Matching Items (52)
Description
The synthesis of the bis(2-diphenylphosphinoethyl)amine chelating ligand (1) was a crucial component in the preparation of non-canonical amino acids (NCAAs) throughout the project. Studies in this project indicated the need to isolate the ligand from its hydrochloride salt form seen in (1) which led to the synthesis of the brown oil, (Ph2PCH2CH2)2NH, (2). The ligand features a phosphine-nitrogen-phosphine group that is not observed in existing NCAAs. Phosphine groups are rarely seen in existing NCAAs and avoided by biochemists because they tend to oxidize before metal addition. In this project, (1) was used in a 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (HATU) mediated method and palladium-catalyzed method to tether an amino acid to the nitrogen atom of the ligand framework. Both methods were monitored through the use of Nuclear Magnetic Resonance (NMR) spectroscopy. While the palladium catalyzed method exhibited little to no coupling, the 31P NMR spectrum obtained for the HATU mediated method did reveal that some coupling had occurred. The unsuccessful attempts to tether an amino acid to (1) led to the hypothesis that the phosphine groups were interfering with the palladium catalyst during the cross-coupling reaction. In an effort to test this hypothesis, (2) was reacted with the dimer, [Rh(nbd)Cl]2, to coordinate the rhodium metal to the free phosphorous arms and the nitrogen atom of the isolated PNP ligand. The PNP-based metal complex was used in the palladium catalyzed method, but cross-coupling was not observed. The new PNP-based metal complex was investigated to demonstrate that it exhibits moisture and air stability.
ContributorsManjarrez, Yvonne (Author) / Trovitch, Ryan (Thesis director) / Stephanopoulos, Nicholas (Committee member) / Herckes, Pierre (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
While DNA and protein nanotechnologies are promising avenues for nanotechnology on their own, merging the two could create more diverse and functional structures. In order to create hybrid structures, the protein will have to undergo site-specific modification, such as the incorporation of an unnatural amino, p-azidophenylalanine (AzF), via Shultz amber codon suppression method, which can then participate in click chemistry with modified DNA. These newly synthesized structures will then be able to self-assemble into higher order structures. Thus far, a surface exposed residue on the aldolase protein has been mutated into an amber stop codon. The next steps are to express the protein with the unnatural amino acid, allow it to participate in click chemistry, and visualize the hybrid structure. If the structure is correct, it will be able to self-assemble.
ContributorsAziz, Ann-Marie (Author) / Stephanopoulos, Nicholas (Thesis director) / Mills, Jeremy (Committee member) / School of Social Transformation (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Extensive efforts have been made to develop efficient and low-cost methods for diagnostics to identify molecular biomarkers that are linked to a wide array of conditions, including cancer. A highly developed method includes utilizing the gene-editing enzyme CRISPR-Cas12a (Cpf1), which demonstrates double-stranded DNase activity with RuvC catalytic domain with high sensitivity and specificity. This DNase activity is RNA-guided and requires a T-rich PAM site on the target sequence for functional cleavage. There have been recent efforts to utilize this DNase activity of Cas12a by combining it with isothermal amplification and analysis by lateral strip tests. This project examined CRISPR-based early detection of microRNA biomarkers. MicroRNA are short RNA molecules that have large roles in post-transcriptional gene regulation. However, due the short length of microRNA and its single-stranded nature, it is challenging to use Cas12a for microRNA detection using existing methods. Thus, this project investigated the potential of two microRNA detection strategies for recognition by CRISPR-Cas12a. These methods were microRNA-splinted ligation with polymerase chain reaction (PCR) and MicroRNA-specific reverse transcriptase PCR (RT-PCR). Gel imaging demonstrated effective amplification of ligated DNA through microRNA-splinted ligation with PCR/RPA. In addition, lateral strips tests showed effective cleavage of the target sequences by Cas12a. However, RT-PCR method demonstrated low amplification by PCR and inefficient poly(A) elongation. This project paves the way for the detection of an extensive range of microRNA biomarkers that are linked to an array of diseases. Future directions include analysis and modifications of RT-PCR method to improve experimental results, extending these detection methods to a larger range of microRNA sequences, and eventually utilizing them for detection in human samples.
