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Genome Res. 17:947-953, 2007
©2007 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/07 $5.00
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Construction of a genome-scale structural map at single-nucleotide resolution

Jason A. Greenbaum1, Bo Pang2, and Thomas D. Tullius1,2,3

1 Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA; 2 Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA

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.

3 Corresponding author.

E-mail tullius{at}bu.edu; fax (617) 353-6466.

[Supplemental material is available online at www.genome.org.]

Article is online at http://www.genome.org/cgi/doi/10.1101/gr.6073107


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