Thiazole orange and Cy3: improvement of fluorescent DNA probes with use of short range electron transfer.
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.
Menacher
Florian
F
University of Regensburg, Institute for Organic Chemistry, Universitätsstrasse 31, Regensburg, Germany.
Rubner
Moritz
M
Berndl
Sina
S
Wagenknecht
Hans-Achim
HA
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
D052160:Benzothiazoles; D015342:DNA Probes; D005456:Fluorescent Dyes; D011804:Quinolines; C051000:thiazole orange