Strange problem with agarose gel electrophoresis

Joseph C. Bagshaw jbagshaw at
Wed Apr 25 09:54:12 EST 2001

The use of red and black to desginate the anode and cathode, respectively,
goes back much further than the advent of kits with multi-colored caps.
It is the standard convention for all electrical devices that input or
output direct current.  I have never seen any part of an electrophesis
apparatus, from power supply to box, that was not so coded.

In my _undergraduate_ course on Recombinant DNA Techniques and
Applications, I remind my students that DNA is highly negatively charged
because of the phosphate groups.  I teach them that because the charge
density on all DNA molecules is the same, all will migrate together in a
DC field in the absence of friction.  I teach them that the agarose gel
enables fractionation by creating frictional resistance, and that the
DNA fragments will always migrate toward the anode.  Finally, I teach them
a simple phrase: "Run to the red".  If they remember that, they will never
commit retrophoresis.

 ********************  HAVE GENES, WILL TRAVEL  ********************
Joe Bagshaw, Worcester Polytechnic Institute
jbagshaw at
Roadkill on the information superhighway.

On 22 Apr 2001, Dr. Hiranya S. Roychowdhury wrote:

> Hehe, Nick, I am glad that at least some us of still get the humor.
> But, seriously, the geometric-dependency among workers are not unique to
> any particular geographic location. Then there are those who are
> color-bound (as in "red capped", "blue capped", "yello capped", etc.) and
> the kit-makers have made it a point to drive these color-codedness of
> reactants to the hilt. So, it is hardly a surprise when the anodes and
> cathodes get referred to as Red and black. It is also not unexpected that
> people would mistake humor for genuine ignorance, and that also,
> alarmingly, shows the level of expectation in the community.
> Hiranya.
> At 12:40 AM 4/22/01 GMT, Nick Theodorakis wrote:
> >In < at>, Dr. Hiranya S.
> >Roychowdhury wrote:
> >
> >[...]
> >
> >Believe it or not, Hiranya, there are some people who are incapable of
> >processing sarcasm or irony, and might have misunderstood you post! ;-P
> >
> >But I am reminded of another story. An un-named postdoc once or twice ran her
> >western blot backwards; she explained that in her grad. lab, the
> apparattus was
> >set up to run "left to right" (or right to left, whatever) and she had
> >remembered the geometric arrangement of the transfer apparattus rather
> than the
> >physical principles involved.
> >
> >Nick
> >
> >--
> >Nick Theodorakis
> >nicholas_theodorakis at
> >"Never, ever, shake a postdoc. Never."
> >
> >
> Dr. Hiranya Sankar Roychowdhury
> College Asst. Prof.
> Molecular Biology,
> Dept. of Chemistry & Biochemistry
> Box 30001 - 3MLS
> New Mexico State University
> Las Cruces, NM 88003
> Lab: (505) 646 4722
> Office: (505) 646 8256
> hroychow at
> ---

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