The early folding intermediates of the tetrahymena ribozyme are kinetically trapped

The "RNA folding problem" is a fundamental and challenging question in cont emporary biophysics. Understanding the mechanism(s) by which RNA molecules fold into compact structures capable of biological activity is important be cause RNA folding is closely tied to cellular regulation and metabolism and catalytic RNAs are potential reagents for gene therapy. Unlike the "protei n folding problem" which has been under study for many decades, the study o f RNA tertiary structure stability and folding is a relatively new field of endeavor. Thus, a detailed understanding of both the thermodynamics;md kin etics of RNA folding are only now beginning to emerge. Kinetic traps have been observed in the late folding steps of the Tetrahyme na ribozyme. In this study we extend our "synchrotron footprinting" analysi s of the Tetrahymena ribozyme (Sclavi, et al., Science 279, 1940-1943, 1998 ) to probe the potential presence of kinetic traps in other steps in the fo lding mechanism. Examination of the folding in 3M urea demonstrates a signi ficant increase in the rates of folding for early folding steps in the form ation of the ribozyme tertiary structure. These data support the conclusion of Williamson and co-workers that the rate-limiting sep in the folding of the Tetrahymena ribozyme is kinetically trapped by native interactions (Roo k et al., J. Mel. Bio., 281, 609-620, 1998). Kinetic trapping also occurs i n the formation of intermediates earlier in the folding reaction, and in th ese cases nonnative interactions may also play a role in the barrier to fol ding.