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The Countable Labs oligo design web tools can be used to design and optimize oligos for Countable PCR assays from existing assays. Here, you can learn how to design a probe additive for your existing hydrolysis probe (HP)-based assay using the PA Designer web tool (currently in Alpha Release version).

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PA Designer

Probe additives (PAs) are oligos with a 3’ quencher and partial complementarity to the 5’ end of a TaqMan hydrolysis probe. This helps to enhance quenching efficiency and suppress background fluorescence that can affect counting accuracy. It is strongly recommended that you include a PA with any TaqMan hydrolysis probe in a Countable PCR assay. For more information about PAs, please visit this page.

The PA Designer web tool will automatically generate a PA sequence for each TaqMan hydrolysis probe sequence and an ordering form with the PA sequences to be used for purchasing from oligo manufacturers.

Using the tool

1. Connect to the PA Designer here.

2. Input your probe sequences: Download the Excel template or manually input the following for each hydrolysis probe:

   • Probe Name: A unique name for your probe (no special characters)
   • 5’ fluorophore
   • Probe sequence
   • Corresponding 3’ quencher: The quencher molecule should correspond to your selected 5' fluorophore.

3. Download Probe-PA pairs as a CSV file.

   • The resulting table will display the generated PA sequences along with key information about both your probes and PA, including Tm, oligo length (bp), and %GC content.

4. Generate and download the order form by inputting the following:

   • Oligo scale: PAs require a minimum scale of 100 nmol
   • Purification method: PAs require HPLC purification

   You can download this file use it for purchasing the PAs from oligo manufacturers.

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After designing the PAs, you are now ready to get started testing your TaqMan hydrolysis probe-based assay on the Countable platform.

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