SCAN g™ a high-throughput assay for detecting small molecule binding to RNA targets

Abstract

A novel optical-based high-throughput screening technology has been developed for increasing the rate of discovering chemical leads against RNA targets. SCAN ĝ.,¢ ( Screen for Compounds with Affinity for Nucleic Acids) is an affinity-based assay that identifies small molecules that bind and recognize structured RNA elements. This technology provides the opportunity to conduct high-throughput screening of a new class of targetsĝ€"RNA. SCAN ĝ.,¢ offers many attractive features including a simple homogeneous format, low screening costs, and the ability to use common laboratory equipment. A SCAN ĝ.,¢ assay was developed for the HCV IRES Loop IIId RNA domain. A high-throughput screen of our entire compound library resulted in the identification of small molecule ligands that bind to Loop IIId. The Zĝ€2 values were greater than 0.8, showing this to be a robust high-throughput screening assay. A correlation between SCAN ĝ.,¢ EC 50 and K D values is reported suggesting the ability to use the assay for compound optimization. © 2009 Society for Biomolecular Sciences.