Fluorescent Substrates

5-(6)-Carboxytetramethylrhodamine (TAMRA) is a fluorescent dye that is used as a probe for DNA-based analysis. It binds to the 5' end of dsDNA, forming an intrastrand duplex. The fluorescence of TAMRA increases when it binds to dsDNA and can be used as a measure of the amount of DNA in a sample. TAMRA has been shown to be useful in the diagnosis of bowel disease and in the investigation of gene expression during body formation. This dye is also used as a marker for covalent linkages and high molecular weight proteins such as cyclin D2.

Single isomer of 5(6)-ROX. It is a fluorescent dye used in RT-PCR methods as an internal reference to determine fluorescence variation that is not associated with the amplification process (plastic of the wells, small differences in concentration or volume, instrument measurements). It produces a constant fluorescence emission signal during the PCR process that is used to normalise the emission produced by the reporter. The fluorescence signal is compatible with most reporters. It is used to label the 5’ end of oligonucleotides as a reporter in the presence of a quencher at the 3’ end (dual labelled probe). During the amplification, the dye is cleaved, and the fluorescence increases proportionally with the amount of the specific sequence amplified during the PCR process. The development of the fluorescence signal is therefore specifically related to the amplification of the target sequence. 6-ROX with NHS-activated carboxylic acids reacts with primary amines.

5-Carboxytetramethylrhodamine - (TAMRA) is a widely employed fluorescent dye (orange/red) that is suitable for different uses. In PCR applications, it has been used as both a reporter at the 5’ or as a quencher at the 3’ end. TAMRA-labelled oligonucleotides have been used to study interactions with DNA or DNA/protein interactions. It is an excellent fluorescent acceptor for FRET applications with a suitable dye pair. It is used as a protein/antibody labelling agent for structural studies, immunochemistry and flow cytometry. Bioconjugation is generally performed through coupling of the carboxylic acid to a primary amine at the N-terminus of a protein, on lysine side chains or amino-modified oligonucleotide.