Thomas,

You can use any pulsed-field gel system and run high-molecular weight, SmaI-digested Dd DNA.
SmaI linearizes mtDNA and does not cut rDNA, so rDNA runs as a nice band above the 56-kb mtDNA with most chromosomal DNA at the exclusion limit.  You could do a Southern or cut the band out.

Mitochondrial DNA replication but no nuclear DNA replication during development of Dictyostelium.
Shaulsky G, Loomis WF.
Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5660-3.

Adam

Adam Kuspa, Ph.D.
Baylor College of Medicine


________________________________________
From: DICTY [[log in to unmask]] On Behalf Of Thomas Winckler [[log in to unmask]]
Sent: Tuesday, March 19, 2013 10:40 AM
To: [log in to unmask]
Subject: [DICTY] Pulsed field electrophoresis

Hi,

I was wondering whether anybody has access to pulsed field electrophoresis and/or experience in separating Dictyostelium chromosomes by whatever method. I would be particularly interested in separating the extrachromosomal rDNA palindrome DNA from the other chromosomes. Background is that we observed integration of the TRE5-A retrotransposon, which is supposed to be specific for tRNA genes, on the rDNA palindrome. I would like to prove that the integrations really occur on the extrachromosomal DNA and not on whatever fragment of the palindrome DNA that may occur on the chromosomes. The idea is to perform PCR on isolated rDNA palindrome DNA to detect our marked TRE5-A elements.

Thanks for any comments.

Kind regards,
Thomas


-------------------------------------------------------
Prof. Dr. Thomas Winckler
Friedrich-Schiller-Universität Jena
Institut für Pharmazie
Lehrstuhl für Pharmazeutische Biologie
Semmelweisstraße 10
D-07743 Jena
Tel. 03641 949841
Fax: 03641 949842
http://www.uni-jena.de/Pharmazeutische_Biologie.html