Weird fragments in my gDNA - (Jan/16/2014 )
I'm extracting DNA from several tissue types (muscle and liver) of teleost fish, with the aim of performing a 5mC ELISA assay.
I've extracted DNA from a few samples as a test for a new DNA prep method, so I could see how the DNA turns out before I did the rest of my samples.
As you can see in the attached picture, I don't just have nice HMW gDNA bands - but I can't figure out what the low molecular weight fragments are. They seem to form 2 distinct bands, but are too small (I think?) for RNA. I don't know 28S/18S rRNA size for fish species, but these fragments are <500bp.
I did an RNase treatment as well - is it possible that these bands are partially degraded RNA?
Thanks very much
The smeary stuff at the bottom of the gel is either degraded DNA or RNA.
Since there are consistently 2 bands of the same size at the low molecular weight region, I would guess that they are RNA rather than degraded DNA. Do keep in mind that RNA do not run like DNA on a non-denaturing gel.