I am working on some DNA extractions and getting some very odd patterns. I am attaching a picture of a gel.
First we carried out a phenol-chloroform extraction. We detected some impurities, so ran a Qiagen DNAeasy clean up on these extractions. This caused some degradation. This is all expected. Some of the P-C only samples were degraded as well, but the extra step caused more degradation.
What is bothering me is the banding pattern observed at low molecular weights. It is more visible in the more degraded samples. Has anybody seen anything like this before?
We have checked for contamination. These are RNase treated. The most stumping thing is the pattern is always stronger in the degraded samples. We have checked the loading buffers. Run the gels with EtBr and gel red. Is the genomic DNA fragmenting in a regular fashion (that sounds crazy).
In the gel pictures, extractions from the same individual are side by side and have the same letter, the number denotes how many extraction steps were taken (1= P-C only, 2= P-C & DNAeasy)
Any ideas, or thoughts are most welcome. Everyone around here is a bit stumped.
This DNA is from various species of bee (Bombus sp.)
Thank you in advance for any help you can provide!