2-D: Orienting first dimension?

Bob Steinberg rsteinbe at etowah.uokhsc.edu
Tue Jun 17 11:38:41 EST 1997

Jerry Kropp wrote:
> Don't laugh...
> I want to run a mess of first dimension (tube) gels and freeze them away
> for later slab gel (second dimension) analysis. So I expel the "worms"
> into a test tube. Now I can no longer tell which end is which.
> I tried injecting a little India ink into the top of the noodle, but it
> didn't stay.
> Tried soaking the ends of the glass tubes containing unexpelled gel in
> bromphenol blue, but the dye wouldn't diffuse into the gel.
> I'm sure all you 2-D studs have solved this problem, so please clue me
> in--via email, please.
> TIA,
> Jerry
> --
> Phonetic isn't
We've never had much problem with this, since the orientation could be
determined after the second dimension was run from the final
autoradiographic or staining pattern. (Also, there is often a
constriction or partial disintegration near the basic end of the gel
caused by the coalescence of H+ and OH- ions at pH 7.) On occasions, we
have cut our gels so that we could run portions of several first
dimension gels on a single second dimension gel-- in this case, we cut
one end at an angle to mark the orientation. I believe O'Farrell used to
deal with this issue by using a needle to insert a small piece of dark
thread at one end of the gel.

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