Interaction of a tricationic meso-substituted porphyrin with guanine-containing polyribonucleotides of various structures.

The interaction of a tricationic water-soluble meso-(N-methylpyridinium)-substituted porphyrin, TMPyP, derived from classic TMPyP4, with double-stranded poly(G)  ⋅  poly(C) and four-stranded poly(G) polyribonucleotides has been studied in aqueous buffered solutions, pH 6.9, of low and near-physiological ionic strengths in a wide range of molar phosphate-to-dye ratios (P/D). To clarify the binding modes of TMPyP to biopolymers various spectroscopic techniques, including absorption and polarized fluorescence spectroscopy, Raman spectroscopy, and resonance light scattering, were used.

Binding of Metallated Porphyrin-Imidazophenazine Conjugate to Tetramolecular Quadruplex Formed by Poly(G): a Spectroscopic Investigation.

The binding of telomerase inhibitor ZnTMPyP(3+)-ImPzn, Zn(II) derivative of tricationic porphyrin-imidazophenazine conjugate, to tetramolecular quadruplex structure formed by poly(G) was studied in aqueous solutions at neutral pH and near physiological ionic strength using absorption and polarized fluorescent spectroscopy techniques. Three binding modes were determined from the dependences of the fluorescence intensity and polarization degree for the porphyrin and phenazine moieties of the conjugate on molar polymer-to-dye ratio (P/D). The first one is outside electrostatic binding of positively charged porphyrin fragments to anionic phosphate groups of the polymer which prevails only at very low P/D values and manifests itself by substantial fluorescence quenching.

Spectroscopic Studies on Binding of Porphyrin-Phenazine Conjugate to Four-Stranded Poly(G).

Binding of a novel cationic porphyrin-imidazophenazine conjugate, TMPyP(3+)-ImPzn, to four-stranded poly(G) was investigated in aqueous solutions of neutral pH under near physiological ionic conditions using absorption, polarized fluorescent spectroscopy and fluorescence titration techniques. In absence of the polymer the conjugate folds into stable internal heterodimer with stacking between the porphyrin and phenazine chromophores. Binding of TMPyP(3+)-ImPzn to poly(G) is realized by two competing ways.

Self-assemblies of tricationic porphyrin on inorganic polyphosphate.

Self-assemblies formed by the new synthesized tricationic porphyrin derivative (TMPyP(3+)) on the polyanionic inorganic polyphosphate (PPS) in aqueous solution were studied using different spectroscopic techniques and DFT calculation method. From the fluorescence quenching of the bound TMPyP(3+) molecules and their Raman spectra we conclude that porphyrin chromophores form the stable π-π stacking-assemblies onto PPS polyanions. The transformation of the Soret band in absorption spectra at different PPS/TMPyP(3+)concentration ratios evidences that the assemblies are mixtures of J- and H-aggregates.

Spectroscopic study on the effect of imidazophenazine tethered to 5'-end of pentadecathymidilate on stability of poly(dA)·(dT)15 duplex.

The effect of imidazo[4,5-d]phenazine (Pzn) attached to the 5(')-end of (dT)(15) oligonucleotide via a flexible linker on the thermal stability of poly(dA)·(dT)(15) duplex was studied in aqueous buffered solution containing 0.1 М NaCl at the equimolar ratio of adenine and thymine bases (100 μM each) using spectroscopic techniques. Duplex formation was investigated by measuring UV absorption and fluorescence melting curves for the Pzn-modified system.

Postsynthetic modification of oligonucleotides with imidazophenazine dye and its effect on duplex stability.

Carboxyalkyl derivative of the intercalating agent imidazo[4,5-b]phenazine was used for the postsynthetic oligonucleotide modification. Model pentadecathymidylate-imidazophenazine conjugate was prepared from 5'-aminoalkyl-modified (dT)(15) by using phosphonium coupling reagent BOP in the presence of 1-hydroxybenzotriazole. Spectral-fluorescent properties of the conjugate were studied.

Effect of Ni2+ and Cd2+ ions on thermally induced conformational transitions in poly(dA)-poly(dT) system.

Effects of Ni(2+) and Cd(2+) ions on thermally induced conformational transitions in the poly(dA)·poly(dT) polynucleotide duplex and poly(dA)·2poly(dT) triplex under near physiological ionic conditions were studied by measurement of UV absorption melting curves and static light scattering intensity. The diagrams of conformational transitions in poly(dA)-poly(dT)-Me(2+) systems were plotted. An aggregation in these polynucleotide systems arises at certain values of the metal ions concentration and the temperature after the polymer dissociation into single strands.

Spectroscopic detection of tetracationic porphyrin H-aggregation on polyanionic matrix of inorganic polyphosphate.

Self-assembly of tetracationic porphyrin TMPyP(4+) onto polyanionic matrix of inorganic polyphosphate (PPS) in aqueous solutions has been studied in a wide range of molar phosphate-to-dye ratios using techniques of polarized fluorescence, absorption, resonance Raman spectroscopy and static light scattering. The binding of TMPyP(4+) to PPS is characterized by the binding constant of 3 x 10(5) M(-1) and the cooperativity parameter of about 150. The fluorescence quenching of the bound TMPyP(4+) evidences the stacking of the porphyrine chromophores.

Fluorescent studies on cooperative binding of cationic pheophorbide-a derivative to polyphosphate.

The cooperative binding of a novel water-soluble cationic derivative of pheophorbide-a (CatPheo-a) to inorganic polyphosphate (PPS) in buffered aqueous solutions was studied by means of polarized fluorescence spectroscopy in a wide range of molar phosphate-to-dye ratios (P/D). Under low P/D values, CatPheo-a forms extended stacking associates on the PPS matrix, while under high P/D the dye binds to PPS in the dimer form. The CatPheo-a self-association is accompanied by 40-fold dye fluorescence quenching and a substantial increase in the fluorescence polarization degree.

Thermodynamic analysis of conformational transitions in oligonucleotide complexes in presence of Na(+) and Mg(2+) ions, using "staggering zipper" model.

Curves of transitions in double (2-->1 transition) and triple (3-->2 transition) complexes of oligonucleotides dA(N1)with dT(N2) in solutions with Na(+) and Mg(2+) are calculated for the case of oligomer lengths from 10 to 500 nucleotides in the wide range of ion concentrations. The calculated curves of transitions and their differential analogs reflect rather exactly the position and form of experimental curves and describe dependences of transition temperatures on the length of molecules, their concentration, and ionic conditions. Values of the nucleation parameter beta for the systems studied are determined by comparison of the calculated and experimental data obtained in a number of works.