The development of novel, peptide based structures for tissue engineering materials has been widely researched, and its popularity can be attributed to advancements in technological analysis methods. Using principles based on protein structure and organization, this work describes the novel self-assembly of depsipeptides, which incorporate alternating esters within a native peptide backbone. Chapter 1 introduces and reviews peptide mimics for their utility for tissue engineering applications. Chapter 2 describes the methodology in synthesizing and characterization a depsipeptide library using both solution and solid phase methods. Chapter 3 discusses the effects of depsipeptide length, concentration, and sequence within a range of ionic concentrations and pH ranges on the self-assembly of depsipeptides into spherical nanostructures, fibers, or hydrogels. Chapter 4 describes proposed methods to increase the rate of gelation, followed by discussions of biocompatibility studies from other self-assembling peptide and modified-peptide systems in vitro and in vivo. The work described in this dissertation demonstrates that the synthesis and self-assembly of a depsipeptide family which alternates esters into a native peptide backbone does not disrupt the formation of higher order structures. This study illustrates the potential to synthesize a wide range of depsipeptides with variable side chains and hydrophobic character, as understanding these effects on self-assembly is imperative to the development of biomimetic materials for tissue engineering applications. / text

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As the feature size of new devices continues to decrease so too does the feasibility of top-down methods of patterning them. In many cases bottom-up methods are replacing the existing methods of assembly, as having building blocks self-organize into the desired structure appears, in many cases, to be a much more advantageous route. Self-assembled nanoparticulate films have a wide range of potential applications; high-density magnetic media, sensing arrays, meta-materials and as seeds for 3D photonic crystals to name a few. Thus, it is critical that we understand the fundamental dynamics of pattern formation on the nanoparticulate and colloidal scale so that we may have better control over the formation and final quality of these structures. We study computationally the self-organization of colloidal particles in 2D using both Monte Carlo and dynamic simulation We present 3 studies employing Monte Carlo simulation. In the first study, Monte Carlo simulations were used to understand the experimental observation of highlyordered 2D arrays of bidisperse, stabilized gold nanoparticles. It was shown that the LS lattice forms with the addition of interparticle forces and a simple compressive force, revealing that bidisperse lattice formation is, in fact, a dynamic process. It was evident that the LS lattice forms in large part because the particles within the lattice reside in their respective interparticle potential wells. In the second Monte Carlo study, this information was used to predict size-ratios and surface coverages for novel lattice structures. These predictions are intended to guide experimentalists in their search for these exciting new structures. In the third study it was shown that polydisperse amounts of amorphous-silicon nanoparticles could form 2D clusters exhibiting long-range orientational order even in the absence of translational order. Monte Carlo simulations were performed, which included lateral capillary forces and a simple stabilizing repulsion, resulting in structures that were strikingly similar to the experimentally observed In the fourth study we used dynamic simulation to study the hydrodynamicallyassisted self-organization of DNA-functionalized colloids in 2D. It was shown that hydrodynamic forces allow a more thorough sampling of phase space than through thermal or Brownian forces alone.

