Investigation of the effect of covalently attached phenazine dye on helix-to-coil transition in mixed poly (rA)-(dT)14 system

Abstract

The effect of imidazo-(4,5-d)-phenazine-N1-β-D-ribofuranoside (Pzn) covalently attached to 3'-end of (dT)₁₄ on conformational transition in a mixed duplex system of poly(rA)•(dT)₁₄ was investigated. The measurements were carried out in Na-cacodylate buffered solution, pH 6.9, containing 0.1 М NaCl, with polynucleotide concentration of 10-300 mkM base pairs. Formation of the poly(rA) complexes with (dT)₁₄ and (dT)₁₄Pzn was studied by thermal denaturation method based on the registration of melting curves by changes in the UV-absorption and the fluorescence intensity of attached phenazine dye. It was found that covalent attachment of imidazophenazin nucleoside derivative substantially increases the thermostability of duplexes formed by (dT)₁₄ with the poly(rA), increasing the temperature of the helix-to-coil transition of 7°С due to intercalation of the dye chromophore between adenine bases. The thermodynamic parameters of helix-to-coil transition for systems studied were determined using the "all-or-none" model. It was shown, that the dye conjugation results in a decrease in the transition enthalpy. However, the observed gain in the free energy of complex formation, ΔG, is provided with the corresponding decrease in entropy change