Alexander Mastroianni

Pyramidal and Chiral Groupings of Gold Nanocrystals Assembled Using DNA Scaffolds

Nanostructures constructed from metal and semiconductor nanocrystals conjugated to and organized by DNA are an emerging class of materials with collective optical properties. We created discrete pyramids of DNA with gold nanocrystals at the tips. By taking small-angle X-ray scattering measurements 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.

Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction 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 100-nm length scale in biology. Here, we substantiate that plasmon rulers can be used to measure dynamical biophysical processes by applying the ruler to a system that has been investigated extensively by 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 1,000 individual dsDNA enzyme substrates could be simultaneously monitored for hours. The kinetic parameters extracted from our single-molecule cleavage trajectories agree well with values obtained in bulk through other methods and confirm well known features of the cleavage process, such as DNA bending before cleavage. Previously unreported dynamical information is revealed as well, for instance, the degree of softening of the DNA just before cleavage. The unlimited lifetime, high temporal resolution, and high signal/noise ratio make the plasmon ruler a unique tool for studying macromolecular assemblies and conformational changes at the single-molecule level.

Direct Nanorod Assembly Using Block Copolymer-Based Supramolecules

Developing routes to control the organization of one-dimensional nanomaterials, such as nanorods, with high precision is critical to generate functional materials since the collective properties depend on their spatial arrangements, interparticle ordering, and macroscopic alignment. We have systematically investigated the coassemblies of nanorods and block copolymer (BCP)-based supramolecules and showed that the energetic contributions from nanorod ligand-polymer interactions, polymer chain deformation, and rod-rod interactions are comparable and can be tailored to disperse nanorods with control over inter-rod ordering and the alignment of nanorods within BCP microdomains. By varying the supramolecular morphology and chemical nature of the nanorods, two highly sought-after morphologies, that is, nanoscopic networks of nanorods and nanorod arrays parallel to cylindrical BCP microdomains can be obtained. The supramolecular approach can be applied to achieve morphological control in nanorod-containing nanocomposites toward fabrication of optical and electronic nanodevices.

Enzymatic Ligation Creates Discrete Multinanoparticle Building Blocks for Self-Assembly

Enzymatic ligation of discrete nanoparticle-DNA conjugates creates nanoparticle dimer and trimer structures in which the nanoparticles are linked by single-stranded DNA, rather than by double-stranded DNA as in previous experiments. Ligation was verified by agarose gel and small-angle X-ray scattering. This capability was utilized in two ways: first, to create a new class of multiparticle building blocks for nanoscale self-assembly and, second, to develop a system that can amplify a population of discrete nanoparticle assemblies.

Probing the Conformational Distributions of Subpersistence Length DNA

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 fluorescence resonance energy transfer) 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 are consistent with a simple wormlike 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 basepairs) 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.

DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals

Significance We developed and applied nanogold labels for DNA complexes with proteins examined by small angle X-ray scattering (SAXS) to follow DNA conformations acting in error detection by the mismatch repair (MMR) system in solution. This technique can examine short or long pieces of DNA and in most solution conditions, including those closest to cellular environments. Thus, we expect the technique to be useful for many biologically important systems involving DNA complexes and conformations. Specifically, we reveal DNA bending followed by straightening by the repair protein MutS at the site of a mismatch as a suitable mechanism for error detection and signaling needed to avoid mutations and cancers and to control microbial stability and evolution in response to environmental stress. DNA metabolism and processing frequently require transient or metastable DNA conformations that are biologically important but challenging to characterize. We use gold nanocrystal labels combined with small angle X-ray scattering to develop, test, and apply a method to follow DNA conformations acting in the Escherichia coli mismatch repair (MMR) system in solution. We developed a neutral PEG linker that allowed gold-labeled DNAs to be flash-cooled and stored without degradation in sample quality. The 1,000-fold increased gold nanocrystal scattering vs. DNA enabled investigations at much lower concentrations than otherwise possible to avoid concentration-dependent tetramerization of the MMR initiation enzyme MutS. We analyzed the correlation scattering functions for the nanocrystals to provide higher resolution interparticle distributions not convoluted by the intraparticle distribution. We determined that mispair-containing DNAs were bent more by MutS than complementary sequence DNA (csDNA), did not promote tetramer formation, and allowed MutS conversion to a sliding clamp conformation that eliminated the DNA bends. Addition of second protein responder MutL did not stabilize the MutS-bent forms of DNA. Thus, DNA distortion is only involved at the earliest mispair recognition steps of MMR: MutL does not trap bent DNA conformations, suggesting migrating MutL or MutS/MutL complexes as a conserved feature of MMR. The results promote a mechanism of mismatch DNA bending followed by straightening in initial MutS and MutL responses in MMR. We demonstrate that small angle X-ray scattering with gold labels is an enabling method to examine protein-induced DNA distortions key to the DNA repair, replication, transcription, and packaging.