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- All Subjects: Nanostructured materials
- Creators: Westerhoff, Paul
- Creators: Yan, Hao
- Member of: ASU Electronic Theses and Dissertations
Description
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Filtration for microfluidic sample-collection devices is desirable for sample selection, concentration, preprocessing, and downstream manipulation, but microfabricating the required sub-micrometer filtration structure is an elaborate process. This thesis presents a simple method to fabricate polydimethylsiloxane (PDMS) devices with an integrated membrane filter that will sample, lyse, and extract the DNA from microorganisms in aqueous environments. An off-the-shelf membrane filter disc was embedded in a PDMS layer and sequentially bound with other PDMS channel layers. No leakage was observed during filtration. This device was validated by concentrating a large amount of cyanobacterium Synechocystis in simulated sample water with consistent performance across devices. After accumulating sufficient biomass on the filter, a sequential electrochemical lysing process was performed by applying 5VDC across the filter. This device was further evaluated by delivering several samples of differing concentrations of cyanobacterium Synechocystis then quantifying the DNA using real-time PCR. Lastly, an environmental sample was run through the device and the amount of photosynthetic microorganisms present in the water was determined. The major breakthroughs in this design are low energy demand, cheap materials, simple design, straightforward fabrication, and robust performance, together enabling wide-utility of similar chip-based devices for field-deployable operations in environmental micro-biotechnology.
ContributorsLecluse, Aurelie (Author) / Meldrum, Deirdre (Thesis advisor) / Chao, Joseph (Thesis advisor) / Westerhoff, Paul (Committee member) / Arizona State University (Publisher)
Created2011
Description
As engineered nanomaterials (NMs) become used in industry and commerce their loading to sewage will increase. However, the fate of widely used NMs in wastewater treatment plants (WWTPs) remains poorly understood. In this research, sequencing batch reactors (SBRs) were operated with hydraulic (HRT) and sludge (SRT) retention times representative of full-scale biological WWTPs for several weeks. NM loadings at the higher range of expected environmental concentrations were selected. To achieve the pseudo-equilibrium state concentration of NMs in biomass, SBR experiments needed to operate for more than three times the SRT value, approximately 18 days. Under the conditions tested, NMs had negligible effects on ability of the wastewater bacteria to biodegrade organic material, as measured by chemical oxygen demand (COD). NM mass balance closure was achieved by measuring NMs in liquid effluent and waste biosolids. All NMs were well removed at the typical biomass concentration (1~2 gSS/L). However, carboxy-terminated polymer coated silver nanoparticles (fn-Ag) were removed less effectively (88% removal) than hydroxylated fullerenes (fullerols; >90% removal), nano TiO2 (>95% removal) or aqueous fullerenes (nC60; >95% removal). Although most NMs did not settle out of the feed solution without bacteria present, approximately 65% of the titanium dioxide was removed even in the absence of biomass simply due to self-aggregation and settling. Experiments conducted over 4 months with daily loadings of nC60 showed that nC60 removal from solution depends on the biomass concentration. Under conditions representative of most suspended growth biological WWTPs (e.g., activated sludge), most of the NMs will accumulate in biosolids rather than in liquid effluent discharged to surface waters. Significant fractions of fn-Ag were associated with colloidal material which suggests that efficient particle separation processes (sedimentation or filtration) could further improve removal of NM from effluent. As most NMs appear to accumulate in biosolids, future research should examine the fate of NMs during disposal of WWTP biosolids, which may occur through composting or anaerobic digestion and/or land application, incineration, or landfill disposal.
