endonuclease

Endonuclease is an enzyme that cleaves the phosphodiester bonds within a nucleic acid chain, cutting at internal sites rather than from the ends. This property distinguishes endonucleases from exonucleases, which remove nucleotides from the termini of a nucleic acid. Endonucleases can act on DNA or RNA and participate in a range of cellular processes, including DNA repair, recombination, RNA processing, and defense against pathogens, as well as in various laboratory techniques.

Endonucleases comprise several major classes. Restriction endonucleases (restriction enzymes) recognize specific DNA sequences and cleave within or near those sites, enabling DNA manipulation in cloning and genetic analysis. Structure-specific endonucleases process DNA at particular structures or damaged sites, such as flaps or junctions, and are involved in repair and replication. RNA endonucleases cleave RNA molecules internally and play roles in RNA maturation and turnover. Nucleases involved in apoptosis and inflammation, such as DNases, also function as endonucleases in cellular catabolic pathways.

Mechanistically, many endonucleases catalyze phosphodiester bond hydrolysis, often using divalent metal ions such as magnesium or manganese to activate a water molecule as a nucleophile. Others employ different catalytic strategies or operate in a metal-independent manner. Specificity ranges from precise sequence recognition to structure- or damage-guided cleavage.

Applications include tools for DNA cloning, genome editing, and molecular diagnostics. Endonucleases are also central to natural cellular processes such as DNA repair and programmed cell death, reflecting their broad importance in biology and biotechnology.