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There is a need for the development of new technologies for the early detection of disease. Diverse initiatives are underway in academia and the pharmaceutical and biotechnology industries to develop highly-sensitive, high-throughput methods to detect disease-relevant biomarkers at the single-cell level. Biomarkers can define the progress of a disease or efficacy of disease treatment, and can include nucleic acids (RNA, DNA), proteins, small molecules, or even specific cells. While discovery research in this area is accelerating, there are a number of current experimental limitations. Most existing methodologies require a relatively large sample size. Also, amplification-based detection technologies are destructive to sample, and errors in amplification can occur, leading to an incorrect diagnosis. Nanomaterial-based devices (nanodevices) offer the promise of label-free, amplification-free detection strategies. Such nanodevices could allow analysis of minute biological samples without the requirement for amplification or incorporation of reporter groups. Loss of sample, due to handling and processing would be minimized and the sample could be recovered for further analysis. Atomic force microscopy (AFM) allows topographic imaging and compressibility/elasticity measurement of biomolecules on solid supports. AFM can enable assays of ligand binding with single molecule detection capability. Certain nucleic acid types, in particular double-stranded (ds) RNA, can act as a biomarker for specific cancers (e.g. leukemia) and viral infection. dsRNA also is of interest since it is a conserved structural feature of precursors to gene-regulatory RNAs, including micro (mi) RNAs and short interfering (si) RNAs. This project demonstrates a single-step, label-free, amplification-free approach for detecting the interaction of biomolecules that bind and/or process dsRNA, using a nanomanipulated, self-assembled monolayer (SAM) of a ds[RNA-DNA] chimera as imprinting matrix, a reference nuclease as imprinting agent, and AFM for imprint-readout. The action of the dsRNA-specific enzyme, ribonuclease III (RNase III), as well as the binding of an inactive, dsRNA-binding RNase III mutant can be permanently recorded by the input-responsive action of a restriction endonuclease that cleaves an ancillary reporter site within the dsDNA segment. The resulting irreversible height change of the arrayed ds[RNA-DNA] chimera, as measured by atomic force microscopy, provides a distinct digital output for each type of input. These findings provide the basis for developing imprinting-based nano-biosensors, and reveal the versatility of AFM as a tool for characterizing the behaviour of highly-crowded biomolecules at the nanoscale. RNA-DNA heteroduplexes are biomarkers for specific inflammatory conditions of genetic origin, and also are the product of capture of an RNA (e.g., miRNA) by a complementary DNA sequence. The approach used here to detect RNA-DNA hybrids is based on the ability of alkylthiol-modified ssDNA molecules to form monolayers and nanomatrices on gold surfaces (as described above) with density-dependent thickness, which increases upon formation of RNA-DNA hybrids following addition of a complementary oligoribonucleotide. Changes in hybrid matrix thickness can be measured by AFM, using a reference monolayer. RNA-DNA hybrid formation as well as subsequent processing by RNase H can be observed as a height increase or decrease, respectively, of the monolayer. When Mg2+ is omitted to prevent RNA cleavage, but not protein binding, a significant height increase is observed. The height increase is not observed with the corresponding ssDNA or ssRNA nanomatrices, and only occurs with nanomatrices having a hybrid density above a defined threshold. The data indicate formation of a stable multimeric RNase H assembly on the hybrid nanomatrix which provides a robust signal that is nondestructive to the RNA. The implications of these findings are discussed with respect to development of novel detection methodologies for RNA, dsRNA, and RNA-DNA hybrids. / Chemistry

The reactivity of chemical warfare agents (CWAs) and CWA simulants on organic and oxide surfaces is not currently well understood, but is of substantial importance to the development of effective sensors, filters and sorbent materials. Polyurethane coatings are used by the armed forces as chemical agent resistive paints to limit the uptake of CWAs on surfaces, while the use of metal oxides has been explored for decontamination and protection purposes. To better understand the chemical nature of the interactions of organophosphonate simulants with these surfaces, an ultra-high vacuum environment was used to isolate the target interactions from environmental gaseous interferences. The use of highly-characterized surfaces, coupled with molecular beam and dosing capabilities, allows for the elucidation of adsorption, desorption, and reaction mechanisms of CWA simulants on a variety of materials. Model urethane-containing organic coatings were designed and applied toward the creation of well-ordered thin films containing carbamate linkages. In addition, novel trisilanolphenyl-polyhedral oligomeric silsesquioxane (POSS) molecules were used to create Langmuir-Blodgett films containing reactive silanol groups that have potential use as sensors and coatings. The uptake and reactivity of organophosphonates and chlorophosphates on these surfaces is the focus of this study. Surfaces were characterized before and after exposure to the phosphates using a number of surface sensitive techniques including: contact angle goniometry, reflection-absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS) and temperature-programmed desorption (TPD) measurements. In conjunction with surface probes, uptake coefficients were monitored according to the King and Wells direct reflection technique. The integration of these analytical techniques provides insight and direction towards the design of more effective chemical agent resistant coatings and aids in the development of more functional strategies for chemical warfare agent decontamination and sensing. / Ph. D.

