hairpin loop (mRNA)

A hairpin loop is an unpaired loop of messenger RNA (mRNA) that is created when an mRNA strand folds and forms base pairs with another section of the same strand. The resulting structure looks like a loop or a U-shape.

Hairpins are a common type of secondary structure in RNA molecules. In RNA, the secondary structure is the basic shape that the sequence of A, C, U, and G nucleotides form after they are linked in series, such a folding or curling of the nucleic acid strand. mRNA hairpins can be formed when two complementary sequences in a single mRNA molecule meet and bind together, after a folding or wrinkling of the molecule. Hairpin loops can also form in DNA molecules, but are most commonly observed in mRNA.

There are many instances of the hairpin loop phenomenon among nucleic acid strands. One example of a hairpin loop is the termination sequence for transcription in some prokaryotes. Once a polymerase meets this loop, it falls of and transcription ends. Another more general example is tRNA, a central player in protein synthesis, which is partially formed by hairpin loops. The tRNA molecule actually contains three hairpin loops that form the shape of a three-leafed clover. One of these hairpin loops contains a sequence called the anticodon, which recognizes and decodes the mRNA molecule three nucleotides (one codon) at a time during translation. This clover-leaf structure supports the eventual connection between every codon, anti-codon and amino acid.