Slanted Bands on Agarose Gels

Chong-Yee Khoo cyk10 at cus.cam.ac.uk
Tue May 24 16:51:13 EST 1994


In article <9405240748.AA15281 at mercury.sfsu.edu> Christopher W Botka,
cwbotka at MERCURY.SFSU.EDU writes:

>Has anyone experienced bands(DNA) that run slanted on an agarose gel? -
>i.e. the bottom of the EtBr stained frag. of DNA seems to be migrating
>faster than the top.  This phenomenon occurs with all samples on the gel
>including the ladder and conc. stds.  However, it only occurs
occasionally,
>and we have not been able to figure out why, although not from lack of
>effort.  We have varied current,  gel set up time, buffer, agarose brand,
>electrical socket (strictly voodoo), to no avail...

How long are you running your gels for? Though the effect is negligible
for short run times, for longer runs, the magnetic field of the earth
begins to interfere. Do you notice this problem with _all_ your gels?
Does the degree of slantedness correlate at all with the length of time
your gel has been running?

One thing you could try would be to try various orientations of your gel
tank, and see whether your gels improve. You could determine magnetic
north
with a hiker's compass. If you can't get your hands on a compass, I find
that a magnet floated on a 42 degree C water bath works quite well.
Remember
to use orange skin for the float, though!

Yours taking-the-piss,

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Chong-Yee Khoo                     E-mail: cyk10 at cus.cam.ac.uk
Wellcome/CRC Institute             Talk:   cyk10 at cy-mac.welc.cam.ac.uk
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