In this study we use AFM-based nanolithography technique to produce nanofeatures of the single strand DNA and LNA probe molecules which are prepared via thiolated nucleic acid self-assembled monolayers (SAMs) on gold substrates. The goal is to observe the topographic changes of the DNA film structures resulting from the formation of rigid double strand DNA when the target and probe DNAs bind together. The so-called hybridization depends strongly on the probe density on the substrate surface. To find the proper probe density for hybridization, we vary the concentration of the probe DNA and search for the optimal conditions for measuring the height changes of the nanofeatures. We also monitor the topographic changes of the DNA nanofeatures in the different target DNA concentrations as a function of time, and the binding isotherms are fitted with the Langmuir adsorption model to derive the equilibrium dissociation constant and maximum hybridization efficiency. In addition, we extend the nanoscale hybridization reaction detection to mismatched DNA:DNA and LNA:DNA hybridization, and observe that topographic change of mismatched hybridization is inconspicuous and rapidly reach equilibrium. The results reveal the apparent difference between the perfect match and mismatch conditions, and validate that this approach can be applied to differentiate the situations for both perfect match and mismatch cases, demonstrating its potentials in the gene chip technology.

Reflection anisotropy spectroscopy (RAS) is a non-destructive optical technique which can be used to measure the surface properties of sample. We use the technique to detect the optical anisotropy of rubbed polyimide thin film. Atomic force microscopy study of rubbed polyimide showed that rubbing produced microgrooves on the surface of the polyimide thin films, and the surface roughness of the polymer thin films increased slightly with the rubbing strength. Reflection anisotropy signals have been found to be generated on the surface of polyimide thin film on completion of mechanical rubbing, and will increase with an increase in the rubbing strength. We also tried to find out the correlation between RA strength of the polyimide alignment layer and pretilt angle of liquid crystal at the rubbed polyimide films.

Improving the identification ability of surfaced-immobilized nucleic acid probes for small size DNA or RNA targets, utilizing optical or electrochemical methods, has been the goal for the gene chip technology. This study focuses on new probe design for introducing hairpin structural features and locked nucleic acid modification. We use three kinds of probes (DNA-LN, DNA-HP and LNA-HP) to prepare recognition layers via self-assembly processes on a gold substrate, and utilize AFM-based nanolithography technique to produce nanofeatures to observe the stiffness changes of oligonucleotide chains resulting from the formation of rigid double stranded duplexes when target sequence hybridizes to the probe. We also monitor the topographic changes upon exposure to the single mismatched and non-complementary targets as a function of time. The results reveal LNA-HP probes exhibit the highest response to discriminating single-point mutation in the base sequence. In addition, we study the effects of salt concentration, reaction temperature and the small size on the hybridization efficiency.

Single molecule force spectroscopy is an important technique to determine the interaction forces between biomolecules. Atomic force microscopy (AFM) is one of the tools used for this purpose. So far, AFMs usually use cantilevers as the force sensors and piezoelectrics as the actuators which may have some drawbacks in terms of speed and noise. In this research, a micromachined membrane actuator was used in two important types of experiments, namely the single molecule pulling and force-clamp based force spectroscopy. These two methods permit a more direct way of probing the forces of biomolecules, giving a detailed insight into binding potentials, and allowing the detection of discrete unbinding forces. To improve the quality of the experiments there is a need for high force resolution, high time resolution and increase in the throughput. This research focuses on using the combination of AFM and membrane based probe structures that have electrostatic actuation capability. The membrane actuators are characterized for range, dynamics, and noise to illustrate their adequacy for these experiments and to show that the complexity they introduce does not affect the noise level in the system. The control system described in this thesis utilizes the novel membrane actuator structures and integrates it into the current AFM setup. This is a very useful tool which can be implemented on any AFM without changing its mechanical architecture. To perform an experiment, all that is needed is to place the membrane actuator on the AFM stage, under the imagining head, and run the control system, which was implemented using LabVIEW. The system allows the user to maintain a precise and continuous control of the force. This was demonstrated by performing a life time experiment using biomolecules. Moreover, by slightly modifying the control scheme, the system allows us to linearize the membrane motion, which is inherently non-linear. The feasibility of using this control system for a variety of loading rate experiments are also demonstrated.

