ABSTRACT Carbohydrates in various forms play vital roles in numerous critical biological processes including cell-cell adhesion and communication, embryo development, immune response, etc. Fluorescent sensors for such carbohydrates have a wide range of potential applications including glucose concentration determination, cell labeling and targeting based on carbohydrate biomarkers, as in vitro diagnostic tools, and biomarker-directed cellular imaging. Our group has been interested in the design and synthesis of multi-boronic acid compounds with well-defined three-dimensional scaffolding for the specific recognition of selected carbohydrate biomarkers. Aberrant expression of carbohydrate antigens such as sialyl Lewis X (sLex), sialyl Lewis A (sLea), Lewis X (Lex), and Lewis Y (Ley) have been associated with tumor formation and metastasis in various cancer types.1-4 As such, for our initial design, we have selected sialyl Lewis X (sLex) as our potential target due to implication in the development of liver and colon cancer.5, 6 Herein, we describe the design, synthesis and evaluation of four such compounds, each having about ten linear steps in its synthesis. In addition to the design of fluorescent probes for cell surface carbohydrates, we also have designed lipophilic boronic acid derivatives as potential fusogenic agents. Due to boronic acid¡¯s ability to bind to 1,2 and 1,3 cis diols, we hypothesize that the aliphatic chain should be able to insert into lipid cellular membrane and the boronic acid units should allow for the ¡°attachment to neighboring cells¡± through complexation with cell surface glycans. Such interactions should allow the boronic acid compounds to bring two or more cells together for fusion. Herein, we have described the methodologies of the design of such compounds. INDEX WORDS: Boronic acid, sialyl Lewis X probe, boronolectin, fluorescence, sensor, cell-cell fusion, fusogen, immunotherapy.

Atomic force microscope (AFM) is an invaluable tool for measurement of pico-Newton to nano-Newton levels of interaction forces in liquid. As such, it is widely used to measure single-molecular interaction forces through dynamic force spectroscopy. In this technique, the interaction force spectra between a specimen on the sharp tip of the cantilever and another specimen on the substrate is measured by repeatedly moving the cantilever in and out of contact with the substrate. By varying the loading rate and measuring the bond rupture force or bond lifetime give researchers information about the strength and dissociation rates of non-covalent bonds, which in turn determines the energy barriers to overcome. Commercially available cantilevers can resolve interaction forces as low as 5 pN with 1 kHz bandwidth in fluid. This resolution can be improved to 1 pN by using smaller cantilevers at the expense of microfabrication constraints and sophisticated detection systems. The pulling speed of the cantilever, which determines the loading rate of the bonds, is limited to the point where the hydrodynamic drag force becomes comparable to the level of the molecular interaction force. This level is around 10 um/s for most cantilevers while higher pulling speeds are required for complete understanding of force spectra. Thus, novel actuators that allow higher loading rates with minimal hydrodynamic drag forces on the cantilevers, and fast, sensitive force sensors with simple detection systems are highly desirable. This dissertation presents the research efforts for the development of membrane-based active probe structures with electrostatic actuation and integrated diffraction-based optical interferometric force detection for single-molecular force measurements. Design, microfabrication and characterization of the probes are explained in detail. A setup including optics and electronics for experimental characterization and biological experiments with the probes membranes is also presented. Finally, biological experiments are included in this dissertation. The "active" nature of the probe is because of the integrated, parallel-plate type electrostatic actuator. The actuation range of the membrane is controlled with the gap height between the membrane and the substrate. Within this range it is possible to actuate the membrane fast, with a speed limited by the membrane dynamics with negligible hydrodynamic drag. Actuating these membrane probes and using a cantilever coupled to the membrane, fast pulling experiments with an order of magnitude faster than achieved by regular AFM systems are demonstrated. The displacement noise spectral density for the probe was measured to be below 10 fm/rtHz for frequencies as low as 3 Hz with differential readout scheme. This noise floor provides a force sensitivity of 0.3 - 3 pN with 1 kHz bandwidth using membranes with spring constants of 1 - 10 N/m. This low inherent noise has a potential to probe wide range of biomolecules. The probes have been demonstrated for fast-pulling and high-resolution force sensing. Feasibility for high throughput parallel operation has been explored. Unique capabilities of the probes such as electrostatic spring constant tuning and thermal drift cancellation in AFM are also presented in this dissertation.

