title: Thiazole orange and Cy3: improvement of fluorescent DNA probes with use of short range electron transfer.
abstract: Thiazole orange was synthetically incorporated into oligonucleotides by using the corresponding phosphoramidite as the building block for automated DNA synthesis. Due to the covalent fixation of the TO dye as a DNA base surrogate, the TO-modified oligonucleotides do not exhibit a significant increase of fluorescence upon hybridization with the counterstrand. However, if 5-nitroindole (NI) is present as a second artificial DNA base (two base pairs away from the TO dye) a fluorescence increase upon DNA hybridization can be observed. That suggests that a short-range photoinduced electron transfer causes the fluorescence quenching in the single strand. The latter result represents a concept that can be transferred to the commercially available Cy3 label. It enables the Cy3 fluorophore to display the DNA hybridization by a fluorescence increase that is normally not observed with this dye.
authors.affiliation: University of Regensburg, Institute for Organic Chemistry, Universitätsstrasse 31, Regensburg, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Menacher
authors.forename: Moritz
authors.initials: M
authors.lastname: Rubner
authors.forename: Sina
authors.initials: S
authors.lastname: Berndl
authors.forename: Hans-Achim
authors.initials: HA
authors.lastname: Wagenknecht
mesh_terms: D052160:Benzothiazoles / Q000737:chemistry*; D015342:DNA Probes; D004583:Electrons; D005456:Fluorescent Dyes / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D011804:Quinolines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D016339:Spectrometry, Mass, Fast Atom Bombardment
chemical_list: D052160:Benzothiazoles; D015342:DNA Probes; D005456:Fluorescent Dyes; D011804:Quinolines; C051000:thiazole orange