ContributorsStaren, Michael Steven (Author) / Green, Alexander (Thesis director) / Stephanopoulos, Nicholas (Committee member) / Diehnelt, Chris (Committee member) / School of Life Sciences (Contributor) / College of Health Solutions (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The dopamine 2 receptor (D2R) is a Class A GPCR which is essential for signaling in the nervous system, and has been implicated in numerous illnesses. While there are over 50 currently approved drugs which act on D2R, the structure has never been determined in detail. Although crystallography has historically been difficult with GPCRs, in recent years many structures have been solved using lipidic cubic phase (LCP) crystallization techniques. Sample preparation for LCP crystallization typically requires optimization of genetic constructs, recombinant expression, and purification techniques in order to produce a sample with sufficient stability and homogeneity. This study compares several genetic constructs utilizing different promoters, fusion proteins, fusion positions, and truncations in order to determine a high quality construct for LCP crystallization of
D2R. All constructs were expressed using the Bac-to-bac baculovirus expression system, then extracted with n-Dodecyl-β-D-Maltoside (DDM) and purified using metal affinity chromatography. Samples were then tested for quantity, purity, and homogeneity using SDS-PAGE, western blot, and size-exclusion chromatography. High quality samples were chosen based on insect cell expression levels, purification yield, and stability estimated by the levels of homomeric protein relative to aggregated protein. A final construct was chosen with which to continue future studies in optimization of thermal stability and crystallization conditions. Future work on this project is required to produce a sample amenable to crystallization. Screening of ligands for co-crystallization,
thermostabilizing point mutations, and potentially optimization of extraction and purification techniques prior to crystallization trials. Solving the D2R structure will lead to an increased understanding of its signaling mechanism and the mechanisms of currently approved drugs, while also providing a basis for more effective structure-based drug design.
D2R. All constructs were expressed using the Bac-to-bac baculovirus expression system, then extracted with n-Dodecyl-β-D-Maltoside (DDM) and purified using metal affinity chromatography. Samples were then tested for quantity, purity, and homogeneity using SDS-PAGE, western blot, and size-exclusion chromatography. High quality samples were chosen based on insect cell expression levels, purification yield, and stability estimated by the levels of homomeric protein relative to aggregated protein. A final construct was chosen with which to continue future studies in optimization of thermal stability and crystallization conditions. Future work on this project is required to produce a sample amenable to crystallization. Screening of ligands for co-crystallization,
thermostabilizing point mutations, and potentially optimization of extraction and purification techniques prior to crystallization trials. Solving the D2R structure will lead to an increased understanding of its signaling mechanism and the mechanisms of currently approved drugs, while also providing a basis for more effective structure-based drug design.
ContributorsErler, Maya Marie (Author) / Liu, Wei (Thesis director) / He, Ximin (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The main objective of this project is to create a hydrogel based material system to capture and release CCRF-CEM Leukemia cancer cells via chemo-mechanical modulation. This system is composed of an aptamer-functionalized hydrogel thin film at the bottom of a microfluidic channel, which changes its film thickness as the temperature of the fluid in the system changes. The functionalized hydrogel film has been created as the primary steps to creating the microfluidic device that could capture and release leukemia cells by turning the temperature of the fluid and length of exposure. Circulating tumor cells have recently become a highly studied area since they have become associated with the likelihood of patient survival. Further, circulating tumor cells can be used to determine changes in the genome of the cancer leading to targeted treatment. First, the aptamers were attached onto the hydrogel through an EDC/NHS reaction. The aptamers were verified to be attached onto the hydrogel through FTIR spectroscopy. The cell capture experiments were completed by exposing the hydrogel to a solution of leukemia cells for 10 minutes at room temperature. The cell release experiments were completed by exposing the hydrogel to a 40°C solution. Several capture and release experiments were completed to measure how many cells could be captured, how quickly, and how many cells captured were released. The aptamers were chemically attached to the hydrogel. 300 cells per square millimeter could be captured at a time in a 10 minute time period and released in a 5 minute period. Of the cells captured, 96% of them were alive once caught. 99% of cells caught were released once exposed to elevated temperature. The project opens the possibility to quickly and efficiently capture and release tumor cells using only changes in temperature. Further, most of the cells that were captured were alive and nearly all of those were released leading to high survival and capture efficiency.
