Restriction site

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Restriction sites, or restriction recognition sites, are locations on a DNA molecule containing specific (4-8 base pairs in length[1]) sequences of nucleotides, which are recognized by restriction enzymes. These are generally palindromic sequences[2](p305) (because restriction enzymes usually bind as homodimers), and a particular restriction enzyme may cut the sequence between two nucleotides within its recognition site, or somewhere nearby. For example, the common restriction enzyme EcoRI recognizes the palindromic sequence GAATTC and cuts between the G and the A on both the top and bottom strands, leaving an overhang (an end-portion of a DNA strand with no attached complement) known as a sticky end[2](p306) on each end of AATT. This overhang can then be used to ligate in (see DNA ligase) 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.[2](p306) 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.[3] 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 complimentary pair of TTAAC which would reduce the functionality of the DNA ligase enzyme.[4]

Applications[edit]

Restriction sites can be used for multiple applications in molecular biology such as identifying restriction fragment length polymorphisms (RFLPs).

References[edit]

  1. ^ Russell, Peter J. (2006). iGenetics: A Mendelian Approach. Benjamin Cummings. ISBN 978-0805346664. 
  2. ^ a b c Lehninger, Albert L.; Nelson, David L.; Cox, Michael M. (2008). Principles of Biochemistry (5th ed.). New York, NY: W.H. Freeman and Company. ISBN 978-0-7167-7108-1. 
  3. ^ Mousavi-Khattat, Mohammad; Rafati, Adele; Gill, Pooria (5 February 2015). "Fabrication of DNA nanotubes using origami-based nanostructures with sticky ends". Journal of Nanostructure in Chemistry. 5 (2): 177–183. doi:10.1007/s40097-015-0148-z. 
  4. ^ Gao, Song; Zhang, Jiannan; Miao, Tianjin; Ma, Di; Su, Ying; An, Yingfeng; Zhang, Qingrui (28 March 2015). "A Simple and Convenient Sticky/Blunt-End Ligation Method for Fusion Gene Construction". Biochemical Genetics. 53 (1-3): 42–48. doi:10.1007/s10528-015-9669-x.