Matching Items (28)
Description
The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino acid in response to one codon. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome enabled the incorporation of both alpha-D-amino acids and beta-amino acids into full length protein. Described in Chapter 2 are five modified ribosomes having modifications in the peptidyltrasnferase center in the 23S rRNA. These modified ribosomes successfully incorporated five different beta-amino acids (2.1 - 2.5) into E. coli dihydrofolate reductase (DHFR). The second project (Chapter 3) focused on the study of the modified ribosomes facilitating the incorporation of the dipeptide glycylphenylalanine (3.25) and fluorescent dipeptidomimetic 3.26 into DHFR. These ribosomes also had modifications in the peptidyltransferase center in the 23S rRNA of the 50S ribosomal subunit. The modified DHFRs having beta-amino acids 2.3 and 2.5, dipeptide glycylphenylalanine (3.25) and dipeptidomimetic 3.26 were successfully characterized by the MALDI-MS analysis of the peptide fragments produced by "in-gel" trypsin digestion of the modified proteins. The fluorescent spectra of the dipeptidomimetic 3.26 and modified DHFR having fluorescent dipeptidomimetic 3.26 were also measured. The type I and II DNA topoisomerases have been firmly established as effective molecular targets for many antitumor drugs. A "classical" topoisomerase I or II poison acts by misaligning the free hydroxyl group of the sugar moiety of DNA and preventing the reverse transesterfication reaction to religate DNA. There have been only two classes of compounds, saintopin and topopyrones, reported as dual topoisomerase I and II poisons. Chapter 4 describes the synthesis and biological evaluation of topopyrones. Compound 4.10, employed at 20 µM, was as efficient as 0.5 uM camptothecin, a potent topoisomerase I poison, in stabilizing the covalent binary complex (~30%). When compared with a known topoisomerase II poison, etoposide (at 0.5 uM), topopyorone 4.10 produced similar levels of stabilized DNA-enzyme binary complex (~34%) at 5 uM concentration.
ContributorsMaini, Rumit (Author) / Hecht, Sidney M. (Thesis advisor) / Gould, Ian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Photosynthesis, one of the most important processes in nature, has provided an energy basis for nearly all life on Earth, as well as the fossil fuels we use today to power modern society. This research aims to mimic the photosynthetic process of converting incident solar energy into chemical potential energy in the form of a fuel via systems capable of carrying out photo-induced electron transfer to drive the production of hydrogen from water. Herein is detailed progress in using photo-induced stepwise electron transfer to drive the oxidation of water and reduction of protons to hydrogen. In the design, use of more blue absorbing porphyrin dyes to generate high-potential intermediates for oxidizing water and more red absorbing phthalocyanine dyes for forming the low potential charge needed for the production of hydrogen have been utilized. For investigating water oxidation at the photoanode, high potential porphyrins such as, bis-pyridyl porphyrins and pentafluorophenyl porphyrins have been synthesized and experiments have aimed at the co-immobilization of this dye with an IrO2-nH2O catalyst on TiO2. To drive the cathodic reaction of the water splitting photoelectrochemical cell, utilization of silicon octabutoxy-phthalocyanines have been explored, as they offer good absorption in the red to near infrared, coupled with low potential photo-excited states. Axially and peripherally substituted phthalocyanines bearing carboxylic anchoring groups for the immobilization on semiconductors such as TiO2 has been investigated. Ultimately, this work should culminate in a photoelectrochemical cell capable of splitting water to oxygen and hydrogen with the only energy input from light. A series of perylene dyes bearing multiple semi-conducting metal oxide anchoring groups have been synthesized and studied. Results have shown interfacial electron transfer between these perylenes and TiO2 nanoparticles encapsulated within reverse micelles and naked nanoparticles. The binding process was followed by monitoring the hypsochromic shift of the dye absorption spectra over time. Photoinduced electron transfer from the singlet excited state of the perylenes to the TiO2 conduction band is indicated by emission quenching of the TiO2-bound form of the dyes and confirmed by transient absorption measurements of the radical cation of the dyes and free carriers (injected electrons) in the TiO2.
