Question

Forward primer: 5'-AGTCTACTCGTAACCGGTTACC-3' Reverse primer: 5'-TAAGGCATCATGGTAACCGGTT-3' The two primers above have the melting temperatures between 55C-80C. What is the reason that these two primers will not bind effectively to the region of DNA that we want to amplify?

Answer 1

Short answer is primers are partially complementary.

Step-by-step explanation:

Forward primer: 5'-AGTCTACTCGTAACCGGTTACC-3'

Reverse primer: 5'-TAAGGCATCATGGTAACCGGTT-3'

When we write reverse primer 5' to 3' we can easily see that

3'-TTGGCCAATGG---5' is complementary to the forward primers'

5'---AACCGGTTACC-3' sequence. So instead of binding to the template DNA these primers might bind each other resulting with reduction of efficiency of DNA amplification.