You have designed a PCR primer with the sequence ATTTTCGCGCG

You have designed a PCR primer with the sequence ATTTTCGCGCGTAGG. The approximate Tm value for this primer is _____oC.

Solution

The Tm or melting point of a primer or DNA strand is an important quantity which determines the temperature t which strand melting takes place in polymerase chain reaction. The sequence given in the question contains a total of 15 nucleotides. For this sequence, the Tm can be calculated according to formula given below:

Tm = 64.9 +41*(aG+bC-16.4)/(cA+dT+aG+bC), where, a, b, c and d represent the number of nucleotides

Here, a = 5, b = 3, c= 2, d=5

Thus, putting in equation,

Tm = 64.9 + 41 (5+3-16.4)/(2+5+5+3) or 64.9 + 41(-8.16)/15

Or Tm = 64.9 -22.74 or 41.36 degree celcius.