Effect of Ethidium on the Formation of Poly(dA) · [poly(dT)]₂ Triplex: A Kinetic Study by Optical Spectroscopic Methods

The kinetics of the formation of triplex poly(dA)-[poly(dT)]₂ from poly(dA)-poly(dT) and poly(dT) is examined by various optical spectroscopic methods, including absorption, circular and linear dichroism (LD) spectroscopy. In the pseudo first order condition, where the poly(dT) concentration is kept lower than that of duplex, the association of the poly(dT) is enhanced by the presence of ethidium; the rate constant is proportional to the amount of ethidium in the mixture. When the concentration of the duplex and the single strand is the same, a spectral change is explained by double exponential curves, indicating that at least two steps are involved, the fast association and slow rearrangement steps. In contrast to the pseudo first order kinetics, the association step in an equimolar condition is not affected by the presence of ethidium. In the rearrangement step, the magnitude of LD decreases with an increase in ethidium concentration, suggesting that the bending of polynucleotide around the intercalation site occurs in the rearrangement step.