Fw: Strange problem with agarose gel electrophoresis

Dr. Hiranya S. Roychowdhury hroychow at nmsu.edu
Sat Apr 21 09:53:30 EST 2001


Hello Phillip,

For resolving small fragments I increase the "gel conc."  I routinely
resolve 100-200 bp comfortably in 2% gels. For quick analytical purposes, I
use "micro gels" made on small glass plates.
Our lab reuses agarose several times for analytical purposes.

And, of course, seeing that I prefer to reuse my agarose, you know at least
I am not the one to go for precast agarose gels at $7 a pop :-(

I am sure you  genomics guys can afford them though ;-)


At 08:47 AM 4/20/01 -0500, Phillip San Miguel wrote:
>"Dr. Hiranya S. Roychowdhury" wrote:
>
>> [...]Anyway, I never understood why TBE is used for short runs in agarose.
>> TBE's
>> 'somewhat' superior buffering may justify its use for overnight runs for
>> genomic digests, etc. and for denaturing PAGE systems, but routine DNA
>> electrophoresis hardly warrants substituting TAE with TBE. Furthermore, if
>> buffer circulation is carried out, TAE is fine even for very long runs in
>> agarose.
>> Dr. Hiranya Sankar Roychowdhury
>> [...]
>
>    At high voltage/cold buffer 0.5x TBE allows substantially reduced
>electrophoresis times. Very nice for small fragments. No trouble resolving
>fragments down to and even below 100 bp. I keep large containers of it in the
>cold box. Back when I usually wanted to run a minigel once or twice a day
I kept
>cast 0.8% agarose gels in 0.5x buffer in the cold box too. I could load a gel
>and have preliminary results 20 minutes later.
>    Try cranking the voltage on your TAE gel and see how long it takes to
melt
>the gel.
>    By the way, how many of you like to *buy* your agarose gels? I got a call
>from a company last week that wanted to sell me a gel rig that (they said)
only
>used their pre-cast gels at $7 a pop!
>
>Phillip SanMiguel
>Purdue Genomics Core Facility
>
>
Dr. Hiranya Sankar Roychowdhury
College Asst. Prof.
Molecular Biology,
Dept. of Chemistry & Biochemistry	
Box 30001 - 3MLS
New Mexico State University
Las Cruces, NM 88003

Lab: (505) 646 4722
Office: (505) 646 8256
hroychow at nmsu.edu

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