Using NCBI Primer-BLAST

NCBI Primer-BLAST can be used to check primers for specificity. It can also be used to design primers (it uses Primer3 for primer design.) We will only use Primer-BLAST to check our primers for specificity, as we will be using Primer3 directly to design our primers.

  • To check your primers for specificity, enter the primer sequences as indicated below (click the image for a larger view).
  • Change the database that will be searched to Genome (because we are using total genomic DNA in our PCR reactions) and the organism to Homo sapiens (usually the default).
  • Click 'Get Primers'.
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