Help me! RNA electrophoresis problem.

Richard V. Giles giles at
Thu Oct 1 07:56:45 EST 1998

Shim Minsub wrote:

> I have a problem when I run RNA formaldehyde gel.  First one is that width of
> band is not equal.  Below 28S RNA, width of band become narrow and shape of 28,
> 18S RNA is heart-shaped, so the resolution is not good.  I use BRL's Horizon 58
> electrophoresis box.
> What is the problem? Please help me.


Not entirely sure what your problem is, but it sounds like an ionic effect to me.
Check that your loading buffer contains 1x MOPS.

An unpleasant option may be to add formaldehyde to the running buffer.  Another
good one is to allow the RNA to settle for 15 minutes or so after loading - before
applying a voltage to the gel.  I've found (empiracly) that all these things
improve resolution in fomaldehyde - agarose gels.


Richard V. Giles Ph.D.
School of Biological Sciences
University of Liverpool
Tel +44/151 794 4389
Fax +44/151 794 4349

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