Matching Items (13)

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Small molecule detection by surface plasmon resonance: improvements in sensitivity and kinetic measurement

Description

Surface plasmon resonance (SPR) has emerged as a popular technique for elucidating subtle signals from biological events in a label-free, high throughput environment. The efficacy of conventional SPR sensors, whose signals are mass-sensitive, diminishes rapidly with the size of the

Surface plasmon resonance (SPR) has emerged as a popular technique for elucidating subtle signals from biological events in a label-free, high throughput environment. The efficacy of conventional SPR sensors, whose signals are mass-sensitive, diminishes rapidly with the size of the observed target molecules. The following work advances the current SPR sensor paradigm for the purpose of small molecule detection. The detection limits of two orthogonal components of SPR measurement are targeted: speed and sensitivity. In the context of this report, speed refers to the dynamic range of measured kinetic rate constants, while sensitivity refers to the target molecule mass limitation of conventional SPR measurement. A simple device for high-speed microfluidic delivery of liquid samples to a sensor surface is presented to address the temporal limitations of conventional SPR measurement. The time scale of buffer/sample switching is on the order of milliseconds, thereby minimizing the opportunity for sample plug dispersion. The high rates of mass transport to and from the central microfluidic sensing region allow for SPR-based kinetic analysis of binding events with dissociation rate constants (kd) up to 130 s-1. The required sample volume is only 1 μL, allowing for minimal sample consumption during high-speed kinetic binding measurement. Charge-based detection of small molecules is demonstrated by plasmonic-based electrochemical impedance microscopy (P-EIM). The dependence of surface plasmon resonance (SPR) on surface charge density is used to detect small molecules (60-120 Da) printed on a dextran-modified sensor surface. The SPR response to an applied ac potential is a function of the surface charge density. This optical signal is comprised of a dc and an ac component, and is measured with high spatial resolution. The amplitude and phase of local surface impedance is provided by the ac component. The phase signal of the small molecules is a function of their charge status, which is manipulated by the pH of a solution. This technique is used to detect and distinguish small molecules based on their charge status, thereby circumventing the mass limitation (~100 Da) of conventional SPR measurement.

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Date Created
2013

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Bleomycin, from start to finish: total synthesis of novel analogues to in vitro fluorescence microscopy imaging

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The bleomycins are a family of glycopeptide-derived antibiotics isolated from various Streptomyces species and have been the subject of much attention from the scientific community as a consequence of their antitumor activity. Bleomycin clinically and is an integral part of

The bleomycins are a family of glycopeptide-derived antibiotics isolated from various Streptomyces species and have been the subject of much attention from the scientific community as a consequence of their antitumor activity. Bleomycin clinically and is an integral part of a number of combination chemotherapy regimens. It has previously been shown that bleomycin has the ability to selectively target tumor cells over their non-malignant counterparts. Pyrimidoblamic acid, the N-terminal metal ion binding domain of bleomycin is known to be the moiety that is responsible for O2 activation and the subsequent chemistry leading to DNA strand scission and overall antitumor activity. Chapter 1 describes bleomycin and related DNA targeting antitumor agents as well as the specific structural domains of bleomycin. Various structural analogues of pyrimidoblamic acid were synthesized and subsequently incorporated into their corresponding full deglycoBLM A6 derivatives by utilizing a solid support. Their activity was measured using a pSP64 DNA plasmid relaxation assay and is summarized in Chapter 2. The specifics of bleomycin—DNA interaction and kinetics were studied via surface plasmon resonance and are presented in Chapter 3. By utilizing carefully selected 64-nucleotide DNA hairpins with variable 16-mer regions whose sequences showed strong binding in past selection studies, a kinetic profile was obtained for several BLMs for the first time since bleomycin was discovered in 1966. The disaccharide moiety of bleomycin has been previously shown to be a specific tumor cell targeting element comprised of L-gulose-D-mannose, especially between MCF-7 (breast cancer cells) and MCF-10A ("normal" breast cells). This phenomenon was further investigated via fluorescence microscopy using multiple cancerous cell lines with matched "normal" counterparts and is fully described in Chapter 4.

