Nucleases

There are two different mechanisms used by various nucleases to cleave the chemical bonds of the DNA or RNA polymer. The most common mechanism is one in which a water molecule is used to break the phosphodiester bond. This is called a hydrolysis reaction. Under most conditions the P-O (phosphorous and oxygen) bond of the DNA or RNA polymer is very stable, and the H₂O molecule is not usually very reactive. However, nucleases that use the hydrolysis mechanism make the H₂O reactive by removing one of the hydrogens to generate a highly reactive OH^- (hydroxyl). The negatively charged OH^- can then attack the P-O bond to cleave the polymer. An alternative mechanism used by some DNA repair endonucleases involves the initial cleavage of a C-O (carbon and oxygen) bond and subsequent P-O bond cleavage. This is called a lyase reaction and does not involve water.