Editing Restriction enzyme (section)

== Recognition site ==
[[File:EcoRV Restriction Site.rsh.svg|thumb|right|A palindromic recognition site reads the same on the reverse strand as it does on the forward strand when both are read in the same orientation]]
Restriction enzymes recognize a specific sequence of nucleotides<ref name="pmid2172084"/> and produce a double-stranded cut in the DNA. The recognition sequences can also be classified by the number of bases in its recognition site, usually between 4 and 8 bases, and the number of bases in the sequence will determine how often the site will appear by chance in any given genome, e.g., a 4-base pair sequence would theoretically occur once every 4^4 or 256bp, 6 bases, 4^6 or 4,096bp, and 8 bases would be 4^8 or 65,536bp.<ref>{{cite web | vauthors = Cooper S |title=Restriction Map |url= http://bioweb.uwlax.edu/genweb/molecular/seq_anal/restriction_map/restriction_map.htm |website=bioweb.uwlax.edu |publisher=University of Wisconsin |access-date=10 May 2021 |date=2003}}</ref> Many of them are [[Palindromic sequence|palindromic]], meaning the base sequence reads the same backwards and forwards.<ref name="pmid11557805">{{cite journal | vauthors = Pingoud A, Jeltsch A | title = Structure and function of type II restriction endonucleases | journal = Nucleic Acids Research | volume = 29 | issue = 18 | pages = 3705–27 | date = September 2001 | pmid = 11557805 | pmc = 55916 | doi = 10.1093/nar/29.18.3705 }}</ref> In theory, there are two types of palindromic sequences that can be possible in DNA. The ''mirror-like'' palindrome is similar to those found in ordinary text, in which a sequence reads the same forward and backward on a single strand of DNA, as in GTAATG. The ''inverted repeat'' palindrome is also a sequence that reads the same forward and backward, but the forward and backward sequences are found in complementary DNA strands (i.e., of double-stranded DNA), as in GTATAC (GTATAC being [[Complementarity (molecular biology)|complementary]] to CATATG).<ref name="isbn0-12-175551-7">{{cite book | author = Clark DP | title = Molecular biology | publisher = Elsevier Academic Press | location = Amsterdam | year = 2005 | isbn = 0-12-175551-7 }}</ref> Inverted repeat palindromes are more common and have greater biological importance than mirror-like palindromes.

[[EcoRI]] digestion produces [[Sticky and blunt ends|"sticky" ends]],

[[Image:EcoRI restriction enzyme recognition site.svg|90px]]

whereas [[SmaI]] restriction enzyme cleavage produces [[Sticky and blunt ends|"blunt" ends]]:

[[Image:SmaI restriction enzyme recognition site.svg|90px]]

Recognition sequences in DNA differ for each restriction enzyme, producing differences in the length, sequence and strand orientation ([[5' end]] or [[3' end]]) of a [[Sticky and blunt ends|sticky-end]] "overhang" of an enzyme restriction.<ref name="pmid11897876">{{cite journal | vauthors = Goodsell DS | title = The molecular perspective: restriction endonucleases | journal = Stem Cells | volume = 20 | issue = 2 | pages = 190–1 | year = 2002 | pmid = 11897876 | doi = 10.1634/stemcells.20-2-190 | s2cid = 222199041 | url = http://theoncologist.alphamedpress.org/content/7/1/82.full.pdf | doi-access = free }}</ref>

Different restriction enzymes that recognize the same sequence are known as [[Isoschizomer|isoschizomers]]. Different enzymes that recognize the same location, but cut at a different position are known as [[neoschizomer]]s.<ref>{{Cite web |title=Isoschizomers {{!}} NEB |url=https://www.neb.com/en/tools-and-resources/selection-charts/isoschizomers |access-date=2025-05-13 |website=www.neb.com}}</ref>