Working From Home: An overview of primer design workflows in MacVector.

Working from home?. We want to help familiarize you with the wide range of functionality in MacVector that you may never have used before. Here’s an overview of workflows for designing, testing, documenting and storing primers. You may not have a PCR machine on the kitchen table, but why not take the time to store all your lab’s regularly used primers in MacVector’s Primer Database.

Amplifying a gene

You can design a set of primers to amplify a gene in as little as three mouse clicks.

  1. Open your sequence.
  2. Open the MAP view, and click on a feature.
  3. Go to ANALYZE | PRIMER DESIGN/TEST(PAIRS).
  4. Click OK.

Design a single targeted primer with a tail.

QuickTest Primer tool gives great flexibility for designing primers with tails or mismatches.

  1. Select a 20 bp region around the location you want your primer to be.
  2. Click ANALYZE > QUICKTEST PRIMER.
  3. Slide the primer along your template until the oligo is optimal.
  4. Add a restriction site or mutation in the optional tail.
  5. Hover over a green (or red) putative restriction site to view the change to your sequence.
  6. Double click on that putative site to add to your primer. Watch how the coding is changed.
  7. Click Add to Database.. to save your primer.
MacVector

Test a pair of primers.

You can map a pair of primers against your template to see how well they would amplify your target.

  1. Open your template sequence
  2. Go to ANALYZE > PRIMER DESIGN/TEST(PAIRS).
  3. For the left primer click USE THIS Primer
  4. Type or paste in your forward primer
  5. Repeat for the reverse primer
  6. Click TEST

To save a primer from QT Primer to the Primer Database.

  1. Open ANALYZE > QUICKTEST PRIMER (INDIVIDUAL)
  2. Design your primer
  3. Click ADD TO…
  4. Give the primer a name and add a comment. Click OK

To save a primer from Primer Design to the Primer Database.

  1. Open ANALYZE > PRIMER DESIGN/TEST (PAIRS)
  2. Design your primer pair
  3. In the spreadsheet right click on a primer
  4. Choose ADD PRIMER TO DATABASE
  5. Give the primer a name and add a comment. Click OK

To use the Primer Database Search:

  1. Open your sequence
  2. Select ANALYZE > PRIMER DATABASE SEARCH
  3. Choose parameters and click OK

Design a primer to match an existing primer from the primer database

The Primer database allows you to store your own collection of primers. You can design new primers to match regularly used ones.

  1. Open your template sequence
  2. Switch to the Map tab and select the region you want to amplify.
  3. Go to ANALYZE | PRIMER DESIGN/TEST(PAIRS).
  4. For the left primer click USE THIS Primer
  5. Use the drop down menu to enter the existing primer from the primer database
  6. Click OK
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