User:Bnarwood/sandbox

Introduction
Exonuclease’s are enzymes diverse in terms of substrate specificity, biochemical properties, and have specialized biological functions. They work in the cellular level by repairing DNA, have roles genetic recombination, help avoid mutations, hydrolyze phosphodiester bonds in DNA from a free end and provide genome stability.

Structure
The structure of exonuclease III was created using an atomic model that was determined by fitting the amounts of three isomorphous heavy atom derivatives into an electron density map. Exonuclease III is a compact of alpha,beta-protein. There are beta-pleated sheets that are anti-parallel and have looped regions where they are linked. These are then surrounded by four alpha helices. The alpha helices form the outside layers of the fold, while the beta sheets form the hydrophobic core.

Function
Exonuclease III is an exodeoxyribonuclease that is a part of the exonuclease family. The large family includes with individuals following the species names, I, III, IV, V, VII. The purpose of the enzyme is to excise mutagenic or toxic strands of DNA. In order to carry out this function the enzyme must delete overhanging nucleotides from the overhanging 3' end of a helical DNA strand. The enzyme is able to initiate the repair process of DNA pieces using specific site directed mutagenesis. ExoIII functions by using a method that repairs DNA using AP Site bonding. This function on the AP site can also be used to cleave phosphodiester bonds in order to produce 5'- termini in the place of what used to be a 3' end. In preforming this action, the enzyme has activated a blocked end of the DNA fragment and prepared it repair.

While ExoIII has many functions it is limited in certain aspects as the enzyme is unable to act on 3' ends that contain more than 4 bases in length, ssDNA or thioester-linked nucleotides.

Regulation
In order to be used, temperature, ionic strength, template sequence and concentration of enzyme to DNA ratio has great effect on the enzyme. When used under specific, controlled conditions the reaction generally proceeds at uniform rates, this makes the enzyme yield rate predictable and ideal for reproduction of tests. ExoIII can be rendered inactive by heating the enzyme to 65° celsius for 15 minutes.

Current Studies
There are many different exonuclease’s and many are still to be discovered in bacteria, current studies are being conducted in E. coli. Many exonuclease’s fall into superfamilies with different domains of life proving that exonuclease III has shown to be ancient. Exonuclease’s evolved early in the history of life and have vital biological roles. Exonuclease III is specifically being studied for its activity and function, the current study conducted by Gachon University investigates the detection of endonuclease III using DNA-templated copper nanoclusters (DNA-CuNCs). The study showed that this enzyme is affected by the concentrations of magnesium and sodium ions.

The applications of this enzyme can produce unidirectional nested deletions, site-directed changes, production of strand-specific labelled areas for site mutagenesis, and preparation of single-stranded substrates for sequencing. This enzyme is used to prepare deletions on the ends of single stranded DNA fragments that are to be used for further study. Studies like these are important because they can be used to detect diseases and may aid in finding better treatments or cures.