title: A DNA minor groove electronegative potential genome map based on photo-chemical probing.
abstract: The double-stranded DNA of the genome contains both sequence information directly relating to the protein and RNA coding as well as functional and structural information relating to protein recognition. Only recently is the importance of DNA shape in this recognition process being fully appreciated, and it also appears that minor groove electronegative potential may contribute significantly in guiding proteins to their cognate binding sites in the genome. Based on the photo-chemical probing results, we have derived an algorithm that predicts the minor groove electronegative potential in a DNA helix of any given sequence. We have validated this model on a series of protein-DNA binding sites known to involve minor groove electrostatic recognition as well as on stable nucleosome core complexes. The algorithm allows for the first time a full minor groove electrostatic description at the nucleotide resolution of any genome, and it is illustrated how such detailed studies of this sequence dependent, inherent property of the DNA may reflect on genome organization, gene expression and chromosomal condensation.
authors.affiliation: Faculty of Health Sciences, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Lindemose
authors.forename: Peter Eigil
authors.initials: PE
authors.lastname: Nielsen
authors.forename: Morten
authors.initials: M
authors.lastname: Hansen
authors.forename: Niels Erik
authors.initials: NE
authors.lastname: Møllegaard
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000528:radiation effects; D053837:DNA Cleavage; D004268:DNA-Binding Proteins / Q000737:chemistry; D016678:Genome; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry; D010782:Photolysis; D055672:Static Electricity; D017974:Uranium Compounds / Q000737:chemistry
chemical_list: D004268:DNA-Binding Proteins; D009707:Nucleosomes; D017974:Uranium Compounds; D004247:DNA