Intercalative interactions of ethidium dyes with triplex structures

Abstract

The binding of phenanthridine dyes to triplex poly(dT)∗poly(dA)·poly(dT) and its precursor duplex poly(dA)·poly(dT) is characterized using linear dichroism and circular dichroism spectroscopy, and thermal denaturation. The two monomeric dyes ethidium bromide and propidium iodide are shown to behave similarly to each other in intercalating into and stabilizing both the duplex and the triplex structures. However, contrary to expectations, the extra cationic side-chain of propidium iodide provides no significant extra stabilization of triplex compared with ethidium bromide, although propidium does stabilize the duplex more than ethidium. The monomeric dyes appear to have somewhat different binding geometries with the duplex and triplex polymers. The dimeric dye ethidium homodimer is found to bis-intercalate in the triplex as well as the duplex but, in contrast to the monomers, no variation in geometry between duplex and triplex is observed. However, although dimer stabilizes the duplex, it has no effect on the thermal stability of the triplex. This lack of binding preferentiality of the dimer for triplex compared with the monomeric dyes indicates greater constraints on the accommodation of a bis-intercalator in the triplex structure than in the duplex.