RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting

Abstract

Radiolysis of water with a synchrotron x-ray beam permits the hydroxyl radical–accessible surface of an RNA to be mapped with nucleotide resolution in 10 milliseconds. Application of this method to folding of the Tetrahymena ribozyme revealed that the most stable domain of the tertiary structure, P4-P6, formed cooperatively within 3 seconds. Exterior helices became protected from hydroxyl radicals in 10 seconds, whereas the catalytic center required minutes to be completely folded. The results show that rapid collapse to a partially disordered state is followed by a slow search for the active structure.