Type-II restriction endonucleases (REs) are enzymes that "recognize" particular DNA sequences, and introduce double-stranded cuts in that sequence. The most important class of REs are the Type-IIP (or just Type-II) enzymes, which have palindromic recognition sites. There are 16 possible 4 bp palindromic* restriction sites; not all possible sites correspond to a known RE activity. REs with 4 bp recognition sites are referred to as "tetraschizomers" or "4-Cutters" There are also alternative enzymes (isoschizomers) that recognize the same site, but cleave it in a different manner. For example, Mbo I and Dpn I both recognize GATC, but the first cuts it 5' to the first base [/GATC] and the second cuts it between the two middle bases [GA/TC]. As well, some enzymes recognize the same site, but cleave it differently according to its state of methylation. For example, Mbo I and Sau3A I both recognize GATC, but the former will not cleave the site if the A base is methylated. Methylation is used by some bacteria to protect its own DNA from self-digestion.

    A palindrome is a word or phrase that reads the same forward or backward: the record is the 15-letter Finnish word for a soap seller,"Saippuakauppias". In the third example above, the recognition site of Alu I is 5'-AGCT-3' such that the complementary strand reads 3'-TCGA-5': the double-stranded 4 bp sequence therefore reads the same in either direction.

    [Click here for further information on Restriction Endonuclease sites].

    HOMEWORK: In writing out a list of 4-cutters, note that the first two letters determine the last two. Using the same principle, calculate the number of possible hexaschizomeric "6-cutters".