Matching Items (34)
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- All Subjects: Chemistry
- Genre: Doctoral Dissertation
- Creators: Gould, Ian
Description
Since the conception of DNA nanotechnology, the field has evolved towards the development of complex, dynamic 3D structures. The predictability of Watson-Crick base pairing makes DNA an unparalleled building block, and enables exceptional programmability in nanostructure shape and size. The work presented in this dissertation focuses on expanding two facets of the field: (1) introducing functionality through the incorporation of peptides to create DNA-peptide hybrid materials, and (2) the development of self-assembling DNA crystal lattices for scaffolding biomolecules. DNA nanostructures have long been proposed as drug delivery vehicles; however, they are not biocompatible because of their low stability in low salt environments and entrapment within the endosome. To address these issues, a functionalized peptide coating was designed to act as a counterion to a six-helix bundle, while simultaneously displaying numerous copies of an endosomal escape peptide to enable cytosolic delivery. This functionalized peptide coating creates a DNA-peptide hybrid material, but does not allow specific positioning or orientation of the peptides. The ability to control those aspects required the synthesis of DNA-peptide or DNA-peptide-DNA conjugates that can be incorporated into the nanostructure. The approach was utilized to produce a synbody where three peptides that bind transferrin with micromolar affinity, which were presented for multivalent binding to optimize affinity. Additionally, two DNA handle was attached to an enzymatically cleavable peptide to link two unique nanostructures. The second DNA handle was also used to constrain the peptide in a cyclic fashion to mimic the cell-adhesive conformations of RGD and PHSRN in fibronectin.
The original goal of DNA nanotechnology was to use a crystalline lattice made of DNA to host proteins for their structural determination using X-ray crystallography. The work presented here takes significant steps towards achieving this goal, including elucidating design rules to control cavity size within the scaffold for accommodating guest molecules of unique sizes, approaches to improve the atomic detail of the scaffold, and strategies to modulate the symmetry of each unique lattice. Finally, this work surveys methodologies towards the incorporation of several guest molecules, with promising preliminary results that constitute a significant advancement towards the ultimate goal of the field.
ContributorsMacCulloch, Tara Lynn (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Borges, Chad (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2021
Description
Interactions between proteins form the basis of almost all biological mechanisms. The majority of proteins perform their functions as a part of an assembled complex, rather than as an isolated species. Understanding the functional pathways of these protein complexes helps in uncovering the molecular mechanisms involved in the interactions. In this thesis, this has been explored in two fundamental ways. First, a biohybrid complex was assembled using the photosystem I (PSI) protein complex to translate the biochemical pathways into a non-cellular environment. This involved incorporating PSI on a porous antimony-doped tin oxide electrode using cytochrome c. Photocurrent was generated upon illumination of the PSI/electrode system alone at microamp/cm2 levels, with reduced oxygen apparently as the primary carrier. When the PSI/electrode system was coupled with ferredoxin, ferredoxin-NADP+ reductase (FNR), and NADP+, the resulting light-powered NADPH production was coupled to a dehydrogenase system for enzymatic carbon reduction. The results demonstrated that light-dependent reduction readily takes place. However, the pathways do not always match the biological pathways of PSI in nature. To create a complex self-assembled system such as the one involving PSI that is structurally well defined, there is a need to develop ways to guide the molecular interactions. In the second part of the thesis, this problem was approached by studying a well-defined system involving monoclonal antibodies (mAbs) binding their cognate epitope sequences to understand the molecular recognition properties associated with protein-protein interactions. This approach used a neural network model to derive a comprehensive and quantitative relationship between an amino acid sequence and its function by using sparse measurements of mAb binding to peptides on a high density peptide microarray. The resulting model can be used to predict the function of any peptide in the possible combinatorial sequence space. The results demonstrated that by training the model on just ~105 peptides out of the total combinatorial space of ~1010, the target sequences of the mAbs (cognate epitopes) can be predicted with high statistical accuracy. Furthermore, the biological relevance of the algorithm’s predictive ability has also been demonstrated.
