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  • Title: Thiazole orange and Cy3: improvement of fluorescent DNA probes with use of short range electron transfer.
    Author: Menacher F, Rubner M, Berndl S, Wagenknecht HA.
    Journal: J Org Chem; 2008 Jun 06; 73(11):4263-6. PubMed ID: 18442293.
    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.
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