DNA Size Discrepency on Agarose Gel

jaydub jaydub at mindless.com
Sat Nov 28 15:09:13 EST 1998


I have run ssDNA samples on an 0.8-percent agarose gel (TAE buffer)
with a "High Mass DNA Ladder".  The ssDNA samples are from bacteriophage
M13 and are all uniform in size, somewhere around 8,000 bases.  The
"High Mass DNA Ladder" is dsDNA and has six bands from 4 kb to 10 kb.

Here is my problem:
I have done three identical runs using these ssDNA samples along with
the Ladder.  The first run gave pleasant results, where my ssDNA bands
were just below the 10 kb standard band, (where they should be).
However, the next two runs, using some of the same samples from the
first run and the same standard, produced different results from the
first.  In these two runs my ssDNA bands were all uniform, but were all
consistently just above the 10 kb standard band.  I know that ssDNA and
dsDNA may run differently, but the last two runs were very consistent
with each other.  (Also, I am sure the ssDNA is quite pure).

If anyone has suggestions or experience on this problem please let me

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