Quantitative Microarray Profiling of DNA-Binding Molecules
- 19 September 2007
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of the American Chemical Society
- Vol. 129 (40) , 12310-12319
- https://doi.org/10.1021/ja0744899
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 β-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 Ka values across the microarray intensity spectrum.Keywords
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