title: DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes.
abstract: Extensive molecular-dynamics (MD) simulations have been used to investigate DNA-dye and DNA-photosensitizer conjugates, which act as reactants in templated reactions leading to the generation of fluorescent products in the presence of specific desoxyribonucleic acid sequences (targets). Such reactions are potentially suitable for detecting target nucleic acids in live cells by fluorescence microscopy or flow cytometry. The simulations show how the attached dyes/photosensitizers influence DNA structure and reveal the relative orientations of the chromophores with respect to each other. Our results will help to optimize the reactants for the templated reactions, especially length and structure of the spacers used to link reporter dyes or photosensitizers to the oligonucleotides responsible for target recognition. Furthermore, we demonstrate that the structural ensembles obtained from the simulations can be used to calculate steady-state UV-vis absorption and emission spectra. We also show how important quantities describing the quenching of the reporter dye via fluorescence resonance energy transfer (FRET) can be calculated from the simulation data, and we compare these for different relative chromophore geometries.
authors.affiliation: Computer-Chemistry-Center and Interdisciplinary Center for Molecular Materials, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.|Cluster of Excellence Engineering of Advanced Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
authors.forename: Frank R
authors.initials: FR
authors.lastname: Beierlein
authors.affiliation: Computer-Chemistry-Center and Interdisciplinary Center for Molecular Materials, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.|Organic Chemistry II, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
authors.forename: Miguel
authors.initials: M
authors.lastname: Paradas Palomo
authors.affiliation: Computer-Chemistry-Center and Interdisciplinary Center for Molecular Materials, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.|Cluster of Excellence Engineering of Advanced Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
authors.forename: Dmitry I
authors.initials: DI
authors.lastname: Sharapa
authors.affiliation: Organic Chemistry II, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
authors.forename: Oleksii
authors.initials: O
authors.lastname: Zozulia
authors.affiliation: Organic Chemistry II, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
authors.forename: Andriy
authors.initials: A
authors.lastname: Mokhir
authors.affiliation: Computer-Chemistry-Center and Interdisciplinary Center for Molecular Materials, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.|Cluster of Excellence Engineering of Advanced Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
authors.forename: Timothy
authors.initials: T
authors.lastname: Clark
mesh_terms: D004247:DNA / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes / Q000737:chemistry*; D008856:Microscopy, Fluorescence; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011789:Quantum Theory; D013056:Spectrophotometry, Ultraviolet
chemical_list: D005456:Fluorescent Dyes; D004247:DNA