Matching Items (460)
Filtering by
- All Subjects: Biochemistry
- Resource Type: Text
Description
This thesis focuses on serial crystallography studies with X-ray free electron lasers
(XFEL) with a special emphasis on data analysis to investigate important processes
in bioenergy conversion and medicinal applications.
First, the work on photosynthesis focuses on time-resolved femtosecond crystallography
studies of Photosystem II (PSII). The structural-dynamic studies of the water
splitting reaction centering on PSII is a current hot topic of interest in the field, the
goal of which is to capture snapshots of the structural changes during the Kok cycle.
This thesis presents results from time-resolved serial femtosecond (fs) crystallography
experiments (TR-SFX) where data sets are collected at room temperature from a
stream of crystals that intersect with the ultrashort femtosecond X-ray pulses at an
XFEL with the goal to obtain structural information from the transient state (S4)
state of the cycle where the O=O bond is formed, and oxygen is released. The most
current techniques available in SFX/TR-SFX to handle hundreds of millions of raw
diffraction patterns are discussed, including selection of the best diffraction patterns,
allowing for their indexing and further data processing. The results include two 4.0 Å
resolution structures of the ground S1 state and triple excited S4 transient state.
Second, this thesis reports on the first international XFEL user experiments in
South Korea at the Pohang Accelerator Laboratory (PAL-XFEL). The usability of this
new XFEL in a proof-of-principle experiment for the study of microcrystals of human
taspase1 (an important cancer target) by SFX has been tested. The descriptions of
experiments and discussions of specific data evaluation challenges of this project in
light of the taspase1 crystals’ high anisotropy, which limited the resolution to 4.5 Å,
are included in this report
In summary, this thesis examines current techniques that are available in the
SFX/TR-SFX domain to study crystal structures from microcrystals damage-free,
with the future potential of making movies of biological processes.
(XFEL) with a special emphasis on data analysis to investigate important processes
in bioenergy conversion and medicinal applications.
First, the work on photosynthesis focuses on time-resolved femtosecond crystallography
studies of Photosystem II (PSII). The structural-dynamic studies of the water
splitting reaction centering on PSII is a current hot topic of interest in the field, the
goal of which is to capture snapshots of the structural changes during the Kok cycle.
This thesis presents results from time-resolved serial femtosecond (fs) crystallography
experiments (TR-SFX) where data sets are collected at room temperature from a
stream of crystals that intersect with the ultrashort femtosecond X-ray pulses at an
XFEL with the goal to obtain structural information from the transient state (S4)
state of the cycle where the O=O bond is formed, and oxygen is released. The most
current techniques available in SFX/TR-SFX to handle hundreds of millions of raw
diffraction patterns are discussed, including selection of the best diffraction patterns,
allowing for their indexing and further data processing. The results include two 4.0 Å
resolution structures of the ground S1 state and triple excited S4 transient state.
Second, this thesis reports on the first international XFEL user experiments in
South Korea at the Pohang Accelerator Laboratory (PAL-XFEL). The usability of this
new XFEL in a proof-of-principle experiment for the study of microcrystals of human
taspase1 (an important cancer target) by SFX has been tested. The descriptions of
experiments and discussions of specific data evaluation challenges of this project in
light of the taspase1 crystals’ high anisotropy, which limited the resolution to 4.5 Å,
are included in this report
In summary, this thesis examines current techniques that are available in the
SFX/TR-SFX domain to study crystal structures from microcrystals damage-free,
with the future potential of making movies of biological processes.