<p>Pattern formation is a mysterious phenomenon occurring at all scales in nature. The beauty of the resulting structures and myriad of resulting properties occurring in naturally forming patterns have attracted great interest from scientists and engineers. One of the most convenient experimental models for studying pattern formation are colloidal particle suspensions, which can be used both to explore condensed matter phenomena and as a powerful fabrication technique for forming advanced materials. In my thesis, I have focused on the study of colloidal patterns, which can be conveniently tracked in an optical microscope yet can also be thermally equilibrated on experimentally relevant time scales, allowing for ground states and transitions between them to be studied with optical tracking algorithms. </p><p>In particular, I have focused on systems that spontaneously organize due to particle-surface and particle-particle interactions, paying close attention to systems that can be dynamically adjusted with an externally applied magnetic or acoustic field. In the early stages of my doctoral studies, I developed a magnetic field manipulation technique to quantify the adhesion force between particles and surfaces. This manipulation technique is based on the magnetic dipolar interactions between colloidal particles and their "image dipoles" that appear within planar substrate. Since the particles interact with their own images, this system enables massively parallel surface force measurements (>100 measurements) in a single experiment, and allows statistical properties of particle-surface adhesion energies to be extracted as a function of loading rate. With this approach, I was able to probe sub-picoNewton surface interactions between colloidal particles and several substrates at the lowest force loading rates ever achieved. </p><p>In the later stages of my doctoral studies, I focused on studying patterns formed from particle-particle interaction, which serve as an experimental model of phase transitions in condensed matter systems that can be tracked with single particle resolution. Compared with other research on colloidal crystal formation, my research has focused on multi-component colloidal systems of magnetic and non-magnetic colloids immersed in a ferrofluid. Initially, I studied the types of patterns that form as a function of the concentrations of the different particles and ferrofluid, and I discovered a wide variety of chains, rings and crystals forming in bi-component and tri-component systems. Based on these results, I narrowed my focus to one specific crystal structure (checkerboard lattice) as a model of phase transformations in alloy. Liquid/solid phase transitions were studied by slowly adjusting the magnetic field strength, which serves to control particle-particle interactions in a manner similar to controlling the physical temperature of the fluid. These studies were used to determine the optimal conditions for forming large single crystal structures, and paved the way for my later work on solid/solid phase transitions when the angle of the external field was shifted away from the normal direction. The magnetostriction coefficient of these crystals was measured in low tilt angle of the applied field. At high tilt angles, I observed a variety of martensitic transformations, which followed different pathways depending on the crystal direction relative to the in-plane field. </p><p>In the last part of my doctoral studies, I investigated colloidal patterns formed in a superimposed acoustic and magnetic field. In this approach, the magnetic field mimics "temperature", while the acoustic field mimics "pressure". The ability to simultaneously tune both temperature and pressure allows for more efficient exploration of phase space. With this technique I demonstrated a large class of particle structures ranging from discrete molecule-like clusters to well ordered crystal phases. Additionally, I demonstrated a crosslinking strategy based on photoacids, which stabilized the structures after the external field was removed. This approach has potential applications in the fabrication of advanced materials. </p><p> My thesis is arranged as follows. In Chapter 1, I present a brief background of general pattern formation and why I chose to investigate patterns formed in colloidal systems. I also provide a brief review of field-assisted manipulation techniques in order to motivate why I selected magnetic and acoustic field to study colloidal patterns. In chapter 2, I present the theoretical background of magnetic manipulation, which is the main technique used in my research. In this chapter, I will introduce the basic knowledge on magnetic materials and theories behind magnetic manipulation. The underlining thermodynamic mechanisms and theoretical/computational approaches in colloidal pattern formation are also briefly reviewed. In Chapter 3, I focus on using these concepts to study adhesion forces between particle and surfaces. In Chapter 4, I focus on exploring the ground states of colloidal patterns formed from the anti-ferromagnetic interactions of mixtures of particles, as a function of the particle volume fractions. In Chapter 5, I discuss my research on phase transformations of the well-ordered checkerboard phase formed from the equimolar mixture of magnetic and non-magnetic beads in ferrofluid, and I focus mainly on phase transformations in a slowly varying magnetic field. In Chapter 6, I discuss my work on the superimposed magnetic and acoustic field to study patterns formed from monocomponent colloidal suspensions under vertical confinement. Finally, I conclude my thesis in Chapter 7 and discuss future directions and open questions that can be explored in magnetic field directed self-organization in colloidal systems.</p> / Dissertation

The formation of large, complex structures from small building blocks through self-assembly is widely seen in proteins and provides a tool for the creation of functional nanoscale devices. However, the factors controlling protein self-assembly are complex and often poorly understood. Peroxiredoxins are a large family of proteins, many of which are able to form a variety of large structures from a small, basic unit. This assembly has been shown to be strongly influenced by the redox state of the enzyme, which functions as a switch, controlling self-assembly. This thesis uses a protein from this family, human peroxiredoxin 3 (hPrx3) as a model system to investigate whether the self-assembly properties of hPrx3 can be influenced by rational protein engineering. Three forms of hPrx3 were purified and examined. These were the wild type and two variants: a mutant (S78A) and a His-tagged form. Size exclusion chromatography showed that each form showed a different ratio of dimers and larger species. Both variants showed preference for larger species, especially in the His-tagged form. This was shown to be partially dependent on metal binding in the His-tagged form. Larger species formed from multiple rings were also identified. SAXS measurement indicated that in the wild type enzyme, higher order species were dodecameric rings. For the His-tagged variant, SAXS measurement showed that the species observed had a different structure than that of the wild type. Electron microscopy showed that higher order structures seen in both wild type hPrx3 and His-tagged hPrx3 were ring shaped, with dimensions consistent with dodecamers. A competitive assay showed that the wild type, with kcat/km values near 2 x 10⁷, consistent with published results. Both variant forms showed evidence of slightly higher activity than the wild type, indicating a link between activity and assembly. A peroxiredoxin from the thermophilic bacteria Thermus aquaticus, TaqPrx was also examined, in an attempt to investigate a peroxiredoxin capable of self-assembly at high temperatures, which would be very useful for a nanoscale device. TaqPrx was cloned, purified and examined, however, no evidence of self-assembly was observed. Protein modelling and dynamic light scattering measurement indicated that the protein purified was monomeric and had a structure. Sparse matrix crystal screening identified conditions that allowed crystal formation, although strongly diffracting crystals were not produced. A novel assay for peroxiredoxin activity was developed, and suggested that TaqPrx shows peroxiredoxin activity. This thesis shows that peroxiredoxins are a useful model system for the investigation of how protein self-assembly is controlled, and how it can be influenced by protein engineering.

