Nucleases are a type of enzyme that can cut the phosphodiester bonds between nucleotides in nucleic acids, like DNA.
The primary purposes of nucleases in DNA are maintenance and repair. Cells use nucleases to make cuts in defecting pieces of DNA, remove the damaged elements, then to allow the cell to insert fresh DNA into the gap.
There are two main types of nucleases based on how they work. Endonucleases, Endonucleases work by targeting the middle of a target molecule. They go straight to the site where they are needed and begin performing work. Exonucleases,Exonucleases work from either end of a nucleic acid.
Nucleases are typically classified as being members of folding families. Their primary structure is not well-conserved, even at active sites.
Researchers have discovered that nucleases play several vital roles in nature, particularly in the realm of DNA repair.
DNA replication is a process that is prone to errors. Despite aeons of evolution, the DNA replication process is not perfect. Environmental conditions in the cell can lead to the generation of mutations - something that evolution depends on for its action in populations of species.
Nucleases find sites where DNA is damaged, “cleave” the existing DNA from the molecule supporting it and then make way for other enzymes to insert new fragments with the correct information.
Nucleases are often also involved in replication proofreading. The basic idea behind this is simple. The nuclease checks that the cell has copied genetic material correctly before dividing. The nuclease removes incorrect nucleotides from the sequences, leaving only those that are exact copies intact.
Nucleases are also involved in base excision repair. AP site formation often happens in dsDNA. Special AP endonucleases remove AP sites by making single-strand breaks around the site.
Nucleases are also implicated in double-strand break repairs. Double strand breaks in DNA happen all the time in cells in living organisms. Ionizing radiation from the universe or x-ray machines penetrates cells, damages molecules, and can sheer DNA in half. Double strand breaks can also happen for reasons the body intends too, such as in meiosis and VDJ recombination.
In both cases, the cell needs a system that can stitch strand breaks back together again. This is the job of nucleases like Mre11, which works together with Rad50.
For a nuclease to repair a section of DNA, it first has to be able to scan it for breaks. Researchers believe that nucleic acid molecules associated with nucleases work using an active recognition process.
Nucleases have the ability to scan DNA for broken target sequences or damage. Nonspecific nucleases do this by travelling up and down the DNA until they find something that looks like a defective sequence which they can repair. Specific nucleases, on the other hand, bind with individual pockets on DNA in a unique way and draws DNA into a deep groove of its DNA-binding domain. In a sense, therefore, these nucleases are sequence-specific and only work on a small subset of the genome.