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The DNA sequence below is 300 bases long. This is only one strand of DNA going from 5 starting at base 1081 to 3 ending at
You want to measure IL-6 inflammatory gene levels in normal mice vs diabetic mice; 1) What results do you expect if you use s
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Answer #1

First, we need to write the complementary strand to the template strand. However, we may not write the entire strand, only the two ends (20 nucleotides long) would suffice. This is because, primers are approximately 20 bp in length, though it may vary depending on one's requirements.

Starting from the base pair 1081,

5'- CAGTATCAGGTGGTGGCCCC-3' (1st 20 nucleotides of the template strand)

3'- GTCATAGTCCACCACCGGGG-5' (complementary strand)

Forward primer will bind to the 3' end og the complementary strand and synthesize DNA in 5'- 3' direction

3'- GTCATAGTCCACCACCGGGG-5'

5'- CAGTATCAGGTGGTGGCCCC-3' (Forward Primer)

Reverse primer can be designed using the template strand.

Here also, primer binds to the 3' end of the template strand and synthesizes DNA in 5' - 3' direction.

3' end of the template strand will be strand from nucleotides 1211 to 1230 (Since we need to find primers for 150 nt long DNA)

5' - CTCTCTCCTCATAGGTGAAA-3' (Template strand)

3' -GAGAGAGGAGTATCCACTTT-5' ( Reverse Primer)

Reverse primer can be written as

5' - TTTCACCTATGAGGAGAGAG-3'

1. Length of DNA sequence = Forward Primer + Reverse Primer + Intervening DNA

In this case, total length of DNA is 150.

Thus,

150 = 20 + 20 + Intervening DNA

150-40 = Intervening DNA

Intervening DNA = 110

Therefore, length of intervening DNA i.e. DNA synthesized using this primer design is 110 nucleotides.

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