Stem-loop

A stem-loop, also known as a hairpin loop, is a secondary structure that can form within single-stranded RNA or DNA molecules. It is characterized by a region of the nucleotide sequence forming a double helix (the stem) that is capped by a loop of unpaired nucleotides.

The stem is formed by complementary base pairing between nucleotides located on the same strand. The base pairing follows the standard Watson-Crick rules (adenine with uracil/thymine, and guanine with cytosine), although wobble base pairs (e.g., guanine-uracil) can also contribute to the stem's stability. The length of the stem, and therefore the number of base pairs it contains, can vary. Longer stems are generally more stable than shorter stems.

The loop is formed by the nucleotides at the end of the stem that are not involved in base pairing. The size of the loop can also vary, but loops typically consist of several unpaired nucleotides. The sequence and size of the loop can influence the stability and function of the stem-loop structure.

Stem-loop structures are important in a variety of biological processes. In RNA, they can act as recognition sites for RNA-binding proteins, play a role in transcriptional termination (as in rho-independent termination in prokaryotes), influence mRNA stability and translation, and contribute to the structure and function of ribozymes and non-coding RNAs. In DNA, they can be involved in replication and DNA repair processes.