An Investigation into Molecular Recognition at a DNA Nanostructure-Metal Interface

Abstract

When developing applications for self-assembling nanostructures, a challenge is to organize the self assembling components within integrated nano-microsystems. One approach is to impart nanostructure recognition properties to patterned surfaces, such that nanostructure placement could be thermodynamically driven. This research focuses upon self assembling nanostructures composed of DNA and their reversible specific assembly upon functionalized planar surfaces. Assembly strategies that have been developed for solution phase assembly are herein demonstrated as potentially appropriate for heterogeneous nanosystem integration.The assembly of DNA nanostructures relies upon unique base pair interactions between single strands. While DNA hybridization that involves many base pairs results in structures that are strongly bound, an assembly strategy that underlies much DNA nanostructure engineering is formation of nanostructures at temperatures at which the interactions are weak. Here, DNA specific nanostructure immobilization is driven by weak forces. Association is characterized using surface sensitive surface plasmon resonance and quartz crystal microbalance methods. The results suggest that future strategies for nanostructure - system integration that require precise nanostructure placement may be accomplished using specific molecular recognition under thermodynamic control.Several methods of solution phase nanostructure characterization are explored. The diffusive properties of DNA nanostructures are examined using dynamic light scattering. Effective hydrodynamic radii are found to be large relative to the nanostructure geometric size. The temperature dependence of light scattering from nanostructures is investigated using both resonance light scattering and nonresonant laser light scattering. Additionally, DNA nanostructure building block and superstructure geometry are interrogated in solution using small angle x-ray scattering. Results derived from comparison of small angle data with simulations of scattering from coarse-grained models are compared with structural information derived from imaging immobilized nanostructures with atomic force microscopy. Finally, plasmon coupling in systems comprised of metal particles of unlike composition is described. Through simulation, three phenomena that contribute to interparticle coupling are explored. Off resonant metal particles positioned in between pairs of particles near resonance are found to promote optical coupling in a manner similar to that provided by bulk dielectric media.