When manually selecting primer and probe sequences using the Primer Express™ software, is there a feature that can evaluate their compliance with Real-Time PCR primer and probe design guidelines?

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Answer

Yes, there is a feature to evaulate complaince of your primer and probe sequences. By copying and pasting the potential primer or TaqMan™ TAMRA probe sequence into the Primer Test Document, you can get % G + C and melting temperature (Tm) information. The Primer/Probe Test can be found by going to TOOLS > PRIMER PROBE TEST TOOL.

If evaluating an MGB probe, you must use the TaqMan™ MGB Quantification option. Guidelines for primer and probe design must be followed as outlined in the Primer Express™ software v3.0 User Manual, which can be found in the Primer Express™ software folder on your computer. You can find a copy on our website as well.

Answer Id: E2155

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I get the following message when trying to start the Primer Express™ software: “Error opening Archive file: Primer Express is unable to open the archive file. Please move this file to another directory and run the Primer Express™ software again to create a new Archive.” How do I solve this problem?

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Answer

This error message can occur while attempting to install the Primer Express software, or sometimes when launching the software after it has been installed on the computer. To create a new archive file, hold down Alt key (to the left of the space bar) while opening the Primer Express™ application. You should get the browser window shown below. Click on “New” to create a New Archive.

The name “PXArchive” will automatically populate in the file name field. You may keep that name or change it to something different. Once you've named the Archive file, click on save. You should now be able to continue with the installation or use of the Primer Express Software.

Answer Id: E2156

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How do I save the primers and probes listed in the Primers Tab search results in Primer Express™ software?

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Click the Save button at the bottom of the Primers page. Open the saved tab delimited text file from within a spreadsheet program, such as Microsoft™ Excel™ software. You may view and modify the file here.

Answer Id: E1796

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Within the Primer Express™ software, what is a "GC Clamp" and what is its impact if I have a GC Clamp at the end of a primer?

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Answer

"GC Clamp" is the number of G or C residues at the 3' end of a primer. In the Primer Express™ software, the GC Clamp can be set to any value, including zero (which is the default). In some cases, a GC Clamp of greater than three will cause no primers to be chosen. When designing primers and probes for Real-Time PCR it is recommended not to have a GC clamp on the 3' end of the primers.

Answer Id: E1797

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I need to see all the primer and probe sequences from an assay design right away. How can I do this?

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Answer

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.

Answer Id: E7513

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Is there a User Manual for Primer Express™ software?

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Yes, there is a Primer Express™ User Manual and an Applications Tutorial that gets loaded into the Primer Express™ software folder when the software is installed onto your computer. In addition, there is the Getting Started Guide: Primer Express™ Software Version 3.0 (http://tools.thermofisher.com/content/sfs/manuals/cms_041902.pdf) and tutorials available on the Primer Express™ product page.

Answer Id: E1000

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Can I use Primer Express™ software on Windows™ 7?

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Answer

Yes, you can use Primer Express™ v3.0.1 on Win7 computers.

Answer Id: E7512

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Where can I find a selected amplicon melting temperature in Primer Express software?

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Answer

You can find the amplicon in the Amplicon Tm column in the Primers and Probes Tab window.

Answer Id: E1798

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