Question about RAPD PCR - (Nov/24/2009 )
My PI brought up a question which I am having trouble figuring out regarding RAPD PCR. I am aware that this technique makes use of an arbitrary random primer. and that:
Different primers used on same genome *may* yield different amplified sequences
Same primers used on different genomes *may* yield different amplified sequences
Her question was: is there an advantage to comparing DNA band patterns by using *different* primers?
And well...since there's a chance that it may yield in different amplified sequences, I guess so...but I am not sure if it's worth the trouble or not. How are we able to know?
Thanks in advance!
With RAPDs you need to use multiple primers in separate reactions across a range of samples to ensure that you are looking at consistent banding patterns and that the results you get from one primer are not biasing your analysis.
You cannot compare different primers on one genome, but you can compare different genomes using one primer.
that makes sense. thank you very much!