ContributorsKetawala, Gihan Kaushyal (Author) / Fromme, Petra (Thesis advisor) / Liu, Wei (Committee member) / Kirian, Richard (Committee member) / Arizona State University (Publisher)
Created2020
Description
Proteins are a large collection of biomolecules that orchestrate the vital
cellular processes of life. The last decade has witnessed dramatic advances in the
field of proteomics, which broadly include characterizing the composition, structure,
functions, interactions, and modifications of numerous proteins in biological systems,
and elucidating how the miscellaneous components collectively contribute to the
phenotypes associated with various disorders. Such large-scale proteomics studies
have steadily gained momentum with the evolution of diverse high-throughput
technologies. This work illustrates the development of novel high-throughput
proteomics platforms and their applications in translational and structural biology. In
Chapter 1, nucleic acid programmable protein arrays displaying the human
proteomes were applied to immunoprofiling of paired serum and cerebrospinal fluid
samples from patients with Alzheimer’s disease. This high-throughput
immunoproteomic approach allows us to investigate the global antibody responses
associated with Alzheimer’s disease and potentially identify the diagnostic
autoantibody biomarkers. In Chapter 2, a versatile proteomic pipeline based on the
baculovirus-insect cell expression system was established to enable high-throughput
gene cloning, protein production, in vivo crystallization and sample preparation for Xray diffraction. In conjunction with the advanced crystallography methods, this endto-end pipeline promises to substantially facilitate the protein structural
determination. In Chapter 3, modified nucleic acid programmable protein arrays
were developed and used for probing protein-protein interactions at the proteome
level. From the perspective of biomarker discovery, structural proteomics, and
protein interaction networks, this work demonstrated the power of high-throughput
proteomics technologies in myriad applications for proteome-scale structural,
functional, and biomedical research.
cellular processes of life. The last decade has witnessed dramatic advances in the
field of proteomics, which broadly include characterizing the composition, structure,
functions, interactions, and modifications of numerous proteins in biological systems,
and elucidating how the miscellaneous components collectively contribute to the
phenotypes associated with various disorders. Such large-scale proteomics studies
have steadily gained momentum with the evolution of diverse high-throughput
technologies. This work illustrates the development of novel high-throughput
proteomics platforms and their applications in translational and structural biology. In
Chapter 1, nucleic acid programmable protein arrays displaying the human
proteomes were applied to immunoprofiling of paired serum and cerebrospinal fluid
samples from patients with Alzheimer’s disease. This high-throughput
immunoproteomic approach allows us to investigate the global antibody responses
associated with Alzheimer’s disease and potentially identify the diagnostic
autoantibody biomarkers. In Chapter 2, a versatile proteomic pipeline based on the
baculovirus-insect cell expression system was established to enable high-throughput
gene cloning, protein production, in vivo crystallization and sample preparation for Xray diffraction. In conjunction with the advanced crystallography methods, this endto-end pipeline promises to substantially facilitate the protein structural
determination. In Chapter 3, modified nucleic acid programmable protein arrays
were developed and used for probing protein-protein interactions at the proteome
level. From the perspective of biomarker discovery, structural proteomics, and
protein interaction networks, this work demonstrated the power of high-throughput
proteomics technologies in myriad applications for proteome-scale structural,
functional, and biomedical research.
ContributorsTang, Yanyang (Author) / LaBaer, Joshua (Thesis advisor) / Anderson, Karen S (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2020
Description
Organic compounds are influenced by hydrothermal conditions in both marine and terrestrial environments. Sedimentary organic reservoirs make up the largest share of organic carbon in the carbon cycle, leading to petroleum generation and to chemoautotrophic microbial communities. There have been numerous studies on the reactivity of organic compounds in water at elevated temperatures, but these studies rarely explore the consequences of inorganic solutes in hydrothermal fluids. The experiments in this thesis explore new reaction pathways of organic compounds mediated by aqueous and solid phase metals, mainly Earth-abundant copper. These experiments show that copper species have the potential to oxidize benzene and toluene, which are typically viewed as unreactive. These pathways add to the growing list of known organic transformations that are possible in natural hydrothermal systems. In addition to the characterization of reactions in natural systems, there has been recent interest in using hydrothermal conditions to facilitate organic transformations that would be useful in an applied, industrial or synthetic setting. This thesis identifies two sets of conditions that may serve as alternatives to commonplace industrial processes. The first process is the oxidation of benzene with copper to form phenol and chlorobenzene. The second is the copper mediated dehalogenation of aryl halides. Both of these processes apply the concepts of geomimicry by carrying out organic reactions under Earth-like conditions. Only water and copper are needed to implement these processes and there is no need for exotic catalysts or toxic reagents.
