Restriction sites, or restriction recognition sites, are located on a
DNA molecule containing specific (4-8 base pairs in length) sequences of
nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
s, which are recognized by
restriction enzyme
A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...
s. These are generally
palindromic sequence
A palindromic sequence is a nucleic acid sequence in a double-stranded DNA or RNA molecule whereby reading in a certain direction (e.g. 5' to 3') on one strand is identical to the sequence in the same direction (e.g. 5' to 3') on the comple ...
s
(because restriction enzymes usually bind as
homodimer
In biochemistry, a protein dimer is a macromolecular complex formed by two protein monomers, or single proteins, which are usually non-covalently bound. Many macromolecules, such as proteins or nucleic acids, form dimers. The word ''dimer'' ha ...
s), and a particular restriction enzyme may cut the sequence between two nucleotides within its recognition site, or somewhere nearby.
Function
For example, the common restriction enzyme
EcoRI
''Eco''RI (pronounced "eco R one") is a restriction endonuclease enzyme isolated from species '' E. coli.'' It is a restriction enzyme that cleaves DNA double helices into fragments at specific sites, and is also a part of the restriction modific ...
recognizes the palindromic sequence GAATTC and cuts between the G and the A on both the top and bottom strands. This leaves an overhang (an end-portion of a
DNA strand with no attached complement) known as a sticky end
on each end of AATT. The overhang can then be used to ligate in (see
DNA ligase
DNA ligase is a specific type of enzyme, a ligase, () that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organ ...
) a piece of DNA with a complementary overhang (another EcoRI-cut piece, for example).
Some restriction enzymes cut DNA at a restriction site in a manner which leaves no overhang, called a blunt end.
Blunt ends are much less likely to be ligated by a DNA ligase because the blunt end doesn't have the overhanging base pair that the enzyme can recognize and match with a complementary pair. Sticky ends of DNA however are more likely to successfully bind with the help of a DNA ligase because of the exposed and unpaired nucleotides. For example, a sticky end trailing with AATTG is more likely to bind with a ligase than a blunt end where both the 5' and 3' DNA strands are paired. In the case of the example the AATTG would have a complementary pair of TTAAC which would reduce the functionality of the DNA ligase enzyme.
Applications
Restriction sites can be used for multiple applications in molecular biology such as identifying restriction fragment length polymorphisms (
RFLPs).
Databases
Several databases exist for restriction sites and enzymes, of which the largest noncommercial database is REBASE. Recently, it has been shown that statistically significant
nullomers
Nullomers are short sequences of DNA that do not occur in the genome of a species (for example, humans), even though they are theoretically possible.
* Nullomers must be under selective pressure - for example, they may be toxic to the cell. Some ...
(i.e. short absent motifs which are highly expected to exist) in virus genomes are restriction sites indicating that viruses have probably got rid of these motifs to facilitate invasion of bacterial hosts.
[Nullomers Database]
contains a comprehensive catalogue of minimal absent motifs many of which might potentially be not-yet-known restriction motifs.
See also
* List of restriction enzyme cutting sites
A restriction enzyme or restriction endonuclease is a special type of biological macromolecule that functions as part of the "immune system" in bacteria. One special kind of restriction enzymes is the class of " homing endonucleases", these being ...
References
{{DEFAULTSORT:Restriction Site
Genetics techniques
Molecular biology
Restriction enzymes