During hemostatic and inflammatory responses, cell adhesion molecules play a major role in regulating the leukocytes and platelets adhesion to vascular surfaces under the hydrodynamic environment of the circulation. Selectin-ligand interactions (bonds) mediate leukocyte rolling on vascular surfaces. The molecular basis for differential ligand recognition by selectins is poorly understood. Using atomic force microscopy (AFM), the kinetics of three mutants L-selectin interacting with surrogates of PSGL-1 and PNAd, is compared with those of wild-type L-selectin. The interaction between glycoprotein Ib (GPIb) and von Willebrand Factor (VWF) mediates platelet translocation at the vascular vessel damage sites, which plays a critical role in initiating the platelets adhesion and thrombus formation. Translocation of platelets on VWF requires a shear threshold, suggesting a possible catch bond at work there. We characterized the kinetics of GPIbα interacting with VWF A1 domain, confirming the catch bond existed. Two type 2B VWD A1 mutants eliminated the catch bond and gave longer low force lifetimes. The prolonged lifetimes at low force resulted in more agglutination of platelets with A1 coated microspheres in flow. During the process of hemostasis, the size of prothrombotic ULVWF affects the affinity of VWF to platelets bearing GPIbα on the membrane. ADAMTS13 has been identified and characterized as a multi-domain metalloprotease that regulate the size of ULVWF. We studied how force regulated the binding and cleavage of ADAMTS13 on VWF. We found the cleavage effects could only be observed after the catastrophic structural change of A1A2A3. The unfolding exposed the ADAMTS13 cleavage site and favored the cleavage. Two protocols using different stretching molecules (GPIbα and CR1) and A1A2A3 immobilization methods revealed the cleavage effects diminished with increasing stretching force. This study elucidated mechanisms of the binding kinetics of L-selectin with different structure components from PSGL-1 and PNAd by structural variants. It also provided new insights into our current knowledge of the dynamic adhesion and regulation of GPIbα-VWF interaction in vivo. Using single molecule method, the chemical catalytic reaction between enzyme and substrate has been targeted. These results help us understand this important enzyme-substrate interaction involved in the hemostasis.

Inorganic-polymer hybrid materials have a high potential to enable major advances in material performance in a wide range of applications. This research focuses on characterizing and tailoring the physics and chemistry of inorganic-polymer interfaces in fabricating high-performance zeolite-polymer mixed-matrix membranes for energy-efficient gas separations. In addition, the topic of novel metal nanoparticle-coated polymer microspheres for optical applications is treated in the Appendix. In zeolite/polymer mixed-matrix membranes, interfacial adhesion and interactions between dope components (zeolite, polymer and solution) play a crucial role in determining interfacial morphology and particle dispersion. The overarching goal is to develop accurate and robust tools for evaluating adhesion and interactions at zeolite-polymer and zeolite-zeolite interfaces in mixed-matrix membrane systems. This knowledge will be used ultimately for selecting proper materials and predicting their performance. This project has two specific goals: (1) development of an AFM methodology for characterizing interfacial interactions and (2) characterization of the mechanical, thermal, and structural properties of zeolite-polymer composites and their correlation to the zeolite-polymer interface and membrane performance. The research successfully developed an AFM methodology to determine interfacial interactions, and these were shown to correlate well with polymer composite properties. The medium effect on interactions between components was studied. We found that the interactions between two hydrophilic silica surfaces in pure liquid (water or NMP) were described qualitatively by the DLVO theory. However, the interactions in NMP-water mixtures were shown to involve non-DLVO forces arising from bridging of NMP macroclusters on the hydrophilic silica surfaces. The mechanism by which nanostructured zeolite surfaces enhanced in zeolite-polymer interfacial adhesion was demonstrated to be reduced entropy penalties for polymer adsorption and increased contact area. ¡¡¡¡¡¡Metal nanoparticle (NP)-coated polymer microspheres have attracted intense interest due to diverse applications in medical imaging and biomolecular sensing. The goal of this project is to develop a facile preparation method of metal-coated polymer beads by controlling metal-polymer interactions. We developed and optimized a novel solvent-controlled, combined swelling-heteroaggregation (CSH) technique. The mechanism governing metal-polymer interaction in the fabrication was determined to be solvent-controlled heteroaggregation and entanglement of NPs with polymer, and the optical properties of the metal/polymer composite beads were shown to make them useful for scattering contrast agent for biomedical imaging and SERS (Surface-Enhanced Raman Scattering) substrates.

