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Weird fragments in my gDNA - (Jan/16/2014 )

Hi guys


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



Attached Image


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.