Tracer Dyes in Agarose

Paul N Hengen pnh at fcs260c2.ncifcrf.gov
Fri Aug 7 10:10:25 EST 1992


In article <1992Aug5.191143.10616 at news2.cis.umn.edu>
horton at molbio.cbs.umn.edu (Robert Horton) writes:

>The reference is BioTechniques 12(5) 679-680 (1992). Cresol red migrates
>between bromophenol blue and xylene cyanol (at ~300bp in a 2% gel) and 
>tartrazine (FD&C yellow #5) migrates well ahead (with the primers in PCRs).
>Many food colors are anionic in TBE, and can be used as tracking dyes,
>and they will have all sorts of different mobilities. I can't find any good
>reason why everyone uses BPB and XCYN, other than tradition.
>-- 
>Bob Horton
>U. of Minnesota
>St. Paul, MN 55108


         ********** PRETTY COLORS ON YOUR GELS **********

Hey, just for fun, make a dye cocktail containing the following:

          10 % w/v ficoll in electrophoresis buffer
          0.05 % w/v xylene cyanol FF (Sigma X-4126) = cyan blue
          0.05 % w/v bromphenol blue (Sigma B-5525) = dark blue
          0.25 % w/v orange G (Sigma O-3756) = yellow
          0.25 % w/v amaranth (Sigma A-1016) = red

These dyes will migrate according to their order above with the red
dye moving the fastest. Or alternatively, make various combinations
in order to color code your DNA samples. For example, put lambda cut
with HindIII in with only blue, the 1 kb ladder in with the red, and
test samples in the yellow. These can also be used to make sure you
haven't added the same sample twice on a gel containing large numbers
of samples by alternating the red and blue, or whatever you like.
You'll really impress those media types when they call on your lab
to publicize your latest great discovery. Since they don't know that
DNA is colorless and want some visual clips for the news, they'll be
amazed at watching the dyes separate by electrophoesis. And if you're
like me (looking for that PCR product that never appears on the gel)
at least you can enjoy the pretty colors during the day ;) !!!


Paul N. Hengen
National Cancer Institute
Frederick Cancer Research and Development Center
Frederick, Maryland 21702-1201 USA



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