The goal of this thesis was the advanced design, fabrication, and application of combined atomic force microscopy - scanning electrochemical microscopy (AFMSECM) probes for high-resolution topographical and electrochemical imaging. The first part of the thesis describes innovative approaches for the optimization of AFM-SECM probe fabrication with recessed frame electrodes. For this purpose, commercial silicon nitride AFM cantilevers were modified using optimized critical fabrication processes including improved metallization for the deposition of the electrode layer, and novel insulation strategies for ensuring localized electrochemical signals. As a novel approach for the insulation of AFM-SECM probes, sandwiched layers of PECVD SixNy and SiO2, and plasma-deposited PFE films were applied and tested. Using sandwiched PECVD SixNy and SiO2 layers, AFM-SECM probes providing straight (unbent) cantilevers along with excellent insulation characteristics facilitating the functionality of the integrated electrode were reproducibly obtained. Alternatively, PFE thin films were tested according to their utility for serving as a mechanically flexible insulating layer for AFM-SECM probes. The electrochemical characterization of PFEinsulated AFM-SECM probes revealed excellent insulating properties at an insulation thickness of only approx. 400 nm. Finally, AFM-SECM cantilevers prepared via both insulation strategies were successfully tested during AFM-SECM imaging experiments. In the second part of this thesis, disk-shaped nanoelectrodes were for the first time integrated into AFM probes for enabling high-resolution AFM-SECM measurements. Disk electrodes with an electrode radius < 100 nm were realized, which provides a significantly improved lateral resolution for SECM experiments performed in synchronicity with AFM imaging. Furthermore, the developed fabrication scheme enables producing AFM-SECM probes with integrated disk nanoelectrodes at significantly reduced time and cost based on a highly reproducible semi-batch fabrication process providing bifunctional probes at a wafer scale. The development of a detailed processing strategy was accompanied by extensive simulation results for developing a fundamental understanding on the electrochemical properties of AFM-SECM probes with nanoscale electrodes, and for optimizing the associated processing parameters. Thus fabricated probes were electrochemically characterized, and their performance was demonstrated via bifunctional imaging at model samples. The third part of this thesis describes the development and characterization of the first AFM tip-integrated potentiometric sensors based on solid-state electrodes with submicrometer dimensions enabling laterally resolved pH imaging. Antimony and iridium oxides were applied as the pH sensitive electrode material, and have been integrated into the AFM probes via conventional microfabrication strategies. The pH response of such AFM tip-integrated integrated pH microsensors was tested for both material systems, and first studies were performed demonstrating localized pH measurements at a model system.

Atomic force microscopy (AFM) is a powerful technique that enables to study biological macromolecules and dynamic biological processes at different scales. It is an excellent tool for imaging of biological objects under various conditions at a nanometer resolution. Force mode of AFM, so called single molecule force spectroscopy (SMFS), allows for investigation of the strength of molecular interactions of different origins established between and within biological molecules. In the present work, SMFS was used to detect and locate structurally and functionally important interactions of sodium/glycine betaine transporter BetP of Corynebacterium glutamicum, which serves as a model system for this class of proteins. Mechanical pulling of BetP molecules embedded into the lipid membranes resulted in a step-wise unfolding of the protein and revealed insights into its structural stability. Effect of the lipid environment, N- and C-terminal extensions on inramolecular interactions of BetP as well as protein activation and ligand binding were investigated in great detail. In another part of this work, I demonstrate an application of the AFM based technique that can record unfolding of a protein under force-clamp conditions. This method directly measures the kinetics of the protein unfolding, allowing for the use of simple methods to analyze the data. For the first time the force-clamp technique was used to describe in detail unfolding kinetics of the membrane protein, i. e. Na+/H+-antiporter NhaA from Escherichia coli. Performed here experiments on NhaA in its functionally active and inactive states demonstrated the advantages of examining unfolding kinetics at the single-molecule level. It was possible to observe unfolding events for pH-activated conformation of NhaA that due to the low frequency of occurrence were not represented in the ensemble average of the single-molecule measurements. As mechanical unfolding, similarly to bond rupture, is a force-dependent process, force-clamp technique can allow for a more direct way of probing protein unfolding and is anticipated to be also useful to examine the folding/unfolding kinetics of other membrane proteins.

Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2002. / Includes bibliographical references. Also available in electronic version. Access restricted to campus users.

Thesis (Ph. D.)--University of Missouri-Columbia, 2003. / Typescript. Vita. Includes bibliographical references (leaves 107-109). Also available on the Internet.