Matching Items (9)
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- All Subjects: nanotechnology
- Genre: Academic theses
- Genre: Masters Thesis
- Creators: Chen, Julian
- Creators: Goryll, Michael
- Status: Published
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
DNA nanotechnology is one of the most flourishing interdisciplinary research fields. Through the features of programmability and predictability, DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales, and more importantly, they can be used as scaffolds for organizing other nanoparticles, proteins and chemical groups. By leveraging these molecules, DNA nanostructures can be used to direct the organization of complex bio-inspired materials that may serve as smart drug delivery systems and in vitro or in vivo bio-molecular computing and diagnostic devices. In this dissertation I describe a systematic study of the thermodynamic properties of complex DNA nanostructures, including 2D and 3D DNA origami, in order to understand their assembly, stability and functionality and inform future design endeavors. It is conceivable that a more thorough understanding of DNA self-assembly can be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications. As a biocompatible nanoscale motif, the successful integration, stabilization and separation of DNA nanostructures from cells/cell lysate suggests its potential to serve as a diagnostic platform at the cellular level. Here, DNA origami was used to capture and identify multiple T cell receptor mRNA species from single cells within a mixed cell population. This demonstrates the potential of DNA nanostructure as an ideal nano scale tool for biological applications.
ContributorsWei, Xixi (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Scientists around the world have been striving to develop artificial light-harvesting antenna model systems for energy and other light-driven biochemical applications. Among the various approaches to achieve this goal, one of the most promising is the assembly of structurally well-defined artificial light-harvesting antennas based on the principles of structural DNA nanotechnology. DNA has recently emerged as an extremely efficient material to organize molecules such as fluorophores and proteins on the nanoscale. It is desirable to develop a hybrid smart material by combining artificial antenna systems based on DNA with natural reaction center components, so that the material can be engineered to convert light energy to chemical energy via formation of a charge-separated state.
Presented here are a series of studies toward this goal. First, self-assembled seven-helix DNA bundles (7HB) with cyclic arrays of three distinct chromophores were developed. The spectral properties and energy transfer mechanisms in the artificial light-harvesting antenna were studied extensively using steady-state and time-resolved methods. Next, engineered cysteine residues in the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides were each covalently conjugated to fluorophores in order to explore the spectral requirements for energy transfer between an artificial light harvesting system and the reaction center. Finally, a structurally well-defined and spectrally tunable artificial light-harvesting system was constructed, where multiple organic dyes were conjugated to 3-arm DNA nanostructure. A reaction center protein isolated from the purple photosynthetic bacterium Rhodobacter sphaeroides was linked to one end of the 3-arm junction to serve as the final acceptor, which converts the photonic energy absorbed by the chromophores into chemical energy by charge separation. This type of model system is required to understand how parameters such as geometry, spectral characteristics of the dyes, and conformational flexibility affect energy transfer, and can be used to inform the development of more complex model light-harvesting systems.
Presented here are a series of studies toward this goal. First, self-assembled seven-helix DNA bundles (7HB) with cyclic arrays of three distinct chromophores were developed. The spectral properties and energy transfer mechanisms in the artificial light-harvesting antenna were studied extensively using steady-state and time-resolved methods. Next, engineered cysteine residues in the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides were each covalently conjugated to fluorophores in order to explore the spectral requirements for energy transfer between an artificial light harvesting system and the reaction center. Finally, a structurally well-defined and spectrally tunable artificial light-harvesting system was constructed, where multiple organic dyes were conjugated to 3-arm DNA nanostructure. A reaction center protein isolated from the purple photosynthetic bacterium Rhodobacter sphaeroides was linked to one end of the 3-arm junction to serve as the final acceptor, which converts the photonic energy absorbed by the chromophores into chemical energy by charge separation. This type of model system is required to understand how parameters such as geometry, spectral characteristics of the dyes, and conformational flexibility affect energy transfer, and can be used to inform the development of more complex model light-harvesting systems.