A number of compounds were synthesized with the ultimate goal being the synthesis of C₂ symmetric molecules which displayed thermotropic liquid crystalline behaviour. The compounds prepared were 4-alkoxy benzophenones, 3,4-bis-alkoxy benzophenones, 4- alkoxy dibenzylidene acetones, 3,4-bis-alkoxy dibenzylidene acetones and 4-alkoxy- 1, 9-diphenyl-nona-l,3,6,8-tetraen-5-ones. The length of the linear alkoxy side chain was varied from C₆H₁₃ to C₁₂H₂₅. All compounds were characterized by FTIR, ¹H, and ¹³C NMR spectroscopy. Mesophase behaviour of the synthesized compounds was investigated using differential scanning calorimetry and polarizing optical microscopy. It was determined that both the alkoxy side chain length, as well as the number of alkoxy side chains have an effect on the ability of this class of C₂ symmetric compounds to selfassemble into liquid crystalline phases. In addition, the overall core size and extent of conjugation also affected mesophase formation. The mono-alkoxy benzophenones and dibenzylidene acetones were non-mesogenic, while all four of the mono-alkoxy 1,9- diphenyl-nona-l,3,6,8-tetraen-5-ones (alkoxy side chain of lengths C₆H₁₃, C₈H₁₇, C₁₀H₂₁ and C₁₂H₂₅)self-assembled into nematic liquid crystalline phases. Increasing the number of alkoxy side chains from one to two per aromatic moiety helped induce liquid crystalline formation: the corresponding bis-C₆H₁₃ benzophenone and bis-C ₆H₁₃, bis C₈H₁₇, and bis-C₁₀H₂₁ dibenzylidene acetones were mesogenic, displaying smectic A (benzophenone) and nematic (dibenzylidene acetone) mesophases respectively.

This thesis deals primarily with supramolecular chemistry based on cucurbit[n]uril (CB[n], n = 7 and 8) host molecules. The research has been focused on the synthesis and characterization of host-guest complexes CB[n] with aromatic guest molecules, and the study of the effects of the host-guest complexation on the chemical reactivity and spectroscopic properties of the included guests, such as their photoreactivity and their UV-visible absorption and emission properties, in aqueous solution. The [4+4] photodimerization of protonated 2-aminopyridine (APH+) occurs stereoselectively to give the anti-trans product as the result of a preferred orientation of two APH+ guests in the cavity of CB[7]. The CB[7] host inhibits photohydration in the course of the photoisomerizations of protonated trans-1,2-bis(4-pyridyl)ethylene and trans-1,2-bis(1-methyl-4-pyridinium)ethylene by including the (4-pyridyl)ethylene portion of the guest, while this is not observed with trans-1,2-bis(1-hexyl-4-pyridinium)ethylene, as preferential inclusion of the hexyl groups leaves the vinyl group vulnerable to photohydration. Very strong CB[7] complexation of (E)-1-ferrocenyl-2-(1-methyl-4-pyridinium)ethylene completely inhibits the (E)→(Z) photoisomerization process. The H/D exchange rates and acidities of the C(2)-proton of cationic imidazolium and thiazolium (including thiamine and thiamine phosphates) carbon acids are decreased upon their complexation with CB[7]. Inclusion of protonated aromatic amines (and aromatic alcohols) in the cavity CB[7] significantly decreases their ground and excited state acidities, such that the emission is switched from the neutral amine to the protonated amine excited state, resulting in changes in the color of fluorescence. The fluorescence of acridizinium cations can be switched off by the formation of 2:1 complexes with CB[8] and then switched back on again by the addition of CB[7] or a competing guest molecule. The stabilization of the deep blue color of the 4,4’-bis(dimethylamino)diphenyl carbonium ion, upon complexation of the corresponding carbinol with CB[7], results from a complexation-induced shift in the carbinol/carbonium ion equilibrium. A dramatic purple to blue color change in pinacyanol chloride upon addition of CB[7] is due to a partial breakup of dye aggregates, upon the interactions of the dye with the host molecule. The CB[n] complexation-induced emission and/or absorption color switch have the potential to be employed in molecular switches and in chemical sensing. / Thesis (Ph.D, Chemistry) -- Queen's University, 2007-08-07 09:21:06.553

No description available.

