Kissing hairpins are formed when a single strand of nucleic acid complements with itself creating loops of RNA in the form of a hairpin. When two hairpins come into contact with each other in vivo, the complementary bases of the two strands form up and begin to unwind the hairpins until a double-stranded RNA (dsRNA) complex is formed or the complex unwinds back to two separate strands due to mismatches in the hairpins. The secondary structure of the hairpin prior to kissing allows for a stable structure with a relatively fixed change in energy. The purpose of these structures is a balancing of stability of the hairpin loop vs binding strength with a complementary strand. Too strong an initial binding to a bad location and the strands will not unwind quickly enough; too weak an initial binding and the strands will never fully form the desired complex. These hairpin structures allow for the exposure of enough bases to provide a strong enough check on the initial binding and a weak enough internal binding to allow the unfolding once a favorable match has been found.
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