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Tracer Dyes in Agarose

Robert Horton horton at molbio.cbs.umn.edu
Wed Aug 5 14:11:43 EST 1992

In article <9207272143.AA00286 at umailsrv0.UMD.EDU> William_D_WARREN at UMAIL.UMD.EDU (ww40) writes:
>>Hello. For some time I've been using a ficoll based loading
>>solution for my agarose gels with both xylene cyanol and
>>bromphenol blue added as tracer dyes.
>     [Stuff deleted]           ...So, I ask if anyone knows of
>>any other dyes that can be used for this purpose? In particular
>>I'm wondering if anyone uses a dye that migrates faster than the
>>bromphenol blue front?
>>Paul N. Hengen
>[address deleted]
>I saw a recent article in Biotechniques about the use of alternative
>dyes - The context of the article was that the BPB and XCYN, if added
>to a PCR reaction prior to amplification will inhibit the reaction.
>The study looked at an number of alternative dyes and additives to
>increase the solution density and found (as I remember) that it is
>possible to add sucrose and one or two of a number of dye alternatives
>to a PCR reaction prior to thermocycling and then directly load the
>samples onto an agarose gel.
>Unfortunately I can't find the article -
>[stuff deleted]
>Good luck

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            /\ "Crash programs fail because of the theory that
U. of Minnesota, CBS  || with nine women pregnant you get a baby a month" 
1479 Gortner Ave.    /||\   -Werner von Braun.  Disclaimer:"Bob who?"
St. Paul, MN 55108    ^^   horton at molbio.cbs.umn.edu/(612) 624-3790

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