title: Molecular recognition of genomic DNA in a condensate with a model surfactant for potential gene-delivery applications.
abstract: The functionality of a gene carrying nucleic acid in an artificial gene-delivery system is important for the overall efficiency of the vehicle in vivo. Here, we have studied a well-known artificial gene-delivery system, which is a condensate of calf thymus DNA (CT-DNA) with a model cationic surfactant cetyltrimethylammonium bromide (CTAB) to investigate the molecular recognition of the genomic DNA in the condensate. While dynamic light scattering (DLS) and circular dichroism (CD) reveal structural aspects of the condensate and the constituting DNA respectively, picosecond resolved polarization gated spectroscopy and Förster resonance energy transfer (FRET) reveal molecular recognition of the genomic DNA in the condensate. We have considered ethidium bromide (EB) and crystal violet (CV), which are well known DNA-binding agents through intercalative (specific) and electrostatic (non-specific) interactions, respectively, as model ligands for the molecular recognition studies. A fluorescent cationic surfactant, Nonyl Acridine Orange (NAO) is considered to be a mimic of CTAB in the condensate. The polarization gated fluorescence of NAO at various temperatures has been used to investigate the local microviscosity of the condensate. The excellent spectral overlap of NAO emission and the absorption spectra of both EB and CV allow us to investigate FRET-distances of the ligands with respect to NAO in the condensate at various temperatures and thermal stability of ligand-binding of the genomic DNA. The thermodynamic properties of the molecular recognition have also been explored using Van't Hoff equation. We have also extended our studies to molecular recognition of the genomic DNA in the condensate as dried thin films. This has important implications for its application in bioelectronics.
authors.affiliation: Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India.
authors.forename: Priya
authors.initials: P
authors.lastname: Singh
authors.affiliation: Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India.
authors.forename: Susobhan
authors.initials: S
authors.lastname: Choudhury
authors.affiliation: Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India.
authors.forename: Goutam Kumar
authors.initials: GK
authors.lastname: Chandra
authors.affiliation: Institute for Condensed Matter Physics, TU Braunschweig, Mendelssohnstrasse 3, 38106 Braunschweig, Germany; Laboratory for Emerging Nanometrology, TU Braunschweig, Mendelssohnstrasse 3, 38106 Braunschweig, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Lemmens
authors.affiliation: Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India. Electronic address: skpal@bose.res.in.
authors.forename: Samir Kumar
authors.initials: SK
authors.lastname: Pal
mesh_terms: D004247:DNA / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer; D008962:Models, Theoretical; D013501:Surface-Active Agents / Q000737:chemistry*; D014162:Transfection
chemical_list: D013501:Surface-Active Agents; D004247:DNA
keywords: DNA condensate; FRET; Gene-delivery vehicle; Molecular recognition; Ultrafast dynamics