Dye to colour DNA samples for PCR

[Robert Horton]

Ciaran Meghen (cmeghen at mail.tcd.ie) wrote:
: Does anyone know of a biologically inert dye for colouring DNA samples used
: in PCR ?  I have tried using a 1:1500 dilution of the food colouring
: 'Brilliant Blue' but this has drastically reduced PCR yields.  Suggestions
: very welcome. 
:
See B. Hoppe, et al., "Gel loading dyes compatible with PCR", BioTechniques
12:679-680(1992).
5X dye is 60% sucrose + ~1mM cresol red. Use the "normal" cresol red from
Aldrich. The solubility of this stuff is right around 1mM, so you can't add too
much. They also sell a more soluble salt, which, people tell me, you can add
too much of.

Samples colored with this dye are much fainter than what you might be used to
with bromophenol blue, etc., but they're plenty visible, especially with the
heavy sucrose, which changes the refractive index, and with proper choice of 
background color behind the gel. Be aware that the color of cresol red changes
from red to pale yellow as the pH drops much below about 7.9. It should be red
in "normal" 10mM Tris pH 8.3 buffer, at room temperature (it will turn yellow
as the sample heats above ~70oC). If you use a buffer of "non-standard" pH, 
you'r eon your own.


Bob Horton (Ph.D.!)   /\ "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