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Date Created
2013

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Plasmonic nanoparticles and their suspensions for solar energy conversion

Description

Plasmon resonance in nanoscale metallic structures has shown its ability to concentrate electromagnetic energy into sub-wavelength volumes. Metal nanostructures exhibit a high extinction coefficient in the visible and near infrared spectrum due to their large absorption and scattering cross sections

Plasmon resonance in nanoscale metallic structures has shown its ability to concentrate electromagnetic energy into sub-wavelength volumes. Metal nanostructures exhibit a high extinction coefficient in the visible and near infrared spectrum due to their large absorption and scattering cross sections corresponding to their surface plasmon resonance. Hence, they can serve as an attractive candidate for solar energy conversion. Recent papers have showed that dielectric core/metallic shell nanoparticles yielded a plasmon resonance wavelength tunable from visible to infrared by changing the ratio of core radius to the total radius. Therefore it is interesting to develop a dispersion of core-shell multifunctional nanoparticles capable of dynamically changing their volume ratio and thus their spectral radiative properties. Nanoparticle suspensions (nanofluids) are known to offer a variety of benefits for thermal transport and energy conversion. Nanofluids have been proven to increase the efficiency of the photo-thermal energy conversion process in direct solar absorption collectors (DAC). Combining these two cutting-edge technologies enables the use of core-shell nanoparticles to control the spectral and radiative properties of plasmonic nanofluids in order to efficiently harvest and convert solar energy. Plasmonic nanofluids that have strong energy concentrating capacity and spectral selectivity can be used in many high-temperature energy systems where radiative heat transport is essential. In this thesis,the surface plasmon resonance effect and the wavelength tuning ranges for different metallic shell nanoparticles are investigated, the solar-weighted efficiencies of corresponding core-shell nanoparticle suspensions are explored, and a quantitative study of core-shell nanoparticle suspensions in a DAC system is provided. Using core-shell nanoparticle dispersions, it is possible to create efficient spectral solar absorption fluids and design materials for applications which require variable spectral absorption or scattering.

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2012

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Plasmonic-based imaging detection of chemical reactions

Description

An imaging measurement technique is developed using surface plasmon resonance. Plasmonic-based electrochemical current imaging (P-ECi) method has been developed to image the local electrochemical current optically, it allows us to measure the current density quickly and non-invasively [1, 2]. In

An imaging measurement technique is developed using surface plasmon resonance. Plasmonic-based electrochemical current imaging (P-ECi) method has been developed to image the local electrochemical current optically, it allows us to measure the current density quickly and non-invasively [1, 2]. In this thesis, we solve the problems when we extand the P-ECi technique to the field of thin film system. The P-ECi signal in thin film structure was found to be directly proportional to the electrochemical current. The upper-limit of thin film thickness to use the proportional relationship between P-ECi signal and EC current was discussed by experiment and simulation. Furthermore, a new algorithm which can calculate the current density from P-ECi signal without any thickness limitation is developed and tested. Besides, surface plasmon resonance is useful phenomenon which can be used to detect the changes in the refractive index near the gold sensing surface. With the assistance of pH indicator, by applied EC potential on the gold film as the working electrode, the detection of H2 evolution reaction can be enhanced. This measurement technique is useful in analyzing local EC information and H2 evolution. References [1] S. Wang, et al., "Electrochemical Surface Plasmon Resonance: Basic Formalism and Experimental Validation," Analytical Chemistry, vol. 82, pp. 935-941, 2010/02/01 2010. [2] X. Shan, et al., "Imaging Local Electrochemical Current via Surface Plasmon Resonance," Science, vol. 327, pp. 1363-1366, March 12, 2010 2010.

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Date Created
2013

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Surface enhanced fluorescence: a classic electromagnetic approach

Description

The fluorescence enhancement by a single Noble metal sphere is separated into excitation/absorption enhancement and the emission quantum yield enhancement. Incorporating the classical model of molecular spontaneous emission into the excitation/absorption transition, the excitation enhancement is calculated rigorously by electrodynamics

