I am using universal 16S rRNA primers to screen samples of genomic fungal DNA for the presence of bacterial DNA. The resulting band should be 1460bps, but there are lots of other bands of larger and smaller sizes when I run my PCR samples. I was wondering if there could possibly be places in the fungal genome where the primers may bind and amplify. In some samples I have seen a band at about the correct size, but we haven't done sequencing yet to verify it. Is there a way to screen a fungal genome for places where the primers might bind to explain the extra bands?
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