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Nucleic Acids Research Advance Access published online on May 21, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp364
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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.

Structural Biology

Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA

Doyoun Kim1, Sanjith Reddy1, Dong Young Kim1, Alexander Rich2, Sangho Lee3, Kyeong Kyu Kim1,* and Yang-Gyun Kim4,*

1Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea,2Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Departments of 3Biological Science and 4Chemistry, Sungkyunkwan University, Suwon 440-746, Korea

*To whom correspondence should be addressed. Email: kkim{at}med.skku.ac.kr Correspondence may also be addressed to Yang-Gyun Kim. Tel: +82 31 299 4563; Fax: +82 31 299 4575; Email: ygkimmit{at}skku.edu; ygkimmit{at}gmail.com

Received February 1, 2009. Revised April 24, 2009. Accepted April 24, 2009.

Base extrusion is a major structural feature at the junction between B- and Z-DNA (the B–Z junction) where a base pair is broken, and the two bases are extruded from the double helix. Despite the demonstration of base extrusion at the B–Z junction, it is not clear whether a similar base extrusion occurs at other types of junctions involving the left-handed Z conformation. Here, we investigate structural changes of bases at three Z-form junctions: DNA B–Z and Z–Z and RNA A–Z junctions. By monitoring fluorescently labeled duplex nucleic acids using 2-aminopurines at various positions relative to the junction point, we show that base extrusion occurs not only at the DNA B–Z junction, but also at the RNA A–Z and DNA Z–Z junctions. Our data suggest that base extrusion is a general feature of Z-form nucleic-acid junctions.


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