APPENDIX A The Restriction Enzymes

Abstract

The restriction enzyme database, REBASE, is a collection of information about restriction enzymes and DNA methylases. More than 2400 restriction enzymes are now known, including 17 different type I specificities, 187 different type II specificities, and 4 different type III specificities. The table contains a listing of all prototype restriction enzymes (types I, II, and III), and some statistics about the numbers of isoschizomers and neoschizomers (enzymes that cleave at a position different from that of the prototype) for each prototype. The most common patterns recognized by type II restriction enzymes are the tetranucleotide and hexanucleotide palindromes. The enzymes recognizing 14 of the 16 possible tetranucleotide palindromes are now known; the two missing sequences are ATAT and TATA. The enzymes recognizing 55 of the 64 possible hexanucleotide palindromes are now known; the missing nine sequences are AAATTT, ATATAT, CGCGCG, CTATAG, TAATTA, TAGCTA, TATATA, TTATAA, and TTGCAA.

REBASE is updated daily. Each month, a set of REBASE data files are released publically and distributed to the scientific community, at no charge, via e-mail. They can also be retrieved by anonymous ftp from vent.neb.com (192.138.220.2). These data files are flat ASCII text files, many of which are designed specifically for use with a variety of software packages such as GCG, IGSuite, GENEPRO, Staden, DNA Strider, Pro-Cite, and PC/Gene. Other data files include a complete set of references, including abstracts, to papers on restriction enzymes and methylases, a list of all commercial suppliers of restriction enzymes and methylases, complete with contact information for...