The fluorescence enhancement by a single Noble metal sphere is separated into excitation/absorption enhancement and the emission quantum yield enhancement. Incorporating the classical model of molecular spontaneous emission into the excitation/absorption transition, the excitation enhancement is calculated rigorously by electrodynamics in the frequency domain. The final formula for the excitation enhancement contains two parts: the primary field enhancement calculated from the Mie theory, and a derating factor due to the backscattering field from the molecule. When compared against a simplified model that only involves the primary Mie theory field calculation, this more rigorous model indicates that the excitation enhancement near the surface of the sphere is quenched severely due to the back-scattering field from the molecule. The degree of quenching depends in part on the bandwidth of the illumination because the presence of the sphere induces a red-shift in the absorption frequency of the molecule and at the same time broadens its spectrum. Monochromatic narrow band illumination at the molecule's original (unperturbed) resonant frequency yields large quenching. For the more realistic broadband illumination scenario, we calculate the final enhancement by integrating over the excitation/absorption spectrum. The numerical results indicate that the resonant illumination scenario overestimates the quenching and therefore would underestimate the total excitation enhancement if the illumination has a broader bandwidth than the molecule. Combining the excitation model with the exact Electrodynamical theory for emission, the complete realistic model demonstrates that there is a potential for significant fluorescence enhancement only for the case of a low quantum yield molecule close to the surface of the sphere. General expressions of the fluorescence enhancement for arbitrarily-shaped metal antennas are derived. The finite difference time domain method is utilized for analyzing these complicated antenna structures. We calculate the total excitation enhancement for the two-sphere dimer. Although the enhancement is greater in this case than for the single sphere, because of the derating effects the total enhancement can never reach the local field enhancement. In general, placing molecules very close to a plasmonic antenna surface yields poor enhancement because the local field is strongly affected by the molecular self-interaction with the metal antenna.

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2013

Plasmonic-based label-free detection and imaging of molecules

Description

Obtaining local electrochemical (EC) information is extremely important for understanding basic surface reactions, and for many applications. Scanning electrochemical microscopy (SECM) can obtain local EC information by scanning a microelectrode across the surface. Although powerful, SECM is slow, the scanning

Obtaining local electrochemical (EC) information is extremely important for understanding basic surface reactions, and for many applications. Scanning electrochemical microscopy (SECM) can obtain local EC information by scanning a microelectrode across the surface. Although powerful, SECM is slow, the scanning microelectrode may perturb reaction and the measured signal decreases with the size of microelectrode. This thesis demonstrates a new imaging technique based on a principle that is completely different from the conventional EC detection technologies. The technique, referred to as plasmonic-based electrochemical imaging (PECI), images local EC current (both faradaic and non-faradaic) without using a scanning microelectrode. Because PECI response is an optical signal originated from surface plasmon resonance (SPR), PECI is fast and non-invasive and its signal is proportional to incident light intensity, thus does not decrease with the area of interest. A complete theory is developed in this thesis work to describe the relationship between EC current and PECI signal. EC current imaging at various fixed potentials and local cyclic voltammetry methods are developed and demonstrated with real samples. Fast imaging rate (up to 100,000 frames per second) with 0.2×3µm spatial resolution and 0.3 pA detection limit have been achieved. Several PECI applications have been developed to demonstrate the unique strengths of the new imaging technology. For example, trace particles in fingerprint is detected by PECI, a capability that cannot be achieved with the conventional EC technologies. Another example is PECI imaging of EC reaction and interfacial impedance of graphene of different thicknesses. In addition, local square wave voltammetry capability is demonstrated and applied to study local catalytic current of platinum nanoparticle microarray. This thesis also describes a related but different research project that develops a new method to measure surface charge densities of SPR sensor chips, and micro- and nano-particles. A third project of this thesis is to develop a method to expand the conventional SPR detection and imaging technology by including a waveguide mode. This innovation creates a sensitive detection of bulk index of refraction, which overcomes the limitation that the conventional SPR can probe only changes near the sensor surface within ~200 nm.

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2011

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Photoluminescence enhancement of Ge quantum dots by exploiting the localized surface plasmon of epitaxial Ag islands

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This dissertation presents research findings regarding the exploitation of localized surface plasmon (LSP) of epitaxial Ag islands as a means to enhance the photoluminescence (PL) of Germanium (Ge) quantum dots (QDs). The first step of this project was to investigate

This dissertation presents research findings regarding the exploitation of localized surface plasmon (LSP) of epitaxial Ag islands as a means to enhance the photoluminescence (PL) of Germanium (Ge) quantum dots (QDs). The first step of this project was to investigate the growth of Ag islands on Si(100). Two distinct families of Ag islands have been observed. “Big islands” are clearly faceted and have basal dimensions in the few hundred nm to μm range with a variety of basal shapes. “Small islands” are not clearly faceted and have basal diameters in the 10s of nm range. Big islands form via a nucleation and growth mechanism, and small islands form via precipitation of Ag contained in a planar layer between the big islands that is thicker than the Stranski-Krastanov layer existing at room-temperature.

