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- All Subjects: nanotechnology
- Creators: Yan, Hao
- Creators: Westerhoff, Paul
Description
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.
ContributorsLi, Zhe (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Seo, Dong-Kyun (Committee member) / Wachter, Rebekka (Committee member) / Arizona State University (Publisher)
Created2012
Description
Repeating tiles made of DNA were used to try to form an indefinitely large structure. Both the tiles and structure were 2D. Two different patterns were tested, one corrugated and one not. Corrugation means that the tiles alternated between facing up and facing down, canceling out any curvature to the tile and creating a slightly corrugated but largely 2D pattern. Annealing methods were also experimented with. Annealing the structure in two, separate steps as opposed to one was tested. Another experiment was comparing cyclic versus linear annealing. A linear decrease in temperatures defines the linear annealing, and a cyclic method involved a linear drop to a certain temperature, followed by a slight increase in temperature and cooling back down again. This cycle is done several times before it continues linear cool down. It was seen that both corrugated and non-corrugated structures could be made. In both cases tiles that make up a larger section of the overall pattern were more successful. This is especially important for the non-corrugated pattern. Linear and 2step annealing methods seem to yield the best results.
ContributorsHunt, Ashley Elizabeth (Author) / Yan, Liu (Thesis director) / Yan, Hao (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05
Description
Originally conceived as a way to scaffold molecules of interest into three-dimensional (3D) crystalline lattices for X ray crystallography, the field of deoxyribonucleic acid (DNA) nanotechnology has dramatically evolved since its inception. The unique properties of DNA nanostructures have promoted their use not only for X ray crystallography, but for a suite of biomedical applications as well. The work presented in this dissertation focuses on both of these exciting applications in the field: 1) Nucleic acid nanostructures as multifunctional drug and vaccine delivery platforms, and 2) 3D DNA crystals for structure elucidation of scaffolded guest molecules.Chapter 1 illustrates how a wide variety of DNA nanostructures have been developed for the delivery of drugs and vaccine components. However, their applications are limited under physiological conditions due to their lack of stability in low salt environments, susceptibility to enzymatic degradation, and tendency for endosomal entrapment. To address these issues, Chapter 2 describes a PEGylated peptide coating molecule was designed to electrostatically adhere to and protect DNA origami nanostructures and to facilitate their cytosolic delivery by peptide-mediated endosomal escape. The development of this molecule will aid in the use of nucleic acid nanostructures for biomedical purposes, such as the delivery of messenger ribonucleic acid (mRNA) vaccine constructs. To this end, Chapter 3 discusses the fabrication of a structured mRNA nanoparticle for more cost-efficient mRNA vaccine manufacture and proposes a multi-epitope mRNA nanostructure vaccine design for targeting human papillomavirus (HPV) type 16-induced head and neck cancers.
DNA nanotechnology was originally envisioned to serve as three-dimensional scaffolds capable of positioning proteins in a rigid array for their structure elucidation by X ray crystallography. Accordingly, Chapter 4 explores design parameters, such as sequence and Holliday junction isomeric forms, for efficient crystallization of 3D DNA lattices. Furthermore, previously published DNA crystal motifs are used to site-specifically position and structurally evaluate minor groove binding molecules with defined occupancies. The results of this study provide significant advancement towards the ultimate goal of the field.
ContributorsHenry, Skylar J.W. (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Anderson, Karen (Thesis advisor) / Blattman, Joseph (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2023
Description
The biological lipid bilayer on cells or the cell membrane is a surface teeming with activity. Several membrane proteins decorate the lipid bilayer to carry out various functionalities that help a cell interact with the environment, gather resources and communicate with other cells. This provides a repertoire of biological structures and processes that can be mimicked and manipulated. Since its inception in the late 20th century deoxyribonucleic acid (DNA) nanotechnology has been used to create nanoscale objects that can be used for such purposes. Using DNA as the building material provides the user with a programmable and functionalizable tool box to design and demonstrate these ideas. In this dissertation, I describe various DNA nanostructures that can insert or interact with lipid bilayers for cargo transport, diagnostics and therapeutics. First, I describe a reversibly gated DNA nanopore of 20.4nm x 20.4nm cross sectional width. Controlled transport of cargoes of various sizes across a lipid bilayer through a channel formed by the DNA nanopore was demonstrated. This demonstration paves the way for a class of nanopores that can be activated by different stimuli. The membrane insertion capability of the DNA nanopore is further utilized to design a nanopore sensor that can detect oligonucleotides of a specific s equence inside a lipid vesicle. The ease with which the sensor can be modified to i dentify different diagnostic markers for disease detection was shown by designing a sensor that can identify the non small cell lung cancer marker micro ribonucleic acid -21 (miRNA21). Finally, I demonstrate the therapeutic capabilities of DNA devices with a DNA tetrabody that can recruit natural killer cells (NK cells) to target cancer cells. The DNA tetrabody functionalized with cholesterol molecules and Her2 affibody inserts into NK cell membrane leading it to Her2 positive cancer cells. This shows that inthe presence of DNA tetrabody, the NK cell activation gets accelerated.
