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PubMed · 15888729

Common patterns in type II restriction enzyme binding sites.

Svetlana Nikolajewa·Andreas Beyer·Maik Friedel·Jens Hollunder·Thomas Wilhelm
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Abstract

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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BacteriophagesBase SequenceBinding SitesDNADNA-Binding ProteinsDeoxyribonucleases, Type II Site-SpecificEscherichia coli K12GC Rich SequenceHydrogen BondingJournal ArticleResearch Support, Non-U.S. Gov't

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Svetlana Nikolajewa, Andreas Beyer, Maik Friedel, Jens Hollunder, Thomas Wilhelm. 2005-05-11. Common patterns in type II restriction enzyme binding sites.. https://doi.org/10.1093/nar%2Fgki575

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