Fluorophores and Quenchers

Dual-labeled probes (also called hydrolyzation probes or TaqMan® probes) are usually labeled with the reporter at the end 5´ and with the quencher placed at the end 3´. Choice of the reporter depends on excitation and emission channels of the used real-time PCR cycler (almost all real-time PCR cyclers provide a channel for fluorescein - FAM).

Today, BHQ (Black Hole Quencher) type quenchers are usually used as quenchers; they quench a broad spectrum of fluorophores and show no autofluorescence. For more detailed information regarding the use and interplay of the most common fluorophores/ reporters and quenchers, please download the flyer “Fluorophores and Quenchers”.

To learn more about our prices, please login to our webshop and download the current price list. Microsynth supplies hydrolyzation probes which are specified in more detail in the table below.

Product Characteristics:

5‘ Label

3‘ Label

0.04 µmol scale1 0.2 µmol scale1

1.0 µmol scale1

Minimum yield2 Average yield2

Minimum yield2

Average yield2

Minimum yield2

Average yield2

FAM

TAMRA

1 OD

5 nmol

3 OD

15 nmol

2 OD

10 nmol

8 OD

40 nmol

10 OD

50 nmol

30 OD

150 nmol

BHQ-1

9 OD

45 nmol

8 OD

40 nmol

25 OD

125 nmol

HEX

TET

TAMRA n/a n/a

2 OD

10 nmol

8 OD

40 nmol

10 OD

50 nmol

30 OD

150 nmol

AlexaFluor 350

FAM

HEX

TET

Dabcyl

n/a n/a

2 OD

10 nmol

5 OD

25 nmol

10 OD

50 nmol

20 OD

100 nmol

AlexaFluor 350

HEX

JOE

TET

ATTO 425/532

Yakima Yellow

(equivalent to VIC)

BHQ-1

n/a n/a

1.5 OD

7.5 nmol

6 OD

30 nmol

8 OD

40 nmol

25 OD

125 nmol

ATTO 647N

ATTO 620

ATTO 550

(equivalent to NED)

Cy3/Cy5

Dyomics 681

ROX

TAMRA

Texas Red

BHQ-2

n/a n/a

1.5 OD

7.5 nmol

4 OD

20 nmol

8 OD

40 nmol

15 OD

75 nmol

If your desired fluorophore or quencher is not listed in this table, please contact us for availability and pricing.


Some Remarks to the Correlation of Yield and Number of Reactions

In the case of real-time PCR, usually one measurement or reaction requires 20 µl of a solution containing the probe at a concentration of 0.2 pmol/µl. As a consequence, one reaction consumes 4 pmol of a probe. For instance, if you order a 5’ FAM + 3’ TAMRA probe at 0.2 µmol synthesis scale we deliver at least 10 nmol of the specified probe to you. Therefore, you can theoretically perform at least 2’500 reactions (whereas the average delivered amount of ~40 nmol is sufficient for ~10'000 reactions).

Calculation of the number of reactions for real-time PCR (quantity of probe: 4 pmol):

# reactions = delivered amount [nmol] * 1’000 / 4

 

How to Order?

  • Enter our webshop
  • Click on DNA and metRNA in the "Oligonucleotide" domain
  • Select either Normal Entry in order to type or copy/paste the desired sequence information etc. or alternatively select Upload Entry by using our convenient Excel Template (can be downloaded during ordering)
  • Simply select your desired 5' and 3' modification, in this way your oligo is recognized and processed as a TaqMan probe (including thorough HPLC or PAGE purification).

1 The synthesis scale represents the initial amount of 3' bases (starting material).

2 Yields indicated in OD260 apply to a probe consisting of 20 DNA bases; Calculation: 1 OD = 5 nmol (please note that this calculation is based on sequences with virtually homogenous distribution of the 4 DNA bases; it may vary for sequences with high GC contents >70% etc.)







Questions?
Write an e-mail or call us at +41-71-722 83 33

Related Downloads
Fluorophores and Quenchers.pdf
Guidelines for use of fluorophores and quenchers in real-time PCR


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