Assembly, Structure and Properties of DNA Programmable Nanoclusters

Finite size nanoclusters can be viewed as a nanoscale analogue of molecules. Just as molecules, synthesized from atoms, give access to new properties, clusters composed of nanoparticles modulate of their functional properties of nanoparticles. In contrast to synthetic chemistry which is a mature field, the creation of nanoscale clusters with well-defined architectures is a new and challenging area of research. My work explores how to assemble model systems of nanoclusters using DNA-programmable interparticle linkages. The simplest clusters of two particles, dimers, allow one to investigate fundamental effects in these systems. Such clusters serve as a versatile platform to understand DNA-mediated interactions, especially in the non-trivial regime where the nanoparticle and DNA chains are comparable in size. I systematically studied a few fundamental questions as follows:;Firstly, we examined the structure of nanoparticle dimers in detail by a combination of X-ray scattering experiments and molecular simulations. We found that, for a given DNA length, the interparticle separation within the dimer is controlled primarily by the number of linking DNA. We summarized our findings in a simple model that captures the interplay of the number of DNA bridges, their length, the particle's curvature and the excluded volume effects. We demonstrated the applicability of the model to our results, without any free parameters. As a consequence, the increase of dimer separation with increasing temperature can be understood as a result of changing the number of connecting DNA.;Later, we investigated the self-assembly process of DNA-functionalized particles in the presence of various lengths of the DNA linkage strands using 3 different pathways. We observed a high yield of dimer formation when significantly long linkers were applied. Small Angle X-ray Scattering revealed two configurations of the small clusters by different pathways. In one case, the interparticle distance increases as the function of linker length. In the other case, the interparticle distance of the cluster decreases with the linker length until the DNA shell thickness of the particles. This result suggests a configuration in which nanoparticles are confined due to the hybridization of flexible linkers from opposite particles' hemispheres. The effect is accompanied by inhibited growth of nanoclusters, resulting in a self-limited cluster assembly.;Secondly, we investigated several types of system including spherical particles and simplest asymmetric structures, Janus particles and dimers interacting with DNA functionalized surface, in which the single stranded DNAs immobilized on surfaces are complementary to DNA grafted on one of cluster particles or on a side of Janus particle, We observed an interesting surface binding behavior: kinetics of surface recognition strongly depends on the design of nanoclusters, the surface oligonucleotide density and a salt concentration. Based on these studies, a new method was developed for a separation of single particles and nanoclusters. Dimers were also applied as basic units to build hierarchical structures.;Thirdly, dimers were applied as a sensor for single-stranded DNA detection. The detection is based on dimer disassembly triggered by binding of target nucleic acid strands. Target detection and disassembly kinetics were followed in real time using dynamic light scattering. The observed disassembly process is in agreement with a two-step kinetic model. The DNA sensing was found to be selective down to the level of a single base mismatch, even in the presence of a high concentration of interference DNA. The method further provides label-free detection of DNA in minutes, and demonstrates the use of this new class of nanoclusters as a powerful platform for nucleic acid sensing.;Lastly, we explored the diffusion properties of nanoclusters in polymer solution. Classical diffusion theory well explains a large number of transport phenomena for molecular, nano and micro-scale systems in simple liquids. However, the question about the diffusion of nano-constructs in complex liquids, particularly when the size of those constructs is comparable to the structural units (polymers) existed in liquid is not well explored. As a model system, the diffusion of dimers of 10nm gold nanoparticles covered with symmetric and asymmetric shells in various concentrations of polyethylene glycol (PEG) solutions was studied by particle tracking method and dynamic light scattering. In the experimental time regime, both dimers with symmetric and asymmetric soft-matter shell exhibit a typical Brownian motion. However, we observed a significant enhancement of diffusion for asymmetric structures compared to the symmetric ones. We systematically studied the effect of cluster structure, solution viscosity and composition on the discovered phenomenon.