A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins A phosphodiester bond is a group of strong covalent bonds between the phosphorus atom in a Phosphate group and two other Molecules over two A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information Older papers may use terms such as "polynucleotidase" or "nucleodepolymerase"^[1].

Introduction

In the late 1960's, scientists Stewart Linn and Werner Arber isolated examples of the two types of enzymes responsible for phage growth restriction in Escherichia coli (E. coli) bacteria ^[2][3]. Werner Arber (born June 3, 1929) is a Swiss Microbiologist and Geneticist. One of these enzymes added a methyl group to the DNA, generating methylated DNA, while the other cleaved unmethylated DNA at a wide variety of locations along the length of the molecule. In Chemistry, a methyl group is a Hydrophobic Alkyl Functional group named after Methane (4 DNA methylation is a type of chemical modification of DNA that can be inherited and subsequently removed without changing the original DNA sequence The first type of enzyme was called a "methylase" and the other a "restriction nuclease". A methylase is an Enzyme that attaches a Methyl group to a Molecule. A restriction enzyme (or restriction Endonuclease) is an Enzyme that cuts double-stranded DNA at specific recognition Nucleotide These enzymatic tools were important to scientists who were gathering the tools needed to "cut and paste" DNA molecules. For a pejorative meaning see Cut and paste job In Human-computer interaction, cut and paste and copy and paste offer What was then needed was a tool that would cut DNA at specific sites, rather than at random sites along the length of the molecule, so that scientists could cut DNA molecules in a predictable and reproducible way. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known

Site-specific nuclease

Structure specific nuclease

For details see flap endonuclease. Flap endonucleases (FENs also known as 5' Nucleases in older references are a class of nucleolytic Enzymes that act as both 5'-3' Exonucleases

Sequence specific nuclease

This important development came when H. O. Smith, K. W. Wilcox, and T. J. Kelley, working at Johns Hopkins University in 1968, isolated and characterized the first restriction nuclease whose functioning depended on a specific DNA nucleotide sequence. Year 1968 ( MCMLXVIII) was a Leap year starting on Monday (link will display full calendar of the Gregorian calendar. A restriction enzyme (or restriction Endonuclease) is an Enzyme that cuts double-stranded DNA at specific recognition Nucleotide Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group Working with Haemophilus influenzae bacteria, this group isolated an enzyme, called HindII, that always cut DNA molecules at a particular point within a specific sequence of six base pairs. Haemophilus influenzae, formerly called Pfeiffer's bacillus or Bacillus influenzae, is a non-motile Gram-negative Coccobacillus HO Smith KW Wilcox and TJ Kelley working at Johns Hopkins University in 1968 isolated and characterized the first Restriction nuclease whose functioning depended on

5' GTYRAC
3' CARYTG

5' GTY  RAC
3' CAR  YTG

They found that the HindII enzyme always cuts directly in the center of this sequence. HO Smith KW Wilcox and TJ Kelley working at Johns Hopkins University in 1968 isolated and characterized the first Restriction nuclease whose functioning depended on Haemophilus influenzae, formerly called Pfeiffer's bacillus or Bacillus influenzae, is a non-motile Gram-negative Coccobacillus R is the eighteenth letter of the modern Latin alphabet. Its name in English is spelled ar (ɑr pronounced or) Adenine is a Purine with a variety of roles in Biochemistry including Cellular respiration, in the form of both the energy-rich Adenosine Guanine is one of the five main Nucleobases found in the Nucleic acids DNA and RNA, the others being Adenine, Cytosine, The letter Y is the twenty-fifth letter in the modern Latin alphabet. Wherever this particular sequence of six base pairs occurs unmodified in a DNA molecule, HindII will cleave both DNA backbones between the 3rd and 4th base pairs of the sequence. Moreover, HindII will only cleave a DNA molecule at this particular site. For this reason, this specific base sequence is known as the "recognition sequence" for HindII. The recognition sequence, also referred to as Recognition site, of any DNA-binding protein motif that exhibits binding specificity refers to the DNA sequence

HindII is only one example of the class of enzymes known as restriction nucleases. In fact, more than 900 restriction enzymes, some sequence specific and some not, have been isolated from over 230 strains of bacteria since the initial discovery of HindII. These restriction enzymes generally have names that reflect their origin--The first letter of the name comes from the genus and the second two letters come from the species of the prokaryotic cell from which they were isolated. For example EcoRI comes from Escherichia coli RY13 bacteria, while HindII comes from Haemophilus influenzae strain Rd. ECOR1_Crystal_Structurershpng|thumb|EcoRI crystal structure]] Eco RI (pronounced "eco R one" is a Nuclease enzyme isolated from certain strains of Haemophilus influenzae, formerly called Pfeiffer's bacillus or Bacillus influenzae, is a non-motile Gram-negative Coccobacillus Numbers following the nuclease names indicate the order in which the enzymes were isolated from single strains of bacteria: EcoRI, EcoRII. ECOR1_Crystal_Structurershpng|thumb|EcoRI crystal structure]] Eco RI (pronounced "eco R one" is a Nuclease enzyme isolated from certain strains of Restriction endonuclease (REase EcoRII (pronounced "eco R two" is an Enzyme of Restriction modification system (RM naturally found in Nucleases are further described by addition of the prefix "endo" or "exo" to the name: The term "endonuclease" applies to nucleases that break nucleic acid chains somewhere in the interior, rather than at the ends, of the molecule. Endonucleases are Enzymes that cleave the Phosphodiester bond within a Polynucleotide chain in contrast to Exonucleases which cleave Phosphodiester A nuclease that functions by removing nucleotides from the ends of the DNA molecule is called an exonuclease. Exonucleases are enzymes (found as individual enzymes or as parts of larger enzyme complexes that cleave Nucleotides one at a time from an end of a polynucleotide chain