ContributorsWang, Yifei (Author) / Westerhoff, Paul (Thesis advisor) / Krajmalnik-Brown, Rosa (Committee member) / Rittmann, Bruce (Committee member) / Hristovski, Kiril (Committee member) / Arizona State University (Publisher)
Created2012
Description
Nanotechnology is becoming increasingly present in our environment. Engineered nanoparticles (ENPs), defined as objects that measure less than 100 nanometers in at least one dimension, are being integrated into commercial products because of their small size, increased surface area, and quantum effects. These special properties have made ENPs antimicrobial agents in clothing and plastics, among other applications in industries such as pharmaceuticals, renewable energy, and prosthetics. This thesis incorporates investigations into both application of nanoparticles into polymers as well as implications of nanoparticle release into the environment. First, the integration of ENPs into polymer fibers via electrospinning was explored. Electrospinning uses an external electric field applied to a polymer solution to produce continuous fibers with large surface area and small volume, a quality which makes the fibers ideal for water and air purification purposes. Indium oxide and titanium dioxide nanoparticles were embedded in polyvinylpyrrolidone and polystyrene. Viscosity, critical voltage, and diameter of electrospun fibers were analyzed in order to determine the effects of nanoparticle integration into the polymers. Critical voltage and viscosity of solution increased at 5 wt% ENP concentration. Fiber morphology was not found to change significantly as a direct effect of ENP addition, but as an effect of increased viscosity and surface tension. These results indicate the possibility for seamless integration of ENPs into electrospun polymers. Implications of ENP release were investigated using phase distribution functional assays of nanoscale silver and silver sulfide, as well as photolysis experiments of nanoscale titanium dioxide to quantify hydroxyl radical production. Functional assays are a means of screening the relevant importance of multiple processes in the environmental fate and transport of ENPs. Four functional assays – water-soil, water-octanol, water-wastewater sludge and water-surfactant – were used to compare concentrations of silver sulfide ENPs (Ag2S-NP) and silver ENPs (AgNP) capped by four different coatings. The functional assays resulted in reproducible experiments which clearly showed variations between nanoparticle phase distributions; the findings may be a product of the effects of the different coatings of the ENPs used. In addition to phase distribution experiments, the production of hydroxyl radical (HO•) by nanoscale titanium dioxide (TiO2) under simulated solar irradiation was investigated. Hydroxyl radical are a short-lived, highly reactive species produced by solar radiation in aquatic environments that affect ecosystem function and degrades pollutants. HO• is produced by photolysis of TiO2 and nitrate (NO3-); these two species were used in photolysis experiments to compare the relative loads of hydroxyl radical which nanoscale TiO2 may add upon release to natural waters. Para-chlorobenzoic acid (pCBA) was used as a probe. Measured rates of pCBA oxidation in the presence of various concentrations of TiO2 nanoparticles and NO3- were utilized to calculate pseudo first order rate constants. Results indicate that, on a mass concentration basis in water, TiO2 produces hydroxyl radical steady state concentrations at 1.3 times more than the equivalent amount of NO3-; however, TiO2 concentrations are generally less than one order of magnitude lower than concentrations of NO3-. This has implications for natural waterways as the amount of nanoscale TiO2 released from consumer products into natural waterways increases in proportion to its use.
ContributorsHoogesteijn von Reitzenstein, Natalia (Author) / Westerhoff, Paul (Thesis advisor) / Herckes, Pierre (Committee member) / Hristovski, Kiril (Committee member) / Arizona State University (Publisher)
Created2015
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
The highly predictable structural and thermodynamic behavior of deoxynucleic acid (DNA) and ribonucleic acid (RNA) have made them versatile tools for creating artificial nanostructures over broad range. Moreover, DNA and RNA are able to interact with biological ligand as either synthetic aptamers or natural components, conferring direct biological functions to the nucleic acid devices. The applications of nucleic acids greatly relies on the bio-reactivity and specificity when applied to highly complexed biological systems.
This dissertation aims to 1) develop new strategy to identify high affinity nucleic acid aptamers against biological ligand; and 2) explore highly orthogonal RNA riboregulators in vivo for constructing multi-input gene circuits with NOT logic. With the aid of a DNA nanoscaffold, pairs of hetero-bivalent aptamers for human alpha thrombin were identified with ultra-high binding affinity in femtomolar range with displaying potent biological modulations for the enzyme activity. The newly identified bivalent aptamers enriched the aptamer tool box for future therapeutic applications in hemostasis, and also the strategy can be potentially developed for other target molecules. Secondly, by employing a three-way junction structure in the riboregulator structure through de-novo design, we identified a family of high-performance RNA-sensing translational repressors that down-regulates gene translation in response to cognate RNAs with remarkable dynamic range and orthogonality. Harnessing the 3WJ repressors as modular parts, we integrate them into biological circuits that execute universal NAND and NOR logic with up to four independent RNA inputs in Escherichia coli.