Thesis (Ph. D.)--University of Kentucky, 2003. / Title from document title page (viewed June 30, 2004). Document formatted into pages; contains xv, 150 p. : ill. Includes abstract and vita. Includes bibliographical references (p. 140-148).

Over the past two decades, the field of molecular sensing has developed into a mature offshoot of molecular recognition, and sensing protocols based on optical signal modulations have enjoyed particularly great success. Such sensing methods are the focus of this dissertation, in which efforts toward the integration of dendrimers and reactands into separate, optically-based sensing platforms are described. To this end, Chapter 1 provides a brief introduction to molecular sensing and its supramolecular underpinnings. The remainder of Chapter 1 is dedicated to dendrimers and their application to molecular recognition and sensing. A discussion of the physicochemical properties of dendrimers is also included to lend perspective on the structure, size, and shape of these macromolecules. The role of dyes and indicators in the elucidation of dendritic structure and function is given special consideration. Finally, selected reports of dendrimers in molecular recognition and optical sensing are summarized. Chapter 2 details original research directed toward the incorporation of dendrimers into molecular sensing ensembles. This use of dendrimers in molecular recognition and sensing is distinguished from those examples described in Chapter 1 by its modular nature. This modularity is achieved through the use of a non-covalent sensing motif based on indicator displacement. The identification and optimization of the appropriate components for use in such dendrimer-based sensing ensembles represents a contribution of the research described herein. An evaluation of indicator dyes for their incorporation into an enantioselective indicator displacement assay (eIDA) for common organic molecules is the subject of the research discussed in Chapter 3. The selected indicator dyes were assessed for use in a novel eIDA that relies on covalent bond formation for the enantioselective signaling of monofunctional organic analytes. A survey of colorimetric methods for the identification and discrimination of amines is included because these compounds served as an initial target in the proposed assay. Optical enantiosensing strategies are also reviewed in light of their relevance to the present work. / text

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Molecular recognition is a major branch of modern organic chemistry, and it resides at the forefront of supramolecular chemistry. Supramolecular chemistry refers to the study of the noncovalent intermolecular interaction that are crucial for biological processes, catalytic systems, the organization of crystalline or solution phase superstructures, and molecular recognition to name a few examples. The following dissertation reports research efforts from the Anslyn group into three topics of fundamental interest to the molecular recognition community: cooperativity, array sensing, and the development of highly selective sensors for minimally functionalized analytes. Chapter 1 is a review of the most fundamental points of molecular recognition as it applies to the experimental work that follows. Intermolecular association phenomena are driven by multiple discrete, noncovalent interactions, and cooperativity is a measure of the efficiency with which these interactions are employed in a given system. Cooperativity is poorly understood despite its ubiquity in biological and molecular recognition contexts. The first synthetic hostguest system exhibiting positive cooperativity in water is reported in Chapter 2. The utility of sensitive but unselective sensors when applied in an array format has recently come to light. Chapter 3 details an array of polyaromatic fluorophores dissolved in an aqueous surfactant solution that was used to sense nitrated explosives. This exceptionally unselective quenching process was able to detect and discriminate nitrated explosives such as RDX and TNT at concentrations as low as 19 [mu]M. Finally, Chapters 4 and 5 report different approaches to the sensing of enantiomeric excess in [alpha]-chiral alcohols using an indicator displacement paradigm. Chapter 4 explores unprecedented efforts to convert the Sharpless catalytic epoxidation system to the first Ti[superscript IV]-based molecular recognition system. Chapter 5 focuses upon a two-stage approach of derivatization of the [alpha]-chiral alcohol to a metal chelating ligand followed by employment of the derivative in an indicator displacement assay. / text