Endonucleases and DNA fragments

A restriction endonuclease functions by "scanning" the length of a DNA molecule. Once it encounters its particular specific recognition sequence, it will bond to the DNA molecule and makes one cut in each of the two sugar-phosphate backbones of the double helix. In Geometry a double helix (plural helices) typically consists of two congruent helices with the same axis differing by a translation The positions of these two cuts, both in relation to each other, and to the recognition sequence itself, are determined by the identity of the restriction endonuclease used to cleave the molecule in the first place. Different endonucleases yield different sets of cuts, but one endonuclease will always cut a particular base sequence the same way, no matter what DNA molecule it is acting on. Once the cuts have been made, the DNA molecule will break into fragments.

Endonucleases and sticky ends

Not all restriction endonucleases cut symmetrically and leave blunt ends like HindII described above. Many endonucleases cleave the DNA backbones in positions that are not directly opposite each other. For example, the nuclease EcoRI has the following recognition sequence:

5'GAATTC
3'CTTAAG

5'---G     AATTC---3'
3'---CTTAA     G---5'

When the enzyme encounters this sequence, it cleaves each backbone between the G and the closest A base residues. ECOR1_Crystal_Structurershpng|thumb|EcoRI crystal structure]] Eco RI (pronounced "eco R one" is a Nuclease enzyme isolated from certain strains of Once the cuts have been made, the resulting fragments are held together only by the relatively weak hydrogen bonds that hold the complementary bases to each other. The weakness of these bonds allows the DNA fragments to separate from one each other. Each resulting fragment has a protruding 5' end composed of unpaired bases. Other enzymes create cuts in the DNA backbone which result in protruding 3' ends. Protruding ends--both 3' and 5'-- are sometimes called "sticky ends" because they tend to bond with complementary sequences of bases. DNA end or sticky end refers to the properties of the end of a Molecule of DNA. In other words, if an unpaired length of bases (5' A A T T 3') encounters another unpaired length with the sequence (3' T T A A 5') they will bond to each other--they are "sticky" for each other. Ligase enzyme is then used to join the phosphate backbones of the two molecules. In Biochemistry, a ligase (from the Latin verb ligāre &mdash "to bind" or "to glue together" is an Enzyme that can catalyse The cellular origin, or even the species origin, of the sticky ends does not affect their stickiness. Any pair of complementary sequences will tend to bond, even if one of the sequences comes from a length of human DNA, and the other comes from a length of bacterial DNA. In fact, it is this quality of stickiness that allows production of recombinant DNA molecules, molecules which are composed of DNA from different sources, and which has given birth to the genetic engineering technology!

Common examples

• Micrococcal nuclease
• S1 nuclease
• P1 nuclease
• HindIII

External links

• Examples of Restriction Enzymes Chart
• Restriction Enzyme Action of EcoRI
• Enzyme glossary
• Nucleases (Main source of the page...)

1. ^ Avery, O. Genetic engineering, Recombinant DNA technology, genetic modification/manipulation (GM and gene splicing are terms that apply to the direct Micrococcal Nuclease (S7 Nuclease or MNase is an Endo - Exonuclease that preferentially digests Single-stranded Nucleic acids. S1 nuclease is an Endonuclease that is active against single-stranded DNA and RNA molecules P1 nuclease is a Nuclease that works on single-stranded DNA as well as RNA Hin dIII is a type II site-specific deoxyribonuclease Restriction enzyme isolated from ''Haemophilus influenzae'' that cleaves the palindromic DNA sequence T. , MacLeod, C. M. , McCarty, M. (1944). Studies on the chemical nature of the substance inducing transformation of pneumococcal types: Induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus type III. J. Exp. Med. 79: 137-158.
2. ^ Linn S. , Arber, W. (1968). Host specificity of DNA produced by Escherichia coli, X. In vitro restriction of phage fd replicative form. Proc. Natl. Acad. Sci. USA. 59:1300-1306
3. ^ Arber, W. , Linn S. (1969) DNA modification and restriction. Annu. Rev. Biochem. 38:467-500