Structural dynamics of catalytic RNA highlighted by fluorescence resonanceenergy transfer

RNA performs a multitude of essential cellular functions involving the main tenance, transfer, and processing of genetic information. The reason probab ly is twofold: (a) Life started as a pre lotic RNA World, in which RNA serv ed as the genetic information carrier and catalyzed all chemical reactions required for its proliferation and (b) some of the RNA World functions were conserved throughout evolution because neither DNA nor protein is as adept in fulfilling them. A particular advantage of RNA is its high propensity t o form alternative structures as required in subsequent steps of a reaction pathway. Here I describe fluorescence resonance energy transfer (FRET) as a method to monitor a crucial conformational transition on the reaction pat hway of the hairpin ribozyme, a small catalytic RNA motif from a self-repli cating plant virus satellite RNA and well-studied paradigm of RNA folding. Steady-state FRET measurements in solution allow one to measure the kinetic s and requirements of docking of its two independently folding domains; tim e-resolved FRET reveals the relative thermodynamic stability of the undocke d (extended, inactive) and docked (active) ribozyme conformations; while si ngle-molecule FRET experiments will highlight the dynamics of RNA at the in dividual molecule level. Similar domain docking events are expected to be a t the heart of many biological functions of RNA, and the described FRET tec hniques promise to be adaptable to most of the involved RNA systems. (C) 20 01 Academic Press.