I am trying to design primers for some miRNAs but I keep getting errors pertaining to my minimum and maximum PCR product size. Any help?
What software are you using for primer design? You should not have to select a min and max PCR product size. I usually design so that my primers flank the sequence before or after 250bp. This should work but double check and make sure all other components are ok.
Skylar King Thank you for your response, I am using the NCBI Primer Blast tool for the design and I am expected to input the expected minimum and maximum amplicon size
What sort of errors are you seeing? If you are putting in a target sequence that is too short, then it can be harder to design primers.
I prefer Primer 3 over NCBI Primer Blast. I would still advise you to include 250bp flanking both sides of the sequence to help design your primers.
Thank you Katie A Burnette the target sequence is indeed short, it is a miRNA of about 25bp. Any idea what I can do?
You'll probably have to put in a longer sequence and tell the program to "flank" that region.
if the target is 25bp, I do not think PCR works. go southern or RNAscope something like that.
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