title: Construction of a genome-scale structural map at single-nucleotide resolution.
abstract: Few methods are available for mapping the local structure of DNA throughout a genome. The hydroxyl radical cleavage pattern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus provides information on the local shape and structure of DNA. We report the construction of a relational database, ORChID (OH Radical Cleavage Intensity Database), that contains extensive hydroxyl radical cleavage data produced from two DNA libraries. We have used the ORChID database to develop a set of algorithms that are capable of predicting the hydroxyl radical cleavage pattern of a DNA sequence of essentially any length, to high accuracy. We have used the prediction algorithm to produce a structural map of the 30 Mb of the ENCODE regions of the human genome.
authors.affiliation: Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.
authors.forename: Jason A
authors.initials: JA
authors.lastname: Greenbaum
authors.forename: Bo
authors.initials: B
authors.lastname: Pang
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Tullius
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D030541:Databases, Genetic; D015723:Gene Library; D015894:Genome, Human; D006801:Humans; D009711:Nucleotides / Q000235:genetics; D011237:Predictive Value of Tests; D017422:Sequence Analysis, DNA
chemical_list: D009711:Nucleotides