This dissertation aims to 1) develop new strategy to identify high affinity nucleic acid aptamers against biological ligand; and 2) explore highly orthogonal RNA riboregulators in vivo for constructing multi-input gene circuits with NOT logic. With the aid of a DNA nanoscaffold, pairs of hetero-bivalent aptamers for human alpha thrombin were identified with ultra-high binding affinity in femtomolar range with displaying potent biological modulations for the enzyme activity. The newly identified bivalent aptamers enriched the aptamer tool box for future therapeutic applications in hemostasis, and also the strategy can be potentially developed for other target molecules. Secondly, by employing a three-way junction structure in the riboregulator structure through de-novo design, we identified a family of high-performance RNA-sensing translational repressors that down-regulates gene translation in response to cognate RNAs with remarkable dynamic range and orthogonality. Harnessing the 3WJ repressors as modular parts, we integrate them into biological circuits that execute universal NAND and NOR logic with up to four independent RNA inputs in Escherichia coli.
ContributorsZhou, Yu (Ph.D.) (Author) / Yan, Hao (Thesis advisor) / Green, Alexander (Thesis advisor) / Woodbury, Neal (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2019
Description
The production and applications of engineered nanomaterials (ENM) has increased rapidly in the last decade, with release of ENM to the environment through the sewer system and municipal wastewater treatment plants (WWTPs) being of concern. Currently, the literature on ENM release from WWTPs and removal of ENM by WWTPs is insufficient and disorganized. There is little quantitative data on the removal of multi-walled carbon nanotubes (MWCNTs), graphene oxide (GO), or few-layer graphene (FLG), from wastewater onto biomass. The removal of pristine and oxidized MWCNTs (O-MWCNTs), graphene oxide (GO), few-layer graphene (FLG) and Tween™ 20-coated Ag ENM by the interaction with biomass were determined by programmable thermal analysis (PTA) and UV-Vis spectrophotometry. The removal of pristine and O-MWCNTs was 96% from the water phase via aggregation and 30-min settling in presence or absence of biomass with an initial MWCNT concentration of 25 mg/L. The removal of 25 mg/L GO was 65% with biomass concentration at or above 1,000 mg TSS/L. The removal of 1 mg/L FLG was 16% with 50 mg TSS/L. The removal of Tween™ 20 Ag ENM with concentration from 0.97 mg/L to 2.6 mg/L was from 11% to 92% with biomass concentration of 500 mg TSS/L to 3,000 mg TSS/L, respectively.
A database of ENM removal by biomass was established by analyzing data from published papers, and non-linear solid-liquid distribution functions were built into the database. A conventional activated sludge (CAS) model was built based on a membrane bioreactor (MBR) model from a previous paper. An iterative numeric approach was adapted to the CAS model to calculate the result of non-linear adsorption of ENM by biomass in the CAS process. Kinetic studies of the CAS model showed the model performance changed mostly in the first 10 days after changing influent chemical oxygen demand (COD) concentration, and reached a steady state after 11 days. Over 60% of ENMs which have distribution coefficients in the database reached higher than 50% removal by the CAS model under general operational conditions. This result suggests that traditional WWTP which include the CAS process can remove many known types of ENMs in certain degree.
A database of ENM removal by biomass was established by analyzing data from published papers, and non-linear solid-liquid distribution functions were built into the database. A conventional activated sludge (CAS) model was built based on a membrane bioreactor (MBR) model from a previous paper. An iterative numeric approach was adapted to the CAS model to calculate the result of non-linear adsorption of ENM by biomass in the CAS process. Kinetic studies of the CAS model showed the model performance changed mostly in the first 10 days after changing influent chemical oxygen demand (COD) concentration, and reached a steady state after 11 days. Over 60% of ENMs which have distribution coefficients in the database reached higher than 50% removal by the CAS model under general operational conditions. This result suggests that traditional WWTP which include the CAS process can remove many known types of ENMs in certain degree.
ContributorsYu, Zhicheng (Author) / Westerhoff, Paul (Thesis advisor) / Rittmann, Bruce (Committee member) / Herckes, Pierre (Committee member) / Arizona State University (Publisher)
Created2015
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