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

Sealing of nicks with 3′ N:oxopurine lesions. (Top panel) The distributions of radiolabeled AppNick intermediate and sealed product during the reaction of Rnl2 at a 3′ A:oxoG nick are plotted versus time. Each datum is the average of three separate kinetic experiments. The curve fits are shown. (Inset) The chemical structure of the A:oxoG pair with oxoG in the syn conformation; (dashed lines) hydrogen-bonding contacts. (Bottom panel) The step 2 and step 3 rate constants for sealing nicks with the indicated 3′-OH N:oxoG and N:oxoA configurations.