Glycans are macromolecules that contain several classes. Glycans can play an important role in biological activities. Studying the cell surface glycans can provide a very powerful way to understand the fundamental process. Also it could help to regulate expected cell response. Thus it is very necessary to have a method to detect cell- surface glycans efficiently. An efficient method for glycan detection is necessary. Metabolic glycan labeling and chemoenzymatic glycan labeling are most commonly used. Chemoenzymatic glycan labeling is a rapid and sensitive method which also has high specificity. This method can be applied in both vitro and vivo. However the availability of unnatural sugar nucleotides functioned by bioorthogonal groups is the main limitation for chemoenzymatic labeling. In this thesis, UDP-GlcNAc and UDP-GalNAc derivatives were prepared for further chemoenzymatic labeling by using chemoenzymatic synthesis method.

Cyanine dyes that absorb light in the near infrared to far red region of the electromagnetic spectrum are desirable as photosensitizers for photodynamic cancer therapy. Light of wavelengths in this range is able to deeply penetrate tissue allowing for practical in vivo use of these dyes. A series of three structurally similar pentamethine cyanine dyes that absorb light ~800 nm to ~500 nm was tested to determine the effects of structural influences on the yields of supercoiled DNA photo-converted to nicked or linear forms. Possible mechanisms and optimal parameters for near- quantitative DNA photocleavage with a symmetrical quinoline pentamethine cyanine dye are discussed.

Glycoscience is important in many areas such as human health, energy and material science. Glycans have been shown to be involved in the pathophysiology of almost every major disease. Additional glycan structure knowledge is required to help advance personal medicine, and pharmaceutical developments, among others. For glycoscience to advance there is a need for large quantities of well-defined glycans and have quick access to glycosyltransferases for manipulating glycan synthesis. Herein, we will cover our efforts on studying the substrate specificities of human glycosyltransferases such as FUT8 and Gn-T V, and their application on N-glycan synthesis. Complex asymmetric N-glycan isomer structures have been related to many diseases such as breast cancer, among others. Synthesis of complex asymmetric N-glycan isomer structures including: alpha-1,6 core-fucosylated, and tri-antennary structures can be achieved by taking advantage of the high specificity of glycosyltransferases that can work as unique catalyst to generate well-defined glycan structures.

Nile red and Nile blue are intensely colored fluorescent dyes from the benzophenoxazine family. Modification of the donor amine with varying alkyl substituents was achieved with the principle aim being to investigate differences, both optical and physical, between dye scaffolds outfitted with secondary amines versus tertiary amines. These changes to the dyes’ architectural framework gave holistic effects to the bulk molecule by modulating hydrophobicity, optical properties, and protein binding constants to human serum albumin.

N-linked glycosylation is the most common post-translational modification (PTM) of proteins that exist in nature. N-glycosylation and change in cells serve as a criterion to monitor the activity of developmental stages and diseases severity. Currently, there is an increasing application of mass spectrometry on glycoprotein for malicious, chronic or acute diseases, such as cancers, rheumatoid arthritis (RA) or influenza. In this dissertation, several mass spectrometric assays have been utilized to, quantitatively and qualitatively, characterize protein N-glycosylation at the glycan, glycopeptide and peptide levels. The goals are to identify serum-based RA biomarker (Chapter 2), or to determine possible glycan structures from monoclonal antibody (Chapter 3), or comprehensively to study one influenza glycoprotein, hemagglutinin (Chapter 4). In Chapter 2, LC-MS/MS with CID as MS 2 is the primary technique that is applied to collect raw data for RA biomarker screening; western blot is the verification method for newfound biomarkers. This mass spectrometry based comparative analysis of N-glycoprotein in RA and healthy patients’ sera reveal 41 potential biomarkers for RA that can be applied in clinical research. Chapter 3 describes another LC-MS/MS based method developed for the structural analysis of N-glycan released from the monoclonal antibody, immunoglobin G. Higher-energy collision dissociation (HCD) was the surprior technique utilized to identify glycopeptide fragments. The results show that 19 and 23 N-glycan structures were determined from standard and modified mAb samples respectively by using SimGlycan software, while 38 and 35 glycan structures were recognized by manually mapping respectively. 13 N-glycoforms, out of 26 overlapped glycan structures, were identified with significant alterations by comparing standard sample (sample A) and modified mAb (sample B) utilizing our method. In Chapter 4, we comprehensively studied hemagglutinin by using LC-MS/MS and MALDI from both proteomic perspective and glycomics prospective. After confirmed and verified protein sequence and glycosylation sites, galactose-specific quantitation was performed with exoglycosidase digestion combined HPLC with fluorescence detection. The MALDI-MS/MS based method was utilized to confirm glycan structures. The results in this dissertation provide insights into the significance of protein glycosylation alterations as RA biomarkers, and these quantitative methods can be reapplied to any other disease biomarkers screening for clinical researchers.

