Matching Items (514)
Filtering by
- All Subjects: Creative Project
Description
DNA has recently emerged as an extremely promising material to organize molecules on nanoscale. The reliability of base recognition, self-assembling behavior, and attractive structural properties of DNA are of unparalleled value in systems of this size. DNA scaffolds have already been used to organize a variety of molecules including nanoparticles and proteins. New protein-DNA bio-conjugation chemistries make it possible to precisely position proteins and other biomolecules on underlying DNA scaffolds, generating multi-biomolecule pathways with the ability to modulate inter-molecular interactions and the local environment. This dissertation focuses on studying the application of using DNA nanostructure to direct the self-assembly of other biomolecular networks to translate biochemical pathways to non-cellular environments. Presented here are a series of studies toward this application. First, a novel strategy utilized DNA origami as a scaffold to arrange spherical virus capsids into one-dimensional arrays with precise nanoscale positioning. This hierarchical self-assembly allows us to position the virus particles with unprecedented control and allows the future construction of integrated multi-component systems from biological scaffolds using the power of rationally engineered DNA nanostructures. Next, discrete glucose oxidase (GOx)/ horseradish peroxidase (HRP) enzyme pairs were organized on DNA origami tiles with controlled interenzyme spacing and position. This study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Finally, a tweezer-like DNA nanodevice was designed and constructed to actuate the activity of an enzyme/cofactor pair. Using this approach, several cycles of externally controlled enzyme inhibition and activation were successfully demonstrated. This principle of responsive enzyme nanodevices may be used to regulate other types of enzymes and to introduce feedback or feed-forward control loops.
ContributorsLiu, Minghui (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2013
Description
DNA is a unique, highly programmable and addressable biomolecule. Due to its reliable and predictable base recognition behavior, uniform structural properties, and extraordinary stability, DNA molecules are desirable substrates for biological computation and nanotechnology. The field of DNA computation has gained considerable attention due to the possibility of exploiting the massive parallelism that is inherent in natural systems to solve computational problems. This dissertation focuses on building novel types of computational DNA systems based on both DNA reaction networks and DNA nanotechnology. A series of related research projects are presented here. First, a novel, three-input majority logic gate based on DNA strand displacement reactions was constructed. Here, the three inputs in the majority gate have equal priority, and the output will be true if any two of the inputs are true. We subsequently designed and realized a complex, 5-input majority logic gate. By controlling two of the five inputs, the complex gate is capable of realizing every combination of OR and AND gates of the other 3 inputs. Next, we constructed a half adder, which is a basic arithmetic unit, from DNA strand operated XOR and AND gates. The aim of these two projects was to develop novel types of DNA logic gates to enrich the DNA computation toolbox, and to examine plausible ways to implement large scale DNA logic circuits. The third project utilized a two dimensional DNA origami frame shaped structure with a hollow interior where DNA hybridization seeds were selectively positioned to control the assembly of small DNA tile building blocks. The small DNA tiles were directed to fill the hollow interior of the DNA origami frame, guided through sticky end interactions at prescribed positions. This research shed light on the fundamental behavior of DNA based self-assembling systems, and provided the information necessary to build programmed nanodisplays based on the self-assembly of DNA.