ContributorsPaxton, Rebecca Joanne (Author) / Stephanopoulos, Nicholas (Thesis director) / He, Ximin (Committee member) / Gould, Ian (Committee member) / Materials Science and Engineering Program (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Polymer-gold composite particles are of tremendous research interests. Contributed by their unique structures, these particles demonstrate superior properties for optical, catalytic and electrical applications. Moreover, the incorporation of “smart” polymers into polymer-gold composite particles enables the composite particles synergistically respond to environment-stimuli like temperature, pH and light with promising applications in multiple areas.
A novel Pickering emulsion polymerization route is found for synthesis of core-shell structured polymer-gold composite particles. It is found that the surface coverage of gold nanoparticles (AuNP) on a polystyrene core is influenced by gold nanoparticle concentration and hydrophobicity. More importantly, the absorption wavelength of polystyrene-gold composite particles is tunable by adjusting AuNP interparticle distance. Further, core-shell structured polystyrene-gold composite particles demonstrate excellent catalyst recyclability.
Asymmetric polystyrene-gold composite particles are successfully synthesized via seeded emulsion polymerization, where AuNPs serve as seeds, allowing the growth of styrene monomers/oligomers on them. These particles also demonstrate excellent catalyst recyclability. Further, monomers of “smart” polymers, poly (N-isopropylacrylamide) (PNIPAm), are successfully copolymerized into asymmetric composite particles, enabling these particles’ thermo-responsiveness with significant size variation around lower critical solution temperature (LCST) of 31°C. The significant size variation gives rise to switchable scattering intensity property, demonstrating potential applications in intensity-based optical sensing.
Multipetal and dumbbell structured gold-polystyrene composite particles are also successfully synthesized via seeded emulsion polymerization. It is intriguing to observe that by controlling reaction time and AuNP size, tetrapetal-structured, tripetal-structured and dumbbell-structured gold-polystyrene are obtained. Further, “smart” PNIPAm polymers are successfully copolymerized into dumbbell-shaped particles, showing significant size variation around LCST. Self-modulated catalytic activity around LCST is achieved for these particles. It is hypothesized that above LCST, the significant shrinkage of particles limits diffusion of reaction molecules to the surface of AuNPs, giving a reduced catalytic activity.
Finally, carbon black (CB) particles are successfully employed for synthesis of core- shell PNIPAm/polystyrene-CB particles. The thermo-responsive absorption characteristics of PNIPAm/polystyrene-CB particles enable them potentially suitable to serve as “smart” nanofluids with self-controlled temperature. Compared to AuNPs, CB particles provide desirable performance here, because they show no plasmon resonance in visible wavelength range, whereas AuNPs’ absorption in the visible wavelength range is undesirable.
A novel Pickering emulsion polymerization route is found for synthesis of core-shell structured polymer-gold composite particles. It is found that the surface coverage of gold nanoparticles (AuNP) on a polystyrene core is influenced by gold nanoparticle concentration and hydrophobicity. More importantly, the absorption wavelength of polystyrene-gold composite particles is tunable by adjusting AuNP interparticle distance. Further, core-shell structured polystyrene-gold composite particles demonstrate excellent catalyst recyclability.
Asymmetric polystyrene-gold composite particles are successfully synthesized via seeded emulsion polymerization, where AuNPs serve as seeds, allowing the growth of styrene monomers/oligomers on them. These particles also demonstrate excellent catalyst recyclability. Further, monomers of “smart” polymers, poly (N-isopropylacrylamide) (PNIPAm), are successfully copolymerized into asymmetric composite particles, enabling these particles’ thermo-responsiveness with significant size variation around lower critical solution temperature (LCST) of 31°C. The significant size variation gives rise to switchable scattering intensity property, demonstrating potential applications in intensity-based optical sensing.
