Question

Your friend is trying to amplify a DNA sequence using PCR, but he didn’t feel too confident about designing the primers, so he ordered two different sets of primers (4 primers total). Unfortunately, neither set produced a visible product when ran on a gel through electrophoresis. Below are the primers that he used and the DNA to be amplified:

DNA template:

5’ ATTCGGACTTG----(750 bases to amplify)----GTCCAGCTAGAGG 3’

3’ TAAGCCTGAAC--------------------------------------CAGGTCGATCTCC 5’

Primer pair #1 (a) 5’ GGACTTG 3’ (b) 5’ GTCCAGC 3’

Primer pair #2 (a) 5’ TTCAGGC 3’ (b) 5’ AGCTGGA 3’

a) With the DNA denatured as below, show where primer pair #1 should anneal. Would this end up in a PCR product, why or why not?

5’ ATTCGGACTTG----(750 bases to amplify)----GTCCAGCTAGAGG 3’

3’ TAAGCCTGAAC--------------------------------------CAGGTCGATCTCC 5’

b) With the DNA denatured as below, show where primer pair #2 should anneal. Would this end up in a PCR product, why or why not?

5’ ATTCGGACTTG----(750 bases to amplify)----GTCCAGCTAGAGG 3’

3’ TAAGCCTGAAC--------------------------------------CAGGTCGATCTCC 5’