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Nucleic Acids Research Advance Access published online on June 23, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp539
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods online

Separation of 1–23-kb complementary DNA strands by urea–agarose gel electrophoresis

Éva Hegedüs1, Endre Kókai2, Alexander Kotlyar3, Viktor Dombrádi2,4 and Gábor Szabó1,*

1Department of Biophysics and Cell Biology, 2Department of Medical Chemistry, University of Debrecen, 4012 Debrecen, Nagyerdei krt. 98, Hungary, 3Department of Biochemistry, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv 69978, Israel and 4HAS Cell Biology and Signalling Research Group, Medical and Health Science Center, University of Debrecen, 4012 Debrecen, Nagyerdei krt. 98, Hungary

*To whom correspondence should be addressed. Tel: +36 52 455 866; Fax: +36 52 532 201; Email: szabog{at}dote.hu; hegeduse{at}dote.hu

Received November 26, 2008. Revised June 8, 2009. Accepted June 9, 2009.

Double-stranded (ds), as well as denatured, single-stranded (ss) DNA samples can be analyzed on urea–agarose gels. Here we report that after denaturation by heat in the presence of 8 M urea, the two strands of the same ds DNA fragment of ~1–20-kb size migrate differently in 1 M urea containing agarose gels. The two strands are readily distinguished on Southern blots by ss-specific probes. The different migration of the two strands could be attributed to their different, base composition-dependent conformation impinging on the electrophoretic mobility of the ss molecules. This phenomenon can be exploited for the efficient preparation of strand-specific probes and for the separation of the complementary DNA strands for subsequent analysis, offering a new tool for various cell biological research areas.


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