How to calculate number of DNA molecules synthesized after 'n' no. cycles with single primer (either only forward primer or reverse primer)? Is there any formula to calculate the DNA yield after such PCR?

Supposing, I am setting a PCR reaction for 100 template DNA molecules for 30 cycles, with only one primer - forward primer for target gene. How many DNA molecules will be generated at the end of 30 cycles. All other conditions remain the same.



1 Answer 1


Technically, if you use only 1 primer, it will not be PCR anymore.

But that's what gonna happen if you have 100 template DNA molecules (made of strand A and complimentary strand B) and abundance of primer (say, 10x, or 1000 molecules):

  1. At first cycle primers will bind to template DNA, but only to one strand (for example, A)
  2. DNA polymerase will extend those primers, creating complimentary strands B'. Some strands B' will be shorter than template because DNA pol is not perfect
  3. DNA-primer complex will melt at the beginning of cycle 2
  4. At the beginning of cycle 2 primer molecules will again bind to template, again to strands A, and process continues

Since there is no step where strand A is being copied, this process will be linear, not a "chain reaction". At each cycle you will get the same amount of strands B'.

It is hard to say how much B' molecules you will get at each cycle, but at the end of 30 cycles, it will be at best 30x of the first cycle. Remember, though, that DNA polymerase degrades, and cycle 30 will be less efficient than cycle 1.

Assuming perfect polymerase, and that extension time is long enough, you will get 100 strands B' on cycle 1, 100 strands B' on cycle 2 and so on. At the end of 30 cycles you will have 30x100 strands B', and 100 strands A and 100 strands B.


You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .