A simple method for identifying the palindromic sequences recognized by restriction endonucleases: the nucleotide sequence of the AvaII site.

Tables specifying the frequencies, distances between and positions of all possible tetra-, penta- and hexanucleotide palindromes in phiX174 and SV40 viral DNAs were prepared by a computer search of their base sequences. A simple method based on these tables is described for identifying the sequence recognized by any specific restriction endonuclease. The method requires experimental determination of the number and approximate sizes of the fragments obtained by digestion of phiX174 RF and SV40 DNAs. Using this method we identified the sequence for AvaII restriction endonuclease as 5'-GG(AT)CC.