Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers
William J. Greenleaf,1*
Kirsten L. Frieda,2
Daniel A. N. Foster,4
Michael T. Woodside,4,5*
Steven M. Block1,3
Riboswitches regulate genes through structural changes in ligand-binding RNA aptamers. With the use of an optical-trapping assay based on in situ transcription by a molecule of RNA polymerase, single nascent RNAs containing pbuE adenine riboswitch aptamers were unfolded and refolded. Multiple folding states were characterized by means of both force-extension curves and folding trajectories under constant force by measuring the molecular contour length, kinetics, and energetics with and without adenine. Distinct folding steps correlated with the formation of key secondary or tertiary structures and with ligand binding. Adenine-induced stabilization of the weakest helix in the aptamer, the mechanical switch underlying regulatory action, was observed directly. These results provide an integrated view of hierarchical folding in an aptamer, demonstrating how complex folding can be resolved into constituent parts, and supply further insights into tertiary structure formation.
1 Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
2 Biophysics Program, Stanford University, Stanford, CA 94305, USA.
3 Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.
4 Department of Physics, University of Alberta, Edmonton AB, T6G 2G7, Canada.
5 National Institute for Nanotechnology, National Research Council of Canada, Edmonton AB, T6G 2M9, Canada.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: sblock{at}stanford.edu (S.M.B); michael.woodside{at}nrc.ca (M.T.W.)
