Quantitative Microarray Profiling of DNA-binding Molecules

Overview

Journal J Am Chem Soc

Publisher American Chemical Society

Specialty Chemistry

Date 2007 Sep 21

PMID 17880081

Citations 35

Authors

James W Puckett

Katy A Muzikar

Josh Tietjen

Christopher L Warren

Aseem Z Ansari

Peter B Dervan

Affiliations

Soon will be listed here.

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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