title: Dynamics of fluorescent dyes attached to G-quadruplex DNA and their effect on FRET experiments.
abstract: FRET spectroscopy is a promising approach for investigating the dynamics of G-quadruplex DNA folds and improving the targeting of G-quadruplexes by potential anticancer compounds. To better interpret such experiments, classical and replica-exchange molecular dynamics simulations and fluorescence-lifetime measurements are used to understand the behavior of a range of Cy3-based dyes attached to the 3' end of G-quadruplex DNA. The simulations revealed that the dyes interact extensively with the G-quadruplex. Identification of preferred dye positions relative to the G-quadruplex in the simulations allows the impact of dye-DNA interactions on FRET results to be determined. All the dyes show significant deviations from the common approximation of being freely rotating and not interacting with the host, but one of the Cy3 dye analogues is slightly closer to this case.
authors.affiliation: Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C (Denmark).|Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark).
authors.forename: Siri
authors.initials: S
authors.lastname: Søndergaard
authors.affiliation: Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark).
authors.forename: Mikayel
authors.initials: M
authors.lastname: Aznauryan
authors.affiliation: Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark).
authors.forename: Emil K
authors.initials: EK
authors.lastname: Haustrup
authors.affiliation: Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C (Denmark).|Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark).
authors.forename: Birgit
authors.initials: B
authors.lastname: Schiøtt
authors.affiliation: Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark). vicb@inano.au.dk.
authors.forename: Victoria
authors.initials: V
authors.lastname: Birkedal
authors.affiliation: Research School of Biology, Australian National University, Linnaeus Way, Canberra ACT 2601 (Australia). ben.corry@anu.edu.au.
authors.forename: Ben
authors.initials: B
authors.lastname: Corry
mesh_terms: D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes / Q000737:chemistry*; D054856:G-Quadruplexes; D009690:Nucleic Acid Conformation
chemical_list: D005456:Fluorescent Dyes
keywords: FRET; G-quadruplexes; dyes/pigments; fluoresecence; molecular dynamics