Poly (caprolactone) (PCL) has been widely studied as a model system for investigating polymer crystallization. In this thesis, PCL crystallization along with other phase transitions in PCL-based polymer blends are studied as Langmuir films at the air/water (A/W) interface. In order to understand the phase behavior of PCL-based blends, surface pressure induced crystallization of PCL in single-component Langmuir monolayers was first studied by Brewster angle microscopy (BAM). PCL crystals observed during film compression exhibit butterfly-shapes. During expansion of the crystallized film, polymer chains detach from the crystals and diffuse back into the monolayer as the crystals "melt". Electron diffraction on Langmuir-Schaefer films suggests that the lamellar crystals are oriented with the chain axes perpendicular to the substrate surface, while atomic force microscopy (AFM) reveals a crystal thickness of ~ 7.6 nm. In addition, the competition between lower segmental mobility and a greater degree of undercooling with increasing molar mass produces a maximum average growth rate at intermediate molar mass. PCL was blended with poly(t-butyl acrylate) (PtBA) to study the influence of PtBA on the morphologies of PCL crystals grown in monolayers. For PCL-rich blends, BAM studies reveal dendritic morphologies of PCL crystals. The thicknesses of the PCL dendrites are ~ 7-8 nm. BAM studies during isobaric area relaxation experiments at different surface pressure reveal morphological transitions from highly branched dendrites, to six-arm dendrites, four-arm dendrites, seaweedlike crystals, and distorted rectangular crystals. In contrast, PCL crystallization is suppressed in PtBA-rich blend films. For immiscible blends of PCL and polystyrene (PS) with intermediate molar masses as Langmuir films, the surface concentration of PCL is the only factor influencing surface pressure below the collapse transition. For PS-rich blends, both BAM and AFM studies reveal that PS nanoparticle aggregates formed at very low surface pressure form networks during film compression. For PCL-rich blends, small PS aggregates serve as heterogeneous nucleation centers for the growth of PCL crystals. During film expansion, BAM images show a gradual change in the surface morphology from highly continuous networklike structures (PS-rich blends) to broken ringlike structures (intermediate composition) to small discontinuous aggregates (PCL-rich blends). / Ph. D.

Controlling the surface morphology and degree of crystallinity of poly(L-lactic acid) (PLLA) substrates have recently attracted considerable attention because of their applications in cell adhesion, tissue engineering, and drug delivery. Several techniques have been used to fabricate PLLA substrates, some of which may be invalid because PLLA can degrade during fabrication processes. This dissertation provides the Langmuir-Blodgett (LB) technique as a mechanism for fabricating PLLA substrates at temperatures where PLLA degradation is uncommon. In order to fully understand surface morphologies of PLLA LB-films, studies of Langmuir monolayers at the air/water (A/W) interface using surface pressure-area (Pi-A) isotherm and Brewster angle microscopy (BAM) are vital. PLLA exhibits a first-order liquid expanded to condensed (LE/LC) phase transition with molar mass dependent critical phenomena, the first such observation for a homopolymer Langmuir monolayer. Atomic force microscopy (AFM) images of PLLA LB-films prepared in the LC phase exhibit well-ordered lamellar structures. Molar mass scaling of lamellar dimensions, x-ray reflectivity, and reflection absorption infrared spectroscopy (RAIRS) measurements on PLLA LB-films are consistent with PLLA existing as single molecule 10/3-helices at the A/W interface. Morphologies observed after collapse of the LC monolayer are dependent upon the collapse mechanism and subsequent thermal treatment. For temperatures below the LE/LC critical temperature (Tc), two mechanisms are identified for the formation of three dimensional structures: a buckling and stacking of lamellar monolayers on top of existing lamellae during constant compression rate experiments, and a modified nucleation and growth mechanism during isobaric area relaxation experiments. PLLA LB-films prepared in different Langmuir film phases at temperatures below Tc all contain lamellae with different surface roughnesses and similar helical content. Conventional thermal annealing studies on PLLA LB-films reveal that well-ordered lamellar features are destroyed after annealing the LB-films at bulk crystallization temperature through a melting-recrystallization process, which is confirmed by RAIRS and AFM. Our results may prove useful for studying critical behavior and experimentally testing scaling predictions for two dimensions, the development and testing of theories for crystallization in confined geometries, and separating the roles that roughness and crystallinity play in cell adhesion and spreading on biocompatible polymer surfaces. / Ph. D.

