Inexplicable DNA degradation in electrophoresis tanks!

Darren Tyson tysondr at
Mon Jan 27 11:50:47 EST 1997

Caroline Jones wrote:
>         We have been running PCR amplified DNA in 2 rows on 1.2% agarose
> gels, made up and run in 1% TAE buffer in horizontal electrophoresis
> tanks.  Since the new year, one tank (A) has been producing gels onwhich
> all samples are degraded, including the size marker, after a 3hr run at
> 90V.  This degradation worsened and progressively spread up the gels for
> subsequent runs.  Any contamination from reagents/ samples was eliminated;
> and the tanks were rinsed in decon-90.  The trays were subjected to both
> 5% HCl and 0.5M NaOH rinses without any apparent improvement.  A tray from
> another uncontaminated tank (B) was then run in tank A, also producing a
> gel with the lower row of samples degraded.  When returned to its own tank
> and run again the samples were still degraded.
>         Do you know of, or, have you experienced similar problems with
> your electrophoresis?  Is it plausible that our tanks could be
> contaminated with an organism which is secreting enzymes into its
> surroundings?  Do you know of anyway to solve this problem?  We would be
> really grateful for any help at all as this is baffling us!  Thanks very
> much!!
>         Caroline Jones.

I think the time that the gel polymerizes makes a big difference.  I
believe if the gel hasn't had enough time to polymerize this could
prevent the DNA from being resolved into distinct bands.  If you think
this could be the problem in your instance, try allowing to polymerize
wrapped in plastic O/N at 4degC (overkill, I know, but it will determine
if this is the problem).


Darren Tyson
Ph.D. Candidate in Cell and Molecular Biology
Saint Louis University
tysondr at or darren at

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