Capillary electrochromatography (CEC) is a major capillary electrophoresis (CE) mode that have been interfaced to mass spectrometry (MS) for sensitive and selective analysis of chiral compounds. This research expands CEC applications in cancer biomarker and chiral CE analysis. Chapter 1 is a review of liquid chromatography-mass spectrometry (LC/MS), gas chromatography-mass spectrometry (GC/MS), and capillary electrophoresis mass spectrometry (CE/MS) for analysis of metabolites in prostate cancer diagnostics and therapies. In this chapter, a literature survey was performed within the databases PubMed, 4 Caplus/Webline and Web of Sciences. A total 17 studies reporting on various analytical platforms for metabolite identification in prostate cancer research, which often include case-control comparison were identified and reviewed. Chapter 2 described the analysis of metabolite biomarkers in prostate cancer tissues by capillary electrochromatography mass spectrometry. In this chapter, a capillary CEC–MS/MS method was developed for the simultaneous determination and separation of eight proofs of concept (POC) metabolites (betaine, malate, proline, N-acetyl aspartate, N-acetylglucosamine, uracil, xanthine, and alanine) as potential prostate cancer diagnostic markers. A polymeric monolith column with a hydrophilic crosslinker and strong anion-exchange mixed-mode has been fabricated by an in situ copolymerization of vinyl benzyl trimethylammonium chloride, and bisphenol A glycerolate dimethacrylate (BisGMA) in the presence of methanol and dodecyl alcohol as porogens and AIBN as initiator. After CEC separation, samples were analyzed by a triple–quadrupole mass spectrometer operated in positive ion mode. After optimization, the data showed that the CEC-MS/MS method using monolithic column achieved a much better chromatographic selectivity compared to coated columns and increased sensitivity than bare fused silica column The effect of mobile phase pH, ACN percentage and additive were studies. Under the optimum mobile phase conditions, this method was carried out to separate and detect eight metabolites in the biopsy sample. The LOD for the metabolites is between 50nM-100nM. This method has successfully used to examine patients’ prostate cancer with an accuracy of 95%. Chapter 3 demonstrates Insights into Chiral Recognition Mechanisms in CEC using linear salvation energy relationship. By varying the linker (amide and carbamate), head group (alanine, leucine, and valine) and chain length (C8, C10 and C12) of the amino acid bound surfactants; monolithic column was made to ultimately understand the factors governing chiral stationary solid phase. Through the comparison of system parameters, we can see that surfactant head group, linker and chain length affect the separation of achiral and chiral compounds. Also, with the same type surfactant, data was presented to show how the trend of LSER parameters and how it affects separation between in CEC. This study showed the predictive capability of LSER to understand the aforementioned intermolecular processes controlling retention and by doing so, be able to quantitatively predict the experimental conditions to achieve an acceptable chiral separation.

The spatio-temporal attributes of intracellular calcium (Ca2+) transients activate various biological functions. These Ca2+ signaling events are triggered extracellularly through different stimuli and controlled intracellularly by the major Ca2+ storage organelle and by numerous Ca2+ pumps, channels, and Ca2+ binding proteins. Ca2+ transients can be significantly altered as a result of defects with signal modulation, leading to different diseases. Because of the fragility and intricacy of the Ca2+ signaling system, with the endo- and sarcoplasmic reticulum at the center, genetically-encoded Ca2+ probes that have been optimized for mammalian expression and fast kinetics are needed to observe global and local Ca2+ changes in different cells. Here, we first report the crystal structure determination of our genetically-encoded Ca2+ sensor CatchER which utilizes EGFP as the scaffold protein. Crystal structures of CatchER were resolved in the Ca2+-free, Ca2+-loaded, and gadolinium-loaded forms at 1.66, 1.20, and 1.78 Å, respectively. Analysis of all three structures established conformational changes in T203 and E222 produce the varying ratios of the neutral and anionic chromophore reflected in the absorbance spectrum where Ca2+ stabilizes the anionic chromophore and enhances the optical output. Since CatchER has miniscule fluorescence when expressed at 37˚C in mammalian cells, we enhanced its brightness by improving the folding at 37˚C, facilitating better chromophore formation. The resulting mutants are the CatchER-T series of Ca2+ sensors with CatchER-T’ having the most improvement in brightness at 37˚C. We also introduced the N149E mutation in the binding site to alter the Kd along with the brightness mutations. The resulting mutants were characterized and found to have weaker Kds compared to wild-type CatchER, similar quantum yields, and altered ratios of the neutral and anionic chromophore in the apo form. Then, CatchER-T’ was applied in situ to monitor Ca2+ changes globally in the ER/SR of C2C12, HEK293, and Cos-7 cells. A new construct consisting of CatchER-T’ and JP-45 was created to monitor local Ca2+ dynamics in the SR lumen of skeletal muscle cells. The results showed a difference between global and local SR Ca2+ release. We also examined the potential and spectroscopic properties to utilize some of our sensors in T cells to monitor the magnesium (Mg2+) flux in immune cells with faulty MagT1 receptors to understand the role of Mg2+ in the immune response.

