kissingloop

Kissing loop is an RNA structural motif in which two hairpin loop regions interact through base pairing between complementary nucleotides within the loops. The interaction is typically inter-molecular, pairing nucleotides in one loop with those in another loop, though it can occur between loops within the same RNA molecule.

Mechanism: A short stretch of base pairs forms initially, often aided by cations and, in some systems, RNA chaperone proteins such as nucleocapsid proteins. If stable, the kissing interaction can rearrange into a more extended duplex via strand displacement, creating a larger helix that connects the two hairpins; in some contexts the kissing loop is a metastable intermediate that can be converted into the mature structure by cellular factors.

Biological context: The best-known example is the dimerization initiation signal loop in the HIV-1 genome, where two copies of the hairpin loop containing a palindromic sequence engage to form kissing dimers that can mature into a longer intermolecular duplex. Kissing loops are also found in other retroviruses, plasmids, and RNA regulatory elements, where loop-loop interactions influence RNA folding, genome packaging, or gene expression.

Structural and experimental notes: Kissing loop interactions are studied by NMR, X-ray crystallography, and cryo-electron microscopy, often inferred from mutational analyses. The stability depends on loop length, sequence complementarity, ionic conditions, and the presence of RNA-binding proteins.

Applications: In RNA nanotechnology, kissing-loop motifs are used to assemble multistranded RNA nanoparticles and regulate assembly pathways.