What if we used 45C instead of 65C as annealing temperature of colony pcr? Is there no band or band on more than we expected (I mean at 3kb instead of 1kb)?
The optimal temperature of annealing for PCR depends on primer sequences. There are a lot of programs on-line that you can use to calculate the right temperature for your PCR. Usually if the temperature is lower you obtain more aspecific products. You should also fix the optimal time of elongation. Many Taq polymerases require 1min for 1 kb.
Perhaps I am not fully understanding your question, but it looks like you are asking what will happen in a PCR run with annealing temperature set to 45oC instead of 65oC? I am also assuming you mean colony PCR as in screening transformed bacteria for positive clones in a cloning experiment?
Your primer will anneal and amplify the target you want (if this should be 1kb, then you will have a band there) at this lower temperature, but you may also have mis-annealing, where a smaller portion of your primer anneals elsewhere and amplifies a different portion of your DNA template. This will cause a competition to be set up between the specific amplification you wanted and any mis-annealing products. It's perfectly possible that at this temperature you will have just the band you wanted, or you may end up with a ladder of bands.
I don't know what you mean by your expected 1kb band becoming a 3kb band.
Why ask? If you did this by accident, then surely you know the answer now - so what happened?
The annealing temperature depends on the primer you designed. 45 instead of the optimal, I guess, 65 could result in non specific amplification which seems to be in your case. Also for colony PCR you have to be careful with the amount of bacteria you add to the PCR mix, too much bacteria result in no amplification or mis-amplification.
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