title: Hydroxyl radical footprints reveal novel structural features around the NF I binding site in adenovirus DNA.
abstract: We have identified a number of as yet unknown structural abnormalities of the NF I-DNA binding site within the inverted terminal repetition of adenovirus DNA by probing it with a hydroxyl radical footprinting technique. NF I binding alters the accessibility of the deoxyribose moieties to hydroxyl radicals both at the 3' and at the 5' side of the recognition sequence 5'-TGG(N)6GCCAA-3'. A smooth bend at the 5' side of the binding sequence is already present in naked linear DNA and it is further enhanced by protein binding. This could be demonstrated not only by hydroxyl radical footprinting but also by studying the temperature dependent mobility during gel electrophoresis of DNA fragments carrying the NF I binding site at circularly permutated positions. We propose that the bent conformation at this site is responsible for facilitating protein/DNA interactions.
authors.affiliation: Institut für Biochemie, Universität München, FRG.
authors.forename: H
authors.initials: H
authors.lastname: Zorbas
authors.forename: L
authors.initials: L
authors.lastname: Rogge
authors.forename: M
authors.initials: M
authors.lastname: Meisterernst
authors.forename: E L
authors.initials: EL
authors.lastname: Winnacker
mesh_terms: D000260:Adenoviruses, Human / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D022762:CCAAT-Enhancer-Binding Proteins; D004279:DNA, Viral / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D003850:Deoxyribonuclease I; D004926:Escherichia coli / Q000235:genetics; D005609:Free Radicals; D005822:Genetic Vectors; D006878:Hydroxides; D017665:Hydroxyl Radical; D008969:Molecular Sequence Data; D051839:NFI Transcription Factors; D009687:Nuclear Proteins; D010957:Plasmids; D012091:Repetitive Sequences, Nucleic Acid; D014157:Transcription Factors; D051840:Y-Box-Binding Protein 1
chemical_list: D022762:CCAAT-Enhancer-Binding Proteins; D004279:DNA, Viral; D004268:DNA-Binding Proteins; D005609:Free Radicals; D006878:Hydroxides; D051839:NFI Transcription Factors; D009687:Nuclear Proteins; D014157:Transcription Factors; D051840:Y-Box-Binding Protein 1; C070856:YBX1 protein, human; D017665:Hydroxyl Radical; D003850:Deoxyribonuclease I