title: Specificity of hydroxylmethyluracil-containing DNA for transcription factor 1: structural insights.
abstract: The genomic materials from some Bacillus subtilis bacteriophages are found to contain 5-(hydroxymethyl)-2'-deoxyuridine in place of thymine. Phage-encoded proteins such as transcription factor 1 specifically and preferentially bind to the minor grooves of these hmU-containing DNA but not to thymine-containing DNA. Data from electrophoretic mobility shift assays suggest that the inherent, localized flexibility of hmU-DNA, which is sequence-specific, is responsible for its discriminative binding. We discuss here, from the NMR-derived structural point of view, how differential DNA flexibility can contribute to specific binding of TF1 to hmU-DNA.
authors.affiliation: Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA.
authors.forename: H M
authors.initials: HM
authors.lastname: Vu
authors.forename: L B
authors.initials: LB
authors.lastname: Pasternack
authors.forename: D R
authors.initials: DR
authors.lastname: Kearns
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D010432:Pentoxyl / Q000031:analogs & derivatives* / Q000737:chemistry; D014764:Viral Proteins
chemical_list: D004268:DNA-Binding Proteins; D009838:Oligodeoxyribonucleotides; C059361:TF1 DNA-binding protein, Bacteriophage SPO1; D014764:Viral Proteins; C008055:5-hydroxymethyluracil; D010432:Pentoxyl; D004247:DNA