Matching Items (56)
Description
Biomolecules can easily recognize its corresponding partner and get bound to it, resulting in controlling various processes (immune system, inter or intracellular signaling) in biology and physiology. Bonding between two partners can be a result of electrostatic, hydrophobic interactions or shape complementarity. It is of great importance to study these kinds of biomolecular interactions to have a detailed knowledge of above mentioned physiological processes. These studies can also open avenues for other aspects of science such as drug development. Discussed in the first part of Chapter 1 are the biotin-streptavidin biomolecular interaction studies by atomic force microscopy (AFM) and surface plasmon resonance (SPR) instrument. Also, the basic working principle of AFM and SPR has been discussed.
The second part of Chapter 1 is discussed about site-specific chemical modification of peptides and proteins. Proteins have been used to generate therapeutic materials, proteins-based biomaterials. To achieve all these properties in protein there is a need for site-specific protein modification.
To be able to successfully monitor biomolecular interaction using AFM there is a need for organic linker molecule which helps one of the investigating molecules to get attached to the AFM tip. Most of the linker molecules available are capable of investigating one type of interaction at a time. Therefore, it is significant to have linker molecule which can monitor multiple interactions (same or different type) at the same time. Further, these linker molecules are modified so that biomolecular interactions can also be monitored using SPR instrument. Described in Chapter 2 are the synthesis of organic linker molecules and their use to study biomolecular interaction through AFM and SPR.
In Chapter 3, N-terminal chemical modification of peptides and proteins has been discussed. Further, modified peptides are attached to DNA thread for their translocation through the solid-state nanopore to identify them. Synthesis of various peptide-DNA conjugates and their nanopore studies have been discussed in this chapter.
The second part of Chapter 1 is discussed about site-specific chemical modification of peptides and proteins. Proteins have been used to generate therapeutic materials, proteins-based biomaterials. To achieve all these properties in protein there is a need for site-specific protein modification.
To be able to successfully monitor biomolecular interaction using AFM there is a need for organic linker molecule which helps one of the investigating molecules to get attached to the AFM tip. Most of the linker molecules available are capable of investigating one type of interaction at a time. Therefore, it is significant to have linker molecule which can monitor multiple interactions (same or different type) at the same time. Further, these linker molecules are modified so that biomolecular interactions can also be monitored using SPR instrument. Described in Chapter 2 are the synthesis of organic linker molecules and their use to study biomolecular interaction through AFM and SPR.
In Chapter 3, N-terminal chemical modification of peptides and proteins has been discussed. Further, modified peptides are attached to DNA thread for their translocation through the solid-state nanopore to identify them. Synthesis of various peptide-DNA conjugates and their nanopore studies have been discussed in this chapter.
ContributorsBiswas, Sudipta (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Redding, Kevin (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2016
Description
Changes to a cell's DNA can result in cancer, which is permanently sustained cellular proliferation. When malfunctioning genes, oncogenes, were verified to be of human origin in the 1970s, drugs were designed to target their encoded, abnormal enzymes. Tyrosine kinases have been established as an oft-modified oncogene enzyme family, but the protein tyrosine phosphatases (PTPs) were not investigated as thoroughly. PTPs have gradually been established as relevant enzymes that work in tandem with tyrosine kinases in cell signaling and are not just "house-keeping" enzymes. Some PTPs are thought to initiate tumorigenesis, and others may play a complementary role after the onset of cancer by extending the duration of cellular signals. Reversible inhibition of these enzymes by an oxalylamino group substituted on an ortho-carboxy aryl have been described in the literature. Modification of the oxalylamino group to favor irreversible inhibition of these cysteine-dependent enzymes may prevent inhibitor efflux by cells and subsequent mutation to gain resistance. Replacement of the oxalylamino group with halogenated propanoate and propenoate esters minimally inhibited cancer cell growth but did not inhibit activity of PTPs. Of the ortho-carboxy aryl structures, a methyl dichloropropanoate (compound 24) and a lactone alkene (compound 29) inhibited cell growth by 50% (GI-50) at micromolar concentrations. The GI-50s for compounds 24 and 29 were 19.9 (DU-145, prostate carcinoma) and 9.4 micromolar (A549, lung cancer), respectively. In contrast, brominated nitro lactones were able to inhibit both cancer cell growth and the activity of PTPs. In a sulforhodamine B assay, these compounds were able to achieve GI-50s as low 5.3 micromolar (compound 33 against BXPC-3, pancreatic adenocarcinoma), and some killed 50% of cancer cells (LC-50) at micromolar concentrations. Compound 33 displayed LC-50 of 23.3 micromolar (BXPC-3), and compound 35 had LC-50s of 32.9 and 32.7 micromolar against BXPC-3 and colon adenocarcinoma (KM20L2), respectively. A single concentration (100 micromolar) inhibition assay of inhibitor PTPs resulted in no enzyme activity for 4 out of 5 PTPs tested with compound 33. Similar results were obtained for compounds 35 and 37. Future analysis will determine if these bromo nitro lactones are irreversibly inhibiting PTPs.