ContributorsDutta, Palash Kanti (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Biogenic silica nanostructures, derived from diatoms, possess highly ordered porous hierarchical nanostructures and afford flexibility in design in large part due to the availability of a great variety of shapes, sizes, and symmetries. These advantages have been exploited for study of transport phenomena of ions and molecules towards the goal of developing ultrasensitive and selective filters and biosensors. Diatom frustules give researchers many inspiration and ideas for the design and production of novel nanostructured materials. In this doctoral research will focus on the following three aspects of biogenic silica: 1) Using diatom frustule as protein sensor. 2) Using diatom nanostructures as template to fabricate nano metal materials. 3) Using diatom nanostructures to fabricate hybrid platform.
Nanoscale confinement biogenetic silica template-based electrical biosensor assay offers the user the ability to detect and quantify the biomolecules. Diatoms have been demonstrated as part of a sensor. The sensor works on the principle of electrochemical impedance spectroscopy. When specific protein biomarkers from a test sample bind to corresponding antibodies conjugated to the surface of the gold surface at the base of each nanowell, a perturbation of electrical double layer occurs resulting in a change in the impedance.
Diatoms are also a new source of inspiration for the design and fabrication of nanostructured materials. Template-directed deposition within cylindrical nanopores of a porous membrane represents an attractive and reproducible approach for preparing metal nanopatterns or nanorods of a variety of aspect ratios. The nanopatterns fabricated from diatom have the potential of the metal-enhanced fluorescence to detect dye-conjugated molecules.
Another approach presents a platform integrating biogenic silica nanostructures with micromachined silicon substrates in a micro
ano hybrid device. In this study, one can take advantages of the unique properties of a marine diatom that exhibits nanopores on the order of 40 nm in diameter and a hierarchical structure. This device can be used to several applications, such as nano particles separation and detection. This platform is also a good substrate to study cell growth that one can observe the reaction of cell growing on the nanostructure of frustule.
Nanoscale confinement biogenetic silica template-based electrical biosensor assay offers the user the ability to detect and quantify the biomolecules. Diatoms have been demonstrated as part of a sensor. The sensor works on the principle of electrochemical impedance spectroscopy. When specific protein biomarkers from a test sample bind to corresponding antibodies conjugated to the surface of the gold surface at the base of each nanowell, a perturbation of electrical double layer occurs resulting in a change in the impedance.
Diatoms are also a new source of inspiration for the design and fabrication of nanostructured materials. Template-directed deposition within cylindrical nanopores of a porous membrane represents an attractive and reproducible approach for preparing metal nanopatterns or nanorods of a variety of aspect ratios. The nanopatterns fabricated from diatom have the potential of the metal-enhanced fluorescence to detect dye-conjugated molecules.
Another approach presents a platform integrating biogenic silica nanostructures with micromachined silicon substrates in a micro
ano hybrid device. In this study, one can take advantages of the unique properties of a marine diatom that exhibits nanopores on the order of 40 nm in diameter and a hierarchical structure. This device can be used to several applications, such as nano particles separation and detection. This platform is also a good substrate to study cell growth that one can observe the reaction of cell growing on the nanostructure of frustule.
