Poly(dA).cntdot.poly(dT) exists in an unusual conformation under physiological conditions: propidium binding to poly(dA).cntdot.poly(dT) and poly[d(A-T)].cntdot.poly[d(A-T)]

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Abstract
The binding of propidium to poly(dA) .cntdot. oly(dT) [poly(deoxyadenylate) poly(thymidylate)] [poly(dA .cntdot. dT)] and to poly[d(A-T)] .cntdot. poly[d(A-T)] [double stranded poly (deoxyadenylyl-thymidylate)] [poly[d(A-T)2]] has been compared under a variety of solution conditions by viscometric titrations, binding studies, and kinetic experiments. The binding of propidium to poly[d(A-T)2] is quite similar to its binding to calf thymus DNA. The interaction with poly(dA .cntdot. dT), however, is quite unusual. The viscosity of a poly(dA .cntdot. dT) solution firs decreases and then increases in a titration with propidium at 18.degree. C. The viscosity of poly [d(A-T)2] shows no decrease in a similar titration. Scatchard plots for the interaction of propidium with poly(dA .cntdot. dT) show the classical upward curvature for positive cooperativity. The curvature decreases as the temperature is increased in binding experiments. A van''t Hoff plot of the observed binding constants yields an apparent positive enthalpy of .apprx. +6 kcal/mol for the propidium-poly(dA .cntdot. dT) interaction. Propidium binding to poly [d(A-T)2] shows no evidence for positive cooperativity, and the enthalpy change for the reaction is .apprx. -9 kcal/mol. Both the magnitude of the dissociation constants and the effects of ionic strength are quite similar for the dissociation of propidium from poly(dA .cntdot. dT) and from poly[d(A-T)2], suggesting that the intercalated states are similar for the 2 complexes. The observed association reactions, under pseudo-1st-order conditions, are quite different. Plots of the observed pseudo-1st-order association rate constant vs. polymer concentration have much larger slopes for propidium binding to poly[d(A-T)2] than to poly(dA .cntdot. dT). These results are interpreted in terms of a fairly standard B conformation for poly[d(A-T)2] which can bind propidium in a manner similar to DNA. Poly(dA .cntdot. dT), however, must have some unusual structural features under normal conditions but can be converted to an intercalated B conformation with the unusual results described above. The polymer conformational transition is characterized by a large positive enthalpy and entropy values which result in a relatively small free-energy change for the transition.