ContributorsSingh, Akanksha (Author) / Woodbury, Neal (Thesis advisor) / Liu, Yan (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2021
Description
MAX phases are an intriguing class of materials with exotic combinations of properties, essentially turning them into metallic ceramics. Despite this unique feature, no commercialization has been accomplished yet. Looking at the state of the art within the MAX phase community, almost all published studies can be summarized using the term “traditional high temperature synthesis”. Contrasting the scientific interest that has been on the rise especially since the discovery of MXenes, the synthetic spectrum has been largely the same as it has been over the past decades.Herein, the newly-emerging sol-gel chemistry is being explored as an alternative non-conventional synthetic approach. Building on the successful sol-gel synthesis of Cr2GaC, this study focuses around the expansion of sol-gel chemistry for MAX phases. Starting with a thorough mechanistic investigation into the reaction pathway of sol-gel synthesized Cr2GaC, the chemical understanding of this system is drastically deepened. It is shown how the preliminary nano-structured metal-oxide species develop into bulk oxides, before the amorphous and disordered
graphite partakes in the reaction and reduces the metals into the MAX phase.
Furthermore, the technique is extended to the two Ge- based MAX phases V2GeC and Cr2GeC, a critical step needed to prove the viability and applicability of the newly developed technique. Additionally, by introducing Mn into the Cr-Ga-C system, a Mn-doping was achieved, and for the first time for (Cr1–xMnx)2GaC, a unit cell increase could be recorded. Based on magnetometry measurements, the currently widely accepted assumption of statistically distributed Mn in the M-layer is challenged.
The versatility of wet chemistry is explored using the model system Cr2GaC. Firstly, the MAX phase can be obtained in a microwire shape leveraging the branched biopolymer dextran, eliminating the need for any post-synthesis machining. Via halide intercalation, the electrical transport properties could be purposefully engineered.
Secondly, leveraging the unique and linear biopolymer chitosan, Cr2GaC was obtained as thick films and dense microspheres, drastically opening potential areas of application for MAX phases. Lastly, hollow microspheres with diameters of tens of μm were synthesized via carboxymethylated dextran. This shape once more opens the door to very specific applications requiring sophisticated structures.
ContributorsSiebert, Jan (Author) / Birkel, Christina (Thesis advisor) / Gould, Ian (Committee member) / Kouvetakis, John (Committee member) / Arizona State University (Publisher)
Created2022
Description
Deoxyribonucleic acid (DNA), a biopolymer well known for its role in preserving genetic information in biology, is now drawing great deal of interest from material scientists. Ease of synthesis, predictable molecular recognition via Watson-Crick base pairing, vast numbers of available chemical modifications, and intrinsic nanoscale size makes DNA a suitable material for the construction of a plethora of nanostructures that can be used as scaffold to organize functional molecules with nanometer precision. This dissertation focuses on DNA-directed organization of metallic nanoparticles into well-defined, discrete structures and using them to study photonic interaction between fluorophore and metal particle. Presented here are a series of studies toward this goal. First, a novel and robust strategy of DNA functionalized silver nanoparticles (AgNPs) was developed and DNA functionalized AgNPs were employed for the organization of discrete well-defined dimeric and trimeric structures using a DNA triangular origami scaffold. Assembly of 1:1 silver nanoparticle and gold nanoparticle heterodimer has also been demonstrated using the same approach. Next, the triangular origami structures were used to co-assemble gold nanoparticles (AuNPs) and fluorophores to study the distance dependent and nanogap dependencies of the photonic interactions between them. These interactions were found to be consistent with the full electrodynamic simulations. Further, a gold nanorod (AuNR), an anisotropic nanoparticle was assembled into well-defined dimeric structures with predefined inter-rod angles. These dimeric structures exhibited unique optical properties compared to single AuNR that was consistent with the theoretical calculations. Fabrication of otherwise difficult to achieve 1:1 AuNP- AuNR hetero dimer, where the AuNP can be selectively placed at the end-on or side-on positions of anisotropic AuNR has also been shown. Finally, a click chemistry based approach was developed to organize sugar modified DNA on a particular arm of a DNA origami triangle and used them for site-selective immobilization of small AgNPs.
ContributorsPal, Suchetan (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Lindsay, Stuart (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012