Mapping the competing barriers that define alternative RNA folding pathways
Joerg Schlatterer
1, Joshua Martin 2, Alain Laederach 2, Michael Brenowitz 1
1: Department of Biochemistry, Albert Einstein College of Medicine
2: Computational and Structural Biology Department, Wadsworth Center
The folding of large RNA molecules into biologically active structures often traverses rugged energy landscapes populated by intermediates possessing either native or non-native structure. To date, a comprehensive and quantitative analysis of the barriers that define the folding landscape has remained experimentally difficult to attain. By combining high-throughput chemical probing and kinetic modeling we report the activation energies for the seven forward transitions that are resolved for the Mg2+-mediated time dependent folding of the Tetrahymena ribozyme. We explore the partitioning of activation barriers into their enthalpic and entropic components for individual steps of folding reactions which include transitions between the unfolded RNA ensemble (U), the intermediates I1 (only the P4-P6 scaffold domain is formed) and I2 (both the peripheral helices and the P4-P6 domain are formed), and the folded RNA (F).