Force spectroscopy of structure formation in single nucleic acid molecules: from hairpins to riboswitches

Michael T. Woodside
National Institute for Nanotechnology, National Research Council of Canada
and Dept. of Physics, University of Alberta

How biological macromolecules self-assemble into complex three-dimensional structures is a fundamental question in biophysics. Recent experimental advances now allow structure formation to be observed directly in single molecules, with high spatial and temporal resolution. I discuss precision optical trapping studies of the folding of various nucleic acids. “Hairpins” of DNA are used to provide a model system for understanding the effects of primary and secondary structure on folding. By changing the hairpin sequence, the free energy landscape for folding is manipulated, allowing the locations and heights of the energy barriers for hairpin folding to be tuned and the presence and position of folding intermediates to be controlled. The complete energy landscape along the reaction coordinate is also reconstructed from high resolution records of reversible folding and compared to a simple predictive model for the folding landscape. RNA “riboswitches” are studied to understand how the folding of more complex molecules can be analysed in term of their constituent parts. A riboswitch controlling the expression of genes regulating adenine biosynthesis is seen to fold in multiple steps that can be identified with the formation of individual hairpin structures, tertiary structures, and ligand binding. The mechanical switching between states that is responsible for gene regulation is observed directly, and the folding energy landscape of the riboswitch is quantified.