ContributorsLin, Kai-Chun (Author) / Ramakrishna, B.L. (Thesis advisor) / Goryll, Michael (Thesis advisor) / Dey, Sandwip (Committee member) / Prasad, Shalini (Committee member) / Arizona State University (Publisher)
Created2014
Description
In the last few years, significant advances in nanofabrication have allowed tailoring of structures and materials at a molecular level enabling nanofabrication with precise control of dimensions and organization at molecular length scales, a development leading to significant advances in nanoscale systems. Although, the direction of progress seems to follow the path of microelectronics, the fundamental physics in a nanoscale system changes more rapidly compared to microelectronics, as the size scale is decreased. The changes in length, area, and volume ratios due to reduction in size alter the relative influence of various physical effects determining the overall operation of a system in unexpected ways. One such category of nanofluidic structures demonstrating unique ionic and molecular transport characteristics are nanopores. Nanopores derive their unique transport characteristics from the electrostatic interaction of nanopore surface charge with aqueous ionic solutions. In this doctoral research cylindrical nanopores, in single and array configuration, were fabricated in silicon-on-insulator (SOI) using a combination of electron beam lithography (EBL) and reactive ion etching (RIE). The fabrication method presented is compatible with standard semiconductor foundries and allows fabrication of nanopores with desired geometries and precise dimensional control, providing near ideal and isolated physical modeling systems to study ion transport at the nanometer level. Ion transport through nanopores was characterized by measuring ionic conductances of arrays of nanopores of various diameters for a wide range of concentration of aqueous hydrochloric acid (HCl) ionic solutions. Measured ionic conductances demonstrated two distinct regimes based on surface charge interactions at low ionic concentrations and nanopore geometry at high ionic concentrations. Field effect modulation of ion transport through nanopore arrays, in a fashion similar to semiconductor transistors, was also studied. Using ionic conductance measurements, it was shown that the concentration of ions in the nanopore volume was significantly changed when a gate voltage on nanopore arrays was applied, hence controlling their transport. Based on the ion transport results, single nanopores were used to demonstrate their application as nanoscale particle counters by using polystyrene nanobeads, monodispersed in aqueous HCl solutions of different molarities. Effects of field effect modulation on particle transition events were also demonstrated.
ContributorsJoshi, Punarvasu (Author) / Thornton, Trevor J (Thesis advisor) / Goryll, Michael (Thesis advisor) / Spanias, Andreas (Committee member) / Saraniti, Marco (Committee member) / Arizona State University (Publisher)
Created2011
Description
In the nano-regime many materials exhibit properties that are quite different from their bulk counterparts. These nano-properties have been shown to be useful in a wide range of applications with nanomaterials being used for catalysts, in energy production, as protective coatings, and in medical treatment. While there is no shortage of exciting and novel applications, the world of nanomaterials suffers from a lack of large scale manufacturing techniques. The current methods and equipment used for manufacturing nanomaterials are generally slow, expensive, potentially dangerous, and material specific. The research and widespread use of nanomaterials has undoubtedly been hindered by this lack of appropriate tooling. This work details the effort to create a novel nanomaterial synthesis and deposition platform capable of operating at industrial level rates and reliability.
The tool, referred to as Deppy, deposits material via hypersonic impaction, a two chamber process that takes advantage of compressible fluids operating in the choked flow regime to accelerate particles to up several thousand meters per second before they impact and stick to the substrate. This allows for the energetic separation of the synthesis and deposition processes while still behaving as a continuous flow reactor giving Deppy the unique ability to independently control the particle properties and the deposited film properties. While the ultimate goal is to design a tool capable of producing a broad range of nanomaterial films, this work will showcase Deppy's ability to produce silicon nano-particle films as a proof of concept.
By adjusting parameters in the upstream chamber the particle composition was varied from completely amorphous to highly crystalline as confirmed by Raman spectroscopy. By adjusting parameters in the downstream chamber significant variation of the film's density was achieved. Further it was shown that the system is capable of making these adjustments in each chamber without affecting the operation of the other.
The tool, referred to as Deppy, deposits material via hypersonic impaction, a two chamber process that takes advantage of compressible fluids operating in the choked flow regime to accelerate particles to up several thousand meters per second before they impact and stick to the substrate. This allows for the energetic separation of the synthesis and deposition processes while still behaving as a continuous flow reactor giving Deppy the unique ability to independently control the particle properties and the deposited film properties. While the ultimate goal is to design a tool capable of producing a broad range of nanomaterial films, this work will showcase Deppy's ability to produce silicon nano-particle films as a proof of concept.
By adjusting parameters in the upstream chamber the particle composition was varied from completely amorphous to highly crystalline as confirmed by Raman spectroscopy. By adjusting parameters in the downstream chamber significant variation of the film's density was achieved. Further it was shown that the system is capable of making these adjustments in each chamber without affecting the operation of the other.
