TaqMan™ QSY2 Probe, 6000 pmole - FAQs

I need to see all the primer and probe sequences from an assay design right away. How can I do this?

You can directly see all the primer and probe sequences from a test design right away using the Primer Express Software. Open the software and choose File => New. Choose either TaqMan MGB Quantification or TaqMan Quantification for Gene Expression Assay design. Copy/paste your gene sequence of interest into the new window and click on the green triangle to get primer/probe designs.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

How can I determine whether the Tm of my custom probe is appropriate?

In general, the target Tm of a TaqMan probe is 70 degrees C. Using the Primer Express Software, you can check the Tm of a MGB or TAMRA probe probe.

Within the software, go to Primer Probe Test Tool and then copy/paste in your sequence of interest to see the Tm. If you need to check for a MGB based probe, make sure to choose Document Type: TaqMan MGB Quantification. If you need to check for a QSY or TAMRA based probe, make sure to choose Document Type: TaqMan Quantification. Real-Time PCR and Digital PCR Applications

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Applications Support Center.

Do I need to redesign my probe when converting from BHQ and other competitor probes to TaqMan QSY/QSY2 Probes?

No, redesign is not necessary when converting from most competitor probes to TaqMan QSY/QSY2 Probes.

Find additional tips, troubleshooting help, and resources within our TaqMan Primers and Probes Support Center.

Is there a need to adjust filter settings on the instrument to utilize Cyanine 5 and Cyanine 5 dyes with TaqMan QSY/QSY2 Probes?

Yes, please make sure to enable the x6m6 filter (6th channel) in the instrument filter settings prior to the qPCR run. This filter is not preselected by default.

Find additional tips, troubleshooting help, and resources within our TaqMan Primers and Probes Support Center.

If I am using Cyanine 5 dye with TaqMan QSY/QSY2 Probes, can I still use Mustang Purple dye as the passive reference dye?

No, these dyes are incompatible as they utilize the same filter set.

Find additional tips, troubleshooting help, and resources within our TaqMan Primers and Probes Support Center.

What are the recommended calibration plates for TaqMan QSY/QSY2 Probes?

For calibration of ABY, JUN, and Cyanine 5 dyes with TaqMan QSY/QSY2 Probes, the complete list of calibration plates for 96 well 0.1 mL, 96 well 0.2 mL, and 384 well plate formats can be found in the TaqMan Assay Multiplex PCR Optimization Guide

For calibration of Cyanine 5.5 dye with TaqMan QSY/QSY2 Probes, please email specialty_oligos@thermofisher.com for calibration plate recommendations.

Find additional tips, troubleshooting help, and resources within our TaqMan Primers and Probes Support Center.

I am looking to order a molecular probe for validation, using specific sequences. How do I order a custom probe?

We do not offer any custom probes for diagnostic purposes.

We do offer custom TaqMan probes for qPCR experiments, which are for Research Use Only.
TaqMan MGB Probe
TaqMan QSY Probe
TaqMan TAMRA Probe
These above probes can be designed in our online tool, Custom TaqMan Probes.

If you would like to order a pre-mix of primers and probe, please check our custom TaqMan Assays.
You can find more information one the Custom TaqMan Gene Expression Assay page on thermofisher.com.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Applications Support Center.

What alternatives do you offer for Cyanine 3 dye/ATTO550N dye and ROX dye/Texas Red dye for use with custom TaqMan probes?

Which buffer is used to reconstitute the TaqMan QSY Probe, 6K, 20K, and 50K pmol (Cat. No. 4482779, 4482777, 4482778) and the TaqMan QSY2 Probe, 6K, 20K, and 50K pmol (Cat. No. A56899, A56900, A56901)?

The TaqMan QSY Probe, 6K, 20K, and 50K pmol (Cat. No. 4482777, 4482778, 4482779) and TaqMan QSY2 Probe, 6K, 20K, and 50K pmol (Cat. No. A56899, A56900, A56901) are reconstituted in 1X TE buffer at a concentration of 100 pmol/µL.

Find additional tips, troubleshooting help, and resources within our TaqMan Primers and Probes Support Center.

What are the excitation and emission profiles for ABY, JUN, Cyanine 5, and Cyanine 5.5 dyes?

ABY dye has an excitation wavelength of 568 nm and emission wavelength of 583 nm.
JUN dye has an excitation wavelength of 606 nm and emission wavelength of 618 nm.
Cynanine 5 dye has an excitation wavelength of 649 nm and emission wavelength of 667 nm.
Cyanine 5.5 dye has an excitation wavelength of 678 nm and emission wavelength of 695 nm.

Please refer to your instrument user guide for additional information on compatibility with different dye channels.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.

I received a shipment of TaqMan probes but I forgot to store them at -20 degrees C and they stayed at room temperature over the weekend. Can you please confirm if the probes are still functional?

TaqMan probes are recommended to be stored at -20 degrees C, but they can be subjected to higher temperature for several days and still retain their quality and stability. Please have a look at our White Paper: Custom Primers and TaqMan Probes shipped at ambient temperature reduce environmental impact and retain their quality and stability, for more details: https://assets.thermofisher.com/TFS-Assets/LSG/brochures/PrimersProbes-ambient-shipping-WhitePaper.pdf

Find additional tips, troubleshooting help, and resources within our TaqMan Primers and Probes Support Center.

What quencher should I use for qPCR multiplexing?

Use QSY quencher for multiplexing up to 4 targets with ABY, JUN, FAM, VIC dyes and use QSY2 quencher for 5- and 6-target multiplexing with Cyanine 5 and Cyanine 5.5 dyes. MGB-NFQ quencher allows for using shorter probes that are more specific and can be used for multiplexing up to 4 targets.

Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Applications Support Center.