ContributorsLoescher, Grant (Author) / Shock, Everett (Thesis advisor) / Hartnett, Hilairy (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2020
Description
Eosinophils are innate immune cells that are most commonly associated with parasite infection and allergic responses. Recent studies, though, have identified eosinophils as cells with diverse effector functions at baseline and in disease. Eosinophils in specific tissue immune environments are proposed to promote unique and specific effector functions, suggesting these cells have the capacity to differentiate into unique subtypes. The studies here focus on defining these subtypes using functional, molecular, and genetic analysis as well as using novel techniques to image these subtypes in situ.
To characterized these subtypes, an in vitro cytokine induced type 1 (E1) and type 2 (E2) eosinophil model was developed that display features and functions of eosinophils found in vivo. For example, E1 eosinophils secrete type 1 mediators (e.g., IL-12, CXCL9 and CXCL10), express iNOS and express increased levels of the surface molecules PDL1 and MHC-I. Conversely, E2 eosinophils release type 2 mediators (e.g., IL4, IL13, CCL17, and CCL22), degranulate and express increased surface molecules CD11b, ST2 and Siglec-F. Completion of differential expression analysis of RNAseq on these subtypes revealed 500 and 655 unique genes were upregulated in E1 and E2 eosinophils, respectively. Functional enrichment studies showed interferon regulatory factor (IRF) transcription factors were uniquely regulated in both mouse and human E1 and E2 eosinophils. These subtypes are sensitive to their environment, modulating their IRF and cell surface expression when stimulated with opposing cytokines, suggesting plasticity.
To identify and study these subtypes in situ, chromogenic and fluorescent eosinophil-specific immunostaining protocols were developed. Methods were created and optimized, here, to identify eosinophils by their granule proteins in formalin fixed mouse tissues. Yet, eosinophil-specific antibodies alone are not enough to identify and study the complex interactions eosinophil subtypes perform within a tissue. Therefore, as part of this thesis, a novel highly-multiplexed immunohistochemistry technique was developed utilizing cleavable linkers to address these concerns. This technique is capable of analyzing up to 22 markers within a single biopsy with single-cell resolution. With this approach, eosinophil subtypes can be studied in situ in routine patient biopsies.
To characterized these subtypes, an in vitro cytokine induced type 1 (E1) and type 2 (E2) eosinophil model was developed that display features and functions of eosinophils found in vivo. For example, E1 eosinophils secrete type 1 mediators (e.g., IL-12, CXCL9 and CXCL10), express iNOS and express increased levels of the surface molecules PDL1 and MHC-I. Conversely, E2 eosinophils release type 2 mediators (e.g., IL4, IL13, CCL17, and CCL22), degranulate and express increased surface molecules CD11b, ST2 and Siglec-F. Completion of differential expression analysis of RNAseq on these subtypes revealed 500 and 655 unique genes were upregulated in E1 and E2 eosinophils, respectively. Functional enrichment studies showed interferon regulatory factor (IRF) transcription factors were uniquely regulated in both mouse and human E1 and E2 eosinophils. These subtypes are sensitive to their environment, modulating their IRF and cell surface expression when stimulated with opposing cytokines, suggesting plasticity.
To identify and study these subtypes in situ, chromogenic and fluorescent eosinophil-specific immunostaining protocols were developed. Methods were created and optimized, here, to identify eosinophils by their granule proteins in formalin fixed mouse tissues. Yet, eosinophil-specific antibodies alone are not enough to identify and study the complex interactions eosinophil subtypes perform within a tissue. Therefore, as part of this thesis, a novel highly-multiplexed immunohistochemistry technique was developed utilizing cleavable linkers to address these concerns. This technique is capable of analyzing up to 22 markers within a single biopsy with single-cell resolution. With this approach, eosinophil subtypes can be studied in situ in routine patient biopsies.