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A series of studies from our lab have investigated the threading polyintercalator approach to sequence specific DNA binding using a 1,4,5,8-naphthalene tetracarboxylic diimide (NDI) intercalating unit connected by flexible peptide linkers. Herein is a report of the sequence specificity, as well as a detailed kinetic analysis, of a threading NDI tetraintercalator. DNase I footprinting using two ~500 base pair DNA fragments containing one designed binding site for the tetraintercalator confirmed highly sequence specific binding. Kinetic analyses include 1H NMR, gel mobility-shift assays, and stopped-flow UV measurements to reveal a polyintercalation binding mode that demonstrates significant similarities between association rate profiles and rate constants for the tetraintercalator binding to its preferred versus a random oligonucleotide sequence. Sequence specificity was found to derive almost entirely from large differences in dissociation rates from the preferred versus random oligonucleotide sequences. Interestingly, the dissociation rate constant of the tetraintercalator complex dissociating from its preferred binding site was extremely slow, corresponding to a 16 day half-life at a benchmark 100 mM [Na+]. This dissociation result for the tetraintercalator is one of the longest bound half-lives yet measured, and to the best of our knowledge, the longest for a DNA binding small molecule. Such a long-lived complex raises the possibility of using threading polyintercalators to disrupt biological processes for extended periods. Current focus is given to deciphering a mechanism for the molecular recognition of the tetraintercalator preferred binding site within a long sequence of DNA. Initial DNase I footprinting results on an approximate 500mer DNA sequence containing three sequential preferred binding sites reveal that the tetraintercalator likely locates its designed binding site by a macro- or microscopic dissociation/re-association type of mechanism. Cooperativity is a possible ally to binding, leaving future studies to distinguish the mechanism for molecular recognition in a manner that is capable of circumventing cooperative binding. Taken together, the threading polyintercalation binding mode presents an interesting topology to sequence specific DNA binding. Extraordinarily long dissociation rates from preferred binding sites offers many future possibilities to disrupt biological processes in vivo. / text

La unión de las propiedades de los CNT con los principios de reconocimiento molecular se presenta como una base adecuada para el desarrollo de sensores altamente específicos. El objetivo de la presente tesis ha sido desarrollar sensores químicos, del tipo transistores de efecto campo (CNTFET), basados en interacciones receptor-analito, mediante el empleo de los nanotubos de pared sencilla (SWCNT), que actúan como transductores de la señal analítica.Las principales etapas de la parte experimental han sido: Crecimiento de SWCNT con la técnica de deposición química en fase vapor. Integración de los SWCNTs en sistemas CNTFET. Empleo del CNTFET como base del sensor en distintos campos utilizando modelos de reconocimiento molecular. Dependiendo del tipo de funcionalización de los SWCNTs se pueden obtener sensores para proteínas, iones, etc. Como resultado, se han desarrollado y estudiado sensores basados en CNTFETs para la detección distintos analitos de interés, como son la Inmunoglobulina G Humana, los iones potasio y el dióxido de azufre. / The general objective of this thesis is to develop chemical sensors whose sensing capacities are based on the principle of molecular recognition and where the transduction is carried out by single-walled carbon nanotubes (SWCNT).The sensing device used is the carbon nanotube field-effect transistor (CNTFET). The new structure of the CNTFET allows nanotubes to be integrated at the surface of the devices, thus exploiting SWCNTs' sensitivity to changes in their environment. The functionalization of SWCNTs with several types of molecular receptors such as antibodies, ion selective membranes, and synthetic receptors, achieve a high selectivity towards the analyte of interest. This thesis shows that CNTFETs can be used for the successful selective detection of different types of target analytes. These can be biomolecules such as antigens, small compounds such as cations or gas-phase compounds such as SO2.