loading dye

[Paul N Hengen]

barbara zangerl (zangerl at vu-wien.ac.at) wrote:

> we are blotting DNA-framgents from 4-6% PAA-gels. The blotted fragments  
> have a size of approximately 300bp. Therefore I would wonder if there is
> anybody who knows a loading dye that shows a visible marker of that size.

Do you really need a dye marker at exactly 300 bp? I use 0.05% Amaranth (Sigma
A-1016) for this, but the red dye migrates faster than 300 bp, at about 40-50
bp. The nice thing is that after electro-blotting you can be assured that if
the dye has been transferred, the DNA will also have been. It also changes
slightly in intensity after UV cross-linking. Be careful though if you plan to
add any dye to a gel-shift experiment because the dye can change the binding
properties of proteins.

@article{Zhang1993,
author = "X. Zhang
     and L. J. L. Duggan
     and P. A. Gottlieb",
title = "Loading dyes used in gel electrophoresis alter
the apparent thermodynamic equilibrium of the {{\em lac}}
repressor-operator complex",
journal = "Anal. Biochem.",
volume = "214",
pages = "580-582",
comment = "dyes bromophenol blue and xylene cyanol in gel shift",
year = "1993"}

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