title: Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays.
abstract: The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores' susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS). Furthermore, the experimental setup allows for the analysis and eventual normalization of Förster-resonance-energy-transfer (FRET) interaction of cyanine-3/cyanine-5 dye combinations on the microarray. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs.
authors.affiliation: Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany. koch@iftc.uni-hannover.de.
authors.forename: Marcel
authors.initials: M
authors.lastname: von der Haar
authors.affiliation: Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany. christopher.heuer@gmx.net.
authors.forename: Christopher
authors.initials: C
authors.lastname: Heuer
authors.affiliation: Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany. paehler@iftc.uni-hannover.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Pähler
authors.affiliation: Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany. vonderhaar@iftc.uni-hannover.de.
authors.forename: Kathrin
authors.initials: K
authors.lastname: von der Haar
authors.affiliation: Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany. lindner@iftc.uni-hannover.de.
authors.forename: Patrick
authors.initials: P
authors.lastname: Lindner
authors.affiliation: Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany. scheper@iftc.uni-hannover.de.
authors.forename: Thomas
authors.initials: T
authors.lastname: Scheper
authors.affiliation: Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany. stahl@iftc.uni-hannover.de.
authors.forename: Frank
authors.initials: F
authors.lastname: Stahl
keywords: DNA; FRET; ROXS; bioanalytics; bioinformatics; cyanine dye; fluorophore; microarray; photobleaching; scanning