Constructing a detailed understanding of the heterogeneous oxidation of atmospheric organic aerosols, both from a mechanistic and kinetic perspective, will enable researchers to predict the fate and lifetime of atmospheric gases and the particles with which they interact. In an effort to develop a more complete understanding of the interfacial reactions of ozone with vinyl-containing organic thin films, self-assembled monolayers that contain vinyl groups positioned precisely at the gas/surface interface were synthesized as model systems for atmospheric organic aerosols. To isolate the reactions of background gases with ozone or surface products, an ultrahigh vacuum surface analysis instrument was designed and constructed to explore the reactions of ozone with the atmospheric model systems. The surface reactions can be monitored in real-time with reflection absorption infrared spectroscopy (RAIRS) and mass spectrometry. The chemical identity of adsorbates on a surface can also be determined before or after a reaction with X-ray photoelectron spectroscopy (XPS). Disordering of the monolayers concurrent with the disappearance of the vinyl group was observed with RAIRS. New bands within the RAIR spectra were observed and assigned to carbonyl or carboxylic acids bound to the surface. Little oxidation of the sulfur head groups and no significant loss of carbon during the reaction was observed with XPS. A mechanism is proposed that includes the cross linking of the hydrocarbon chains within the monolayer, which impedes further oxidation of the sulfur head group and limits desorption of the chains. By RAIRS, the kinetics of the oxidation of the vinyl groups were tracked and an observed rate constant was determined by monitoring the changes in IR absorbance of the C=C bond. With the aid of the rate constant, an initial reaction probability for the collisions of ozone with vinyl groups positioned precisely at an interface was determined. The reaction probability is approximately three orders of magnitude greater than the reaction probability for an analogous gas-phase reaction, which demonstrates that the gas/surface interface plays an important role in this reaction. The results presented in this thesis should help develop a more detailed understanding of the interfacial reactions of pure ozone at surfaces. / Ph. D.

This dissertation describes the impact of defects on monolayer properties for self-assembled monolayers (SAMs) created by interfacial patterning methods. When forming a two-dimensional interfacial pattern with n-alkanethiols on gold, the desired electrochemical properties are those of a homogeneous, solution adsorbed monolayer. However, even well-ordered SAMs contain a small degree of defects, especially at domain boundaries where two nucleating domains converge. Patterning a surface creates user-defined domain boundaries within the monolayer, potentially having a significant impact on the properties of the interface. This dissertation investigates the effect that user-created domain boundaries have on the properties of a monolayer, as studied by electrochemical impedance spectroscopy. Two patterning methods are investigated for creating user-defined domain boundaries: the soft lithography method of contact printing and site-selective reductive desorption. The electrochemical properties of homogeneous contact printed monolayers are measured and compared to those of monolayers prepared by solution adsorption. The contact printed monolayers are found to have dramatically different impedance behavior from the solution prepared monolayers, consistent with the contact printed monolayers having greater defect density. In addition, these studies show that the overall defect density depends on the concentration of the solutions used for contact printing. In this work, simple patterns are created by contact printing a pattern onto the substrate and then backfilling the remaining gold substrate by solution adsorption. Backfilling with the same alkanethiol used to create the pattern generates a homogeneous monolayer; however, it is found that the contact printed/backfilled monolayer has an impedance intermediate between the homogeneous contact printed and the homogeneous solution adsorbed monolayer. This result suggests that the backfilling process also saturates the pinhole defects associated with the contact printed areas. In addition to exploring defects that arise from contact printing, simple patterns with user-defined defects, created by site-selective reductive desorption (SSRD), were also investigated. Following the backfill step, the impedance behavior of the SSRD produced patterns was similar to that of the impedance of the initial pattern before backfilling. This important result implies that the domain boundaries play the most important role in defining the overall impedance of the patterned interface. / Ph. D.