Single Molecule Experiments Reveal the Role that Energy Landscapes Play in Biological Processes
In biology, the energy of a protein or nucleic acid molecule as a function of its physical conformation is of critical importance. It controls the folding of proteins into their native, active conformations, and it determines how much work processive enzymes must do in order to access information stored in DNA or RNA sequences. I will describe a new technique we have developed for measuring the energy of a DNA or RNA molecule as a function of its extension using an optical trap. I will describe a theoretical framework we have developed for relating the energy as a function of extension to the energy as a function of conformation, which is more directly related to biological function. Finally, I will describe what we have learned by applying this technique to several important biological systems. One example is an messenger RNA molecule which forms a pseudoknot that is known to induce a ribosomal frame shift. The frame shift interferes with synthesis of a co-factor for HIV infection. Measuring the energy landscape for disruption of this molecule we have found that it occupies a statistical ensemble of conformations which provide dramatically different levels of resistance to disruption by a translating ribosome. Micro-RNA molecules that enhance the frame-shift efficiency in vivo are found to work by altering the statistical ensemble of the molecule. Another molecule we have studied is a DNA G-quadruplex structure. G quadruplex is a novel form of DNA in which a single strand organizes itself around planar quinine tetrads. G-quadruplex in the pre-transcribed regions of genes may couple torsional strain to gene expression levels, and G-quadruplex in the human telomeric repeat sequence may play a role in the inhibition of telomerase. In our optical trap based studies, we have found that G-quadruplex in a highly cooperative structure which provides strong resistance to disruption by force, but which is vulnerable to disruption by thermal fluctuations. These features have interesting implications for the competition between G-quadruplex and ordinary duplex DNA, and for the ability of G-quadruplex to interfere with processive enzymes.