Kinetic mechanism of nick sealing by T4 RNA ligase 2 and effects of 3′-OH base mispairs and damaged base lesions

Effects of 3′-OH N:pyrimidine mispairs on the kinetics of nick sealing. (Top panel) The distributions of radiolabeled AppNick intermediate and sealed product during the reaction of Rnl2 at a 3′ C:C mispaired nick are plotted versus time. Each datum is the average of three separate kinetic experiments. The curve fits to the kinetic scheme are shown. (Bottom panel) The step 2 and step 3 rate constants for sealing nicks with the indicated 3′-OH N:pyrimidine configurations.