Homing endonucleases are double stranded DNases that have large, asymmetric recognition sites (12-40 base pairs) and coding sequences that are usually embedded in either introns or inteins (1). Introns are spliced out of precursor RNAs, while inteins are spliced out of precursor proteins (2,3). Homing endonucleases are named using conventions similar to those of restriction endonucleases with intron-encoded endonucleases containing the prefix, “I-” and intein endonucleases containing the prefix, “PI-”(1,7).

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 standard restriction endonucleases, homing endonucleases tolerate some sequence degeneracy within their recognition sequence (5,6). As a result, their observed sequence specificity is typically in the range of 10-12 base pairs.

Homing endonucleases do not have stringently-defined recognition sequences in the way that restriction enzymes do. That is, single base changes do not abolish cleavage but reduce its efficiency to variable extents. The precise boundary of required bases is generally not known. The recognition sequence listed is one site that is known to be recognized and cleaved.

4 homing endonucleases are available from NEB:

References:

1. Belfort, M. and Roberts, R.J. (1997) Nucleic Acids Res., 25, 3379–3388.
2. Dujon, B. et al. (1989) Gene, 82, 115–118.
3. Perler, F.B. et al. (1994) Nucleic Acids Res., 22, 1125–1127.
4. Jasin, M. (1996) Trends in Genetics, 12, 224–228.
5. Gimble, F.S. and Wang, J. (1996) J. Mol. Biol., 263, 163–180.
6. Argast, M.G. et al. (1998) J. Mol. Biol., 280, 345–353.
7. Roberts, R.J. et al. (2003) Nucleic Acids Res., 31, 1805–1812.