DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes

Journal article


Publication Details

Author(s): Beierlein F, Paradas Palomo M, Sharapa D, Zozulia O, Mokhir A, Clark T
Journal: Plos One
Publication year: 2016
Volume: 11
Journal issue: 7
Pages range: e0160229


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.


FAU Authors / FAU Editors

Beierlein, Frank Dr.
Computer-Chemie-Centrum
Clark, Timothy apl. Prof. Dr.
Computer-Chemie-Centrum
Mokhir, Andriy Prof. Dr.
Professur für Organische Chemie
Paradas Palomo, Miguel Dr.
Lehrstuhl für Organische Chemie II
Sharapa, Dmytro
Sonderforschungsbereich 953/2 Synthetische Kohlenstoffallotrope
Zozulia, Oleksii
Professur für Organische Chemie


Additional Organisation
Exzellenz-Cluster Engineering of Advanced Materials


How to cite

APA:
Beierlein, F., Paradas Palomo, M., Sharapa, D., Zozulia, O., Mokhir, A., & Clark, T. (2016). DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes. Plos One, 11(7), e0160229. https://dx.doi.org/10.1371/journal.pone.0160229

MLA:
Beierlein, Frank, et al. "DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes." Plos One 11.7 (2016): e0160229.

BibTeX: 

Last updated on 2019-14-03 at 12:01