"Ghost" bands in plasmid preps?

Paul E Wiehl wiehlp at oak.cats.ohiou.edu
Mon Nov 29 11:17:28 EST 1999


The band that you see might be "irreverisibly denatured" plasmid DNA.
Birnboim and Doly show a band on their gel on page 1518 of an alkaline
extraction procedure of plasmid DNA. Nucleic Acid Research Vol 7 #6 1979
Pages 1513-1523.
						P.Wiehl

On Wed, 24 Nov 1999, Bernard Murray, PhD wrote:

> In article <383C5889.ED006DEB at cc.umanitoba.ca>, Rob Kirkpatrick
> <kirkpat at cc.umanitoba.ca> wrote:
> 
> > Simon Dawson wrote:
> > 
> > > Hi all,
> > >         Does anyone ever see what I can only call "ghost' bands if they
> > > over-expose an ethidium bromide stained agarose gel of plasmid DNA? They
> > > usually appear to run somewhat faster than what I would think is the
> > > supercoiled DNA band and you only seem to see them if you overexpose the
> > > gel.
> > >     Any thoughts? Ignore them (they don't seem to cause any problems with
> > > subsequent manipulations)? I'm curious to know if anyone else sees something
> > > like it.
> 
> > I'm told these are random cleaved DNA fragments that result
> > from excess exposure
> > to NaOH in the lysis step and that they are resistant to endonuclease
> > cleavage.
> > But, I'm am not an expert on this and am somewhat interested in the answers to
> > this question as well.
> 
> Paul Hengen tells the story in his March 1994 TIBS column and
> the text is available here;
>     ftp://ftp.ncifcrf.gov/pub/methods/TIBS/mar94.txt
> 
> The ghost band usually runs about the same MW as ssDNA of
> "non-denatured" plasmid.  I don't believe "random cleavage"
> is involved.
> 
>    Bernard
> 
> -- 
> Bernard P. Murray, PhD
> bpmurray at cgl . ucsf . edu
> Department of Cellular & Molecular Pharmacology, UCSF
> 
> 





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