Quantitative microarray profiling of DNA-binding molecules |
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Authors: | Puckett James W Muzikar Katy A Tietjen Josh Warren Christopher L Ansari Aseem Z Dervan Peter B |
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Institution: | Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA. |
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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 Ka values across the microarray intensity spectrum. |
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