ContributorsLi, Wei (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Proteins and peptides fold into dynamic structures that access a broad functional landscape, however, designing artificial polypeptide systems continues to be a great chal-lenge. Conversely, deoxyribonucleic acid (DNA) engineering is now routinely used to build a wide variety of two dimensional and three dimensional (3D) nanostructures from simple hybridization based rules, and their functional diversity can be significantly ex-panded through site specific incorporation of the appropriate guest molecules. This dis-sertation describes a gentle methodology for using short (8 nucleotide) peptide nucleic acid (PNA) linkers to assemble polypeptides within a 3D DNA nanocage, as a proof of concept for constructing artificial catalytic centers. PNA-polypeptide conjugates were synthesized directly using microwave assisted solid phase synthesis or alternatively PNA linkers were conjugated to biologically expressed proteins using chemical crosslinking. The PNA-polypeptides hybridized to the preassembled DNA nanocage at room tempera-ture or 11 ⁰C and could be assembled in a stepwise fashion. Time resolved fluorescence anisotropy and gel electrophoresis were used to determine that a negatively charged az-urin protein was repelled outside of the negatively charged DNA nanocage, while a posi-tively charged cytochrome c protein was retained inside. Spectroelectrochemistry and an in-gel luminol oxidation assay demonstrated the cytochrome c protein remained active within the DNA nanocage and its redox potential decreased modestly by 10 mV due to the presence of the DNA nanocage. These results demonstrate the benign PNA assembly conditions are ideal for preserving polypeptide structure and function, and will facilitate the polypeptide-based assembly of artificial catalytic centers inside a stable DNA nanocage. A prospective application of assembling multiple cyclic γ-PNA-peptides to mimic the oxygen-evolving complex (OEC) catalytic active site from photosystem II (PSII) is described. In this way, the robust catalytic capacity of PSII could be utilized, without suffering the light-induced damage that occurs by the photoreactions within PSII via triplet state formation, which limits the efficiency of natural photosynthesis. There-fore, this strategy has the potential to revolutionize the process of designing and building robust catalysts by leveraging nature's recipes, and also providing a flexible and con-trolled artificial environment that might even improve them further towards commercial viability.
ContributorsFlory, Justin David (Author) / Fromme, Petra (Thesis advisor) / Yan, Hao (Committee member) / Buttry, Daniel (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2014
Description
ABSTRACT The unique structural features of deoxyribonucleic acid (DNA) that are of considerable biological interest also make it a valuable engineering material. Perhaps the most useful property of DNA for molecular engineering is its ability to self-assemble into predictable, double helical secondary structures. These interactions are exploited to design a variety of DNA nanostructures, which can be organized into both discrete and periodic structures. This dissertation focuses on studying the dynamic behavior of DNA nanostructure recognition processes. The thermodynamics and kinetics of nanostructure binding are evaluated, with the intention of improving our ability to understand and control their assembly. Presented here are a series of studies toward this goal. First, multi-helical DNA nanostructures were used to investigate how the valency and arrangement of the connections between DNA nanostructures affect super-structure formation. The study revealed that both the number and the relative position of connections play a significant role in the stability of the final assembly. Next, several DNA nanostructures were designed to gain insight into how small changes to the nanostructure scaffolds, intended to vary their conformational flexibility, would affect their association equilibrium. This approach yielded quantitative information about the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect. Finally, a multi-helical DNA nanostructure was used as a model `chip' for the detection of a single stranded DNA target. The results revealed that the rate constant of hybridization is strongly dominated by a rate-limiting nucleation step.
ContributorsNangreave, Jeanette (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian J.-L. (Committee member) / Seo, Dong Kyun (Committee member) / Arizona State University (Publisher)
Created2011
Description
A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences were isolated from a pool of random TNA molecules. This implicates a possible chemical framework capable of crosstalk between TNA and RNA. Further, this shows that heredity and evolution are not limited to the natural genetic system based on ribofuranosyl nucleic acids. Another alternative genetic system, glycerol nucleic acid (GNA) undergoes intrasystem pairing with superior thermalstability compared to that of DNA. Inspired by this property, I demonstrated a minimal nanostructure composed of both left- and right-handed mirro image GNA. This work suggested that GNA could be useful as promising orthogonal material in structural DNA nanotechnology.
ContributorsZhang, Su (Author) / Chaut, John C (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011
Description
DNA and RNA are generally regarded as one of the central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology witnessed the success of usage of DNA/RNA as programmable molecules to construct nano-objects with predefined shapes and dynamic molecular machines for various functions. From the perspective of structural design with nucleic acid, there are basically two types of assembly method, DNA tile based assembly and DNA origami based assembly, used to construct infinite-sized crystal structures and finite-sized molecular structures. The assembled structure can be used for arrangement of other molecules or nanoparticles with the resolution of nanometers to create new type of materials. The dynamic nucleic acid machine is based on the DNA strand displacement, which allows two nucleic acid strands to hybridize with each other to displace one or more prehybridized strands in the process. Strand displacement reaction has been implemented to construct a variety of dynamic molecular systems, such as molecular computer, oscillators, in vivo devices for gene expression control.
