Question

2. Design a primer pair (5 nucleotides each) to amplify only exon 2 of the gene model below. Use the primer pair you designed to model 3 cycles of DNA replication. 5..CGTGACTGATCATGGAGCTACGATCGACTCTCGAAGCTCTAGACGCTCTCGAGAGCTCTCGAATTAGATCGTAATTGCGGTTCA...3'

Answer 1

In order to design the primer pair for amplifying exon 2 of the given gene model, we will first draw the complementary sequence to that given to make it double stranded. Further, since we only want to amplify exon 2, we will consider only that sequence and design the forward and reverse primers for it.

Here is how it can be done.

The given sequence is:

5'-CTCGAAGCTCTAGACGCTCTC-3'

3'-GAGCTTCGAGATCTGCGAGAG-5' (complementary strand)

The forward primer will be on the complementary strand in 5'-3' direction.

3'-GAGCTTCGAGATCTGCGAGAG-5'

5'-CTCGA-3' (Forward primer)

The reverse primer will be on the template strand in 5'-3' direction.

5'-CTCGAAGCTCTAGACGCTCTC-3'

  3'-GAGAG-5' (Reverse Primer)

This reverse primer will be written in 5'-3' direction i.e. 5'-GAGAG-3'

Thus the primer pair for the amplification of exon 2 is :

5'-CTCGA-3' (Forward primer)

5'-GAGAG-3' (Reverse Primer)