Exonucleases

Exonucleases are enzymes that remove nucleotides one by one from the ends of polynucleotide chains, releasing nucleoside monophosphates as products. They differ from endonucleases, which cleave phosphodiester bonds within a molecule rather than at the ends. Exonucleases act on RNA and/or DNA substrates and can process single-stranded or double-stranded nucleic acids, depending on the enzyme.

Directionality is a key feature. 3' to 5' exonucleases remove nucleotides from the 3' end toward the 5' end, while 5' to 3' exonucleases remove from the 5' end toward the 3' end. Some exonucleases have preferences for particular structures or substrates, such as single-stranded regions, double-stranded DNA, or RNA, and their activity can be influenced by cofactors and cellular conditions.

Biological roles include proofreading during DNA replication, processing DNA during repair pathways, trimming RNA during turnover and maturation, and the removal of primer or adapter sequences in various replication and repair contexts. Exonucleases also participate in RNA quality control and degradation of defective nucleic acids.

Mechanistically, many exonucleases require divalent metal ions (commonly magnesium or manganese) at their active sites and catalyze hydrolysis of phosphodiester bonds. They vary in processivity and regulation, and can function as part of larger nucleic acid-processing complexes.

In biotechnology and research, exonucleases are used to modify or clean up nucleic acids, generate defined overhangs, or remove unwanted nucleic acids from samples, highlighting their practical utility alongside their cellular roles.