title: Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes.
abstract: A wide variety of organic dyes form, under certain conditions, clusters know as J- and H-aggregates. Cyanine dyes are such a class of molecules where the spatial proximity of several dyes leads to overlapping electron orbitals and thus to the creation of a new energy landscape compared to that of the individual units. In this work, we create artificial H-aggregates of exactly two Cyanine 3 (Cy3) dyes by covalently linking them to a DNA molecule with controlled subnanometer distances. The absorption spectra of these coupled systems exhibit a blue-shifted peak, whose intensity varies depending on the distance between the dyes and the rigidity of the DNA template. Simulated vibrational resolved spectra, based on molecular orbital theory, excellently reproduce the experimentally observed features. Circular dichroism spectroscopy additionally reveals distinct signals, which indicates a chiral arrangement of the dye molecules. Molecular dynamic simulations of a Cy3-Cy3 construct including a 14-base pair DNA sequence verified chiral stacking of the dye molecules.
authors.affiliation: Faculty of Physics and Center for NanoScience (CENS), Ludwig-Maximilians-Universität München (LMU) , Geschwister-Scholl-Platz 1, 80539 Munich, Germany.
authors.forename: Francesca
authors.initials: F
authors.lastname: Nicoli
authors.affiliation: Department Chemie, Ludwig-Maximilians-Universität München (LMU) , Butenandt Straße 11, 81377 Munich, Germany.
authors.forename: Matthias K
authors.initials: MK
authors.lastname: Roos
authors.affiliation: Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, CB3 0HE Cambridge, United Kingdom.
authors.forename: Elisa A
authors.initials: EA
authors.lastname: Hemmig
authors.affiliation: Chemistry Department, University of Cambridge , Lensfield Road, CB2 1EW Cambridge, United Kingdom.
authors.forename: Marco
authors.initials: M
authors.lastname: Di Antonio
authors.affiliation: Department Chemie, Ludwig-Maximilians-Universität München (LMU) , Butenandt Straße 11, 81377 Munich, Germany.
authors.forename: Regina
authors.initials: R
authors.lastname: de Vivie-Riedle
authors.affiliation: Faculty of Physics and Center for NanoScience (CENS), Ludwig-Maximilians-Universität München (LMU) , Geschwister-Scholl-Platz 1, 80539 Munich, Germany.
authors.forename: Tim
authors.identifier: http://orcid.org/0000-0002-0040-0173
authors.initials: T
authors.lastname: Liedl
mesh_terms: D002232:Carbocyanines / Q000737:chemistry*; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation
chemical_list: D002232:Carbocyanines; C089187:cyanine dye 3; D004247:DNA