ContributorsFirth, Peter (Author) / Holman, Zachary C (Thesis advisor) / Kozicki, Michael (Committee member) / Goryll, Michael (Committee member) / Arizona State University (Publisher)
Created2015
Description
Design and development of optical sensors for the detection of specific targets, e.g., ions, molecules, proteins, light polarizations, is one of the most essential research topics in the field of nanophotonics that paves the way for significant technological progressions in chemical and biomarker detections, polarimetric imaging and other sensing related applications. In this dissertation, three designs of optical sensors based on plasmonic and dielectric nanostructures are thoroughly studied for the applications in chemicals, biomarkers and light polarization detection. Firstly, a plasmonic nanoantenna structure, which is composed of complementary anisotropic nanobars and nanoapertures featuring strong localized electric field enhancement at nanogap region, demonstrates both high sensitivity refractometric detection and specific infrared fingerprint detection for chemical sensing. Specifically, the sensor can probe monolayer thin octadecanethiol with a large resonance shift of 136 nm and all four characteristic infrared fingerprints detected. Secondly, a bio-inspired double-layered metasurface structure, which is made of dielectric nanoantenna and plasmonic nanogratings, mediates strong optical chirality and enables the selection of circularly polarized light handedness (extinction ratio ≥ 35) with high transmission efficiency (≥ 80%). The structure can be further integrated on-chip with linear polarizers for highly precise full-Stokes polarimetric detection with minimum transmission loss. Lastly, a gold nanoparticle based colorimetric assay is designed for high sensitivity, specificity and rapid detection of infectious diseases related biomarkers. The complete design workflows from critical reagents productions, rapid detection protocol to assay characterizations are extensively studied. Detection of Ebola virus disease biomarker, secreted glycoprotein, within 20 minutes are experimentally demonstrated with limit of detection down to ~40 pM and a broad detection range from 10 pM to 1 µM.
The designs of the three sensors propose novel and versatile design concepts for the development of sensing devices in the detection of chemicals, biomarkers and light polarization. The efforts in the fundamental theoretical analysis and experimental demonstrations are expected to provide valuable contents to the optical sensor researches and to potentially inspire new sensor designs for broad sensing applications in the future.
ContributorsChen, Xiahui (Author) / Wang, Chao (Thesis advisor) / Zhao, Yuji (Committee member) / Wang, Liping (Committee member) / Goryll, Michael (Committee member) / Arizona State University (Publisher)
Created2021
Description
The discovery of DNA helical structure opened the door of modern molecular biology. Ned Seeman utilized DNA as building block to construct different nanoscale materials, and introduced a new field, know as DNA nanotechnology. After several decades of development, different DNA structures had been created, with different dimension, different morphology and even with complex curvatures. In addition, after construction of enough amounts DNA structure candidates, DNA structure template, with excellent spatial addressability, had been used to direct the assembly of different nanomaterials, including nanoparticles and proteins, to produce different functional nanomaterials. However there are still many challenges to fabricate functional DNA nanostructures. The first difficulty is that the present finite sized template dimension is still very small, usually smaller than 100nm, which will limit the application for large amount of nanomaterials assembly or large sized nanomaterials assembly. Here we tried to solve this problem through developing a new method, superorigami, to construct finite sized DNA structure with much larger dimension, which can be as large as 500nm. The second problem will be explored the ability of DNA structure to assemble inorganic nanomaterials for novel photonic or electronic properties. Here we tried to utilize DNA Origami method to assemble AuNPs with controlled 3D spacial position for possible chiral photonic complex. We also tried to assemble SWNT with discrete length for possible field effect transistor device. In addition, we tried to mimic in vivo compartment with DNA structure to study internalized enzyme behavior. From our results, constructed DNA cage origami can protect encapsulated enzyme from degradation, and internalized enzyme activity can be boosted for up to 10 folds. In summary, DNA structure can serve as an ideal template for construction of functional nanomaterials with lots of possibilities to be explored.
ContributorsZhao, Zhao (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Seo, Dong-Kyun (Committee member) / Arizona State University (Publisher)
Created2013