ContributorsNAZAROFF, CHRISTOPHER D. (Author) / Guo, Jia (Thesis advisor) / Rank, Matthew A (Thesis advisor) / LaBaer, Joshua (Committee member) / Williams, Peter (Committee member) / Arizona State University (Publisher)
Created2020
Description
Integrins are a family of αβ heterodimeric transmembrane receptors. As an important class of adhesion receptors, integrins mediate cell adhesion, migration, and transformation through bidirectional signaling across the plasma membrane. Among the 24 different types of integrins, which are notorious for their capacity to recognize multiple ligands, the leukocyte integrin αMβ2 (Mac-1) is the most promiscuous member. In contrast to other integrins, Mac1 is unique with respect to its preference for cationic ligands. In this thesis, a new Mac-1 cationic ligand named pleiotrophin (PTN) is uncovered. PTN is an important cytokine and growth factor. Its activities in mitogenesis and angiogenesis have been extensively researched, but its function on immune cells was not widely explored. In this research, the cell biology and biochemical evidences show that PTN can regulate various Mac-1-expressing cells functions through the activation of the extracellular signal regulated kinases. Direct interactions between PTN and the αM I-domain, the major ligand-binding domain of Mac-1, has been shown using biolayer interferometry analyses and confirmed by solution NMR spectroscopy. The binding epitopes and the binding mechanism of PTN and αM I-domain interaction were further revealed by peptide array analysis and microscale thermophoresis. The data suggested that PTN’s thrombospondin type-1 repeat (TSR) domains and αM I-domain metal-ion-dependent adhesion site (MIDAS) are the major binding sites. In addition, this interaction followed a novel metal-ion independent binding mechanism which has not been found in other integrins. After a series of characterizations of αM I-domain using both experimental and computational methods, it showed that activated αM I-domain is significantly more dynamic than inactive αM I-domain, and the dynamics seem to modulate the effect of Mg2+ on its interactions with cationic ligands. To further explore the PTN induced Mac-1 structure rearrangement, intact Mac-1 was studied by negative stain electron microscopy. The results showed that the Mac-1 exhibited a very heterogeneous conformation distribution in detergents. In contrast, the Mac-1 adopted predominantly the bent conformation in phospholipid nanodisc condition. This Mac-1 nanodisc model provides a new platform for studying intact Mac-1 activation mechanism in a more physiologically relevant manner in the future.
ContributorsShen, Di (Author) / Wang, Xu (Thesis advisor) / Van Horn, Wade (Committee member) / Yarger, Jeffery (Committee member) / Arizona State University (Publisher)
Created2020
Description
Mixed-ionic electronic conducting (MIEC) oxides have drawn much attention from researchers because of their potential in high temperature separation processes. Among many materials available, perovskite type and fluorite type oxides are the most studied for their excellent oxygen ion transport property. These oxides not only can be oxygen adsorbent or O2-permeable membranes themselves, but also can be incorporated with molten carbonate to form dual-phase membranes for CO2 separation.
Oxygen sorption/desorption properties of perovskite oxides with and without oxygen vacancy were investigated first by thermogravimetric analysis (TGA) and fixed-bed experiments. The oxide with unique disorder-order phase transition during desorption exhibited an enhanced oxygen desorption rate during the TGA measurement but not in fixed-bed demonstrations. The difference in oxygen desorption rate is due to much higher oxygen partial pressure surrounding the sorbent during the fixed-bed oxygen desorption process, as revealed by X-ray diffraction (XRD) patterns of rapidly quenched samples.
