6594 Nucleic Acids Research, 2010, Vol. 38, No. 19 Figure 3. Lack of endonucleolytic activity in MeP-half-site reactions of Cre(R173A, Y324G). Reactions and product analysis were performed as described under Figure 2. The results of SDS–PAGE and denaturing PAGE analyses are shown in A and B, respectively. The predicted positions of migration of the covalent intermediate and the hydrolysis product (HP) are indicated. The incubation time for the control reaction without addition of Cre(R173A, Y324G) was 24 h. Figure 4. Lack of strand cleavage or hydrolysis in a P-half-site by Cre(R173A). The half-site substrate was identical in sequence to that employed in the reactions shown in Figures 2 and 3, except that it contained a scissile phosphate instead of methylphosphonate. Reactions were analyzed as described in the legends for Figures 2 and 3. (A) SDS-PAGE. (B) Urea-PAGE.