Nucleases

DNA and RNA are polymers made by linking together smaller units called nucleotides. Nucleases are enzymes that break the chemical bonds, called phosphodiester bonds, that hold the nucleotides of DNA or RNA polymers together. Enzymes that cleave the phosphodiester bonds of DNA are called deoxyribonucleases, and enzymes that cleave the phosphodiester bonds of RNA are called ribonucleases.

Nucleases can be divided into two classes, exonucleases and endonucleases, based on the positions of the cleaved bonds within the DNA or RNA polymers. The exonucleases are involved in trimming the ends of RNA and DNA polymers, cleaving the last phosphodiester bond in a chain. This cleavage results in the removal of a single nucleotide from the polymer. If the enzyme removes nucleotides from the 3′ ("three prime") end, it is referred to as a 3′ exonuclease. If cleavage is at the 5′ end, the enzyme is called a 5′ exonuclease. The endonucleases cleave phosphodiester bonds of DNA or RNA at positions other than at the end of the polymer. The cutting reactions of the endonucleases produce fragments of DNA or RNA.

Individual nucleases frequently show preferences for various structures of DNA and RNA. Some nucleases prefer single-stranded polymers, while Nucleases are distinguished by their sites of attack. Exonucleases attack the end of a chain, while endonucleases attack intern postions. In reality, the nucleotide polymer could range in length from dozens to thousands of units. others prefer double-stranded polymers. Some nucleases cleave at specific nucleotide sequences, and others cleave at positions in the polymers independent of nucleotide sequence. Exonucleases can show preference for DNA ends that are correctly base-paired or for ends that are mispaired. Some endonucleases involved in DNA repair recognize damaged nucleotides and cleave phosphodiester bonds at these sites. The preferences exhibited by the nucleases reflect the wide biological functions for these enzymes.