I have just used the qiagen PCR clean up kit to clean up my PCR products before sequencing. My pcr products were pretty neat before clean up (ie. no visible mispriming or primer dimers on the gel), but when I run the samples after PCR clean up I am seeing a very unusual stain on the gel that I haven't seen before.
The loading dye has 3 dyes that should be represented at the following:
xylene cyanol - 1000-600bp
bromophenol blue - 200-<100bp
orange g - <100-<100bp
on the gel you can see the faint marks where the dyes are, but I can't explain the bright mark at the base of the gel. Initially I thought it was the loading dye, but I can't see any reason why any of those dyes should interfere with ethidium bromide.
does any one know what it is?
addition details: 2% gel, 100bp ladder, pcr products are approximately 144bp long, so they're as expected. I have seen primer dimers in previous samples (not at clean up stage) and they occur around 40bp.
to me it looks like a high etbr stain spot but I don't understannnd whyy