Stem-loop intramolecular
base pairing is a pattern that can occur in single-stranded
DNA or, more commonly, in
RNA. The structure is also known as a
hairpin or
hairpin loop. It occurs when two regions of the same strand, usually complementary in
nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA
secondary structures.