Plate cleaning "redux"

Skip Vaught, Brian Coullahan, Mark Schwartz, and Felisa Blackmer Skip Vaught, Brian Coullahan, Mark Schwartz, and Felisa Blackmer
Thu Apr 29 03:50:26 EST 1999

Hello again, sequencing friends,

Thanks for your excellent responses to my query about plate cleaning.  It's
clear that there are several approaches to good results.

Well, I'm slightly embarrassed, no, make that very embarrassed to admit
that it happened again on one of yesterday's gels.  It happened on a set of
plates that worked perfectly the day before.  "That's odd", I said to
myself, "how could a build up of comtaminating molecules on the gel side of
the plates be so abrupt as to effect  mobility in one day?"  As I forlornly
looked around for the most corrosive liquid I could find to immerse the
plates into (say, a couple of nights in chromerge), I noticed something
that may, or may not, shed some light on the mystery. The notched plate was
on backwards! (Whew, this admission is very cathartic.)

We etch vertical lines on the corners of our plates so that they are always
oriented correctly. But, because vertical lines are symmetrical, you have
to look closely to determine what side the etch is on (we are  going to
etch something asymmetrical on the glass to eliminate goofs, and I'm going
to insist that every technician orient the plates in the drying rack the
same way).

What do you folks think?  Can the "dirty" side of a plate affect mobility?
Those of you who hand wash certainly notice that the gel side of the plates
sheet water beautifully, while the "dirty" side has areas that bead water
and other areas that sheet.  The beading is especially prominent on the
"dirty" side of the notched plate where the rubber seal  of the upper
buffer chamber contacts the glass.  If the plate was reversed, this contact
point would be right at that critical area of the gel where the bands
"stack up".

We hand wash our plates and only occasionaly soak (after trouble). Those of
you who responded to my query who soak your plates routinely or those who
do the hot DI water rinse never seem to have a problem.  Could it be that
with your methods, both sides of the plates are so scrupulously clean that
an inadvertent reversal would have no impact?

Your responses are welcomed.

Best regards,

Skip Vaught
DNA Sequencing Service
University of Arizona


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Skip Vaught-     jev at u.arizona.edu
Brian Coullahan- coullaha at u.arizona.edu
Mark Schwartz-   schwartm at u.arizona.edu
Amy Raymond-     raymonda at u.arizona.edu

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