endonucleases

Endonucleases are nucleases that cleave phosphodiester bonds within a nucleic acid chain, as opposed to exonucleases which trim nucleotides from the ends. They act on DNA or RNA and can be sequence-specific or nonspecific. Cleavage can produce blunt ends or cohesive (sticky) ends, and may introduce single-strand nicks or double-strand breaks.

In DNA, restriction enzymes are a prominent class of sequence-specific endonucleases that recognize short motifs and cut within or near those sites. Other DNA endonucleases such as DNase I are nonspecific and hydrolyze DNA without a fixed recognition sequence. Some endonucleases, called nicking endonucleases, cleave only one strand. In genome editing, engineered endonucleases such as zinc finger nucleases, TALENs, and CRISPR-Cas systems introduce targeted double-strand breaks to enable modification.

In RNA, endonucleases cleave internal phosphodiester bonds of RNA. RNase A family enzymes and RNase H are examples; RNases play roles in RNA maturation, turnover, and defense.

Mechanistically, many endonucleases require divalent metal ions (commonly Mg2+ or Mn2+) and employ catalytic strategies that involve nucleophilic attack on the phosphate backbone. The products may include 3' hydroxyl and 5' phosphate ends.

Applications include molecular cloning, DNA footprinting, and genome editing; sample preparation uses DNase to remove DNA, while restriction enzymes enable mapping and construction of recombinant DNA. In biology, endonucleases participate in DNA replication, repair, recombination, and programmed cell death.