Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence

DA Hiller, JM Fogg, AM Martin, JM Beechem… - Biochemistry, 2003 - ACS Publications
DA Hiller, JM Fogg, AM Martin, JM Beechem, NO Reich, JJ Perona
Biochemistry, 2003ACS Publications
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 …
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 koff 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 kcat, which is limited by the cleavage and product dissociation steps. Measurement of kon and koff 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.
ACS Publications
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