Simultaneous DNA Binding and Bending by EcoRV Endonuclease Observed by Real-Time Fluorescence

The complete catalytic cycle of EcoRV endonuclease has been observed by combining fluorescence anisotropy with fluorescence resonance energy transfer (FRET) measurements. Binding, bending, and cleavage of substrate oligonucleotides were monitored in real time by rhodamine-x anisotropy and by FRET between rhodamine and fluorescein dyes attached to opposite ends of a 14-mer DNA duplex. For the cognate GATATC site binding and bending are found to be nearly simultaneous, with association and bending rate constants of (1.45−1.6) × 108 M-1 s-1. On the basis of the measurement of k off by a substrate-trapping approach, the equilibrium dissociation constant of the enzyme−DNA complex in the presence of inhibitory calcium ions was calculated as 3.7 × 10-12 M from the kinetic constants. Further, the entire DNA cleavage reaction can be observed in the presence of catalytic Mg2+ ions. These measurements reveal that the binding and bending steps occur at equivalent rates in the presence of either Mg2+ or Ca2+, while a slow decrease in fluorescence intensity following bending corresponds to k cat, which is limited by the cleavage and product dissociation steps. Measurement of k on and k off in the absence of divalent metals shows that the DNA binding affinity is decreased by 5000-fold to 1.4 × 10-8 M, and no bending could be detected in this case. Together with crystallographic studies, these data suggest a model for the induced-fit conformational change in which the role of divalent metal ions is to stabilize the sharply bent DNA in an orientation suitable for accessing the catalytic transition state.