, with complementary unpaired regions elsewhere in the RNA chain. Beside double-helical or stem regions and hairpins, which result from intramolecular base pairing, interior and bulge loops, bifurcations, and bifurcation loops can be recognized. The chapter describes the characteristics of a simple type of pseudoknot. This type of pseudoknot has a widespread occurrence and has a coaxial stacking. It should be emphasized that this coaxial stacking, though strongly suggested by the models of the tRNA-like structures, is an assumption for which direct proof remains unavailable. The minimal number of base pairs in each stem is found presently to be three base pairs.