Smiles on Southerns

[Paul N Hengen]

In article <158hl8INN5dj at agate.berkeley.edu> scottk at nuclease.berkeley.edu (Number Ten Ox) writes:
>In article <3653 at fcs280s.ncifcrf.gov>, pnh at fcs260c2.ncifcrf.gov 
>(Paul N Hengen) writes:
>
>|> -> Problems can occur when there is overloading with DNA, the
>|> concentration of agarose is too high, or you've pushed it so
>|> that the gel runs faster than normal. This causes a trailing
>|> effect, mostly due to shearing of the DNA. If you're using very
>                         ^^^^^^^^^^^^^^^^^^^
>
>Huh? Can you explain how shearing the DNA causes it to *trail*
>on a gel?
>

Oops. I realize that the original posting was for the electrophoresis
of restriction fragments of total genomic DNA, or was it?

Here, I was referring to a method of separating large plasmid DNA
(cccDNA) using a cell lysis technique within the well of an agarose
gel for use in Southern blots. Shearing and/or nicking of the cccDNA
in such a gel causes a trailing effect.

The method is described in the following book chapter:

L.D. Kuykendall and P.N. Hengen. 1988. Microbial Genetics
of Legume Root Nodulation and Nitrogen Fixation. In: Biological
Nitrogen Fixation: Recent Advances. N.S. Subba Rao (ed.). Oxford and
IBH Publishers, New Delhi.

Paul N. Hengen
National Cancer Institute
Frederick Cancer Research and Development Center
Laboratory of Mathematical Biology
P.O. Box B
Frederick, Maryland 21702-1201 USA
voice: (301) 846-5581
FAX: (301) 846-5598
e-mail: pnh at ncifcrf.gov