This track displays the predicted hydroxyl radical cleavage
intensity on naked DNA for each nucleotide in the ENCODE regions.
Because the hydroxyl radical cleavage intensity is proportional to the solvent
accessible surface area of the deoxyribose hydrogen atoms
(Balasubramanian et al., 1998), this track represents a structural
profile of the DNA in the ENCODE regions.
Please visit the ORChID web site maintained by the Tullius group for
access to experimental hydroxyl radical cleavage data, and to a server
which can be used to predict the cleavage pattern for any input sequence.
Display Conventions and Configuration
This track may be configured in a variety of ways to highlight different
aspects of the displayed data. The graphical configuration options
are shown at the top of the track description page. For more information,
configuration help link.
Hydroxyl radical cleavage intensity predictions were performed using
an in-house sliding tetramer window (STW) algorithm. This algorithm
draws data from the ·OH Radical Cleavage Intensity Database
(ORChID), which contains more than 150 experimentally determined cleavage
patterns. These predictions are fairly accurate, with a Pearson
coefficient of 0.88 between the predicted and experimentally
determined cleavage intensities. For more details on the hydroxyl
radical cleavage method, see below for reference (Greenbaum et al. 2007).
The STW algorithm has been cross-validated by removing each test
sequence from the training set and performing a prediction. The
mean correlation coefficient (between predicted and experimental
cleavage patterns) from this study was 0.88.
These data were generated through the combined effort of
Bo Pang at MIT,
at The La Jolla Institute for Allergy and Immunology and
Eric Bishop and
Tom Tullius of Boston University.
Balasubramanian B, Pogozelski WK, and Tullius TD
DNA strand breaking by the hydroxyl radical is governed by the
accessible surface areas of the hydrogen atoms of the DNA backbone.
Proc. Natl. Acad. Sci. USA 95(17), 9738-9743 (1998).
Price MA, and Tullius TD
Using the Hydroxyl Radical to Probe DNA Structure.
Meth. Enzymol. 212, 194-219 (1992).
Tullius TD. Probing DNA Structure with Hydroxyl Radicals.
In Current Protocols in Nucleic Acid Chemistry, (eds.
Beaucage, S.L., Bergstrom, D.E., Glick, G.D. and Jones, R.A.) (Wiley, 2001),
Greenbaum JA, Pang B, and Tullius TD
Construction of a genome-scale structural map at single-nucleotide resolution.
Genome Res. 17(6), 947-953 (2007).