Thermodynamics of Interactions of Water-Soluble Porphyrins with RNA Duplexes.

We characterized the interactions of meso-tetrakis(4N-(2-hydroxyethyl)pyridinium-4-yl) porphyrin (TEtOHPyP4), meso-tetrakis(4N-allylpyridinium-4-yl) porphyrin (TAIPyP4) and meso-tetrakis(4N-metal- lylpyridinium-4-yl) porphyrin (TMetAIPyP4) with the poly(rA)poly(rU) and poly(rl)poly(rC) ANA duplexes between 18 and 45 °C by employing circular dichroism, light absorption, and fluorescence intensity spectroscopic measurements. Our results suggest that TEtOHPyP4 and TAIPyP4 intercalate into the poly- (rA)poly(rU) and poly(rl)poly(rC) host duplexes, while TMetAIPyP4 associates with these RNA duplexes by forming outside-bound, self-stacked aggregates. We used our temperature-dependent absorption titration data to determine the binding constants and stoichiometry for each porphyrin-RNA binding event studied in this work. From the temperature dependences of the binding constants, we calculated the binding free energies, ΔGb, enthalpies, ΔHb, and entropies, ΔSb. For each RNA duplex, the binding enthalpy, ΔHb, is the most favorable for TEtOHPyP4 (an intercalator) followed by TAIPyP4 (an intercalator) and TMetAIPyP4 (an outside binder). On the other hand, for each duplex, external self-stacking of TMetAIPyP4 produces the most favorable change in entropy, ΔSb, followed by the intercalators TAIPyP4 and TEtOHPyP4. Thus, our results suggest that the thermodynamic profile of porphyrin-RNA binding may correlate with the binding mode. This correlation reflects the differential nature of molecular forces that stabilize/destabilize the two modes of binding-intercalation versus external self-stacking along the host duplex. [ABSTRACT FROM AUTHOR]