Construction of a genome-scale structural map at single-nucleotide resolution.
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.
Greenbaum
Jason A
JA
Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.
Pang
Bo
B
Tullius
Thomas D
TD
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
D009711:Nucleotides