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3' DDQ I or DDQ II Double-Dye probes

Doube-Dye LNA Probes

The optimal length of Double-Dye Oligonucleotide probes with a 3’ Deep Dark Quencher (I or II) is 25 bases. In case extra long Double-Dye Oligonucleotides probes are required, Deep Dark Quencher II, BHQ-1® and BHQ-2® can be coupled internally.


DescriptionSize Reference USD  
DD Probe 5' FAM + 3' DDQ I 40 nmol scale - 1 probe1 probe PB-DD401-004 198.00Configure...
DD Probe 5' FAM + 3' DDQ I 200 nmol scale - 1 probe1 probe PB-DD401-020 258.00Configure...
DD Probe 5' FAM + 3' DDQ I 1000 nmol scale - 1 probe1 probe PB-DD401-100 396.00Configure...
DD Probe 5' ROX + 3' DDQ II 40 nmol scale - 1 probe1 probe PB-DD416-004 270.00Configure...
DD Probe 5' ROX + 3' DDQ II 200 nmol scale - 1 probe1 probe PB-DD416-020 330.00Configure...
DD Probe 5' ROX + 3' DDQ II 1000 nmol scale - 1 probe1 probe PB-DD416-100 480.00Configure...
DD Probe 5' Yakima Yellow® + 3' DDQ I 40 nmol scale - 1 probe1 probe PB-DD440-004 348.00Configure...
DD Probe 5' Yakima Yellow® + 3' DDQ I 200 nmol scale - 1 probe1 probe PB-DD440-020 402.00Configure...
DD Probe 5' Yakima Yellow® + 3' DDQ I 1000 nmol scale - 1 probe1 probe PB-DD440-100 563.00Configure...
DD Probe 5' DYOMICS + 3' DDQ I 40 nmol scale - 1 probe1 probe PB-DD480-004 On RequestConfigure...
DD Probe 5' DYOMICS + 3' DDQ I 200 nmol scale - 1 probe1 probe PB-DD480-020 On RequestConfigure...
DD Probe 5' DYOMICS + 3' DDQ I 1000 nmol scale - 1 probe1 probe PB-DD480-100 On RequestConfigure...
DD Probe 5' TAMRA + 3 'DDQ II 40 nmol scale - 1 probe1 probe PB-DD500-004 300.00Configure...
DD Probe 5' TAMRA + 3' DDQ II 200 nmol scale - 1 probe1 probe PB-DD500-020 354.00Configure...
DD Probe 5' TAMRA + 3' DDQ II 1000 nmol scale - 1 probe1 probe PB-DD500-100 480.00Configure...
DD Probe 5' Texas Red® + 3' DDQ II 40 nmol scale - 1 probe1 probe PB-DD530-004 300.00Configure...
DD Probe 5' Texas Red® + 3' DDQ II 200 nmol scale - 1 probe1 probe PB-DD530-020 354.00Configure...
DD Probe 5' Texas Red® + 3' DDQ II 1000 nmol scale - 1 probe1 probe PB-DD530-100 480.00Configure...
DD Probe 5' Dragonfly Orange™ + 3' DDQ II 40 nmol scale - 1 probe1 probe PB-DD545-004 300.00Configure...
DD Probe 5' Dragonfly Orange™ + 3' DDQ II 200 nmol scale - 1 probe1 probe PB-DD545-020 354.00Configure...
DD Probe 5' Dragonfly Orange™ + 3' DDQ II 1000 nmol scale - 1 probe1 probe PB-DD545-100 480.00Configure...
DD Probe 5' Cy® 3 + 3' DDQ II 40 nmol scale - 1 probe1 probe PB-DD550-004 300.00Configure...
DD Probe 5' Cy® 3 + 3' DDQ II 200 nmol scale - 1 probe1 probe PB-DD550-020 354.00Configure...
DD Probe 5' Cy® 3 + 3' DDQ II 1000 nmol scale - 1 probe1 probe PB-DD550-100 480.00Configure...
DD Probe 5' Cy5® + 3' DDQ II 40 nmol scale - 1 probe1 probe PB-DD555-004 300.00Configure...
DD Probe 5' Cy5® + 3' DDQ II 200 nmol scale - 1 probe1 probe PB-DD555-020 354.00Configure...
DD Probe 5' Cy5® + 3' DDQ II 1000 nmol scale - 1 probe1 probe PB-DD555-100 480.00Configure...
DD Probe 5' ATTO + 3' DDQ 40 nmol scale - 1 probe1 probe PB-DD590-004 325.00Configure...
DD Probe 5' ATTO + 3' DDQ 200 nmol scale - 1 probe1 probe PB-DD590-020 393.00Configure...
DD Probe 5' ATTO + 3' DDQ 1000 nmol scale - 1 probe1 probe PB-DD590-100 547.00Configure...
More info on the Purifications page

More info

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.

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 Quencher® 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 Quencher®, Deep Dark Quencher I and TAMRA can be coupled internally.

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Literature & Resources

Product citations


CHEN J. et al., "Activity-Induced Expression of Common Reference Genes in Individual CNS Neurons", Laboratory Investigation, vol. 81, n°6, p. 913-916, June 2001


VERLINDEN L. et al., "Previtamin D3 with a trans-Fused Decalin CD-ring Has Pronounced Genomic Activity", The Journal of Biological Chemistry, vol. 278, n°37, p. 35476-35482, September 2003


CHARBONNIER Y. et al., "A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus", BMC Genomics, 17;6:95, June 2005


EBNER K. et al., "Molecular Detection and Quantitative Analysis of the Entire Spectrum of Human Adenoviruses by a Two-Reaction Real-Time PCR Assay", Journal of Clinical Microbiology, vol. 43, n° 7, p. 3049-3053, July 2005


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