Thermal unwinding of Polyadenylic·Polyuridylic acid complex with TMPyP4 porphyrin in aqueous solutions

Abstract

Abstract The molecular mechanism of Poly(A)•Poly(U) (Polyadenylic•Polyuridylic acid) polyribonucleotide denaturation was studied through a combination of molecular dynamics (MD) simulations and UV–Vis-melting experiments. UV–Vis absorption spectra of Poly(A)•Poly(U) were measured at different temperatures (20–70 °C) both in the absence and presence of porphyrin-ligand TMPyP4 in equilibrated aqueous solutions (pH 7.0). Thermal behavior of double-stranded structure of Poly(A)•Poly(U) altered by formation of the ternary [Poly(A)•Poly(U)]*(TMPyP4)n complexes was studied with the help of a new semi-soft chemometrics procedure, based on the analyses of fractions of species in solution versus temperature. The melting temperature in the presence of porphyrin is 1.2 °C higher than that for pure polyribonucleotide, which indicates that porphyrin binding contributes to the suppression of transition between the native ordered structure of Poly(A)•Poly(U) and disordered state. MD simulations were performed for the binding of TMPyP4 to (rA)12•(rU)12 oligonucleotide to provide molecular-level insight into the mechanism of duplex dsRNA melting in the presence of TMPyP4. The results of MD simulations suggest a molecular mechanism of thermal stabilization of the native structure through the accommodation of TMPyP4 in double-stranded structure of (rA)12•(rU)12 oligonucleotide groove close to the end of the ordered region of stacked nucleobase pairs.