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 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.
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