The epigenetic post-translational modifications (PTMs) of histone proteins are numerous and have an important role in regulating cellular development. Molecular recognition elements that can bind directly to epigenetic PTMs have previously been developed. The most synthetically accessible of these are a family of molecules called monoaryl-trisulfonate calix[4]arenes. The initial goal of this thesis was to develop research tools consisting of these asymmetrically-derivatized calixarenes immobilized onto a solid resin for the purpose of enrichment of PTM-bearing species. Seven novel resin-immobilized calixarene reagents were created and employed in batch-wise pulldown experiments, as well as chromatographic separations. These experiments produced mixed results: poor efficacy was demonstrated in batch-binding experiments but total separation of certain PTM bearing peptides was achieved in a chromatographic approach. During these studies, a subset of these calixarenes were found to undergo self-association in water in a fashion not previously observed for calixarenes. Secondary goals of the thesis were to create new examples of this self-associating motif, and to characterize and develop structure-function relationships for their assemblies. Eight new self-associating calixarenes were developed and characterized extensively by 1H NMR, isothermal titration calorimetry (ITC), and X-ray crystallography. Self-association was shown to be enthalpically driven with Kd values ranging from 1-20 mM. The dimeric assembly behaviours were remarkably consistent across many different family members, and were shown to persist even in highly competitive media like mock blood and urine. This system represents a novel class of ordered calixarenes assemblies that operate in biological media. / Graduate / 2016-12-23

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In this work, the synthesis and characterization of functionalized biosurfaces that can be used for bioseparations and bio-nanotechnology are reported. A novel protein purification technique that incorporates chelating ligands and polymers onto the same chromatographic matrix is explored. A polysaccharide based gel, agarose, was modified systematically with hybrid ligands of the chelator iminodiacetic acid (IDA) and the polymer polyethylene glycol (PEG). The PEG molecule acts as a blocking polymer that can allow only small proteins to permeate onto the matrix surfaces and form conventional immobilized metal ion affinity chromatographic (IMAC) interactions with the chelators. Kinetic studies of chelator and polymer attachment were performed in order to effectively control the chelator and polymer densities on the matrix. Studies with different PEG surface densities and their effects on the adsorption of several proteins (e.g. myoglobin, lysozyme and bovine serum albumin (BSA)) were evaluated to characterize these new hybrid size exclusion IMAC (SEIMAC) matrices. An exclusion effect was observed while adsorption as observed in IMAC systems took place.Functionalization schemes and procedures were extended in the activation and incorporation of affinity ligands on inorganic surfaces such as gold surfaces. Functional gold platforms were explored for development of nano-interconnects via functionalized self assembled monolayers (FSAMs) on gold to attach specific affinity ligands as linkers to immobilize biomolecules, such as microtubules (MTs). MTs eventually could be utilized as self assembling structures and templates for fabrication of nano-scale bio-interconnect arrays and networks. In this work, different organothiols were used to form FSAMs and anti-glutathione S-transferase was attached as a linker to utilize the attachment of MT cap proteins, gamma-tubulin. The gamma-tubulin could recognize specifically a heterodimer of the MTs and can provide a nucleation center for MT growth. Several methodologies were employed including photolithographic methods and the use of photoreactive compounds for proper micro/nano scale dual protein functionalization of surfaces with homogeneous affinity ligands and with heterogeneous ligands as well.

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The competition between two molecules of similar polarity for adsorption sites on the stationary phase is discussed in light of rapid kinetics of adsorption and desorption, and of the effects of temperature, acetonitrile, surfactant (cyclohexylaminopropane sulfonic acid, CAPS) and salt concentrations on the retention of the thyroid hormones (3,5-diiodothyronine, T2; 3,3',5-triiodothyronine, T3 and thyroxine, T4). A three parameter equation relates the surfactant concentration and ionic strength to the retention of the hormones and is analyzed in terms of the Stern-Gouy-Chapman theory. A second order polynomial describes the temperature dependency and permits the evaluation of the enthalpy, entropy and heat capacity, demonstrating a reduction in the molecular motion of the analyte with increasing surfactant and acetonitrile concentrations. The equation parameters for linear or non-linear equations, using data sets with or without homogeneous variances, are evaluated using a Simplex optimization procedure that uses one of two proposed optimization criteria. The construction and operation of a computer based gradient programmer for HPLC is described. A surfactant mediated gradient elution with electrochemical detection is examined for the analysis of serum thyroid hormones.

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Applications taking advantage of fluorine-fluorine interactions for separations are a recent analytical trend, with benefits in terms of cost, ease of use and specificity cited as advantages of these so-called “fluorous” techniques. While most current fluorous separations employ columns packed with microspheres, columns based on entrapped microspheres, porous polymer monoliths (PPMs) and open tubes all represent viable alternatives to conventional packed capillaries. In this thesis, the design, optimization and implementation of fluorous stationary phases based on all three of these new technologies are explored. Development of methods and techniques using these systems are presented, with factors affecting their performance being examined. Doing this, the specificity of the fluorous interaction can also be explored, and potential applications for these new materials can be discussed. For the work with entrapped microspheres, the columns that were formed did not prove to have an advantage over those that were unentrapped. Although affixing spheres within a matrix is known to have benefits in terms of bed stability over repeated use, the inclusion of a polymer coating proved to represent a greater concern for the availability of the bead-based stationary phases. Layers of polymer forming over the surface were shown to limit the access of analytes to the entrapped microspheres, restricting the usefulness of these materials. The work with fluorous monoliths proved the most successful, providing clear evidence of improved selectivity when compared to analogs made without fluorination. Fluorous retention specificity was also effectively examined, with secondary effects probed and compared to those that had been discussed for commercially-available fluorous microspheres. Results showed that the monoliths were very much in-line with what had already been seen for sphere-based systems, with residual substrate character providing only a slight contribution to the observed separations. Finally, development of open-tubular columns based on microstructured optical fibers was the most speculative of the projects discussed here. The introduction of a fluorous stationary phase through silanization was demonstrated to be an effective method for imparting chromatographic selectivity into these columns, and controllable factors such as treatment protocol and silane character were shown to affect the performance of the resulting materials. / Thesis (Ph.D, Chemistry) -- Queen's University, 2011-05-06 17:03:14.803