abstract: Deoxyribonucleic acid (DNA) has been treated as excellent building material for nanoscale construction because of its unique structural features. Its ability to self-assemble into predictable and addressable nanostructures distinguishes it from other materials. A large variety of DNA nanostructures have been constructed, providing scaffolds with nanometer precision to organize functional molecules. This dissertation focuses on developing biologically replicating DNA nanostructures to explore their biocompatibility for potential functions in cells, as well as studying the molecular behaviors of DNA origami tiles in higher-order self-assembly for constructing DNA nanostructures with large size and complexity. Presented here are a series of studies towards this goal. First, a single-stranded DNA tetrahedron was constructed and replicated in vivo with high efficiency and fidelity. This study indicated the compatibility between DNA nanostructures and biological systems, and suggested a feasible low-coast method to scale up the preparation of synthetic DNA. Next, the higher-order self-assembly of DNA origami tiles was systematically studied. It was demonstrated that the dimensional aspect ratio of origami tiles as well as the intertile connection design were essential in determining the assembled superstructures. Finally, the effects of DNA hairpin loops on the conformations of origami tiles as well as the higher-order assembled structures were demonstrated. The results would benefit the design and construction of large complex nanostructures. / Dissertation/Thesis / Ph.D. Biochemistry 2012

No description available.

No description available.

Self-assembly, templation and biomimetics are three important, overlapping areas in supramolecularChemistry. Some contributions to these three areas are introduced. Novel substituted trispyridylmethanol derived ligands were synthesized to mimic the active site of carbonic anhydrase. The key two-step process in constructing the trispyridylmethanol core structure is proven to be more efficient than the traditional one-step synthesis. Self-assembly is a very efficient way to form nanoscale structure from relatively simple subunits. Tetraphenylmethane-based subunits were synthesized. The result of self-assembly reactions demonstrated the formation of 1~3 nm sized molecules in one step. Potential multi-generation self-assembly on this subunit is also discussed. A novel and efficient approach for the synthesis of large aromatic crown ethers, using resorcinarenes as templates, has been developed. This simple threestep process generated a new family of aromatic crown ethers in up to 50% overall yield. As intermediates from these three-step syntheses, a large variety of molecular "baskets", which have been shown to be excellent hosts for adamantanes, have also been obtained.

Synthetic Laponite-clay particles with a platelet-like shape display strong gelation when dispersed in aqueous solutions because of their positively charged rims and negatively charged flat surfaces. In this thesis, my aim was to modify the surfaces of these clay particles such that we can both access their liquid crystalline (LC) discotic phase and further build transparent and mechanically resilient coatings with a 3D "brick-and-mortar" structure that is similar to that observed in natural mother of pearl (nacre). I first introduce a simple strategy that successfully suppresses Laponite's ageing phenomenon and enables the system's isotropic-to-LC phase transition. By grafting Laponite particle surfaces with comb-like polymers, poly (L-lysine)-g-poly (ethylene glycol) (PLL-PEG), I was able to screen negative surface charges and ensure steric stabilisation. Besides using long-chain polymers, I also coated the positively charged Laponite rims with small, barrel-shaped molecules cucurbit[7]uril (CB[7]). By carefully tuning the ratio between CB[7] and Laponite, the system experienced a macroscopic phase separation into a Laponite-poor suspension and a birefringent LC gel. Inspired by the hierarchical structure of nacre, here I also demonstrate a simple approach to fabricate polymer-clay hybrid films via a water-evaporation process. In this third method, Laponite platelets were bridged by natural abundant polymers (carboxymethyl cellulose) through hydrogen bonding. This hybrid material possesses high transparency, flexibility and an outstanding fire-retardant property. After Ca2+ ion-coordination of these cellulose-Laponite composite films, the interface between the polymers and clays was further strengthened, leading to enhanced mechanical properties along with improved thermal- and water-resistance. I also present that using Dextran as a depletant, sterically stabilised Laponite can access its liquid crystal phase under low clay concentration. Finally, I show that Laponite can be coated with various polymers (PEO, chitosan, sodium alginate) for the purpose of obtaining LC gels and hybrid films. I believe that our findings on surface-modification of clay particles can open new routes to large-scale and inexpensive production of bio-inspired functional materials.

