Ksp632I, a novel class-IIS restriction endonuclease from Kluyvera sp. strain 632 with the asymmetric hexanucleotide recognition sequence: 5'-CTCTTC(N)1-3' 3'-GAGAAG(N)4-5'

A new class-IIS restriction endonuclease, Ksp632I, with novel sequence specificity has been discovered in a non-pathogenic species of Kluyvera. The presence of only a single site-specific activity in this Kluyvera sp. strain 632 enables Ksp632I to be isolated in highly purified form free of contaminating nucleases. Ksp632I recognition sites and cleavage positions were deduced using experimental and computer-assisted mapping and sequencing. The cleavage specificity corresponds to the sequence 5'-CTCTTCN decreases NNN-N-3' 3'-GAGAAGN-NNN increases N-5'. The enzyme recognizes an asymmetric hexanucleotide sequence and cleaves in the presence of Mg2+ ions specific phosphodiester bonds in both DNA strands, 1 and 4 nucleotides distal to the recognition sequence. The staggered cuts generate 5'-protruding ends with single-stranded 5'-phosphorylated trinucleotides. Several slow cleavage sites for Ksp632I were observed on lambda cI857Sam7 DNA. Ksp632I may complement other class-IIS enzymes in the universal restriction approach and may serve as a tool for generating defined unidirectional deletions or insertions.