This thesis is an experimental investigation on the binding of self-assembling peptides to oligodeoxynucleotides (ODNs) and the characterization of the resulting peptide-ODN complexes/aggregates, the first key step in the development of a peptide-based gene delivery system. Effects of pH, charge distribution along the peptide backbone, and oligonucleotide sequences on the peptide-ODN binding were investigated by a series of physicochemical methods. UV-Vis absorption and fluorescence anisotropy experiments demonstrate that aggregates are formed after mixing the peptide and ODN in aqueous solution. The aggregates in solution can be centrifuged out. Based on this property, the fraction of ODNs incorporated in the peptide-ODN aggregates can be obtained by comparing the UV-Vis absorption of the solution before and after centrifugation. Binding isotherms are generated by a binding density function analysis of the UV absorbance results. The binding parameters are extracted from the analysis of the binding isotherms based on the McGhee and von Hippel model. Equilibrium binding parameter studies show that the binding of two self-assembling peptides, EAK16-II and EAK 16-IV, to model single and double-stranded ODNs at pH 4 is stronger than at pH 7, and that no binding occurs at pH 11. These results demonstrate that electrostatic interactions play an important role in the EAK-ODN binding because EAKs are more positively charged at low pH. EAKs bind more strongly to dG16 than to the other ODN sequences dC16 and dGC16. This demonstrates that the hydrogen bond might be involved because they promote the binding of the lysine residues of the peptide to dG16 to a greater extent than to dC16. The charge distribution along the peptides is found to have an effect on the binding. EAK16-IV, whose positively charged residues are clustered at one end of the peptide, binds to the ODNs more strongly than EAK16-II, whose positively charged residues are distributed throughout the peptide chain, at the same pH. The binding process of EAKs to the ODNs was investigated by fluorescence anisotropy and static light scattering experiments. The results show that individual EAK and ODN molecules complex first, followed by the aggregation of these complexes into large aggregates. The nature of the resulting peptide-ODN complexes/aggregates is examined by UV-Vis absorption, fluorescence anisotropy, and PAGE experiments. The results demonstrate that free EAK, free ODNs, and small EAK-ODN complexes, which can not be centrifuged out, exist in the supernatant, and that large aggregates are collected in the pellets after centrifugation of the solution. The size of the resulting EAK-ODN complexes/aggregates measured by AFM and DLS is around a few hundreds of nanometers at low EAK concentrations. The accessibility of the ODNs to the quencher in the solution is reduced by 40 % and 60 % after binding to EAK16-II and EAK16-IV, respectively, as determined by fluorescence quenching experiments on EAK-ODN mixture solutions. An ODN protection from Exonuclease 1 degradation is provided by the EAK16-II or EAK16-IV matrix when they are mixed with the ODNs at pH 4. However, the ODNs are protected to a much lower degree when the EAK-ODN aggregates are prepared at pH 7. The EAK-ODN aggregates prepared at pH 7 are found to dissociate more easily than those prepared at pH 4 when they are incubated with exonuclease I solution at pH 9.5. These results suggest that the ODN protection afforded by the EAK-ODN aggregates is correlated with their structural stability after being incubated with the nuclease solution. The stability of the EAK-ODN aggregates after dilution is determined by UV-Vis absorption. No detectable dissociation of the aggregates is observed over 20 hrs after a 5- and 10-fold dilution of the solution in the same buffer used for their preparation. The EAK-ODN aggregates remain stable after the solutions are centrifuged, and re-dissolved in fresh buffer solutions. The ability of an EAK matix to protect ODNs from nuclease degradation together with its biocompatibility and low-toxicity suggests that EAK self-assembling peptides could be used as carriers for gene delivery.

The field of nanotechnology has enabled scientists to perform fascinating engineering manipulations of biological substrates. Systems of DNA are now able to perform algorithmic computations by way of constructing biological modules composed of DNA macromolecules and using laboratory techniques available to biological sciences. The tile assembly model is an established model of biomolecular computing: using properties of DNA macromolecules to define constructions of self-assembling biological systems. The existing tile assembly model uses the concept of DNA tiles conceptually shaped as squares and exposes the tiles to carefully controlled biological conditions. The result is that under this process we can design and create these systems to compute solutions to algorithmic problems. Hexagons are the only two-dimensional regular polygon other than squares that can tile a plane infinitely leaving no space uncovered, where only translations of the initial polygon is allowed. Therefore hexagon-shaped DNA tiles can be defined to cover a planar surface, with the notable difference of six adjacent tiles per position versus the four adjacent neighbours in traditional four sided tiles. In this thesis, we will define a generalization of the tile assembly model that supports six-sided DNA tiles, in addition to the traditional four sides. We will introduce a problem known as the 0-1 Knapsack problem that is currently unsolved with square tiles. Moreover, a solution to the problem was attempted by tile assembly model researchers, however we show there is an error in their solution. After we analyze their solution and discover the shortcomings of square tiles under those constraints, we then show this fault is not applicable to hexagon tiles. Therefore, we show that the 0-1 Knapsack problem is solvable using hexagon shaped tiles.