Designing and testing primers in MacVector – part 1

MacVector has many different primer tools for different purposes. In this, the first of a series of articles I want to present an overview of primer design in MacVector, and when it’s best to use which tool. I’ll also talk about what’s coming next in future releases.

Design Primers (Primer3)

The most flexible tool was introduced in MacVector 10. It provides a interface to Primer3. The dialogue is meant to be as flexible as possible and can cope with testing, designing, and even to find matching primers for a known one. You can also design internal primers for use in realtime and qPCR.

Out of all the primer tools Design Primers (Primer3) is the most tightly integrated into the MacVector point and click way of working. From the Map view you can design a pair of primers to amplify a feature in as little as three mouse clicks.

Primer3_Capture2.jpg

PCR Primer Pairs

PCR Primer Pairs has been in MacVector for many versions. The output is a text file and a graphical non-interactive map, however, it is very detailed and shows extra information that you may need. For example it will provide the optimal Tm to use for your PCR (rather than the Tm of your product and primer sequences). By default this tool will show pairs of primers to produce a specific product size, rather than amplify a certain region. To do this you need to specify two flanking regions.

Test PRIMER PAIRS

Whereas the output from this tool is fairly rudimentary, it does provide extra data about your primers that Design Primers will not. For example the optimal Tm to use for your PCR. It will also supply details about which bases could potentially form primer-primer or primer-dimer bonds. It will also show a more detailed view of the actual alignment formed between primer and template. Use this tool if Design Primers fails with stringent primer-primer interaction values.

Sequencing Primers/Probes

So far this is your only option for designing sequencing primers in MacVector. It produces a fairly detailed report, but does not show the actual location of the priming site.

Test Sequencing Primers/Probes

Again this is your only option for testing an existing sequencing primer. It produces a fairly detailed report that is similar to the text report provided by Test PRIMER PAIRS.

In the next post I’ll talk about Primer3 in more detail and how to design pairs of primers for usual cases. I’ll also show you some tips to get more out of this tool.

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