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Nucleic Acids Research 2005 33(8):2726-2733; doi:10.1093/nar/gki575
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Published online 11 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Common patterns in type II restriction enzyme binding sites

Svetlana Nikolajewa, Andreas Beyer, Maik Friedel, Jens Hollunder and Thomas Wilhelm*

Institute of Molecular Biotechnology Beutenbergstrasse 11, D-07745 Jena, Germany

*To whom correspondence should be addressed. Tel: +49 3641 65 6208; Fax: +49 3641 65 6191; Email: wilhelm{at}imb-jena.de

Received April 1, 2005. Revised April 26, 2005. Accepted April 26, 2005.

Restriction enzymes are among the best studied examples of DNA binding proteins. In order to find general patterns in DNA recognition sites, which may reflect important properties of protein–DNA interaction, we analyse the binding sites of all known type II restriction endonucleases. We find a significantly enhanced GC content and discuss three explanations for this phenomenon. Moreover, we study patterns of nucleotide order in recognition sites. Our analysis reveals a striking accumulation of adjacent purines (R) or pyrimidines (Y). We discuss three possible reasons: RR/YY dinucleotides are characterized by (i) stronger H-bond donor and acceptor clusters, (ii) specific geometrical properties and (iii) a low stacking energy. These features make RR/YY steps particularly accessible for specific protein–DNA interactions. Finally, we show that the recognition sites of type II restriction enzymes are underrepresented in host genomes and in phage genomes.


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