If a 20bp primer differs from template DNA by 20bp, can PCR work? - (Aug/28/2010 )
I was trying to PCR-amplify using a primer of around 20bp and it work.
Now when I check my data it seems to me that the primer they gave me to work with has a difference of 7bp in relation to the template DNA.
I wanted to ask if 7bp difference between primer and DNA template should normally make the PCR not work. In this case I might have entered the data (the primer sequence) in my notebook incorrecly.
Or would the PCR still work with the 7bp difference?
It depends on where the differences are and on your PCR conditions -- generally speaking, if the differences at the 3' end, it will not work, if they're in the middle or scattered through out the primer it might work, and if they're at the 5' end, it will work.