We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle X-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average value (as in ensemble FRET) or an extreme value (as in cyclization), and in principle provides a more robust data set for assessing the suitability of theoretical models. Our experimental results for dsDNA comprising 42-94 basepairs (bp) are consistent with a simple worm-like chain model of dsDNA elasticity, whose behavior we have determined from Monte Carlo simulations that explicitly represent nanoparticles and their alkane tethers. A persistence length of 50 nm (150 bp) gave a favorable comparison, consistent with the results of single-molecule force-extension experiments on much longer dsDNA chains, but in contrast to recent suggestions of enhanced flexibility at these length scales.

Nanostructures constructed from metal and semiconductor nanocrystals conjugated to, and organized by DNA are an emerging class of material with collective optical properties. We created discrete pyramids of DNA with gold nanocrystals at the tips. By taking small angle X-ray scattering (SAXS) measurments from solutions of these pyramids we confirmed that this pyramidal geometry creates structures which are more rigid in solution than linear DNA. We then took advantage of the tetrahedral symmetry to demonstrate construction of chiral nanostructures.

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.