title: Micelle induced dissociation of DNA-ligand complexes: The effect of ligand binding specificity.
abstract: We investigate the SDS micelle induced dissociation of a small fluorescent ligand 4',6-diamidino-2-phenylindole (DAPI) bound to DNAs of varying sequences. Steady state and time resolved fluorescence measurements affirm minor groove binding of DAPI to poly(dA).poly(dT) and calf thymus DNA while it intercalates in poly(dG).poly(dC). Calorimetric measurements identify the former mode to be entropy driven and the intercalation to be enthalpy driven. Addition of SDS micelles extracts the ligand out of the DNA and relocates it into the micelle independent of the DNA-ligand binding mode. This process is found to be endothermic which is compensated by a huge gain in the entropy. Circular dichroism measurements indicate that the micelles do not affect the structure of DNAs, however, binding and un-binding of DAPI can introduce noticeable alteration in the DNA structure and consequently on the associated hydration which is reflected in solvation measurement. Consideration of a simple two step equilibrium model seems inadequate to account for the observed thermodynamic costs in the dissociation process. The results have been discussed on the basis of an intricate enthalpy-entropy balance.
authors.affiliation: Department of Chemical Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India.
authors.forename: Animesh
authors.initials: A
authors.lastname: Patra
authors.affiliation: Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India.
authors.forename: Soumitra
authors.initials: S
authors.lastname: Hazra
authors.affiliation: Department of Chemical Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India.
authors.forename: Nirnay
authors.initials: N
authors.lastname: Samanta
authors.affiliation: Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India. Electronic address: gskumar@iicb.res.in.
authors.forename: Gopinatha
authors.initials: G
authors.lastname: Suresh Kumar
authors.affiliation: Department of Chemical Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India. Electronic address: rajib@bose.res.in.
authors.forename: Rajib Kumar
authors.initials: RK
authors.lastname: Mitra
mesh_terms: D000818:Animals; D002151:Calorimetry; D002417:Cattle; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D008024:Ligands; D008823:Micelles; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D008024:Ligands; D008823:Micelles; D004247:DNA; C427203:calf thymus DNA
keywords: Hydration; Hydrophobic sink; Spectroscopy; Thermodynamics