Thesis (Ph.D.)--University of Delaware, 2007. / Principal faculty advisor: Joel P. Schneider, Dept. of Chemistry & Biochemistry. Includes bibliographical references.

Elastin is a polymeric protein of the extracellular matrix that imparts the characteristics of extensibility and elastic recoil to tissues. Recombinant polypeptides based on the domain structures and sequences of human elastin self-assemble into organized fibrous structures, with physical properties similar to those of native polymeric elastin. Elastin self-assembly is initiated by a temperature-induced phase separation, called coacervation. Previous to this work, coacervation temperature had been the only parameter available to measure propensity for self-assembly. A variety of techniques were developed using spectrophotometry, microscopy, and rheometry to differentiate the stages of self-assembly, thereby enabling independent observation and quantitation of each stage, and allowing investigations into properties of polypeptides and solution conditions affecting these stages. Kinetic analysis of self-assembly yielded two additional parameters: coacervation velocity and maturation velocity. Examining the effects of agitation, salt concentration, temperature, polypeptide concentration, size of a polypeptide, hydrophobic domain sequence, and cross-linking domain structure on the kinetics demonstrated that coacervation and maturation are independent stages of self-assembly involving distinct mechanisms. Microscopic observations showed that protein-rich droplets of coacervate grew by coalescence to a stable droplet size, which correlated to differences in maturation velocities between polypeptides. Coacervate droplet growth appeared limited by the formation of organized polypeptide at the surface of the droplets, decreasing surface fluidity. Many of the general principles of the physical chemistry of colloids and emulsions appeared to apply to the formation, growth and stabilization of coacervates of the elastin-like polypeptides. Self-assembly in the presence of non-elastin, matrix-associated proteins showed that these proteins maintained the coacervate as small droplets, which sometimes flocculated into fibre-like structures. Rheometry demonstrated a second temperature-induced transition above the coacervation temperature, which resulted in gelation and viscoelastic characteristics similar to microgels. Together, these observations have resulted in a greater level of understanding of the entire self-assembly process, and provided a comprehensive model of elastin-like polypeptide self-assembly that relates to in vivo assembly of elastic fibres.

The atomic force microscope (AFM) was used to study a series of self-assembled systems: alkanethiol self-assembled monolayer (SAM), diblock copolymer thin film, solid supported lipid bilayer membrane, and microgel with double interpenetrating polymer network. In the first system, packing and restructuring of self-assembled monolayers as exhibited by several alkanethiol systems (1-hexanethiol, 1-decanethiol, 11-ferrocenyl-1-undecanethiol) is demonstrated using conducting probe AFM (CP-AFM). Pressure is induced by an AFM tip, and simultaneously, electrical behavior is measured via detection of tunneling currents between metallic tip and substrate. The behavior is fit using a mechanical model that attempts to predict the observed junction resistance as a function of applied force with consideration for mechanical restructuring of the monolayer at higher loads. CP-AFM is also used to study self-assembled thin film of the diblock copolymer polystyrene- block-polyferrocenylsilane (PS-b-PFS) on gold substrate. Simultaneous height and electrical current imaging verify the phase separation of the two blocks of the polymer and additionally, distinguish each block due to differential conductivity. The phase separation of multi-component phospholipid bilayers (phosphatidylcholine/ sphingomyelin/ cholesterol) on supporting substrate into liquid-ordered and liquid-disordered phases is demonstrated using both topographical imaging, and the use of force map analysis through tip indentation and rupture measurements. The segregation and differential mechanical stiffness of the phases help to understand the important role of mechanical stability and rigidity membranes. An automated batch analysis process was implemented to facilitate the procedure. The mechanical properties of microfluidically produced microgels (cross-linked sodium alginate and poly(N-isopropylacrylamide)) are measured using indentation experiments, to evaluate the suitability of these gels as cell-mimics. Nanoscale heterogeneities were avoided by using a tipless cantilever. This body of work shows that the alginate content of these microgels can be varied to tune their mechanical properties and that a platform for mechanical measurement of cell and cell-mimics is possible.

