RNAHairpins

RNA hairpins are common RNA secondary structures characterized by an intramolecular base pairing that forms a stem of paired nucleotides terminated by a loop of unpaired nucleotides. The paired region, or stem, typically consists of several to more than a dozen base pairs, while the loop is usually a short sequence of unpaired nucleotides. The arrangement is also referred to as a stem-loop.

Hairpins arise when a single-stranded RNA contains complementary sequences that can fold back on themselves. The stability of a hairpin depends on stem length, GC content, loop size, and the presence of mismatches or bulges. Tetraloops and certain loop motifs can confer additional stability and influence recognition by proteins.

RNA hairpins occur in many RNA molecules and serve diverse roles. In mRNA, hairpins in untranslated regions can regulate translation by affecting ribosome access or mRNA stability. In transfer RNA and ribosomal RNA, hairpin elements contribute to proper folding and function. Hairpin structures also predominate in the processing of microRNA precursors (pre-miRNA), which are cleaved to yield mature miRNAs. In riboswitches and aptamers, hairpin motifs participate in ligand sensing and binding.

From a research perspective, hairpins are studied by experimental probing methods such as chemical modification or enzymatic probing and by computational prediction tools that minimize free energy to predict secondary structure (for example, Mfold, RNAfold). Pseudoknots and other higher-order interactions can build on hairpin stems, creating more complex topologies.

Overall, RNA hairpins are fundamental motifs in RNA structure and function, influencing folding, stability, and molecular interactions across diverse RNA families and applications in biotechnology and nanotechnology.