agarose gel electrophoresis

[Paul N Hengen]

Andreas Rump (arump at imb-jena.de) wrote:

> I have observed the following phenomenon several times: when I cut 
> out a piece of agarose gel containing a single DNA band and place this
> piece of gel on it's side, then I see two bands. This means, that the
> same DNA moves through the gel on two different levels (x and y, see
> Figure), one near the bottom of the gel and one near the surface. 
> Both bands are discrete, although the slot has been completely filled
> with sample and one would expect that the DNA enters the gel at the
> whole heigth of the gel and would move as one broad band.

I have seen it too. Do you use a tracking dye that migrates faster than
the DNA front? Does the same separation happen if you exclude the dye?

--
*******************************************************************************
* Paul N. Hengen, Ph.D.                           /--------------------------/*
* National Cancer Institute                       |Internet: pnh at ncifcrf.gov |*
* Laboratory of Mathematical Biology              |   Phone: (301) 846-5581  |*
* Frederick Cancer Research and Development Center|     FAX: (301) 846-5598  |*
* Frederick, Maryland 21702-1201 USA              /--------------------------/*
* - - -  Methods FAQ list -> ftp://ftp.ncifcrf.gov/pub/methods/FAQlist - - -  *
* -  TIBS column archive -> http://www-lmmb.ncifcrf.gov/~pnh/readme.html - -  *
* - The BEST Molecular Biology HomePage -> http://www-lmmb.ncifcrf.gov/~pnh/  *
*******************************************************************************