Methods for the characterization and selection of rna target motifs that bind compounds of pharmaceutical use

Abstract

Methods are disclosed for identifying an RNA fragment that mimics the structure of a defined or undefined target RNA molecule to which a compound binds inside of a cell resulting in retardation of cell growth or cell death. Methods using these RNA fragments for identifying unknown compounds of pharmaceutical interest, and for identifying unknown RNA targets for use in treating disease are disclosed. These methods and compositions are used in screening for novel antibiotics, bacteriostatics, or modifications thereof or for identifying compounds useful to alter expression levels of proteins encoded by mRNA. The methods involve providing random DNA fragments from DNA which encodes RNA target molecules, cloning such fragments to create a plasmid library of same; transfecting cells which contain the native RNA target molecule with the plasmid library and exposing the cells to one or more of test compounds. Cells transfected with an RNA fragment that mimics the target molecule will survive in culture, and cells transfected with fragments which do not mimic the molecule will suffer defects in growth. The mimicking RNA fragment is isolated and provides structural information about the target. The fragment and the information derived from it are then used to screen or design binding compounds.