title: Spectroscopic and calorimetric investigations on the binding of phenazinium dyes safranine-O and phenosafranine to double stranded RNA polynucleotides.
abstract: RNA targeting through small molecules that can selectively bind specific RNA structures is an important current strategy in therapeutic drug development. Towards this strategy a comparative study on the interaction of two phenazinium dyes, safranine-O and phenosafranine to double stranded RNAs, poly(I).poly(C), poly(A).poly(U) and poly(C).poly(G) was performed. Spectrophotometric and spectrofluorimetric studies revealed non-cooperative binding of the dyes to the duplex RNA with binding constants of the order 10(5)M(-1) with a higher affinity of safranine-O to poly(I).poly(C) followed by poly(A).poly(U) and poly(C).poly(G). Anisotropy and fluorescence quenching results confirmed an intercalation mode of binding for the dyes on these RNAs. Binding induced conformational changes in the RNA polynucleotides were revealed from circular dichroism data. Thermal melting study and DSC experiments demonstrated stabilization of dye-RNA complexes. Calorimetric studies revealed that the binding was accompanied by a large positive entropy term with a small negative enthalpy contributions. Significant hydrophobic forces in the complexation of the double stranded RNAs with the dyes were confirmed from the negative heat capacity changes. Enthalpy-entropy compensation was also observed in the binding. Parsing of the Gibbs energy suggested a larger non-electrostatic contribution in all the cases. The results presented here may be helpful to design new types of RNA-based therapeutic agents.
authors.affiliation: Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
authors.forename: Baishakhi
authors.initials: B
authors.lastname: Saha
authors.affiliation: Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India. Electronic address: gskumar@iicb.res.in.
authors.forename: Gopinatha Suresh
authors.initials: GS
authors.lastname: Kumar
mesh_terms: D002151:Calorimetry; D002152:Calorimetry, Differential Scanning; D002942:Circular Dichroism; D004396:Coloring Agents / Q000737:chemistry / Q000378:metabolism; D019277:Entropy; D007364:Intercalating Agents / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation / Q000528:radiation effects; D009994:Osmolar Concentration; D010619:Phenazines / Q000737:chemistry / Q000378:metabolism*; D011119:Polynucleotides / Q000737:chemistry / Q000378:metabolism; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000378:metabolism*; D013050:Spectrometry, Fluorescence; D013053:Spectrophotometry; D044366:Transition Temperature; D014466:Ultraviolet Rays
chemical_list: D004396:Coloring Agents; D007364:Intercalating Agents; D010619:Phenazines; D011119:Polynucleotides; D012330:RNA, Double-Stranded; C011977:phenosafranine; C009195:safranine T
keywords: Calorimetry; Phenazinium dyes; Phenosafranine; Safranine-O; Spectroscopy; ds RNAs