Effect of intercalative binding compared to external binding on Z/B equilibrium of poly d(GMe5C) using fluorescent oxazolopyridocarbazoles as probes

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Abstract
Using the fluorimetric determination of the binding isotherms in combination with circular dichroism, we have investigated the effect of the binding of the intercalating chromophore oxazolopyridocarbazole (OPC) to poly d(Gme5C) on B/Z equilibrium, compared to the effect of the external binder OPC derivative pentyl‐2‐OPC. The intercalating OPC appears to be very efficient in reversing left‐handed poly d(Gme5C) into the right‐handed conformation, according to a cooperative mode. For each OPC molecule intercalated into the B form, 7 base pairs were switched from the Z to B conformation. In contrast, the binding of the external binder pentyl‐OPC resulted in a limited Z to B transition, involving the switch of 1.4 base pairs from the Z to B conformation. Moreover, OPC appears much more efficient than pentyl‐OPC in inhibiting both the extent and kinetics of the salt‐induced B/Z transition. At low drug to DNA ratio (D/P = 1/50), a 7‐fold and 1.5‐fold inhibition of the B/Z transition kinetics occurs in the presence of OPC and pently‐OPC, respectively. These features are discussed in terms of the difference existing between the entropic contribution in the DNA binding of intercalating agents, compared to external binders.