ContributorsAbraham, Leeza (Author) / Yan, Hao (Thesis advisor) / Liu, Uan (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2023
Description
As a rapidly evolving field, nucleic acid nanotechnology focuses on creating functional nanostructures or dynamic devices through harnessing the programmbility of nucleic acids including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), enabled by the predictable Watson-Crick base pairing. The precise control over the sequence and structure, along with the development of simulation softwares for the prediction of the experimental implementation provides the base of designing structures or devices with arbitrary topology and operational logic at nanoscale. Over the past 40 years, the thriving field has pushed the boundaries of nucleic acids, from originally biological macromolecules to functional building blocks with applications in biomedicine, molecular diagnostics and imaging, material science, electronics, crystallography, and more have emerged through programming the sequences and generating the various structures or devices. The underlying logic of nucleic acid programming is the base pairing rule, straightforward and robust. While for the complicated design of sequences and quantitative understanding of the programmed results, computational tools will markedly reduced the level of difficulty and even meet the challenge not available with manual effort. With this thesis three individual projects are presented, with all of them interweaving theory/computation and experiments. In a higher level abstraction, this dissertation covers the topic of biophysical understanding of the dynamic reactions, designing and realizing complex self-assembly systems and finally super-resolutional imaging. More specifically, Chapter 2 describes the study of RNA strand displacement kinetics with dedicated model extracting the reaction rates, providing guidelines for the rational design and regulation of the strand displacement reactions and eventually biochemical processes. In chapter 3 the platform for the design of complex symmetry of the self-assembly target and first experimental implementation of the assembly of pyrochlore lattices with DNA origamis are presented, which potentially can be applied to manipulate lights as optical materials. Chapter 4 focuses on the in solution characterization of the periodicity of DNA origami lattices with super-resolutional microscopy, with algorithms in development for three dimensional structural reconstruction.
ContributorsLiu, Hao (Author) / Yan, Hao (Thesis advisor) / Sulc, Petr (Thesis advisor) / Guo, Jia (Committee member) / Heyden, Matthias (Committee member) / Arizona State University (Publisher)
Created2023
Description
Peptide-based vaccines represent a promising strategy to develop personalized treatments for cancer immunotherapy. Despite their specificity and low cost of production, these vaccines have had minimal success in clinical studies due to their lack of immunogenicity, creating a need for more effective vaccine designs. Adjuvants can be incorporated to enhance their immunogenicity by promoting dendritic cell activation and antigen cross-presentation. Due to their favorable size and ability to incorporate peptides and adjuvants, nanoparticles represent an advantageous platform for designing peptide vaccines. One prime example is RNA origami (RNA-OG) nanostructures, which are nucleic acid nanostructures programmed to assemble into uniform shapes and sizes. These stable nanostructures can rationally incorporate small molecules giving them a wide array of functions. Furthermore, RNA-OG itself can function as an adjuvant to stimulate innate immune cells. In the following study, self-adjuvanted RNA-OG was employed as a vaccine assembly platform, incorporating tumor peptides onto the nanostructure to design RNA-OG-peptide nanovaccines for cancer immunotherapy. RNA-OG-peptide was found to induce dendritic cell activation and antigen cross-presentation, which mobilized tumor-specific cytotoxic T cells to elicit protective anti-tumor immunity in tumor-bearing mice. These findings demonstrate the therapeutic potential of RNA-OG as a stable, carrier-free nanovaccine platform. In an attempt to further enhance the efficacy by optimizing the amount of peptides assembled, RNA-OG was complexed with polylysine-linked peptides, a simple strategy that allowed peptide amounts to be varied. Interestingly, increasing the peptide load led to decreased vaccine efficacy, which was correlated with an ineffective CD8+ T cell response. On the other hand, the vaccine efficacy was improved by decreasing the amount of peptide loaded onto RNA-OG, which may have attributed to greater complex stability compared to the high peptide load. These results highlight a simple strategy that can be used to optimize vaccine efficacy by altering the load of assembled peptides. These studies advance our understanding of RNA-OG as a peptide vaccine platform and provide various strategies to improve the design of peptide vaccines for translation into cancer immunotherapy.