This thesis will focus on the computational design of structural and dynamic nucleic acid systems, particularly for new type of DNA structure design and high precision control of gene expression in vivo. Firstly, a new type of fundamental DNA structural motif, the layered-crossover motif, will be introduced. The layered-crossover allow non-parallel alignment of DNA helices with precisely controlled angle. By using the layered-crossover motif, the scaffold can go through the 3D framework DNA origami structures. The properties of precise angle control of the layered-crossover tiles can also be used to assemble 2D and 3D crystals. One the dynamic control part, a de-novo-designed riboregulator is developed that can recognize single nucleotide variation. The riboregulators can also be used to develop paper-based diagnostic devices.
This thesis will focus on the computational design of structural and dynamic nucleic acid systems, particularly for new type of DNA structure design and high precision control of gene expression in vivo. Firstly, a new type of fundamental DNA structural motif, the layered-crossover motif, will be introduced. The layered-crossover allow non-parallel alignment of DNA helices with precisely controlled angle. By using the layered-crossover motif, the scaffold can go through the 3D framework DNA origami structures. The properties of precise angle control of the layered-crossover tiles can also be used to assemble 2D and 3D crystals. One the dynamic control part, a de-novo-designed riboregulator is developed that can recognize single nucleotide variation. The riboregulators can also be used to develop paper-based diagnostic devices.
ContributorsHong, Fan, Ph. D (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Green, Alexander A. (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2019
Description
How do you convey what’s interesting and important to you as an artist in a digital world of constantly shifting attentions? For many young creatives, the answer is original characters, or OCs. An OC is a character that an artist creates for personal enjoyment, whether based on an already existing story or world, or completely from their own imagination.
As creations made for purely personal interests, OCs are an excellent elevator pitch to talk one creative to another, opening up opportunities for connection in a world where communication is at our fingertips but personal connection is increasingly harder to make. OCs encourage meaningful interaction by offering themselves as muses, avatars, and story pieces, and so much more, where artists can have their characters interact with other creatives through many different avenues such as art-making, table top games, or word of mouth.
In this thesis, I explore the worlds and aesthetics of many creators and their original characters through qualitative research and collaborative art-making. I begin with a short survey of my creative peers, asking general questions about their characters and thoughts on OCs, then move to sketching characters from various creators. I focus my research to a group of seven core creators and their characters, whom I interview and work closely with in order to create a series of seven final paintings of their original characters.
As creations made for purely personal interests, OCs are an excellent elevator pitch to talk one creative to another, opening up opportunities for connection in a world where communication is at our fingertips but personal connection is increasingly harder to make. OCs encourage meaningful interaction by offering themselves as muses, avatars, and story pieces, and so much more, where artists can have their characters interact with other creatives through many different avenues such as art-making, table top games, or word of mouth.
In this thesis, I explore the worlds and aesthetics of many creators and their original characters through qualitative research and collaborative art-making. I begin with a short survey of my creative peers, asking general questions about their characters and thoughts on OCs, then move to sketching characters from various creators. I focus my research to a group of seven core creators and their characters, whom I interview and work closely with in order to create a series of seven final paintings of their original characters.