Multipetal and dumbbell structured gold-polystyrene composite particles are also successfully synthesized via seeded emulsion polymerization. It is intriguing to observe that by controlling reaction time and AuNP size, tetrapetal-structured, tripetal-structured and dumbbell-structured gold-polystyrene are obtained. Further, “smart” PNIPAm polymers are successfully copolymerized into dumbbell-shaped particles, showing significant size variation around LCST. Self-modulated catalytic activity around LCST is achieved for these particles. It is hypothesized that above LCST, the significant shrinkage of particles limits diffusion of reaction molecules to the surface of AuNPs, giving a reduced catalytic activity.
Finally, carbon black (CB) particles are successfully employed for synthesis of core- shell PNIPAm/polystyrene-CB particles. The thermo-responsive absorption characteristics of PNIPAm/polystyrene-CB particles enable them potentially suitable to serve as “smart” nanofluids with self-controlled temperature. Compared to AuNPs, CB particles provide desirable performance here, because they show no plasmon resonance in visible wavelength range, whereas AuNPs’ absorption in the visible wavelength range is undesirable.
ContributorsZhang, Mingmeng (Author) / Dai, Lenore L (Committee member) / Phelan, Patrick E (Committee member) / Otanicar, Todd P (Committee member) / Lin, Jerry (Committee member) / He, Ximin (Committee member) / Arizona State University (Publisher)
Created2015
Description
Origami and Kirigami are two traditional art forms in the world. Origami, from
‘ori’ meaning folding, and ‘kami’ meaning paper is the art of paper folding. Kirigami, from ‘kiri’ meaning cutting, is the art of the combination of paper cutting and paper folding. In this dissertation, Origami and kirigami concepts were successively utilized in making stretchable lithium ion batteries and three-dimensional (3D) silicon structure which both provide excellent mechanical characteristics.
‘ori’ meaning folding, and ‘kami’ meaning paper is the art of paper folding. Kirigami, from ‘kiri’ meaning cutting, is the art of the combination of paper cutting and paper folding. In this dissertation, Origami and kirigami concepts were successively utilized in making stretchable lithium ion batteries and three-dimensional (3D) silicon structure which both provide excellent mechanical characteristics.
ContributorsSong, Zeming (Author) / Jiang, Hanqing (Thesis advisor) / Dai, Lenore (Committee member) / Yu, Hongbin (Committee member) / He, Ximin (Committee member) / Arizona State University (Publisher)
Created2016
Description
Solar energy is leading in renewable energy sources and the aspects surrounding the efforts to harvest light are gaining importance. One such aspect is increasing the light absorption, where heliotropism comes into play. Heliotropism, the ability to track the sun across the sky, can be integrated with solar cells for more efficient photon collection and other optoelectronic systems. Inspired by plants, which optimize incident sunlight in nature, several researchers have made artificial heliotropic and phototropic systems. This project aims to design, synthesize and characterize a material system and evaluate its application in a phototropic system. A gold nanoparticle (Au NP) incorporated poly(N-isopropylacrylamide) (PNIPAAm) hydrogel was synthesized as a photo-thermo-responsive material in our phototropic system. The Au NPs generate heat from the incident via plasmonic resonance to induce a volume phase change of the thermo-responsive hydrogel PNIPAAm. PNIPAAm shrinks or swells at temperature above or below 32°C. Upon irradiation, the Au NP-PNIPAAm micropillar actuates, specifically bending toward the incident light and precisely following the varying incident angle.
