2.1.16.4: In Silico PCR

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    From LibreTexts, under CC BY-NC-SA 4.0, as the source states it; its equations are written in TeX, which the PDF shows typeset. This page at LibreTexts.

    Using the primer sequences, one can determine the size and/or location of a PCR product. This can be done using BLAST or with a program like UGENE.

    Using BLAST

    1. Primers for the PV92 insertion.
      • Forward primer: 5′ GGATCTCAGGGTGGGTGGCAATGCT 3′
      • Reverse primer: 5′ GAAAGGCAAGCTACCAGAAGCCCCAA 3′
    2. Visit BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch.
    3. Paste both primers:
      • GGATCTCAGGGTGGGTGGCAATGCTGAAAGGCAAGCTACCAGAAGCCCCAA
      • Remove the 5′ and 3′ numbers.
    4. Choose “Somewhat Similar”.
      • Locate the locus of the product and the size.

    Using Ugene

    1. Exercise using a human D-Loop Primers.
      • Forward Primer 5’-TTAACTCCACCATTAGCACC-3’
      • Reverse Primer 5’-GAGGATGGTGGTCAAGGGAC-3’
    2. Download the sample Genbank file: Human Mitochondrial Genome.
    3. Open the file in Ugene.
    4. Select the “In Silico PCR” button on the far right (double helix button).
      • Insert forward and reverse primers in the appropriate spaces.

    primerbutton

    5. A PCR product should be noted for one of the sequences after pressing “Find Products anyway“.

    This page titled 2.1.16.4: In Silico PCR was last modified on Mon, 28 Aug 2023 17:40:44 GMT and is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Shannon Clark.