= RNA hairpin
{c}
An \b[RNA hairpin] is a <stem-loop> formed when two regions of one <RNA> strand make <base pairs>, leaving an intervening unpaired loop. It is a local <RNA secondary structure> motif: covalent continuity runs through the loop while pairing brings separated parts of the sequence together. The motif does not require a second RNA molecule and need not describe the fold of the whole RNA.
For an original sequence illustration, consider `5'-GGCCUUCGGGCC-3'`. Pair positions1–12,2–11,3–10 and4–9. The four pairs are G–C, G–C, C–G and C–G, leaving positions5–8, `UUCG`, as a four-nucleotide loop. Thus four pairs use eight <nucleotides>, and the loop supplies four more, giving twelve in total. The corresponding illustrative dot-bracket notation is `((((....))))`. This proposed pairing is a structural example, not an experimental demonstration that an isolated sequence occupies only that conformation.
A four-residue loop is an <RNA tetraloop>. Both the paired stem and the loop sequence influence stability. In a 2010 experiment, researchers optically melted24 stem–loop sequences containing common tetraloops and determined their thermodynamic parameters. Measuring <absorbance> as <temperature> changes connects sequence differences to an experimental folding transition rather than inferring stability from the number of pairs alone.<Thermodynamic characterization of naturally occurring RNA tetraloops by Justin P. Sheehy and others>[Abstract and Materials and Methods: optical melting and thermodynamic analysis of24 sequences.]{ref}
A two-state model makes <RNA hairpin melting> quantitative. If only folded F and unfolded U states are allowed, set $K=[F]/[U]=\exp[-\Delta G/(RT)]$, with $\Delta G=G_F-G_U$ and $R$ the <molar gas constant>. The folded fraction is $K/(1+K)$. A stipulated $\Delta G=-RT\ln4$ gives $K=4$ and folded fraction $0.8$; equal free energies give $0.5$. These model fractions are not the paper's measurements. Alternative folds, non-two-state transitions and assay conditions can require a richer interpretation.
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