Chemical genetics makes use of small molecules to study protein function. Small molecules can permit selective, temporal, and dose-dependent control over the functions of a target protein. In order to study a proteome comprehensively, this approach requires specific activating and inactivating ligands for every protein in the network. Herein is described a novel microarray approach to identifying small molecule-protein binding interactions. An automated platform was developed to facilitate the delivery of compounds resulting from solid-phase, diversity-oriented synthesis into both phenotypic and protein-binding assays. Diverse collections of small molecules were spatially arrayed and covalently captured onto glass microscope slides containing up to 10,800 small molecule features. The small molecule microarrays were probed with a panel of tagged yeast proteins, resulting in over one million individual binding assays. Retesting positives in a secondary binding assay, using surface plasmon resonance, validated the microarray approach. Finally, microarrays were used to identify a small molecule that binds to Hap3p, a yeast transcription factor subunit, and inhibits Hap3p-regulated transcription in vivo.
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