electrophoretic mobility

Joseph C. Bagshaw jbagshaw at wpi.edu
Sun Aug 8 05:47:33 EST 1999

The mobility of not only the dyes but also the DNA fragments is influenced
by the composition of the loading buffer.  If you cut the same DNA with,
e.g., Eco RI, Bam HI and Hind III and load the digests directly into a gel
in TBE, you will get three slightly different mobilities.  If it's
important to have samples run the same, precipitate with EtOH after
digestion and then dissolve everything in the same buffer.

********************  HAVE GENES, WILL TRAVEL  ********************
Joe Bagshaw, Worcester Polytechnic Institute
jbagshaw at wpi.edu
Roadkill on the information superhighway.

On Thu, 5 Aug 1999, C.S. Wilding wrote:

> This is probably one of those things that I should know the answer to 
> or be able to apply myself to but I don't and can't so:
> When electrophoresing (through 0.8% agarose in 1xTBE) some restriction 
> digested DNA samples, why do samples cut with EcoRI in NEB's Eco buffer 
> (50mM NaCl, 100mM Tris-HCl, 10mM MgCl2, 0.025% Triton X-100) "appear to 
> run slower" than uncut DNA or Eco cut in NEB buffer#2 (10mM Tris-HCl, 
> 10mM MgCl2, 50mM NaCl, 1mM DTT). I say "appear to run slower" as this 
> is based solely on the migration of the bromophenol blue and xylene 
> cyanol which is equal in uncut (no buffer) and #2, but much slower in 
> those with the Eco-specific buffer.
> Craig.

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