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Custom DNA Probes
Choosing the Right Probe
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There are a selection of possible probes that can be used for qPCR and each has advantages for different applications. The summary below highlights the applications of commonly used probes.
| Application Reference Guide |
| (For additional product information, click on the column headers below.) |
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SYBR® Green I |
Dual-Labeled Probes |
Dual-Labeled LNA® Probes |
Molecular Beacons* |
LightCycler® Probes* |
Scorpions™ Probes* |
| APPLICATION |
| Mass screening |
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| Microarray validation |
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| Multiple target genes / few samples |
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| SNP detection |
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| Allelic discrimination |
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| Pathogen detection |
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| Multiplex |
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| Viral load quantification |
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| Gene expression |
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| Gene copy determination |
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| End point genotyping |
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| End point genotyping |
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| *LNA can be incorporated into the probes for improved specificity. |
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| Spectral Properties Table |
| Dye |
Max.
EX (nm) |
Max.
EM (nm) |
Compatible
Quencher |
| 6-FAM™ |
494 |
515 |
BHQ-1, TAMRA |
| JOE™ |
520 |
548 |
BHQ-1, TAMRA |
| TET™ |
521 |
536 |
BHQ-1, TAMRA |
| Cal Fluor® Gold 5401 |
520 |
548 |
BHQ-1 |
| HEX™2 |
535 |
555 |
BHQ-1, TAMRA |
| Cal Fluor® Orange 5602 |
522 |
541 |
BHQ-1 |
| TAMRA™ |
555 |
576 |
BHQ-2 |
| Cy3® |
550 |
570 |
BHQ-2 |
| Quasar® 5703 |
548 |
566 |
BHQ-2 |
| Cal Fluor® Red 5904 |
565 |
588 |
BHQ-2 |
| ROX™ |
573 |
602 |
BHQ-2 |
| Texas Red® |
583 |
603 |
BHQ-2 |
| Cy5® |
651 |
674 |
BHQ-3 |
| Quasar 6705 |
647 |
667 |
BHQ-3 |
| Cy5.5® |
675 |
694 |
BHQ-3 |
1JOE/TET alternative
2VIC® alternative
3Cy3 alternative
4TAMRA alternative
5Cy5 alternative |
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| Fluorophores and Instrument Compatibility Table |
| Platform |
SYBR
Green I |
FAM |
HEX |
JOE |
ROX |
TET |
Cy3 |
Cy5 |
TAMRA |
Texas
Red |
LC Red
640 |
LC Red
705 |
| ABI 7900HT |
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| ABI 7300 |
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| ABI 7500 |
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| ABI 7700 |
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| ABI 7000 |
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| Bio-Rad iCycler iQ |
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| Bio-Rad Opticon® 2 |
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| Bio-Rad Chromo4™ |
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| Stratagene Mx4000® |
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| Stratagene Mx3000P® |
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| Stratagene Mx3005P® |
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| Roche LightCycler® |
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| Roche LightCycler 2 |
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| Roche LightCycler 480 |
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| Cepheid SmartCycler® |
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| Cepheid SmartCycler II |
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| Corbett Rotor-Gene™ 6000 |
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| Eppendorf Mastercycler® realplex |
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| Note: Not all qPCR instruments or fluorophores are listed. Contact the instrument manufacturer for details on compatible fluorophores |
Sigma® is a licensed supplier of a variety of dyes and quenchers and continually adds to its portfolio of new chemistries. For assistance in the design of your probe and/or assays, submit your request at sigma.com/designmyprobe.
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