Elastin is a polymeric protein of the extracellular matrix that imparts the characteristics of extensibility and elastic recoil to tissues. Recombinant polypeptides based on the domain structures and sequences of human elastin self-assemble into organized fibrous structures, with physical properties similar to those of native polymeric elastin. Elastin self-assembly is initiated by a temperature-induced phase separation, called coacervation. Previous to this work, coacervation temperature had been the only parameter available to measure propensity for self-assembly. A variety of techniques were developed using spectrophotometry, microscopy, and rheometry to differentiate the stages of self-assembly, thereby enabling independent observation and quantitation of each stage, and allowing investigations into properties of polypeptides and solution conditions affecting these stages. Kinetic analysis of self-assembly yielded two additional parameters: coacervation velocity and maturation velocity. Examining the effects of agitation, salt concentration, temperature, polypeptide concentration, size of a polypeptide, hydrophobic domain sequence, and cross-linking domain structure on the kinetics demonstrated that coacervation and maturation are independent stages of self-assembly involving distinct mechanisms. Microscopic observations showed that protein-rich droplets of coacervate grew by coalescence to a stable droplet size, which correlated to differences in maturation velocities between polypeptides. Coacervate droplet growth appeared limited by the formation of organized polypeptide at the surface of the droplets, decreasing surface fluidity. Many of the general principles of the physical chemistry of colloids and emulsions appeared to apply to the formation, growth and stabilization of coacervates of the elastin-like polypeptides. Self-assembly in the presence of non-elastin, matrix-associated proteins showed that these proteins maintained the coacervate as small droplets, which sometimes flocculated into fibre-like structures. Rheometry demonstrated a second temperature-induced transition above the coacervation temperature, which resulted in gelation and viscoelastic characteristics similar to microgels. Together, these observations have resulted in a greater level of understanding of the entire self-assembly process, and provided a comprehensive model of elastin-like polypeptide self-assembly that relates to in vivo assembly of elastic fibres.

The atomic force microscope (AFM) was used to study a series of self-assembled systems: alkanethiol self-assembled monolayer (SAM), diblock copolymer thin film, solid supported lipid bilayer membrane, and microgel with double interpenetrating polymer network. In the first system, packing and restructuring of self-assembled monolayers as exhibited by several alkanethiol systems (1-hexanethiol, 1-decanethiol, 11-ferrocenyl-1-undecanethiol) is demonstrated using conducting probe AFM (CP-AFM). Pressure is induced by an AFM tip, and simultaneously, electrical behavior is measured via detection of tunneling currents between metallic tip and substrate. The behavior is fit using a mechanical model that attempts to predict the observed junction resistance as a function of applied force with consideration for mechanical restructuring of the monolayer at higher loads. CP-AFM is also used to study self-assembled thin film of the diblock copolymer polystyrene- block-polyferrocenylsilane (PS-b-PFS) on gold substrate. Simultaneous height and electrical current imaging verify the phase separation of the two blocks of the polymer and additionally, distinguish each block due to differential conductivity. The phase separation of multi-component phospholipid bilayers (phosphatidylcholine/ sphingomyelin/ cholesterol) on supporting substrate into liquid-ordered and liquid-disordered phases is demonstrated using both topographical imaging, and the use of force map analysis through tip indentation and rupture measurements. The segregation and differential mechanical stiffness of the phases help to understand the important role of mechanical stability and rigidity membranes. An automated batch analysis process was implemented to facilitate the procedure. The mechanical properties of microfluidically produced microgels (cross-linked sodium alginate and poly(N-isopropylacrylamide)) are measured using indentation experiments, to evaluate the suitability of these gels as cell-mimics. Nanoscale heterogeneities were avoided by using a tipless cantilever. This body of work shows that the alginate content of these microgels can be varied to tune their mechanical properties and that a platform for mechanical measurement of cell and cell-mimics is possible.