title: Specific minor groove solvation is a crucial determinant of DNA binding site recognition.
abstract: The DNA sequence preferences of nearly all sequence specific DNA binding proteins are influenced by the identities of bases that are not directly contacted by protein. Discrimination between non-contacted base sequences is commonly based on the differential abilities of DNA sequences to allow narrowing of the DNA minor groove. However, the factors that govern the propensity of minor groove narrowing are not completely understood. Here we show that the differential abilities of various DNA sequences to support formation of a highly ordered and stable minor groove solvation network are a key determinant of non-contacted base recognition by a sequence-specific binding protein. In addition, disrupting the solvent network in the non-contacted region of the binding site alters the protein's ability to recognize contacted base sequences at positions 5-6 bases away. This observation suggests that DNA solvent interactions link contacted and non-contacted base recognition by the protein.
authors.affiliation: Department of Biological Sciences, 607 Cooke Hall, University at Buffalo, Buffalo, NY 14260, USA.
authors.forename: Lydia-Ann
authors.initials: LA
authors.lastname: Harris
authors.affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
authors.forename: Loren Dean
authors.initials: LD
authors.lastname: Williams
authors.affiliation: Department of Biological Sciences, 607 Cooke Hall, University at Buffalo, Buffalo, NY 14260, USA koudelka@buffalo.edu.
authors.forename: Gerald B
authors.initials: GB
authors.lastname: Koudelka
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D011485:Protein Binding; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; C034261:P22 repressor protein, Enterobacteria phage P22; D012097:Repressor Proteins; D014764:Viral Proteins; D004247:DNA