The pseudodielectric functions of epitaxial Ag islands on Si(100) substrates were investigated with spectroscopic ellipsometry. Comparing the experimental pseudodielectric functions obtained for Si with and without Ag islands clearly identifies a plasmon mode with its dipole moment perpendicular to the surface. This observation is confirmed using a simulation based on the thin island film (TIF) theory. Another mode parallel to the surface may be identified by comparing the experimental pseudodielectric functions with the simulated ones from TIF theory. Additional results suggest that the LSP energy of Ag islands can be tuned from the ultra-violet to the infrared range by an amorphous Si (α-Si) cap layer.

Heterostructures were grown that incorporated Ge QDs, an epitaxial Si cap layer and Ag islands grown atop the Si cap layer. Optimum growth conditions for distinct Ge dot ensembles and Si cap layers were obtained. The density of Ag islands grown on the Si cap layer depends on its thickness. Factors contributing to this effect may include the average strain and Ge concentration on the surface of the Si cap layer.

The effects of the Ag LSP on the PL of Ge coherent domes were investigated for both α-Si capped and bare Ag islands. For samples with low-doped substrates, the LSPs reduce the Ge dot-related PL when the Si cap layer is below some critical thickness and have no effect on the PL when the Si cap layer is above the critical thickness. For samples grown on highly-doped wafers, the LSP of bare Ag islands enhanced the PL of Ge QDs by ~ 40%.

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2015

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Optical methods for studying cell mechanics

Description

Mechanical properties of cells are important in maintaining physiological functions of biological systems. Quantitative measurement and analysis of mechanical properties can help understand cellular mechanics and its functional relevance and discover physical biomarkers for diseases monitoring and therapeutics.

This dissertation presents

Mechanical properties of cells are important in maintaining physiological functions of biological systems. Quantitative measurement and analysis of mechanical properties can help understand cellular mechanics and its functional relevance and discover physical biomarkers for diseases monitoring and therapeutics.

This dissertation presents a work to develop optical methods for studying cell mechanics which encompasses four applications. Surface plasmon resonance microscopy based optical method has been applied to image intracellular motions and cell mechanical motion. This label-free technique enables ultrafast imaging with extremely high sensitivity in detecting cell deformation. The technique was first applied to study intracellular transportation. Organelle transportation process and displacement steps of motor protein can be tracked using this method. The second application is to study heterogeneous subcellular membrane displacement induced by membrane potential (de)polarization. The application can map the amplitude and direction of cell deformation. The electromechanical coupling of mammalian cells was also observed. The third application is for imaging electrical activity in single cells with sub-millisecond resolution. This technique can fast record actions potentials and also resolve the fast initiation and propagation of electromechanical signals within single neurons. Bright-field optical imaging approach has been applied to the mechanical wave visualization that associated with action potential in the fourth application. Neuron-to-neuron viability of membrane displacement was revealed and heterogeneous subcellular response was observed.

All these works shed light on the possibility of using optical approaches to study millisecond-scale and sub-nanometer-scale mechanical motions. These studies revealed ultrafast and ultra-small mechanical motions at the cellular level, including motor protein-driven motions and electromechanical coupled motions. The observations will help understand cell mechanics and its biological functions. These optical approaches will also become powerful tools for elucidating the interplay between biological and physical functions.

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2016

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Surface Plasmon Resonance (SPR) bio-sensors to detect target molecules in undiluted human serum

Description

Biosensors aiming at detection of target analytes, such as proteins, microbes, virus, and toxins, are widely needed for various applications including detection of chemical and biological warfare (CBW) agents, biomedicine, environmental monitoring, and drug screening. Surface Plasmon Resonance (SPR), as

