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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 Ka values across the microarray intensity spectrum.

SUBMITTER: Puckett JW 

PROVIDER: S-EPMC3066056 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature

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Quantitative microarray profiling of DNA-binding molecules.

Puckett James W JW   Muzikar Katy A KA   Tietjen Josh J   Warren Christopher L CL   Ansari Aseem Z AZ   Dervan Peter B PB  

Journal of the American Chemical Society 20070919 40


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 C  ...[more]

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