Research on using perovskite oxides as CO2-permeable dual-phase membranes was subsequently conducted. Two CO2-resistant MIEC perovskite ceramics, Pr0.6Sr0.4Co0.2Fe0.8 O3-δ (PSCF) and SrFe0.9Ta0.1O3-δ (SFT) were chosen as support materials for membrane synthesis. PSCF-molten carbonate (MC) and SFT-MC membranes were prepared for CO2-O2 counter-permeation. The geometric factors for the carbonate phase and ceramic phase were used to calculate the effective carbonate and oxygen ionic conductivity in the carbonate and ceramic phase. When tested in CO2-O2 counter-permeation set-up, CO2 flux showed negligible change, but O2 flux decreased by 10-32% compared with single-component permeation. With CO2 counter-permeation, the total oxygen permeation flux is higher than that without counter-permeation.
A new concept of CO2-permselective membrane reactor for hydrogen production via steam reforming of methane (SRM) was demonstrated. The results of SRM in the membrane reactor confirm that in-situ CO2 removal effectively promotes water-gas shift conversion and thus enhances hydrogen yield. A modeling study was also conducted to assess the performance of the membrane reactor in high-pressure feed/vacuum sweep conditions, which were not carried out due to limitations in current membrane testing set-up. When 5 atm feed pressure and 10-3 atm sweep pressure were applied, the membrane reactor can produce over 99% hydrogen stream in simulation.
Oxygen sorption/desorption properties of perovskite oxides with and without oxygen vacancy were investigated first by thermogravimetric analysis (TGA) and fixed-bed experiments. The oxide with unique disorder-order phase transition during desorption exhibited an enhanced oxygen desorption rate during the TGA measurement but not in fixed-bed demonstrations. The difference in oxygen desorption rate is due to much higher oxygen partial pressure surrounding the sorbent during the fixed-bed oxygen desorption process, as revealed by X-ray diffraction (XRD) patterns of rapidly quenched samples.
Research on using perovskite oxides as CO2-permeable dual-phase membranes was subsequently conducted. Two CO2-resistant MIEC perovskite ceramics, Pr0.6Sr0.4Co0.2Fe0.8 O3-δ (PSCF) and SrFe0.9Ta0.1O3-δ (SFT) were chosen as support materials for membrane synthesis. PSCF-molten carbonate (MC) and SFT-MC membranes were prepared for CO2-O2 counter-permeation. The geometric factors for the carbonate phase and ceramic phase were used to calculate the effective carbonate and oxygen ionic conductivity in the carbonate and ceramic phase. When tested in CO2-O2 counter-permeation set-up, CO2 flux showed negligible change, but O2 flux decreased by 10-32% compared with single-component permeation. With CO2 counter-permeation, the total oxygen permeation flux is higher than that without counter-permeation.
A new concept of CO2-permselective membrane reactor for hydrogen production via steam reforming of methane (SRM) was demonstrated. The results of SRM in the membrane reactor confirm that in-situ CO2 removal effectively promotes water-gas shift conversion and thus enhances hydrogen yield. A modeling study was also conducted to assess the performance of the membrane reactor in high-pressure feed/vacuum sweep conditions, which were not carried out due to limitations in current membrane testing set-up. When 5 atm feed pressure and 10-3 atm sweep pressure were applied, the membrane reactor can produce over 99% hydrogen stream in simulation.