Potassium ion channels play a key role in the generation and propagation of action potentials. The S4-S5 linker peptide (L45) is believed to be responsible for the anesthetic/alcohol response of voltage-gated K+ channels. We investigated this region to define the structural basis of 1-alkanol binding site in dShaw2 K+ channel. L45 peptides derived from dShaw2 and hKv3.4 K+ channel, which, if part of the complete channel, demonstrate different sensitivity to 1-alcohols. Specifically, dShaw2 is alcohol sensitive and hKv3.4 is alcohol resistant. Structural analysis of L45 with NMR and CD suggested a direct correlation between alpha-helicity and the inhibition of dShaw2 channel by 1-butanol. We used CD and NMR to determine the structure of L45 peptides in micelles and vesicles. We measured spin-lattice relaxation time (T1) and determined the location and surface accessibility of L45 in micelles. These experiments confirm that L45 of dShaw2 adopts an α-helical conformation, partially buried in the membrane and parallel to the surface. The binding and accumulation of rev proteins to an internal loop of RRE (rev responsive element) of unspliced mRNA precursors is a key step of propagation of human immunodeficiency (HIV) virus. Molecules that interfere with this process can be expected to show anti-HIV activity. Our work is based on an assumption that zinc fingers could compete with rev proteins, therefore impeding the life cycle of HIV and stopping its infection. We studied the influence of different cations, anions, and the concentration of salts and osmolytes on the binding affinity with Polyacrylamide Gel Electrophoresis (PAGE) and Isothermal Titration Calorimetry (ITC). We conclude that the types of anions and/or cations and their concentrations affect the enthalpy and entropy of the binding interacitons. Using a gel assay, we confirm that there are three products in RNA-Protein reaction, and both EDTA and salts (and their concentrations) in the gel or samples interfere with RNA-protein complex mobility.

Photodynamic therapy (PDT) is a cancer treatment method in which a photosensitizer, light of a particular wavelength, and also oxygen are used to destroy cancerous cells. Cancer cells absorb the photosensitizing agent which is injected into the body, and it is triggered to cause cell destruction upon absorption of light. This occurs because of the excitation of the photosensitizer produces reactive oxygen species that induce a cascade of cellular and molecular events in the body. Photosensitizing agents that can photo-cleave DNA at long wavelengths are highly demanded in PDT, because the long wavelengths of light can penetrate through tissue deeply compared to visible light. While most of the photosensitizers are activated at wavelengths less than 690 nm, penetration of light continues to increase at increasing wavelengths. In this thesis, photosensitizers that can be activated to oxidize DNA with long wavelengths of light will be discussed. Using quinoline cyanine dyes, here we report the first example of DNA photocleavage at a wavelength of light above 800 nm.

Six polyamine anthracene conjugates (Ants) were studied that take advantage of the polyamine transporter system (PTS) to target specific cancer. The structural features of the Ants involve planar aromatic anthracene that has highly cytotoxicity properties and a polyamine chain similar to natural polyamine, which is taken up by eukaryote cells expressing the PTS actively. Experimental data show that Ants with di-substituted polyamine chains have significantly higher DNA binding affinities than the mono-substituted anthracene conjugates. The high ionic conditions (~150 mM NaCl and 260 mM KCl) in the eukaryote cell nucleus extensively impair the apparent DNA binding of the Ants, but may further reinforce DNA structural stability. Combining the published cytotoxicity of the PTS data with the DNA interaction data reported here, the di-substituted polyamine anthracene conjugates have the highest potential to, after cellular uptake via PTS, bind to DNA.