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RNA secondary structure

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Secondary structure of a ciliate telomerase RNA

The secondary structure of a RNA refers to the basepairing interactions within a single molecule or set of interacting molecules of RNA. Some nucleotides of a RNA molecule can pair with each other via hydrogen bonds and form a stable structure.[1]

Types of RNA secondary structural motifs

Hairpin loop

Main article: Hairpin loop

A hairpin loop is a structure in which the pairing of intramolecular base pairs occurs. It takes place when two regions of the same molecule, usually forming a palindrome, form pairs to constitute a double helix ending in a loop unpaired.

Internal loop


Bulge loop

External Loop


  1. Ye, Yuzhen; Tang, Haixu (2008). "2-Dynamic Programming Algorithms For Biological Sequence and Structure Comparison". In Mandoiu, Ion I.; Zelikovsky, Alexander. Bioinformatics Algorithms: Techniques and Applications. New Jersey: John Wiley & Sons. p. 19-20.