Question

A labeled primer that is known to hybridize to human DNA at 60 different sites in the genome is used to prime human DNA for the PCR reaction. A six base pair sequence (GACATT) is used as an unlabelled return primer for this PCR reaction. The resulting solution (after 20 thermal cycles) is run on an electrophoresis gel. On the average, how long (in base pairs) will the DNA produced in the above PCR experiment be?

Answer 1

The average length of the DNA produced is 36 base pairs.

How to find average length?

To calculate the average length of the DNA produced in this experiment, consider the following factors:

Length of the labeled primer: This primer hybridizes to human DNA at 60 different sites, implying its length is variable and can be anywhere between 6 and 60 base pairs. For simplicity, let's assume an average length of 30 base pairs for the labeled primer.

Length of the unlabeled return primer: This primer is a fixed sequence of 6 base pairs (GACATT).

Specificity of the primers: Although the labeled primer can bind at multiple locations, the specific binding site used in each PCR cycle will determine the length of the amplified fragment. We can assume random selection of binding sites for simplicity.

Therefore, the average length of the DNA produced can be calculated as:

Average length = Length of labeled primer + Length of unlabeled return primer

Average length = 30 base pairs + 6 base pairs

= 36 base pairs

Answer 2

The information is not complete in the question to say clearly that how long will be the PCR amplified product. Firstly, it is mentioned that the primer sequence would bind to 60 different sites in the genome. So, there will be 60 different PCR products. Each PCR product could be of different length. This is because we don't know that what is the length of each gene which is going to be amplified in all those 60 cases. Therefore, it is not possible to say what would be the length (in base pairs) of each PCR product as well as the average length. More information is needed to conclude.