endonucleolytic

Endonucleolytic describes the action of endonucleases, enzymes that cleave phosphodiester bonds within a nucleic acid strand rather than at its ends. This internal cleavage produces fragments with new 5' and 3' ends and contrasts with exonucleolytic activity, which removes nucleotides from the ends of a molecule.

In biology, endonucleases participate in a variety of processes, including DNA repair, recombination, and RNA processing. In DNA repair, certain endonucleases introduce nicks or incisions near damaged sites to enable downstream processing; examples include AP endonucleases that cleave at abasic sites and structure-specific nucleases such as XPG and ERCC1-XPF involved in nucleotide excision repair. In molecular biology, restriction endonucleases, such as many Type II enzymes, recognize specific DNA sequences and cleave at defined sites, a foundation for cloning and genetic analysis. Non-specific endonucleases like DNase I cleave DNA without a fixed sequence and help in DNA turnover and degradation.

In RNA metabolism, endonucleolytic activity is also essential. Endoribonucleases such as RNase A and RNase H cleave RNA or RNA–DNA hybrids, and endonucleolytic steps are involved in RNA maturation and intron processing. Some RNA-catalyzed reactions involve ribozymes with endonucleolytic activity, including self-splicing introns.

Biochemically, many endonucleases require divalent metal ions for catalysis and employ mechanisms that in many enzymes involve two metal ions coordinating water nucleophiles to cleave the phosphodiester backbone. Endonucleolytic activity is a central concept across genetics, molecular biology, and biomedicine, reflecting internal cleavage rather than processing from molecule ends.