Question

The forward and reverse PCR primers used for the amplification of a VNTR locus on chromosome number 4 are 20 bases and 21 bases long, respectively. The 3’ base of the forward primer is 53 bases away from the first repeat. The 3’ base of the reverse primer is 28 bases away from the first repeat in that direction. Each repeat unit is 60 bases in length. A person has, on one of their number 4 chromosomes, 6 repeats. How long (in bp) should its PCR product be?

Answer 1

The repeats which occur together on a chromosome are referred to as VNTR. The length of each repeat is 60bp.

The first primer is 20bp and is 53 bp away from 1st repeat. Therefore, the total length of sequence amplified by the first primer till 1st repeat = 20+53 = 73bp. Beyond this point 6 repeats on 60 bp are present, hence, the length becomes = 73 + (60X6) = 433bp.

Now the reverse primer which is 21bp in length is located 28bp from the repeat on its side. Reverse primer comes from the opposite direction, so it must be present after the 6 repeats.

The total length of the amplified region = 433 + 28 + 21 = 482 bp.