ContributorsWu, Han-Chun (Author) / Lin, Jerry Y.S. (Thesis advisor) / Deng, Shuguang (Committee member) / Jiao, Yang (Committee member) / Emady, Heather (Committee member) / Muhich, Christopherq (Committee member) / Arizona State University (Publisher)
Created2020
Description
Glycans are complex biological sugar polymers that are commonly found covalently attached to proteins, lipids, and lipoproteins. About 50% of all mammalian proteins are glycosylated. Aberrant glycosylation is a hallmark of most types of cancer, and glycosylation changes that occur in this disease are known to facilitate tumor development. In this dissertation, a bottom-up approach to glycomics, “glycan node analysis”, which is a method based on glycan linkage analysis that quantifies unique glycan features, such as “core fucosylation”, “α2-6 sialylation”, “β1-6 branching”, and “bisecting GlcNAc”, as single analytical signals by gas chromatography-mass spectrometry (GC-MS), was applied to cancer cell lines, antibodies, extracellular vesicles, and low density lipoproteins to understand the mechanisms leading to aberrant glycosylation in cancer, and to understand the role of blood plasma glycan sialylation in cancer immunity. Specific tumor antigens such as β1-6-branching, β1-4-branching, bisecting GlcNAc, antennary fucosylation, and Tn antigen (GalNAc-Ser/Thr), were found to be regulated by IL-6 in HepG2 cells; fewer glycan features were regulated by IL-1β. Additionally, neuraminidase enzyme treatment of alpha-1 antitrypsin IgG demonstrates how glycan node analysis can be used to detect relative changes in “α2-6-sialylation” along with corresponding increases in terminal galactose.
Extracellular vesicles (EVs) derived from metastatic and non-metastatic cancer cell lines displayed upregulated or downregulated expression of several specific glycan nodes, particularly 3-GlcNAc, which represents hyaluronic acid. EVs displayed several glycan features that distinguished them from the whole blood plasma glycome. These results were promising for developing new diagnostic strategies in cancer.
A “liquid phase permethylation” procedure for glycan node analysis that does not require spin columns was applied for the first time to whole biological specimens, and it demonstrated potential clinical utility in detecting specific tumor antigens. Significantly different glycan node profiles were found among three cancer cell lines and in peripheral blood mononuclear cells from healthy donors.
Changes in glycosylation and mechanisms regulating glycan changes were studied extensively in cancer cells. Subsequently, it is reported how glycosylation changes can have an impact in cancer immunity. A novel role for oxidized-desialylated low density lipoprotein in cancer immunity is reported, and its implications in cancer and atherosclerosis are discussed.
ContributorsAguilar Diaz de leon, Jesús Salvador (Author) / Borges, Chad R (Thesis advisor) / Williams, Peter (Committee member) / Wang, Xu (Committee member) / Arizona State University (Publisher)
Created2021
Description
Staphylococcus aureus permanently asymptomatically colonizes one-third of humans, yet is an opportunistic pathogen causing life threatening diseases. Diagnosing S. aureus infections requires differentiating S. aureus from the human commensal Staphylococcus epidermidis, which beneficially colonizes the skin of all people. These studies aimed to characterize the volatile metabolites of S. aureus and S. epidermidis, and to measure the influence of growth medium on the discovery of volatile organic compounds that differentiate them. Headspace solid-phase microextraction and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry detected 337 S. aureus and S. epidermidis headspace volatiles produced during aerobic growth in four complex media. Analyses revealed that only 20 – 40% of staph volatiles are produced by both species in any one medium. Using principal components and hierarchical clustering analyses of the staphylococcal volatiles showed individual clustering of S. aureus and S. epidermidis independent of culturing media but clustering of replicate cultures by growth medium within species. Subsets of volatiles produced in common by both species, or in common across all four media, revealed volatilome differences between S. aureus and S. epidermidis based on the volatiles’ relative abundances. When analyzing volatiles by relative abundances, culturing staph in media containing free glucose (brain heart infusion and tryptic soy broth) revealed volatilomes dominated by acids and esters (67%). The low-glucose media (lysogeny broth and Mueller-Hinton broth) yielded ketones in greatest relative abundances, yet also produced highly dissimilar volatilome compositions. The staphylococcal volatilome is strongly influenced by the nutritional composition of growth medium, especially free glucose availability, which is robustly evident when analyzing the relative abundances of the volatiles, compared to their presence versus absence. Future work will evaluate more strains of each species, testing the universality of these results. Prospective analyses involve hypotheses testing on the role of catabolite repression control and glucose availability on the volatilome, with plans to model in vitro culture conditions that replicate in vivo volatilomes. Studies assessing correlations of virulence to species-specific volatilome responses to free glucose may identify pathogenic strains of S. epidermidis and other staphylococcal commensals.