Biosensors aiming at detection of target analytes, such as proteins, microbes, virus, and toxins, are widely needed for various applications including detection of chemical and biological warfare (CBW) agents, biomedicine, environmental monitoring, and drug screening. Surface Plasmon Resonance (SPR), as a surface-sensitive analytical tool, can very sensitively respond to minute changes of refractive index occurring adjacent to a metal film, offering detection limits up to a few ppt (pg/mL). Through SPR, the process of protein adsorption may be monitored in real-time, and transduced into an SPR angle shift. This unique technique bypasses the time-consuming, labor-intensive labeling processes, such as radioisotope and fluorescence labeling. More importantly, the method avoids the modification of the biomarker’s characteristics and behaviors by labeling that often occurs in traditional biosensors. While many transducers, including SPR, offer high sensitivity, selectivity is determined by the bio-receptors. In traditional biosensors, the selectivity is provided by bio-receptors possessing highly specific binding affinity to capture target analytes, yet their use in biosensors are often limited by their relatively-weak binding affinity with analyte, non-specific adsorption, need for optimization conditions, low reproducibility, and difficulties integrating onto the surface of transducers. In order to circumvent the use of bio-receptors, the competitive adsorption of proteins, termed the Vroman effect, is utilized in this work. The Vroman effect was first reported by Vroman and Adams in 1969. The competitive adsorption targeted here occurs among different proteins competing to adsorb to a surface, when more than one type of protein is present. When lower-affinity proteins are adsorbed on the surface first, they can be displaced by higher-affinity proteins arriving at the surface at a later point in time. Moreover, only low-affinity proteins can be displaced by high-affinity proteins, typically possessing higher molecular weight, yet the reverse sequence does not occur. The SPR biosensor based on competitive adsorption is successfully demonstrated to detect fibrinogen and thyroglobulin (Tg) in undiluted human serum and copper ions in drinking water through the denatured albumin.

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Date Created
2015

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Large-Scale Kinetic Analyses of Protein-Protein Interactions: Advancing the Understanding of Post Translational Modifications in Biological Regulation

Description

Signal transduction networks comprising protein-protein interactions (PPIs) mediate homeostatic, diseased, and therapeutic cellular responses. Mapping these networks has primarily focused on identifying interactors, but less is known about the interaction affinity, rates of interaction or their regulation. To better understand

Signal transduction networks comprising protein-protein interactions (PPIs) mediate homeostatic, diseased, and therapeutic cellular responses. Mapping these networks has primarily focused on identifying interactors, but less is known about the interaction affinity, rates of interaction or their regulation. To better understand the extent of the annotated human interactome, I first examined > 2500 protein interactions within the B cell receptor (BCR) signaling pathway using a current, cutting-edge bioluminescence-based platform called “NanoBRET” that is capable of analyzing transient and stable interactions in high throughput. Eighty-three percent (83%) of the detected interactions have not been previously reported, indicating that much of the BCR pathway is still unexplored. Unfortunately, NanoBRET, as with all other high throughput methods, cannot determine binding kinetics or affinities. To address this shortcoming, I developed a hybrid platform that characterizes > 400 PPIs quantitatively and simultaneously in < 1 hour by combining the high throughput and flexible nature of nucleic programmable protein arrays (NAPPA) with the quantitative abilities of surface plasmon resonance imaging (SPRi). NAPPA-SPRi was then used to study the kinetics and affinities of > 12,000 PPIs in the BCR signaling pathway, revealing unique kinetic mechanisms that are employed by proteins, phosphorylation and activation states to regulate PPIs. In one example, activation of the GTPase RAC1 with nonhydrolyzable GTP-γS minimally affected its binding affinities with phosphorylated proteins but increased, on average, its on- and off-rates by 4 orders of magnitude for one-third of its interactions. In contrast, this phenomenon occurred with virtually all unphosphorylated proteins. The majority of the interactions (85%) were novel, sharing 40% of the same interactions as NanoBRET as well as detecting 55% more interactions than NanoBRET. In addition, I further validated four novel interactions identified by NAPPA-SPRi using SDS-PAGE migration and Western blot analyses. In one case, we have the first evidence of a direct enzyme-substrate interaction between two well-known proto-oncogenes that are abnormally regulated in > 30% of cancers, PI3K and MYC. Herein, PI3K is demonstrated to phosphorylate MYC at serine 62, a phosphosite that increases the stability of MYC. This study provides valuable insight into how PPIs, phosphorylation, and GTPase activation regulate the BCR signal transduction pathway. In addition, these methods could be applied toward understanding other signaling pathways, pathogen-host interactions, and the effect of protein mutations on protein interactions.

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Date Created
2018