An insight into the interaction of phenanthridine dyes with polyriboadenylic acid: Spectroscopic and thermodynamic approach Suman Das ⇑ , Sultana Parveen, Ankur Bikash Pradhan Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700 032, India highlights  Two dyes ethidium bromide and propidium iodide bind to single stranded polyriboadenylic acid.  Binding affinity is greater for propidium iodide than ethidium bromide.  Binding are characterized by both negative enthalpy and entropy changes.  Ionic strength dependence of binding revealed lesser electrolytic contribution to the binding process. graphical abstract We have investigated the interaction of two phenanthridine ligands namely ethidium bromide and pro- pidium iodide with single and double stranded polyriboadenylic acid using various spectroscopic tech- niques. Both of them were found to bind with the single stranded polymer, while no interaction was observed with the double stranded one. Thermodynamic studies revealed that in both the cases the bind- ing were characterized by negative enthalpy and negative entropy changes. Ionic strength dependence studies revealed a lesser electrolytic contribution to the total Gibbs free energy change in both the cases compared to the non-electrolytic contribution. Our results may be of potential use in the design of spe- cific phenanthridine derivatives and understanding the structure activity relationship for improved ther- apeutic applications. article info Article history: Received 6 June 2013 Received in revised form 17 August 2013 Accepted 23 August 2013 Available online 31 August 2013 Keywords: Single stranded RNA Propidium iodide Ligand-RNA interaction Spectroscopic study Thermodynamics Salt dependence abstract Interaction of two phenanthridine dyes, namely ethidium bromide (EB) and propidium iodide (PI) with polyriboadenylic acid was investigated using various spectroscopic techniques. They were found to bind only with the single stranded form of the polymer, while no affinity was observed for the double stranded form. Enhanced binding observed for PI compared to EB may be attributed to the presence of external alkyl chain in PI. Thermodynamic studies showed negative enthalpy and negative entropy changes for the binding of both the dyes. Salt dependent studies revealed a lesser electrolytic contribution compared to the nonelectrolytic contribution to the total Gibbs free energy change in each case. This indicated importance of hydrophobic and van der Waal’s interaction for the binding process. Overall, the binding data and detail energetics of interaction presented here would be helpful in the design of phenanthridine based molecules that interact with specific RNA structure. Ó 2013 Elsevier B.V. All rights reserved. 1386-1425/$ - see front matter Ó 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.saa.2013.08.106 ⇑ Corresponding author. Tel.: +91 94 3437 3164/033 2457 2349; fax: +91 33 2414 6266. E-mail addresses: sumandas10@yahoo.com (S. Das), parveen.sultana.ju@gmail.- com (S. Parveen), ankurpradhan727@gmail.com (A.B. Pradhan). Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 118 (2014) 356–366 Contents lists available at ScienceDirect Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy journal homepage: www.elsevier.com/locate/saa