Literature DB >> 17880081

Quantitative microarray profiling of DNA-binding molecules.

James W Puckett1, Katy A Muzikar, Josh Tietjen, Christopher L Warren, Aseem Z Ansari, Peter B Dervan.   

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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Year:  2007        PMID： 17880081      PMCID： PMC3066056          DOI： 10.1021/ja0744899

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN： 0002-7863            Impact factor:   15.419


  25 in total

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2.  Footprinting methods for analysis of pyrrole-imidazole polyamide/DNA complexes.

Authors:  J W Trauger; P B Dervan
Journal:  Methods Enzymol       Date:  2001       Impact factor: 1.600

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