Hairpin loop

A hairpin loop or stem-loop is a structure that can occur in single-stranded DNA. In this structure, 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. The hairpin loops vary in length from 7 to 20bp. The resulting structure is a building block of many RNA secondary structures. Intrinsic termination is a mechanism in prokaryotes that causes RNA transcription to be stopped. Intrinsic terminators include hairpin loops followed by a run of U residues.