title: A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.
abstract: DNA shape variation and the associated variation in minor groove electrostatic potential are widely exploited by proteins for DNA recognition. Here we show that the hydroxyl radical cleavage pattern is a quantitative measure of DNA backbone solvent accessibility, minor groove width, and minor groove electrostatic potential, at single nucleotide resolution. We introduce maps of DNA shape and electrostatic potential as tools for understanding how proteins recognize binding sites in a genome. These maps reveal periodic structural signals in yeast and Drosophila genomic DNA sequences that are associated with positioned nucleosomes.
authors.forename: Eric P
authors.initials: EP
authors.lastname: Bishop
authors.forename: Remo
authors.initials: R
authors.lastname: Rohs
authors.forename: Stephen C J
authors.initials: SC
authors.lastname: Parker
authors.forename: Sean M
authors.initials: SM
authors.lastname: West
authors.forename: Peng
authors.initials: P
authors.lastname: Liu
authors.forename: Richard S
authors.initials: RS
authors.lastname: Mann
authors.forename: Barry
authors.initials: B
authors.lastname: Honig
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Tullius
mesh_terms: D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry; D030561:Databases, Nucleic Acid; D017665:Hydroxyl Radical / Q000737:chemistry*; D009707:Nucleosomes / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D004268:DNA-Binding Proteins; D009707:Nucleosomes; D017665:Hydroxyl Radical; D004247:DNA