ContributorsBergkamp, Jesse J (Author) / Moore, Ana L (Thesis advisor) / Mariño-Ochoa, Ernesto (Thesis advisor) / Gust, Devens J (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2013
Description
The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using orthogonal aminoacyl-tRNA synthetase/tRNA pairs in conjunction with nonsense, rare, or 4-bp codons. There has been considerable progress in developing new types of amino acids, in identifying novel methods of tRNA aminoacylation, and in expanding the genetic code to direct their position. Chemical aminoacylation of tRNAs is accomplished by acylation and ligation of a dinucleotide (pdCpA) to the 3'-terminus of truncated tRNA. This strategy allows the incorporation of a wide range of natural and unnatural amino acids into pre-determined sites, thereby facilitating the study of structure-function relationships in proteins and allowing the investigation of their biological, biochemical and biophysical properties. Described in Chapter 1 is the current methodology for synthesizing aminoacylated suppressor tRNAs. Aminoacylated suppressor tRNACUAs are typically prepared by linking pre-aminoacylated dinucleotides (aminoacyl-pdCpAs) to 74 nucleotide (nt) truncated tRNAs (tRNA-COH) via a T4 RNA ligase mediated reaction. Alternatively, there is another route outlined in Chapter 1 that utilizes a different pre-aminoacylated dinucleotide, AppA. This dinucleotide has been shown to be a suitable substrate for T4 RNA ligase mediated coupling with abbreviated tRNA-COHs for production of 76 nt aminoacyl-tRNACUAs. The synthesized suppressor tRNAs have been shown to participate in protein synthesis in vitro, in an S30 (E. coli) coupled transcription-translation system in which there is a UAG codon in the mRNA at the position corresponding to Val10. Chapter 2 describes the synthesis of two non-proteinogenic amino acids, L-thiothreonine and L-allo-thiothreonine, and their incorporation into predetermined positions of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine. Here, the elaborated proteins were site-specifically derivitized with a fluorophore at the thiothreonine residue. The synthesis and incorporation of phosphorotyrosine derivatives into DHFR is illustrated in Chapter 3. Three different phosphorylated tyrosine derivatives were prepared: bis-nitrobenzylphosphoro-L-tyrosine, nitrobenzylphosphoro-L-tyrosine, and phosphoro-L-tyrosine. Their ability to participate in a protein synthesis system was also evaluated.
ContributorsNangreave, Ryan Christopher (Author) / Hecht, Sidney M. (Thesis advisor) / Yan, Hao (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2013
Description
Mitochondria produce most of the ATP needed for the cell as an energy source. It is well known that cellular respiration results in oxidative damage to the cell due to the production of reactive oxygen species (ROS). Mitochondrial dysfunction is believed to contribute to a number of degenerative diseases; because of this the mitochondrial respiratory chain is considered as potential drug target. A few series of idebenone analogues with quinone, pyridinol and pyrimidinol redox cores have been synthesized and evaluated as antioxidants able to protect cellular integrity and, more specifically, mitochondrial function. The compounds exhibited a range of activities. The activities observed were used for the design of analogues with enhanced properties as antioxidants. Compounds were identified which provide better protection against oxidative stress than idebenone, and it is thought that they do so catalytically.
ContributorsArce Amezquita, Pablo M (Author) / Hecht, Sidney M. (Thesis advisor) / Moore, Ana (Committee member) / Rose, Seth (Committee member) / Arizona State University (Publisher)
Created2012
Description
Solar energy is a promising alternative for addressing the world's current and future energy requirements in a sustainable way. Because solar irradiation is intermittent, it is necessary to store this energy in the form of a fuel so it can be used when required. The light-driven splitting of water into oxygen and hydrogen (a useful chemical fuel) is a fascinating theoretical and experimental challenge that is worth pursuing because the advance of the knowledge that it implies and the availability of water and sunlight. Inspired by natural photosynthesis and building on previous work from our laboratory, this dissertation focuses on the development of water-splitting dye-sensitized photoelectrochemical tandem cells (WSDSPETCs). The design, synthesis, and characterization of high-potential porphyrins and metal-free phthalocyanines with phosphonic anchoring groups are reported. Photocurrents measured for WSDSPETCs made with some of these dyes co-adsorbed with molecular or colloidal catalysts on TiO2 electrodes are reported as well. To guide in the design of new molecules we have used computational quantum chemistry extensively. Linear correlations between calculated frontier molecular orbital energies and redox potentials were built and tested at multiple levels of theory (from semi-empirical methods to density functional theory). Strong correlations (with r2 values > 0.99) with very good predictive abilities (rmsd < 50 mV) were found when using density functional theory (DFT) combined with a continuum solvent model. DFT was also used to aid in the elucidation of the mechanism of the thermal relaxation observed for the charge-separated state of a molecular triad that mimics the photo-induced proton coupled electron transfer of the tyrosine-histidine redox relay in the reaction center of Photosystem II. It was found that the inclusion of explicit solvent molecules, hydrogen bonded to specific sites within the molecular triad, was essential to explain the observed thermal relaxation. These results are relevant for both advancing the knowledge about natural photosynthesis and for the future design of new molecules for WSDSPETCs.
