Thermodynamics of Interactions of Water-Soluble Porphyrins with RNA Duplexes

Abstract

We characterized the interactions of meso-tetrakis(4N-(2-hydroxyethyl)pyridinium-4-yl) porphyrin (TEtOHPyP4), meso-tetrakis(4N-allylpyridinium-4-yl) porphyrin (TAlPyP4), and meso-tetrakis(4N-metallylpyridinium-4-yl) porphyrin (TMetAlPyP4) with the poly(rA)poly(rU) and poly(rI)poly(rC) RNA duplexes between 18 and 45 degrees C by employing circular dichroism, light absorption, and fluorescence intensity spectroscopic measurements. Our results suggest that TEtOHPyP4 and TAlPyP4 intercalate into the poly(rA)poly(rU) and poly(rI)poly(rC) host duplexes, while TMetAlPyP4 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, DeltaG(b), enthalpies, DeltaH(b), and entropies, DeltaS(b). For each RNA duplex, the binding enthalpy, DeltaH(b), is the most favorable for TEtOHPyP4 (an intercalator) followed by TAlPyP4 (an intercalator) and TMetAlPyP4 (an outside binder). On the other hand, for each duplex, external self-stacking of TMetAlPyP4 produces the most favorable change in entropy, DeltaS(b), followed by the intercalators TAlPyP4 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.

A spectroscopic investigation of the interaction between c-MYC DNA and tetrapyridinoporphyrazinatozinc(II)

“…Outside binding without stacking is demonstrated by a small red shift (about 6-8 nm) and hypochromicity (10%) or even hyperchromicity of the soret band. Outside binding with stacking is indicated by variable effects on the soret band [21][22][23]. Accordingly, for both forms of DNA, the changes of the first and the second stages are intermediate between those expected for intercalative and outside binding modes.…”

Thermodynamics of interaction ofmeso-tetra-(4N-oxyethylpyridyl) porphyrin and its Cu(II)- and Co(II)- containing derivatives with A and B forms of DNA

“…Our previous studies of interaction of water soluble meso-tetra-(4N-oxyethylpyridyl) porphyrin and its Cu(II)-and Co(II)-containing derivatives (CuTOEPyP4 and CoTOEPyP4) with B-DNA of calf thymus have shown that at high ionic strengths TOEPyP4 and CuTOEPyP4 prefer the intercalative binding mechanism, and CoTOEPyP4, which has an axial ligand, binds only externally in the major groove of DNA [17][18][19]. In this paper, the comparative study of interaction of these porphyrins with A-and Bform DNA at low ionic conditions is conducted.…”

Thermodynamic Profile of Interaction of Porphyrins With Nucleic Acids

“…In our previous works we have characterized the binding of four novel water soluble porphyrins to nucleic RNA duplexes [5][6][7][8] . We estimated their binding modes and binding thermodynamics.…”

“…The concentrations of double-stranded polynucleotides were determined spectroscopically using molar extinction coefficients presented in our pervious papers 5,6 . All spectroscopic measurements were performed in 0.1 BPSE buffer (1BPSE = 6 mM Na 2 HPO 4 + 2 mM NaH 2 PO 4 + 185 mM NaCl + 1 mM Na 2 EDTA), pH 7.0, µ = 0.02.…”

“…All absorption and fluorescence titration experiments were carried out by stepwise addition of aliquots of a stock solution of NA to the porphyrin as previously described 5 . Visible absorption spectra of porphyrins in Soret region in the absence and presence of the RNA duplexes were collected at 18, 25, 35, and 45 °C using Perkin Elmer Lambda 800 UV/VIS spectrophotometer.…”