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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 Universal Multiplex (UM)-based assays using the UM Converter web tool (currently in Alpha Release version).

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UM Converter

To create Universal Multiplex (UM) assays, a UM adapter sequence is appended to each forward primer. This tool first analyzes your existing primer sequences for potential issues that could hinder assay performance, such as primer secondary structures, primer dimer, or cross-reactivity between sequences. After these checks, the UM Converter automatically identifies and appends the optimal UM adapter sequence to each of your forward primers, creating UM primers suitable for multiplexing up to four targets.

Using the tool

1. Connect to the UM Converter here.
2. Upload assay information using the Excel template form or fill in the table for each target with:
   • Target name: A unique name for your DNA sequence of interest (no special characters)
   • Amplicon sequence (optional)
   • Probe sequence (optional)
   • Forward primer sequence
   • Reverse primer sequence
3. Click 'Run cross-reactivity check'. This step analyzes whether there are significant interactions across the provided primer sequences. The list of significant interaction is for information only. It can be used to interpret if any primers need to be redesigned to reduce the level of undesirable interactions before proceeding to designing the UM assay.
4. Once the result of the cross-reactivity is displayed, you can proceed to click 'Run UM primer design' to generate the designs for UM sequences. The design process may take a few minutes.
5. Download converted UM primer set: The resulting table contains up to 5 designs for the set of provided primers with the UM adapter sequences appended to the forward primers. The design with the least amount of unfavorable interactions after the addition of UM adapter sequences is ranked highest. In most cases, we recommend using the first solution (i.e. the first row in the resulting table).

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After performing the UM design, you are now ready to get started testing your UM assay on the Countable platform.

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