ContributorsMéndez-Hernández, Dalvin D (Author) / Moore, Ana L (Thesis advisor) / Mujica, Vladimiro (Thesis advisor) / Gust, Devens J. (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Natural photosynthesis dedicates specific proteins to achieve the modular division of the essential roles of solar energy harvesting, charge separation and carrier transport within natural photosynthesis. The modern understanding of the fundamental photochemistry by which natural photosynthesis operates is well advanced and solution state mimics of the key photochemical processes have been reported previously. All of the early events in natural photosynthesis responsible for the conversion of solar energy to electric potential energy occur within proteins and phospholipid membranes that act as scaffolds for arranging the active chromophores. Accordingly, for creating artificial photovoltaic (PV) systems, scaffolds are required to imbue structure to the systems. An approach to incorporating modular design into solid-state organic mimics of the natural system is presented together with how conductive scaffolds can be utilized in organic PV systems. To support the chromophore arrays present within this design and to extract separated charges from within the structure, linear pyrazine-containing molecular ribbons were chosen as candidates for forming conductive linear scaffolds that could be functionalized orthogonally to the linear axis. A series of donor-wire-acceptor (D-W-A) compounds employing porphyrins as the donors and a C60 fullerene adduct as the acceptors have been synthesized for studying the ability of the pyrazine-containing hetero-aromatic wires to mediate photoinduced electron transfer between the porphyrin donor and fullerene acceptor. Appropriate substitutions were made and the necessary model compounds useful for dissecting the complex photochemistry that the series is expected to display were also synthesized. A dye was synthesized using a pyrazine-containing heteroaromatic spacer that features two porphyrin chromophores. The dye dramatically outperforms the control dye featuring the same porphyrin and a simple benzoic acid linker. A novel, highly soluble 6+kDa extended phthalocyanine was also synthesized and exhibits absorption out to 900nm. The extensive functionalization of the extended phthalocyanine core with dodecyl groups enabled purification and characterization of an otherwise insoluble entity. Finally, in the interest of incorporating modular design into plastic solar cells, a series of porphyrin-containing monomers have been synthesized that are intended to form dyadic and triadic molecular-heterojunction polymers with dedicated hole and electron transport pathways during electrochemical polymerization.
ContributorsWatson, Brian Lyndon (Author) / Gust, Devens (Thesis advisor) / Gould, Ian (Committee member) / Moore, Ana L (Committee member) / Arizona State University (Publisher)
Created2013
Description
The bleomycins are a family of glycopeptide-derived antibiotics isolated from various Streptomyces species and have been the subject of much attention from the scientific community as a consequence of their antitumor activity. Bleomycin clinically and is an integral part of a number of combination chemotherapy regimens. It has previously been shown that bleomycin has the ability to selectively target tumor cells over their non-malignant counterparts. Pyrimidoblamic acid, the N-terminal metal ion binding domain of bleomycin is known to be the moiety that is responsible for O2 activation and the subsequent chemistry leading to DNA strand scission and overall antitumor activity. Chapter 1 describes bleomycin and related DNA targeting antitumor agents as well as the specific structural domains of bleomycin. Various structural analogues of pyrimidoblamic acid were synthesized and subsequently incorporated into their corresponding full deglycoBLM A6 derivatives by utilizing a solid support. Their activity was measured using a pSP64 DNA plasmid relaxation assay and is summarized in Chapter 2. The specifics of bleomycin—DNA interaction and kinetics were studied via surface plasmon resonance and are presented in Chapter 3. By utilizing carefully selected 64-nucleotide DNA hairpins with variable 16-mer regions whose sequences showed strong binding in past selection studies, a kinetic profile was obtained for several BLMs for the first time since bleomycin was discovered in 1966. The disaccharide moiety of bleomycin has been previously shown to be a specific tumor cell targeting element comprised of L-gulose-D-mannose, especially between MCF-7 (breast cancer cells) and MCF-10A ("normal" breast cells). This phenomenon was further investigated via fluorescence microscopy using multiple cancerous cell lines with matched "normal" counterparts and is fully described in Chapter 4.
