Hi,
While we are doing genotyping of mice, we observed non-specific band which has main band size.
So we had 3 negative controls : (1) Taq only (2) Taq + primer (3) Taq +gDNA
Surprisingly, we got a 300bp~ band in (2) Taq + primer sample.
Is this a primer contamination?
Is it possible to have a 300bp~ band because of primer contamination?
Thanks in advance.
Sohee
At this size, primer dimer is very unlikely. Seems like your primers picked up something with the enzyme - 16S primers eg could easily do that. Can try to run less cycles and/or run a blast search on your primers
Péter Gyarmati, thanks for your advice! We had 40 cycles in total, which might be too much. We could optimize the PCR cycle in 35 cycles or less. Thanks!
Your taq plus primer and dna picks up this band as well. I agree it is too big for primer dimer but it could be a contaminant in the water used to prepare reagents. If it was post pcr contamination I would expect to see the larger proper band amplifying as well
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