Swelling ratio tests, bending angle tests with a static incident light and bending tests with varying angles were carried out on hydrogel samples with varying Au NP concentrations. Swelling ratios ranging from 1.45 to 2.9 were recorded for pure hydrogel samples and samples with very low Au NP concentrations. Swelling ratios of 2.41 and 3.37 were calculated for samples with low and high concentrations of Au NPs, respectively. A bending of up to 88° was observed in Au NP-hydrogel pillars with a low Au NP concentration with a 90° incident angle. The light tracking performance was assessed by the slope of the pillar Bending angle (response angle) vs. Incident light angle plot. A slope of 1 indicates ideal tracking with top of the pillar being normal to the incident light, maximizing the photon absorption. Slopes of 0.82 and 0.56 were observed for the low and high Au NP concentration samples. The rapid and precise incident light tracking of our system has shown the promise in phototropic applications.
Swelling ratio tests, bending angle tests with a static incident light and bending tests with varying angles were carried out on hydrogel samples with varying Au NP concentrations. Swelling ratios ranging from 1.45 to 2.9 were recorded for pure hydrogel samples and samples with very low Au NP concentrations. Swelling ratios of 2.41 and 3.37 were calculated for samples with low and high concentrations of Au NPs, respectively. A bending of up to 88° was observed in Au NP-hydrogel pillars with a low Au NP concentration with a 90° incident angle. The light tracking performance was assessed by the slope of the pillar Bending angle (response angle) vs. Incident light angle plot. A slope of 1 indicates ideal tracking with top of the pillar being normal to the incident light, maximizing the photon absorption. Slopes of 0.82 and 0.56 were observed for the low and high Au NP concentration samples. The rapid and precise incident light tracking of our system has shown the promise in phototropic applications.
ContributorsGopalakrishna, Hamsini (Author) / He, Ximin (Thesis advisor) / Holman, Zachary C (Committee member) / Wang, Liping (Committee member) / Arizona State University (Publisher)
Created2016
Description
This thesis presents systematic studies on angle dependent Raman and Photoluminescence (PL) of a new class of layered materials, Transition Metal Trichalcogenides (TMTCs), which are made up of layers possessing anisotropic structure within the van-der-Waals plane. The crystal structure of individual layer of MX3 compounds consists of aligned nanowire like 1D chains running along the b-axis direction. The work focuses on the growth of two members of this family - ZrS3 and TiS3 - through Chemical Vapor Transport Method (CVT), with consequent angle dependent Raman and PL studies which highlight their in-plane optically anisotropic properties. Results highlight that the optical properties of few-layer flakes are highly anisotropic as evidenced by large PL intensity variation with polarization direction (in ZrS3) and an intense variation in Raman intensity with variation in polarization direction (in both ZrS3 and TiS3).
Results suggest that light is efficiently absorbed when E-field of the polarized incident excitation laser is polarized along the chain (b-axis). It is greatly attenuated and absorption is reduced when field is polarized perpendicular to the length of 1D-like chains, as wavelength of the exciting light is much longer than the width of each 1D chain. Observed PL variation with respect to the azimuthal flake angle is similar to what has been previously observed in 1D materials like nanowires. However, in TMTCs, since the 1D chains interact with each other, it gives rise to a unique linear dichroism response that falls between 2D and 1D like behavior. These results not only mark the very first demonstration of high PL polarization anisotropy in 2D systems, but also provide a novel insight into how interaction between adjacent 1D-like chains and the 2D nature of each layer influences the overall optical anisotropy of Quasi-1D materials. The presented results are anticipated to have impact in technologies involving polarized detection, near-field imaging, communication systems, and bio-applications relying on the generation and detection of polarized light.
Results suggest that light is efficiently absorbed when E-field of the polarized incident excitation laser is polarized along the chain (b-axis). It is greatly attenuated and absorption is reduced when field is polarized perpendicular to the length of 1D-like chains, as wavelength of the exciting light is much longer than the width of each 1D chain. Observed PL variation with respect to the azimuthal flake angle is similar to what has been previously observed in 1D materials like nanowires. However, in TMTCs, since the 1D chains interact with each other, it gives rise to a unique linear dichroism response that falls between 2D and 1D like behavior. These results not only mark the very first demonstration of high PL polarization anisotropy in 2D systems, but also provide a novel insight into how interaction between adjacent 1D-like chains and the 2D nature of each layer influences the overall optical anisotropy of Quasi-1D materials. The presented results are anticipated to have impact in technologies involving polarized detection, near-field imaging, communication systems, and bio-applications relying on the generation and detection of polarized light.