ContributorsBozeman, Trevor C (Author) / Hecht, Sidney M. (Thesis advisor) / Chaput, John (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2013
Description
Reactive oxygen species (ROS) are a series of molecules, ions, and radicals derived from oxygen that possess remarkable reactivity. They act as signaling molecules when their concentration in cells is within a normal range. When the levels of ROS increase, reaching a concentration in which the antioxidants cannot readily quench them, oxidative stress will affect the cells. These excessive levels of ROS result in direct or indirect ROS-mediated damage of proteins, nucleic acids, and lipids. Excessive oxidative stress, particularly in chronic inflammation, has been linked with mutations and carcinogenesis. One of the main targets of ROS in severe oxidative stress is mitochondrial DNA (mtDNA). The synthesis of analogues of alpha-tocopherol is described as potential compounds with the ability to remediate defective mitochondria. An interesting possibility for eradicating cancer cells is to selectively target them with oxidative species while avoiding any deleterious effects on healthy cells. To accomplish this, analogues of the beta-hydroxyhistidine moiety of the antitumor agent bleomycin (BLM) were synthesized. The first part of this thesis focuses on the synthesis of simplified analogues of alpha-tocopherol. These analogues possess a bicyclic pyridinol as the antioxidant core and an alkyl group as the lipophilic chain to mimic alpha-tocopherol. Additionally, analogues with a completely oxidized pyridinol core were synthesized. Some of these analogues showed promising properties against ROS production and lipid peroxidation. The protection they conferred was shown to be tightly regulated by their concentration. The second part of this thesis focuses on the synthesis of analogues of beta-hydroxyhistidine. BLMs are glycopeptides that possess anticancer activity and have been used to treat testicular carcinomas, Hodgkin's lymphoma, and squamous cell carcinomas. The activity of BLM is based on the degradation of DNA, or possibly RNA, caused by a Fe(II)-BLM complex in the presence of O2. The beta-hydroxyhistidine moiety of BLM contributes to metal coordination via two ligands: the N-3 nitrogen atom of imidazole and possibly the nitrogen atom of the amide. A series of beta-hydroxyhistidine analogues has successfully been synthesized.
ContributorsArmendáriz Guajardo, José Israel (Author) / Hecht, Sidney M. (Thesis advisor) / Moore, Ana (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
The first chapter reviews three decades of artificial photosynthetic research conducted by the A. Moore, T. Moore, and D. Gust research group. Several carotenoid (Car) and tetrapyrrole containing molecules were synthesized and investigated for excitation energy transfer (EET), photoregulation, and photoprotective functions. These artificial photosynthetic compounds mimicked known processes and investigated proposed mechanisms in natural systems. This research leads to a greater understanding of photosynthesis and design concepts for organic based solar energy conversion devices. The second and third chapters analyze the triplet energy transfer in carotenoid containing dyads. Transient absorption, time-resolved FTIR and resonance Raman spectra revealed that in a 4-amide linked carotenophthalocyanine dyads the Car triplet state is shared across the larger conjugated system, which is similar to protein complexes in oxygenic photosynthetic organisms. In a carotenopurpurin dyad (CarPur) a methylene ester covalent bond prevents the purpurin (Pur) from influencing the Car triplet based on the transient absorption, time-resolved FTIR and resonance Raman spectra. Thus CarPur resembles the antenna proteins from anoxygenic photosynthetic bacteria. Additional examples of carotenoporphyrin dyads further demonstrates the need for orbital overlap for ultrafast triplet energy transfer and the formations of possible intramolecular charge transfer state. The fourth chapter studies a 4-amino phenyl carotenophthalocyanine and its model compounds using high temporal resolution transient absorption spectroscopy techniques. EET from the Car second excited (S2) state to the phthalocyanine (Pc) was determined to be 37% and a coupled hot ground state (S*)/Pc excited state spectrum was observed. Excitation of the tetrapyrrole portion of the dyad did not yield any kinetic differences, but there was an S* signal during the excited states of the dyad. This demonstrates the EET and photoregulating properties of this artificial photosynthetic compound are similar to those of natural photosynthesis. The last chapter covers the synthesis of silicon Pc (SiPc) dyes and the methods for attaching them to gold nanoparticles and flat gold surfaces. SiPc attached to patterned gold surfaces had unperturbed fluorescence, however the selectivity for the gold was low, so alternative materials are under investigation to improve the dye's selectivity for the gold surface.
