Hello,
I'm using PCR to assess the differences between the banding patterns of a microsatellite in different salamander species. In my resulting gel, there's extra unclear bands underneath the clear bands in the A.texanum and A. laterale samples, and above A. jeffersonianum's clear bands. What do these unclear bands indicate?
Hi,
I think most probably these bands represent non-specific amplicons or primer dimer.
Hello Zhi Xiong Chong
Thank you for your reply. But if those bands are primer dimers, they should appear in all 8 lanes, are they not? Since all 8 lanes have identical MasterMix solution. It's interesting that each species has a unique extra band
Kareem Alshudaifat But why does the primer dimers have a different length travelled for each species and they are very consistent for one species too. If they are primer dimers, all lanes should have extra bands at identical position, do they not?
Kareem Alshudaifat Sorry that I did not indicate it on the photo but yes, the second lane is the control water. However, if the extra band is caused by a contaminant, why are these contaminant bands show up at the identical position within one species, but differ between the three species?
Hello Pamela Rubí Cejudo Nevarez
I interpret those extra bands as non-specifics, which apparently are quite common in microsatellite analysis.
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