Quantitative microarray profiling of DNA-binding molecules
Abstract
A high-throughput Cognate Site Identity (CSI) microarray platform interrogating all 524 800 10-base pair variable sites is correlated to quantitative DNase I footprinting data of DNA binding pyrrole-imidazole polyamides. An eight-ring hairpin polyamide programmed to target the 5 bp sequence 5'-TACGT-3' within the hypoxia response element (HRE) yielded a CSI microarray-derived sequence motif of 5'-WWACGT-3' (W = A,T). A linear beta-linked polyamide programmed to target a (GAA)_3 repeat yielded a CSI microarray-derived sequence motif of 5'-AARAARWWG-3' (R = G,A). Quantitative DNase I footprinting of selected sequences from each microarray experiment enabled quantitative prediction of K_a values across the microarray intensity spectrum.
Additional Information
© 2007 American Chemical Society. Received July 3, 2007. This work was supported by the National Institutes of Health (GM27681 to P.B.D. and A.Z.A). We thank the Beckman Institute Sequence Analysis Facility for DNA sequencing.Attached Files
Accepted Version - nihms278094.pdf
Supplemental Material - ja0744899_si_001.pdf
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Additional details
- PMCID
- PMC3066056
- Eprint ID
- 66741
- Resolver ID
- CaltechAUTHORS:20160509-104244669
- GM-27681
- NIH
- Created
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2016-05-17Created from EPrint's datestamp field
- Updated
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2021-11-11Created from EPrint's last_modified field