RNA gel electrophoresis

Nick Theodorakis nick_theodorakis at hotmail.com
Sun Mar 7 17:34:25 EST 2004

On 7 Mar 2004 10:24:44 -0000, spnekju at iop.kcl.ac.uk wrote:


>I am running anRNA gell at 80mV but the band are running int he wrong direction- I have checked all the connections and they are correct - the bands I am getting are very strong. Why could they be running in the wrong direction?

You don't give enough details to make a definitive diagnosis, so I'm
going to have to use a crystal ball to guess. Here is my guess:

(1) You are running a typical formaldehyde/MOPS/agarose horizontal gel

(2) You have ethidium bromide in the sample buffer.

(3) When you look at the gel with a UV-transilluminator, you see a
bright fluorescent band migrating toward the negative electrode.

If I have guessed right, then you have it set up correctly, What you
are actually seeing is the unbound ethidium (which is positively
charged) correctly migrating toward the negative end. The RNA (which
is usually not as bright) should be going the other way, if look

If I have guessed wrong, write back with more details.


Nick Theodorakis
nick_theodorakis at hotmail.com
nicholas_theodorakis [at] urmc [dot] rochester [dot] edu 

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