ContributorsJenkins, Carrie L. (Author) / Bean, Heather D (Thesis advisor) / Buetow, Kenneth H (Committee member) / Lake, Douglas (Committee member) / Wilson-Rawls, Jeanne (Committee member) / Arizona State University (Publisher)
Created2021
Description
This dissertation focuses on the structure-function relationships of nanomaterials (NMs) and some of their applications in environmental engineering. The aim is to investigate NMs of different surface chemistries and assess their interactions with biological models, evaluate the weathering impact and degradation parameters to improve polymer coatings, test their efficiency for contaminant removal and provide further understanding in the safe design of nanomaterials. Nanoecotoxicological risk assessment currently suffers from a lack of testing procedures adapted to nanomaterials. Graphene oxide (GO) is a carbon nanomaterial (CNM) that consists of a single layer of carbon atoms arranged in a hexagonal network. It is decorated with a high density of oxygen functional groups including epoxide and hydroxyl moieties on the basal planes and carboxylic and carbonyl groups at the edges. The changes in surface chemistry give GO unique properties that can be tailored for a function. Additionally, because of its simple synthesis and flexible chemistry, GO has been a popular building block of many composite CNMs. In environmental engineering, specifically, water treatment, GO has been studied by itself or as a composite for pollutant removal, biofouling reduction, and as an antimicrobial agent, just to name a few. Like GO, silver (Ag) is another NM widely used in water treatment for its biocidal properties. Despite the recent growth in this field, a fundamental understanding of the function-structure relationships in NMs is still progressing. Through a systematic set of experiments, the structure-properties-function and structure-properties-hazard relationships were investigated. These relationships can be used to establish guidelines to engineer “safe-by-design” functional nanomaterials, where materials are tailored to enhance their function while minimizing their inherent biological or environmental hazard.
ContributorsBarrios, Ana Cecilia (Author) / Perreault, Francois (Thesis advisor) / Abbaszadegan, Morteza (Committee member) / Conroy-Ben, Otakuye (Committee member) / Hua-Wang, Qing (Committee member) / Arizona State University (Publisher)
Created2021
Description
Since the inception of DNA nanotechnology, DNA has found itself poised as one of the most robust self-assembling building blocks due to its well understood double helix structure formed by two anti-parallel strands of DNA held together by hydrogen bond from nucleobases which also provides the material programmability due to the well-understood Watson Crick base pairing rules. These capabilities have led to the exponential increase in publications showing off intricate and remarkable designs alongside ever-expanding applications. However, as the field expands there is an apparent lack of chemical diversity and functionality. To combat this my research focused on creating hybrid peptide oligonucleotide conjugates (POC) where the conjugated peptide could add chemical and structural diversity using the 20 canonical amino acids and various peptide secondary structures. In this work, I conjugate DNA to the self-assembling peptide building block the coiled coil. The coiled coil motif is formed from the self-assembly of two or more α-helical peptides and, like DNA, the coiled coil has well understood programmability. Together as a conjugate, the DNA and coiled coil, create a new self-assembling building block capable of two orthogonal self-assembling modes that can work in tandem. In this work, I used DNA coiled coil conjugates to show the capability to create first of their kind hybrid DNA/coiled coil one-dimensional fibers (chapter 2), integrate proteins (chapter 3), and to create hybrid cage structures (chapter 4). Finally, a POC hydrogel is created using the polypeptide gelatin with DNA crosslinks to create a reversible stiffening gel using toe-hold mediated strand displacement (chapter 5).
ContributorsBuchberger, Alex Richard (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Mills, Jeremy (Committee member) / Van Horn, Wade (Committee member) / Arizona State University (Publisher)
Created2021