title: Common patterns in type II restriction enzyme binding sites.
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.
authors.affiliation: Institute of Molecular Biotechnology Beutenbergstrasse 11, D-07745 Jena, Germany.
authors.forename: Svetlana
authors.initials: S
authors.lastname: Nikolajewa
authors.forename: Andreas
authors.initials: A
authors.lastname: Beyer
authors.forename: Maik
authors.initials: M
authors.lastname: Friedel
authors.forename: Jens
authors.initials: J
authors.lastname: Hollunder
authors.forename: Thomas
authors.initials: T
authors.lastname: Wilhelm
mesh_terms: D001435:Bacteriophages / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry / Q000378:metabolism*; D048168:Escherichia coli K12 / Q000235:genetics; D020862:GC Rich Sequence; D006860:Hydrogen Bonding
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA; D015252:Deoxyribonucleases, Type II Site-Specific