What is restriction enzyme star activity?
The precise specificity of the approximately 3,000 known restriction enzymes for their >200 different target sequences could be considered their most interesting characteristic. Although all restriction enzymes bind DNA nonspecifically, under optimal conditions the difference in cleavage rates at the cognate site and the next best site (single-base substitution) is very high. For example, the rate difference for EcoR I at its cognate site (5′-GAATTC-3′) and next best site (5-TAATTC-3) is of the order of 105 (1). Similarly, for EcoR V, cleavage at its cognate site (5′-GATATC-3′) is 106 times faster than at the next best site (5′-GTTATC-3′; 2). However, under nonoptimal conditions, the differences in cleavage rates between cognate and next-best sites change dramatically for many enzymes. This loss of fidelity or increase in cleavage at sites similar to the cognate site is commonly referred to as star activity. A number of reaction parameters can increase the rate of cleavage at star site
