smeared 1st sequencing runs

brett brett at BORCIM.WUSTL.EDU
Thu May 22 15:22:30 EST 1997

I fail to see how Dudley's method is superior to an occasional soak in lye,
rinse with water and rain-x treatment. in between i just prefer water - the
universal solvent and much cheaper and easier than all those other steps. But
hey, if you've got nothing else to worry about....

>The #1 problem I've seen with poorly performing sequencing gels (either
>pouring poorly or running poorly) is lack of elbow grease in the
>cleaning step.
>I have no affiliation with Gold Biotech, but I do use their sequestrip
>and sequesoap and recommend them over chloroform and NaOH soaks. 
>They'll give you a free sample.  The Sequestrip does remove Rain-X,
>which is good or bad, depending on how you look at it (L always
>re-siliconize, so I think it's good).  It takes me about 20 min from the
>time I start washing to the time I reassemble my rig.  Here's what I do:
>1) Scrape the plates with a razorblade to get rid of chunky stuff, and
>wash off.
>2) Working one plate at a time, pour a few mls of strip on the plate and
>scrub scrub scrub well with kimwipes..  Get a lottle elbow grease into
>it.  Rinse off the strip and repeat (this is probably excessive, but I'm
>like that with cleaning).
>3) Pour some sequesoap onto the plate and scrub.  Rinse and repeat (I've
>found two soapings to be important).
>4) Shake excess water off and scrub with some 95-100% ethanol.  Scrub
>well with kimwipes--change when soaked.  Repeat.
>5) Let the plates totally dry, and with a couple of clean, dry kimwipes
>between your hand and the plate, feel the plate surface.  Move your hand
>all over the plate applying light pressure.  It should glide smoothly. 
>Wherever the kipwipes encounter friction, scrub that spot with ethanol.
>6) To siliconize a plate, apply two coats of rain-X (or whatever), let
>dry a minute or so, and with a damp kimwipe, wipe off the excess.
>It may take a try or two to figure this all out (people always look at
>me quizically when I try to explain the "feel the plate" idea...), but
>you should get very clean plates.
>One word of caution:  don't press down really really hard on a plate
>that's spanning a sink.  It could be bad.
>I hope this helps!
>--- --- ---
>Richard J. Dudley (rdudley at                            
>Department of Neurobiology                    
>University of Alabama School of Medicine       
Brett Lindenbach
Dept Molecular Microbiology
Washington University School of Medicine
St Louis, MO

"One thousand miles an hour, I'm just like anyone.
I want to feel the road of tar beneath the wheel
named extinction" - Pixies

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