question about agarose gel - (Jul/28/2007 )
Dear all, I met a problem when I was checking my agarose gel in UV light. I saw some DNA sample was still staying in the vial. They did not run on the agarose gel. Only little sample run on the gel. I never met such problem before. I do not why. 
well there are many reasons for this observation
1- the DNA was not clean enough, as a result it is bound to junk and unable to migrate into the gel matrix
2- after EtOH percipitation, very little of the DNA was actually disolved back into solution. As a resulty the DNA isn't actually in solution, but exist as small insoluble pellets floating in about. Again DNA be recalcitrant to resuspension maybe due to the DNA being dirty (a clean DNA pellet even one of large size should go into solution with little or no help). Alternatively over drying (using a heating block) may result in the same problem, of insoluble pellet.
3- If you are running a dense gel >1.5% agarose, bacterial genome DNA (which sometimes gets pulled down in a bad plasmid prep) will more or less sit in the well. Being so big, they can't migrate far.
4- if you are running genomic DNA, well aside from (1 and 2), your restriction digestis may have failed (due to reason 1)
5- lastly (and this very rarely happens), there is too much salt in the DNA prep. I have only seen this once, when an undergrad resuspended his DNA prep. with working loading dye made by diluted the stock with NaAc solution. 
Yes, every year you learn more things. My theory here, is that if enough ions is in the prep, the salt ions get moved in preference to the DNA. Thus the DNA stands still.
ya, it happens at times.
do not poke the gel too much with the tip while loading
do not poke the gel too much with the tip while loading
and after pipetting, some samples also go out with the tip...
do not poke the gel too much with the tip while loading
and after pipetting, some samples also go out with the tip...
One other thing -very simple error- that has not been mentioned is if your gel is not totally hardened, ie you load your DNA (esp. genomic DNA) before the matrix has formed completely you find that some can get stuck up in the wells-
In my opinion,THe 'DNA' staying in the vial is actually protein.
protein could not run on the agarose gel commonly.
I agree with redmission.
The protein somehow able to shine more and you can see one whole big shining part in your vial.
Try to clean up before running the samples in the agarose.
The protein somehow able to shine more and you can see one whole big shining part in your vial.
Try to clean up before running the samples in the agarose.
oh...I did not know that the protein can be seen under UV light...