ContributorsYip, Theresa (Author) / Chang, Yung (Thesis advisor) / Borges Florsheim, Esther (Committee member) / Lake, Douglas (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2024
Description
The volume of end-of-life photovoltaic (PV) modules is increasing as the global PV market increases, and the global PV waste streams are expected to reach 250,000 metric tons by the end of 2020. If the recycling processes are not in place, there would be 60 million tons of end-of-life PV modules lying in the landfills by 2050, that may not become a not-so-sustainable way of sourcing energy since all PV modules could contain certain amount of toxic substances. Currently in the United States, PV modules are categorized as general waste and can be disposed in landfills. However, potential leaching of toxic chemicals and materials, if any, from broken end-of-life modules may pose health or environmental risks. There is no standard procedure to remove samples from PV modules for chemical toxicity testing in the Toxicity Characteristic Leaching Procedure (TCLP) laboratories as per EPA 1311 standard. The main objective of this thesis is to develop an unbiased sampling approach for the TCLP testing of PV modules. The TCLP testing was concentrated only for the laminate part of the modules, as they are already existing recycling technologies for the frame and junction box components of PV modules. Four different sample removal methods have been applied to the laminates of five different module manufacturers: coring approach, cell-cut approach, strip-cut approach, and hybrid approach. These removed samples were sent to two different TCLP laboratories, and TCLP results were tested for repeatability within a lab and reproducibility between the labs. The pros and cons of each sample removal method have been explored and the influence of sample removal methods on the variability of TCLP results has been discussed. To reduce the variability of TCLP results to an acceptable level, additional improvements in the coring approach, the best of the four tested options, are still needed.
ContributorsLeslie, Joswin (Author) / Tamizhmani, Govindasamy (Thesis advisor) / Srinivasan, Devarajan (Committee member) / Kuitche, Joseph (Committee member) / Arizona State University (Publisher)
Created2018
Description
Flame retardants (FRs) are applied to variety of consumer products such as textiles and polymers for fire prevention and fire safety. Substantial research is ongoing to replace traditional FRs with alternative materials that are less toxic, present higher flame retardancy and result in lower overall exposure as there are potential health concerns in case of exposure to popular FRs. Carbonaceous nanomaterials (CNMs) such as carbon nanotubes (CNTs) and graphene oxide (GO) have been studied and applied to polymer composites and electronics extensively due to their remarkable properties. Hence CNMs are considered as potential alternative materials that present high flame retardancy. In this research, different kinds of CNMs coatings on polyester fabric are produced and evaluated for their use as flame retardants. To monitor the mass loading of CNMs coated on the fabric, a two-step analytical method for quantifying CNMs embedded in polymer composites was developed. This method consisted of polymer dissolution process using organic solvents followed by subsequent programmed thermal analysis (PTA). This quantification technique was applicable to CNTs with and without high metal impurities in a broad range of polymers. Various types of CNMs were coated on polyester fabric and the efficacy of coatings as flame retardant was evaluated. The oxygen content of CNMs emerged as a critical parameter impacting flame retardancy with higher oxygen content resulting in less FR efficacy. The most performant nanomaterials, multi-walled carbon nanotubes (MWCNTs) and amine functionalized multi-walled carbon nantoubes (NH2-MWCNT) showed similar FR properties to current flame retardants with low mass loading (0.18 g/m2) and hence are promising alternatives that warrant further investigation. Chemical/physical modification of MWCNTs was conducted to produce well-dispersed MWCNT solutions without involving oxygen for uniform FR coating. The MWCNTs coating was studied to evaluate the durability of the coating and the impact on the efficacy during use phase by conducting mechanical abrasion and washing test. Approximately 50% and 40% of MWCNTs were released from 1 set of mechanical abrasion and washing test respectively. The losses during simulated usage impacted the flame retardancy negatively.