ContributorsWongCarter, Katherine (Author) / Moore, Ana L (Thesis advisor) / Gust, Devens (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Small molecules have proven to be very important tools for exploration of biological systems including diagnosis and treatment of lethal diseases like cancer. Fluorescent probes have been extensively used to further amplify the utilization of small molecules. The manipulation of naturally occurring biological targets with the help of synthetic compounds is the focus of the work described in this thesis.
Bleomycins (BLMs) are a class of water soluble, glycopeptide-derived antitumor antibiotics consisting of a structurally complicated unnatural hexapeptide and a disaccharide, clinically used as an anticancer chemotherapeutic agent at an exceptionally low therapeutic dose. The efficiency of BLM is likely achieved both by selective localization within tumor cells and selective binding to DNA followed by efficient double-strand cleavage. The disaccharide moiety is responsible for the tumor cell targeting properties of BLM. A recent study showed that both BLM and its disaccharide, conjugated to the cyanine dye Cy5**, bound selectively to cancer cells. Thus, the disaccharide moiety alone recapitulates the tumor cell targeting properties of BLM. Work presented here describes the synthesis of the fluorescent carbohydrate conjugates. A number of dye-labeled modified disaccharides and monosaccharides were synthesized to study the nature of the participation of the carbamoyl moiety in the mechanism of tumor cell recognition and uptake by BLM saccharides. It was demonstrated that the carbamoylmannose moiety of BLM is the smallest structural entity capable for the cellular targeting and internalization, and the carbamoyl functionality is indispensible for tumor cell targeting. It was also confirmed that BLM is a modular molecule, composed of a tumor cell targeting moiety (the saccharide) attached to a cytotoxic DNA cleaving domain (the BLM aglycone). These finding encouraged us to further synthesize carbohydrate probes for PET imaging and to conjugate the saccharide moiety with cytotoxins for targeted delivery to tumor cells.
The misacylated suppressor tRNA technique has enabled the site-specific incorporation of noncanonical amino acids into proteins. The focus of the present work was the synthesis of unnatural lysine analogues with nucleophilic properties for incorporation at position 72 of the lyase domain of human DNA polymerase beta, a multifunctional enzyme with dRP lyase and polymerase activity.
Bleomycins (BLMs) are a class of water soluble, glycopeptide-derived antitumor antibiotics consisting of a structurally complicated unnatural hexapeptide and a disaccharide, clinically used as an anticancer chemotherapeutic agent at an exceptionally low therapeutic dose. The efficiency of BLM is likely achieved both by selective localization within tumor cells and selective binding to DNA followed by efficient double-strand cleavage. The disaccharide moiety is responsible for the tumor cell targeting properties of BLM. A recent study showed that both BLM and its disaccharide, conjugated to the cyanine dye Cy5**, bound selectively to cancer cells. Thus, the disaccharide moiety alone recapitulates the tumor cell targeting properties of BLM. Work presented here describes the synthesis of the fluorescent carbohydrate conjugates. A number of dye-labeled modified disaccharides and monosaccharides were synthesized to study the nature of the participation of the carbamoyl moiety in the mechanism of tumor cell recognition and uptake by BLM saccharides. It was demonstrated that the carbamoylmannose moiety of BLM is the smallest structural entity capable for the cellular targeting and internalization, and the carbamoyl functionality is indispensible for tumor cell targeting. It was also confirmed that BLM is a modular molecule, composed of a tumor cell targeting moiety (the saccharide) attached to a cytotoxic DNA cleaving domain (the BLM aglycone). These finding encouraged us to further synthesize carbohydrate probes for PET imaging and to conjugate the saccharide moiety with cytotoxins for targeted delivery to tumor cells.
The misacylated suppressor tRNA technique has enabled the site-specific incorporation of noncanonical amino acids into proteins. The focus of the present work was the synthesis of unnatural lysine analogues with nucleophilic properties for incorporation at position 72 of the lyase domain of human DNA polymerase beta, a multifunctional enzyme with dRP lyase and polymerase activity.
ContributorsBhattacharya, Chandrabali (Author) / Hecht, Sidney M. (Thesis advisor) / Moore, Ana (Committee member) / Gould, Ian R (Committee member) / Arizona State University (Publisher)
Created2014