DNA determinants in sequence-specific recognition by Xmal endonuclease

Abstract

The Xmal endonuclease recognizes and cleaves the sequence C↓CCGGG. Magnesium is required for catalysis, however, the enzyme forms stable, specific complexes with DNA in the absence of magnesium. An association constant of 1.2 × 109/M was estimated for the affinity of the enzyme for a specific 195 bp fragment. Competition assays revealed that the site-specific association constant represented an ∼104 increase in affinity over that for non-cognate sites. Missing nucleoside analyses suggested an interaction of the enzyme with each of the cytosines and guanines within the recognition site. Recognition of each of the guanines was also indicated by dimethylsulfate interference footprinting assays. The phosphates 5′ to the guanines within the recognition site appeared to be the major sites of interaction of Xmal with the sugar-phosphate backbone. No significant interaction of the protein was observed with phosphates flanking the recognition sequence. Comparison of the footprinting patterns of Xmal with those of the neoschizomer Smal (CCC↓GGG) revealed that the two enzymes utilize the same DNA determinants in their specific interaction with the CCCGGG recognition site. © 1995 Oxford University Press.