ContributorsNosaka, Takayuki (Author) / Herckes, Pierre (Thesis advisor) / Westerhoff, Paul (Committee member) / Wang, Qing Hua (Committee member) / Arizona State University (Publisher)
Created2018
Description
Ion exchange sorbents embedded with metal oxide nanoparticles can have high affinity and high capacity to simultaneously remove multiple oxygenated anion contaminants from drinking water. This research pursued answering the question, “Can synthesis methods of nano-composite sorbents be improved to increase sustainability and feasibility to remove hexavalent chromium and arsenic simultaneously from groundwater compared to existing sorbents?” Preliminary nano-composite sorbents outperformed existing sorbents in equilibrium tests, but struggled in packed bed applications and at low influent concentrations. The synthesis process was then tailored for weak base anion exchange (WBAX) while comparing titanium dioxide against iron hydroxide nanoparticles (Ti-WBAX and Fe-WBAX, respectively). Increasing metal precursor concentration increased the metal content of the created sorbents, but pollutant removal performance and usable surface area declined due to pore blockage and nanoparticle agglomeration. An acid-post rinse was required for Fe-WBAX to restore chromium removal capacity. Anticipatory life cycle assessment identified critical design constraints to improve environmental and human health performance like minimizing oven heating time, improving pollutant removal capacity, and efficiently reusing metal precursor solution. The life cycle environmental impact of Ti-WBAX was lower than Fe-WBAX as well as a mixed bed of WBAX and granular ferric hydroxide for all studied categories. A separate life cycle assessment found the total number of cancer and non-cancer cases prevented by drinking safer water outweighed those created by manufacture and use of water treatment materials and energy. However, treatment relocated who bore the health risk, concentrated it in a sub-population, and changed the primary manifestation from cancer to non-cancer disease. This tradeoff was partially mitigated by avoiding use of pH control chemicals. When properly synthesized, Fe-WBAX and Ti-WBAX sorbents maintained chromium removal capacity while significantly increasing arsenic removal capacity compared to the parent resin. The hybrid sorbent performance was demonstrated in packed beds using a challenging water matrix and low pollutant influent conditions. Breakthrough curves hint that the hexavalent chromium is removed by anion exchange and the arsenic is removed by metal oxide sorption. Overall, the hybrid nano-sorbent synthesis methods increased sustainability, improved sorbent characteristics, and increased simultaneous removal of chromium and arsenic for drinking water.
ContributorsGifford, James McKay (Author) / Westerhoff, Paul (Thesis advisor) / Hristovski, Kiril (Thesis advisor) / Chester, Mikhail (Committee member) / Arizona State University (Publisher)
Created2016
Description
Deoxyribonucleic acid (DNA) has emerged as an attractive building material for creating complex architectures at the nanometer scale that simultaneously affords versatility and modularity. Particularly, the programmability of DNA enables the assembly of basic building units into increasingly complex, arbitrary shapes or patterns. With the expanding complexity and functionality of DNA toolboxes, a quantitative understanding of DNA self-assembly in terms of thermodynamics and kinetics, will provide researchers with more subtle design guidelines that facilitate more precise spatial and temporal control. This dissertation focuses on studying the physicochemical properties of DNA tile-based self-assembly process by recapitulating representative scenarios and intermediate states with unique assembly pathways.
First, DNA double-helical tiles with increasing flexibility were designed to investigate the dimerization kinetics. The higher dimerization rates of more rigid tiles result from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. Next, the thermodynamics and kinetics of single tile attachment to preformed “multitile” arrays were investigated to test the fundamental assumptions of tile assembly models. The results offer experimental evidences that double crossover tile attachment is determined by the electrostatic environment and the steric hindrance at the binding site. Finally, the assembly of double crossover tiles within a rhombic DNA origami frame was employed as the model system to investigate the competition between unseeded, facet and seeded nucleation. The results revealed that preference of nucleation types can be tuned by controlling the rate-limiting nucleation step.
The works presented in this dissertation will be helpful for refining the DNA tile assembly model for future designs and simulations. Moreover, The works presented here could also be helpful in understanding how individual molecules interact and more complex cooperative bindings in chemistry and biology. The future direction will focus on the characterization of tile assembly at single molecule level and the development of error-free tile assembly systems.
First, DNA double-helical tiles with increasing flexibility were designed to investigate the dimerization kinetics. The higher dimerization rates of more rigid tiles result from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. Next, the thermodynamics and kinetics of single tile attachment to preformed “multitile” arrays were investigated to test the fundamental assumptions of tile assembly models. The results offer experimental evidences that double crossover tile attachment is determined by the electrostatic environment and the steric hindrance at the binding site. Finally, the assembly of double crossover tiles within a rhombic DNA origami frame was employed as the model system to investigate the competition between unseeded, facet and seeded nucleation. The results revealed that preference of nucleation types can be tuned by controlling the rate-limiting nucleation step.
The works presented in this dissertation will be helpful for refining the DNA tile assembly model for future designs and simulations. Moreover, The works presented here could also be helpful in understanding how individual molecules interact and more complex cooperative bindings in chemistry and biology. The future direction will focus on the characterization of tile assembly at single molecule level and the development of error-free tile assembly systems.
ContributorsJiang, Shuoxing (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Hayes, Mark (Committee member) / Wang, Xu (Committee member) / Arizona State University (Publisher)
Created2016