ContributorsCote, Jacqueline (Author) / Button, Melissa M (Thesis director) / Dove-Viebahn, Aviva (Committee member) / School of Art (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
In the past ten years, the United States’ sound recording industries have experienced significant decreases in employment opportunities for aspiring audio engineers from economic imbalances in the music industry’s digital streaming era and reductions in government funding for career and technical education (CTE). The Recording Industry Association of America reports promises of music industry sustainability based on increasing annual revenues in paid streaming services and artists’ high creative demand. The rate of new audio engineer entries in the sound recording subsection of the music industry is not viable to support streaming artists’ high demand to engineer new music recordings. Offering CTE programs in secondary education is rare for aspiring engineers with insufficient accessibility to pursue a post-secondary or vocational education because of financial and academic limitations. These aspiring engineers seek alternatives for receiving an informal education in audio engineering on the Internet using video sharing services like YouTube to search for tutorials and improve their engineering skills. The shortage of accessible educational materials on the Internet restricts engineers from advancing their own audio engineering education, reducing opportunities to enter a desperate job market in need of independent, home studio-based engineers. Content creators on YouTube take advantage of this situation and commercialize their own video tutorial series for free and selling paid subscriptions to exclusive content. This is misleading for newer engineers because these tutorials omit important understandings of fundamental engineering concepts. Instead, content creators teach inflexible engineering methodologies that are mostly beneficial to their own way of thinking. Content creators do not often assess the incompatibility of teaching their own methodologies to potential entrants in a profession that demands critical thinking skills requiring applied fundamental audio engineering concepts and techniques. This project analyzes potential solutions to resolve the deficiencies in online audio engineering education and experiments with structuring simple, deliverable, accessible educational content and materials to new entries in audio engineering. Designing clear, easy to follow material to these new entries in audio engineering is essential for developing a strong understanding for the application of fundamental concepts in future engineers’ careers. Approaches to creating and designing educational content requires translating complex engineering concepts through simplified mediums that reduce limitations in learning for future audio engineers.
ContributorsBurns, Triston Connor (Author) / Tobias, Evan (Thesis director) / Libman, Jeff (Committee member) / Department of Information Systems (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
There has been a recent push for queer fiction, especially in the young adult genre, whose focus is gay and lesbian relationships. This growth is much needed in terms of visibility and the furthering of acceptance, but there are still subjects within the LGBTQ+ community that need to be addressed, including bisexual, asexual, and non-binary erasure. There are many people who claim that these identities do not exist, are labels used as a stepping stone on one's journey to discovering that they are homosexual, or are invented excuses for overtly promiscuous or prudish behavior. The existence of negative stereotypes, particularly those of non-binary individuals, is largely due to a lack of visibility and respectful representation within media and popular culture. However, there is still a dearth of non-binary content in popular literature outside of young adult fiction. Can You See Me? aims to fill the gap in bisexual, asexual, and non-binary representation in adult literature. Each of the four stories that make up this collection deals with an aspect of gender and/or sexuality that has been erased, ignored, or denied visibility in American popular culture. The first story, "We'll Grow Lemon Trees," examines bisexual erasure through the lens of sociolinguistics. A bisexual Romanian woman emigrates to Los Angeles in 1989 and must navigate a new culture, learn new languages, and try to move on from her past life under a dictatorship where speaking up could mean imprisonment or death. The second story "Up, Down, All Around," is about a young genderqueer child and their parents dealing with microaggressions, examining gender norms, and exploring personal identity through imaginary scenarios, each involving an encounter with an unknown entity and a colander. The third story, "Aces High," follows two asexual characters from the day they're born to when they are 28 years old, as they find themselves in pop culture. The two endure identity crises, gender discrimination, erasure, individual obsessions, and prejudice as they learn to accept themselves and embrace who they are. In the fourth and final story, "Mile Marker 72," a gay Mexican man must hide in plain sight as he deals with the death of his partner and coming out to his best friend, whose brother is his partner's murderer.
ContributorsOchser, Jordyn M. (Author) / Bell, Matt (Thesis director) / Free, Melissa (Committee member) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Pandora is a play exploring our relationship with gendered technology through the lens of artificial intelligence. Can women be subjective under patriarchy? Do robots who look like women have subjectivity? Hoping to create a better version of ourselves, The Engineer must navigate the loss of her creation, and Pandora must navigate their new world. The original premiere run was March 27-28, 2018, original cast: Caitlin Andelora, Rikki Tremblay, and Michael Tristano Jr.
ContributorsToye, Abigail Elizabeth (Author) / Linde, Jennifer (Thesis director) / Abele, Kelsey (Committee member) / Department of Information Systems (Contributor) / Economics Program in CLAS (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05