National Research Council of Canada. National Institute for Nanotechnology
Optical Trapping Applications, OTA 2015, 12 April 2015 through 15 April 2015
Diffusion; Molecules; Nucleic acids; Regulatory compliance; Biological molecule; Diffusive process; Equilibrium fluctuation; High dimensionality; Mechanical loads; Multi dimensional; Single molecule force spectroscopy; Structure formations; Optical tweezers
Folding of proteins and nucleic acids involves diffusion over a multidimensional energy landscape. Optical tweezers provide a powerful method for measuring this landscape using single-molecule force spectroscopy, whereby individual molecules are unfolded and refolded under mechanical load applied by the tweezers and the resulting changes in extension of the molecule are monitored to follow changes in the molecular structure. Methods are discussed for measuring energy landscapes, approximated as a 1D projection of the full multi-dimensional energy surface, via equilibrium fluctuations of the extension or non-equilibrium force-ramps. The correct approach for determining the diffusion coefficient for structural changes from such measurements, wherein the effects of instrumental compliance and time resolution are taken into account, is described. Finally, the approximation of folding as a 1D diffusive process is shown to be good for simple molecules like DNA hairpins, despite the high dimensionality of the full folding problem.