Applied Biosystems™ TaqMan™ QSY and QSY2 Probes

Catalog No.	Product Type	Quantity
A56901	QSY2 Probe	50,000 pmole
44-827-77	QSY Probe	6000 pmol
44-827-78	QSY Probe	20,000 pmol
44-827-79	QSY Probe	50,000 pmol
A56899	QSY2 Probe	6000 pmole
A56900	QSY2 Probe	20,000 pmole

Catalog No. A56901 Supplier Applied Biosystems™ Supplier No. A56901

Description

Applied Biosystems TaqMan QSY and QSY2 probes are dual-labeled probes used for real-time PCR. TaqMan QSY and QSY2 Probes are designed for optimal sensitivity and performance in multiplexed qPCR experiments for detection of up to 6 targets.

Applied Biosystems TaqMan QSY and QSY2 probes are dual-labeled probes used for real-time PCR with Cyanine 5 (Cy5) and Cyanine 5.5 (Cy5.5) reporter dyes. TaqMan QSY and QSY2 Probes are designed for optimal sensitivity and performance in multiplexed qPCR experiments for detection of up to 6 targets. Current users of dark quencher probes, such as Black Hole Quencher (BHQ™) probes, can design custom QSY and QSY2 probes without changing probe sequences.

All TaqMan QSY and QSY2 probes are HPLC-purified and verified by mass spectrometry to help ensure lot-to-lot reproducibility between batches. Thermo Fisher Scientific has been a leader in qPCR probe manufacturing for over 20 years, with expertise in probe synthesis in a facility that is certified to ISO 13485. TaqMan QSY and QSY2 probes can be used for viral pathogen and microbial detection in research samples for healthcare and biopharmaceutical development needs.

Applied Biosystems TaqMan QSY and QSY2 probes are dual-labeled probes used for real-time PCR. They are designed for optimal sensitivity and performance in multiplexed qPCR experiments for detection of up to six targets. Current users of dark quencher probes, such as Black Hole Quencher (BHQ™) probes, can design custom QSY and QSY2 probes without changing probe sequences.

All TaqMan QSY and QSY2 probes are HPLC-purified and verified by mass spectrometry to help ensure lot-to-lot reproducibility between batches. Thermo Fisher Scientific has been a leader in qPCR probe manufacturing for over 20 years, with expertise in probe synthesis in a facility that is certified to ISO 13485. TaqMan QSY and QSY2 probes can be used for viral pathogen and microbial detection in research samples for healthcare and biopharmaceutical development needs.

Features of TaqMan QSY and QSY2 probes include:

• Cyanine 5 and Cyanine 5.5 reporter dyes—new TaqMan QSY2 probes include Cyanine 5 and Cyanine 5.5 reporter dyes, now enabling you to multiplex up to six targets
• Increased sensitivity compared to probes from another leading supplier—detect low-abundance targets, impurities, and fluctuations in bioproduction more accurately
• Multiplexing performance without compromise—use QSY for multiplexing up to four targets with ABY, JUN, FAM, and VIC and use QSY2 for 5th and 6^th target multiplexing with Cyanine 5 and Cyanine 5.5
• Better performance retention when scaling up—consistent performance from singleplex to 6-plex creates a smoother assay development experience
• TaqMan QSY and QSY2 probes have greater dynamic range compared to probes from another leading supplier—enables more accurate detection of a greater range of analyte concentrations
• Get started quickly—BHQ probe sequences can be converted to QSY and QSY2 versions with no redesign needed
• Compatible with our master mixes and validated on our instruments—get increased confidence in the performance of the probes in your lab to help get your products to market faster
• Part of the Thermo Fisher Scientific qPCR ecosystem—our teams can support you in all components of the real‐time PCR (qPCR) workflow

Guaranteed yield
The unit size you select is based on the minimum amount we will deliver, not on synthesis starting amount. Ensure that you are considering the guaranteed yield (amount of probe you are actually receiving) when calculating price per reaction.

Approximate ship times

• 4 to 10 days in North America
• 5 to 10 days in Europe

Calibration
For calibration of ABY, JUN, and Cyanine 5, the complete list of calibration plates for 96-well, 0.1 mL; 96-well, 0.2 mL; and 384-well plate formats are in the Multiplexing Optimization Guide in the document section. For Calibration of Cyanine 5.5, please email your request to specialty_oligos@thermofisher.com.

We also offer Applied Biosystems custom primers and other types of TaqMan probes.

Need a different dye or concentration or a larger lot size? The TaqMan Custom Assay and Oligo Service offers custom products that you can tailor to meet your experimental needs.

Specifications

• 3'Primer Modification: QSY 2
• 5'Primer Modification: Cyanine 5, Cyanine 5.5
• Content And Storage: 1 tube containing a dual-labeled probe in solution or dried down. Store at –15°C to –25°C.
• Detection Method: Primer-probe
• Form: Liquid or Dried Down
• Format: Tube
• PCR Method: qPCR
• Reaction Speed: Fast
• For Use With (Equipment): 7500 System, 7500 Fast System, 7900HT System, StepOne™, StepOnePlus™, ViiA™ 7 System, QuantStudio™ 3, QuantStudio™ 5, QuantStudio™ 6 Flex, QuantStudio™ 7 Flex, QuantStudio 6 Pro, QuantStudio 7 Pro, QuantStudio™ 12k Flex
• Green Features: Sustainable packaging
• Internal Probe Modification: None
• Product Line: TaqMan
• Product Type: QSY2 Probe
• Purification Method: HPLC
• Quantity: 50,000 pmole
• Shipping Condition: Room Temperature

Frequently Asked Questions (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.

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

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.

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.

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.

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.

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.

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

Cyanine 3 dye/ATTO550N dye alternative: ABY dye (Excitation: 550 ± 10 nm; Emission: 586 ± 10 nm)

ROX dye/Texas Red dye alternative: JUN dye (Excitation: 580 ± 10 nm; Emission: 623 ± 14 nm)

Please email specialty_oligos@thermofisher.com for more information.

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.

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.

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

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.