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Double Dye probes

All in probes

Double-Dye Oligonucleotides have a fluorescent reporter dye and a quencher at their 5’ and 3’ ends, respectively. Double-Dye Oligonucleotides are designed to anneal between the upstream and downstream PCR primers. The Tm of the Double-Dye Oligonucleotide probe must be higher than the upstream primer, to avoid a situation where the later primer is already being extended while the Double-Dye Oligonucleotide probe is not yet annealed. 

Double dye probes
During the elongation phase, the DNA polymerase cleaves the fluorescent dyes from the probe which starts to emit a fluorescent signal. The signal is then recorded in real time.

During the amplification process, the 5’>3’ exonuclease activity of the Taq DNA polymerase cleaves the fluorophore from the probe. Since the fluorophore is no longer subjected to FRET quenching, it starts to fluoresce. This fluorescence can be measured, and the level is directly proportional to the amount of target DNA accumulating during the PCR reaction. 

Eurogentec is a supplier of Double-Dye Oligonucleotide probes and offers the largest number of fluorescent reporters and quenchers. Double-Dye Oligonucleotide probes with TAMRA or various non-fluorescent quenchers (e.g. the Black Hole QuencherTM family) and a variety of fluorescent dyes can be conveniently ordered using our web ordering interface. 

Furthermore, as many applications, like genotyping or gene expression profiling, are requiring small amounts of several different probes, Eurogentec has developed a high-throughput platform to produce high quality small scale Real-Time qPCR Double-Dye probes. All Double-Dye Oligonucleotides are HPLC purified. They are controlled by analytical HPLC and MALDI-TOF Mass Spectrometry. Double-Dye Oligonucleotides are provided lyophilized in individual tubes. The optimal recommended length of Double-Dye Oligonucleotide probes is 25 bases. The maximum length of Double-Dye Oligonucleotides is 35 bases. In case of extra long Double-Dye Oligonucleotides probes are required, quenchers like Black Hole QuencherTM, Deep Dark Quencher I and TAMRA can be coupled internally.


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