Recognition Sequences in the Restriction Endonucleases

The nature of specific protein-nucleic acid interaction between restriction endonucleases (RE) and their recognition sequences (RS) was studied by bioinformatics methods. It was found that the frequency of 5-6 residue long RS-like oligonucleotides is unexpectedly high in the nucleic acid sequence of the corresponding RE (p<0.05 and p<0.001 respectively, n=7). There is an extensive conservation of these RS-like sequences in RE isoschizomers. A review of the seven available crystallographic studies showed that the amino acids coded by codons that are subsets of recognition sequences were often closely located to the RS itself and they were in many cases directly adjacent to the codon-like triplets in the RS. Ten examples of this codon amino acid colocalization are presented. The distance between the nitrogen and oxygen atoms of the co-localized molecules is short, 3.74+/-0.46 Å (mean +/S.E.), indicating that an interaction between the nucleicand amino acids might occur.