Homing endonuclease recognition sites are extremely rare. For example, an 18 base pair recognition sequence will occur only once in every 7 x 1010 base pairs of random sequence. This is equivalent to only one site in 20 mammalian-sized genomes (4). However, unlike restriction endonucleases, homing endonucleases tolerate some sequence degeneracy within their recognition sequence (5,6). That is, single base changes do not abolish cleavage but reduce its efficiency to variable extents. As a result, their observed sequence specificity is typically in the range of 10-12 base pairs.
(1) Belfort, M. and Roberts, R.J. (1997) Nucleic Acids Res., 25, 3379–3388. PMID: 9254693
(2) Dujon, B. et al. (1989) Gene, 82, 115–118. PMID: 2555261
(3) Perler, F.B. et al. (1994) Nucleic Acids Res., 22, 1125–1127. PMID: 8165123
(4) Jasin, M. (1996) Trends in Genetics, 12, 224–228. PMID: 8928227
(5) Gimble, F.S. and Wang, J. (1996) J. Mol. Biol., 263, 163–180. PMID: 8913299
(6) Argast, M.G. et al. (1998) J. Mol. Biol., 280, 345–353. PMID: 9665841
(7) Roberts, R.J. et al. (2003) Nucleic Acids Res., 31, 1805–1812. PMID: 12654995
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Watch as Geoff Wilson, Restriction Enzyme Division Head, describes the interaction of restriction enzymes and substrate DNA using computer models generated from x-ray crystallography data.
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