DNA question

Question

Below is a theoretical section of DNA. Design two primers that are 10 base pairs (bp) long that
will amplify this section of DNA in a PCR reaction (‘N’ refers to non-specific ‘nucleotide’).

3’–A C gT g A A C T g C C T nnn......nnnC C gT g T A T C T C T T–5’
5’–T g C A C T T g A C g g A nnn......nnnggC A C A T A g A g A A–3’

Answer 1

Sonia:

Here are some tips that will help you answer this question:

1) The primers need to anneal perfectly to the template

2) ***Don't forget that the two strands of DNA are ANTI-parallel (note that the 5' and 3' ends of the two sequences are opposite one another)

3) The 'magic' of PCR is that each PRODUCT of one primer can act as a TEMPLATE for future rounds. So what relationship must the two primers have to one another such that the PRODUCT of primer 1 is the TEMPLATE for primer 2 and vice versa? Which DIRECTION must each primer 'go' for this to happen (remember DNA synthesis is FROM the 5' end adding ONTO the 3' end). Should they sit on the SAME strand or DIFFERENT strands?

 

Cheers

Bruce