Role of the Third Strand in the Binding of Proflavine and Pt-Proflavine to Poly(rA)·2poly(rU): A Thermodynamic and Kinetic Study

Abstract

The interactions of triple strands of poly(rA)·2poly(rU) with proflavine (PR) and the proflavine cis-platinum derivative [{PtCl (tmen)}2{NC13H7(NCH2CH2)2}]+ (PRPt) are examined at pH 7.0, T = 25 °C, and 0.2 M ionic strength by spectrophotometry, spectrofluorometry, circular dichroism, viscosimetry, stopped-flow, and T-jump relaxation techniques. The melting experiments demonstrate that both drugs tend to destabilize the triplex structure, although the PRPt effect is more relevant. By contrast, both drugs tend to slightly stabilize the duplex structure. The viscosity and circular dichroism measurements show that, at a low dye-to-polymer ratio (CD/CP), the binding is intercalative, whereas at high CD/CP values, the external binding dominates. The binding kinetics and equilibria have been investigated over the CD/CP region, where intercalation is operative. Both drugs bind to the RNA triplex according to the excluded site model. With PR, two kinetic effects have been observed, whereas with PRPt, only one has been observed. The results are interpreted according to the reaction schemes D + S ⇄ DSI, with PRPt, and D + S ⇄ DSI ⇄ DSII, with PR. The electrostatic contribution to the formation activation energy for DSI is similar (40%) for both systems. The results suggest that DSI is a partially intercalated species. Absence of the second step with PRPt is put down to groove interaction of the Pt-containing moiety, which prevents the PR residue from further penetration through the base pairs to form the fully intercalated complex, DSII. Comparison with the binding of the same drugs to the duplex reveals that the occupation of the major groove in poly(rA)·2poly(rU) by the third strand plays a critical role in the kinetic behavior.