Endonucleolytically

Endonucleolytically is an adverb used to describe enzymatic action that cleaves phosphodiester bonds within a nucleic acid strand, generating internal breaks rather than trimming from the ends. This mode of action is carried out by endonucleases, a diverse class of enzymes that act on DNA or RNA molecules.

Endonucleolytic cleavage can be site-specific or non-specific. Site-specific endonucleases, such as restriction enzymes, recognize defined sequences and cut within or near those sites. Non-specific endonucleases, including DNase I, RNase A, and RNase H, cleave internal bonds without strict sequence requirements. Many endonucleases require cofactors such as divalent metal ions (for example Mg2+ or Mn2+) to activate water molecules for the hydrolysis of phosphodiester bonds; others function by different catalytic mechanisms.

Biological roles include DNA repair and recombination, RNA processing, and defense against pathogens. Examples include restriction enzymes used in molecular cloning, nucleotide excision repair nucleases like XPG and FEN1, and programmable endonucleases such as those used in genome editing (e.g., Cas9) which introduce double-strand breaks endonucleolytically at targeted genomic loci. In RNA biology, endonucleolytic processing by ribonucleases helps generate mature RNAs.

Endonucleolytically contrasts with exonucleolytic activity, which removes nucleotides from ends of nucleic acids. The term is common in biochemistry and molecular biology when describing the mode of action of nucleases and nucleic acid-processing enzymes.