Use of Plasmon Coupling to Reveal the Dynamics of DNA Bending and Cleavage by Single EcoRV \nRestriction Enzymes

Pairs of Au nanoparticles have recently been proposed as plasmon rulers based on the dependence of their light scattering on the interparticle distance. Preliminary work has suggested that plasmon rulers can be used to measure and monitor dynamic distance changes over the 1 to 100nm length scale in biology. Here, we substantiate that plasmon rulers can be used to effectively measure dynamical biophysical processes by applying the ruler to a system that has been investigated extensively using ensemble kinetic measurements: the cleavage of DNA by the restriction enzyme EcoRV. Temporal resolutions of up to 240 Hz were obtained, and the end-to-end extension of up to 1000 individual dsDNA enzyme substrates could be monitored in parallel for hours. The single molecule cleavage trajectories acquired here agree well with values obtained in bulk through other methods, and confirm well-known features of the cleavage process, such as the fact that the DNA is bent prior to cleavage. New dynamical information is revealed as well, for instance, the degree of softening of the DNA just prior to cleavage. The unlimited life time, high temporal resolution, and high signal/noise make the plasmon ruler an excellent tool for studying macromolecular assemblies and conformational changes at the single molecule level.