nuclease

A nuclease is an enzyme that cleaves nucleic acids by hydrolyzing phosphodiester bonds within DNA or RNA. They vary in substrate specificity (DNA, RNA, or both) and in the manner of cleavage: endonucleases cut within the nucleic acid chain, while exonucleases remove nucleotides from one or both ends of a polynucleotide.

Endonucleases include restriction enzymes, which are sequence-specific DNA endonucleases used in molecular cloning; DNases that cut DNA non-specifically; RNases such as RNase A that cleave RNA at the phosphodiester backbone; and RNase H that degrades the RNA strand of RNA–DNA hybrids. Some enzymes act on both DNA and RNA. Exonucleases, such as Exonuclease I and Exonuclease III, remove nucleotides from chain ends, generating defined products.

Mechanistically, many nucleases require divalent metal ions, commonly Mg2+ or Mn2+, to activate water or stabilize charged intermediates, though some, like RNase A, use a catalytic triad of amino acids independent of metal ions. Biologically, nucleases participate in DNA replication, repair, recombination, RNA processing, and degradation, and they form part of host defense and programmed cell death pathways. In biotechnology, nucleases are used to remove nucleic acids from preparations, to map cleavage sites, and to cut DNA at defined locations with restriction enzymes.