Mutual influence between contiguous TMPyP4 ligands when bound to a synthetic double-stranded Poly(A)-Poly(U)

• Computational procedure for evaluation the intrinsic binding constants.
• Calculation of equilibrium parameters using a new modification of conditional probabilities method.
• Binding model governed by the cooperativity of ligand binding to a biopolymer.
• Theoretical analysis and experimental result were well matched.

The cooperativity of TMPyP4 ligand binding to Poly(A)-Poly(U) polynucleotide were monitored in this study by fluorescence spectroscopy and UV–Vis absorbance spectroscopy. To solve the equilibrium binding model between a dye and substrate, a new computational approach has been proposed based collectively on Principal Component Analysis and the conditional probabilities method. This approach suggest that the absorbance and fluorescence variance during a titration is determined by spectral species formed in stepwise saturation of binding sites on Poly(A)-Poly(U) with porphyrin and a conformational changes on a macromolecule. Spectral species assigned to different forms of polymer–ligand complexes whose existences in equilibrium were postulated by the conditional probabilities method. The binding of TMPyP4 molecule to the Poly(A)-Poly(U) enhances the binding of additional molecules to that same receptor. The intrinsic binding constant to an isolated binding site lgKin = 6.4, the cooperativity parameter ω = 5.0, and number of monomers occupied by a ligand n = 2 (25 °C; pH 7) were calculated based upon the non-linear least-squares fitting procedure.

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