ContributorsPant, Anupum (Author) / Tongay, Sefaattin (Thesis advisor) / Alford, Terry Lynn (Committee member) / He, Ximin (Committee member) / Arizona State University (Publisher)
Created2016
Description
Silicone compounds have a very low surface energy due to highly flexible Si-O-Si backbone and large number of –CH3 groups, but these compounds are extremely hydrophobic and thus have limited applications in aqueous formulations. Modification of such silicone compounds by grafting hydrophilic chains provides a wide range of silicone products called "Silicone Surfactants". Silicone surfactants are surface active agents which get adsorbed at the air-water interface thereby, reducing the interfacial tension. Some of the larger applications of silicone surfactant are in the manufacture of plastic foams, in personal care products and as spreading and wetting agents (Hill, R.M, 2002).
In this thesis, a series of silicone surfactant graft copolymers were synthesized via hydrosilylation reaction. Poly(ethylene glycol) (PEG) of different chain length was grafted to a hydrophobic Poly(methylhydrosiloxane) (PMHS) backbone to improve the final hydrophilicity. Also, a positively charged quaternary ammonium salt (allyltriethylammonium bromide) was grafted to the PMHS backbone. The objective of this thesis was to synthesize polymers in predefined ratios of the above mentioned side groups and utilize these polymers to-
1) Study the effect of PEG chain length and its composition on the hydrophilicity of the polymer.
2) Study the effect of PEG: ammonium salt ratio on the surface tension of aqueous systems.
Analysis of FT-IR and 1H NMR spectra of the polymers confirmed the predicted structure. The absence of characteristic Si-H absorbance peak at 2160 cm-1 in FT-IR spectra indicates consumption of silane groups along the polymer backbone. The actual moles of the side chain grafted on the backbone are calculated by 1H NMR peak integration. The results of contact angle studies indicated an increase in hydrophilicity with an increase in the composition of PEG in molecule. A 2*2 factorial DOE analysis reported that the fraction of Si-H bonds converted to PEG grafts was the critical factor towards increasing the hydrophilicity (p value of 0.015). Surface tension studies report that the air-water interfacial tension of the synthesized polymers is between 28mN/m – 45mN/m. The amount of Si-H was concluded to be the deciding factor in lowering the surface tension.
In this thesis, a series of silicone surfactant graft copolymers were synthesized via hydrosilylation reaction. Poly(ethylene glycol) (PEG) of different chain length was grafted to a hydrophobic Poly(methylhydrosiloxane) (PMHS) backbone to improve the final hydrophilicity. Also, a positively charged quaternary ammonium salt (allyltriethylammonium bromide) was grafted to the PMHS backbone. The objective of this thesis was to synthesize polymers in predefined ratios of the above mentioned side groups and utilize these polymers to-
1) Study the effect of PEG chain length and its composition on the hydrophilicity of the polymer.
2) Study the effect of PEG: ammonium salt ratio on the surface tension of aqueous systems.
Analysis of FT-IR and 1H NMR spectra of the polymers confirmed the predicted structure. The absence of characteristic Si-H absorbance peak at 2160 cm-1 in FT-IR spectra indicates consumption of silane groups along the polymer backbone. The actual moles of the side chain grafted on the backbone are calculated by 1H NMR peak integration. The results of contact angle studies indicated an increase in hydrophilicity with an increase in the composition of PEG in molecule. A 2*2 factorial DOE analysis reported that the fraction of Si-H bonds converted to PEG grafts was the critical factor towards increasing the hydrophilicity (p value of 0.015). Surface tension studies report that the air-water interfacial tension of the synthesized polymers is between 28mN/m – 45mN/m. The amount of Si-H was concluded to be the deciding factor in lowering the surface tension.
ContributorsSingh, Pummy (Author) / Green, Matthew (Thesis advisor) / He, Ximin (Committee member) / Lind, Mary Laura (Committee member) / Arizona State University (Publisher)
Created2016