ContributorsFadgen, Casey Joseph (Author) / Rose, Seth D (Thesis advisor) / Francisco, Wilson (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012
Description
A potential new class of cancer chemotherapeutic agents has been synthesized by varying the 2 position of a benzimidazole based extended amidine. Compounds 6-amino-2-chloromethyl-4-imino-1-(2-methansulfonoxyethyl)-5-methyl-1H-benzimidazole-7-one (1A) and 6-amino-2-hydroxypropyl-4-imino-1-(2-methansulfonoxyethyl)-5-methyl-1H-benzimidazole-7-one (1B) were assayed at the National Cancer Institute's (NCI) Developmental Therapeutic Program (DTP) and found to be cytotoxic at sub-micromolar concentrations, and have shown between a 100 and a 1000-fold increase in specificity towards lung, colon, CNS, and melanoma cell lines. These ATP mimics have been found to correlate with sequestosome 1 (SQSTM1), a protein implicated in drug resistance and cell survival in various cancer cell lines. Using the DTP COMPARE algorithm, compounds 1A and 1B were shown to correlate to each other at 77%, but failed to correlate with other benzimidazole based extended amidines previously synthesized in this laboratory suggesting they operate through a different biological mechanism.
ContributorsDarzi, Evan (Author) / Skibo, Edward (Thesis advisor) / Gould, Ian (Committee member) / Francisco, Wilson (Committee member) / Arizona State University (Publisher)
Created2011
Description
Due to its difficult nature, organic chemistry is receiving much research attention across the nation to develop more efficient and effective means to teach it. As part of that, Dr. Ian Gould at ASU is developing an online organic chemistry educational website that provides help to students, adapts to their responses, and collects data about their performance. This thesis creative project addresses the design and implementation of an input parser for organic chemistry reagent questions, to appear on his website. After students used the form to submit questions throughout the Spring 2013 semester in Dr. Gould's organic chemistry class, the data gathered from their usage was analyzed, and feedback was collected. The feedback obtained from students was positive, and suggested that the input parser accomplished the educational goals that it sought to meet.
ContributorsBeerman, Eric Christopher (Author) / Gould, Ian (Thesis director) / Wilkerson, Kelly (Committee member) / Mosca, Vince (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2013-05
The Effect of ZnS and Other Metal Sulfides on cis-1,2-dimethylcyclohexane at Hydrothermal Conditions
Description
Reactions between minerals and organic compounds in hydrothermal systems (high temperature and presence of H2O) are critical in the Earth’s deep carbon cycle and may have implications in the origins of life. Previous work demonstrated that in the absence of a mineral, hydrothermal reaction of cis- and trans-1,2-dimethylcyclohexane is extremely slow and resulted in the formation of many products. However, in the presence of sphalerite (ZnS), the reaction rate is significantly increased and it results in the formation of one main product, the corresponding stereoisomer. Following similar methods, we demonstrated that the sphalerite used in the reaction of cis-1,2-dimethylcyclohexane to the trans- stereoisomer visually changes structure via SEM. Additionally, we ran the experiments in sealed glass tubes, which unlike previously used gold tubes, do not react with the organics and provides more volume for larger amounts of mineral to be used. Finally, we investigated the role of other metal sulfides (FeS and PbS) in organic transformation reactions and analyzed their resulting physical structure. We found the role of FeS catalysis to be ambiguous and that PbS seemed to have no effect in the transformation reactions. We also found the glass tube data using ZnS to track previously published data with the same reactions in gold tubes. Our reactions were run without pressurizing the reaction vessels and at 300°C indicating pressure is not main factor in product formation (compare 1000 bar and 300°C).
ContributorsMchenry, Austin Ryan (Author) / Gould, Ian (Thesis director) / Johnson, Kristin (Committee member) / Department of Psychology (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Perovskite solar cells are one of the rising stars in the solar cell industry. This thesis explores several approaches to enhance the properties of the perovskite layer and the solar cell devices in which they operate. They include studies of different antisolvent additives during spin coating of triple cation perovskites, the use of surfactants to improve the quality of perovskite film microstructures, the applicability of a new fabrication process, and the value of post-deposition thermal and chemical annealing processes.This thesis experimentally analyzes different antisolvents, viz., ethyl acetate, isopropyl alcohol, toluene, and chlorobenzene. It focuses on the antisolvent-assisted crystallization method to achieve homogenous nucleation of the perovskite film. Of all the antisolvents, ethyl acetate-treated films gave the best-performing device, achieving a power conversion efficiency of 15.5%.
This thesis also analyzes the effects of mixed antisolvents on the qualities of triple-cation perovskites. Different solution concentrations of chlorobenzene in ethyl acetate and isopropyl alcohol in ethyl acetate are optimized for optimal supersaturation to achieve enlarged perovskite grains. Evaluations are discussed in the context of solution polarity and boiling point of the antisolvents, where 25% chlorobenzene in ethyl acetate antisolvent mixture shows the best film properties.
Another study discusses a new fabrication process called electrical field-assisted direct ink deposition for large-scale printing of perovskite solar cells. This process involves the formation of nanodroplets under an electrical field deposited onto ITO/glass substrates. As a result, smooth Poly (3,4-ethylene dioxythiophene) polystyrene sulfonate layers are
ii
produced with an average effective electrical resistivity of 4.15104 0.26 -m compared to that of spin-coated films.
A successive chapter discusses the studies of the electrical field-assisted direct ink deposition of the photoactive CH3NH3PbI2 (MAPbI3) layer. Its focus is on the post-deposition chemical annealing of the MAPbI3 films in methylamine gas, termed as methylamine gas-assisted healing and growth of perovskite films. This treatment improved the smoothness, reduced porosity, increased density, and generated more uniform grain sizes. Moreover, it improved the inter-grain boundary contacts by eliminating secondary, fine-grained boundary structures. Mechanisms behind the initial liquefaction of the MAPbI3 film's subsequent re-solidification are discussed.
ContributorsGogoi, Banashree (Author) / Alford, Terry (Thesis advisor) / Petuskey, William (Thesis advisor) / Gould, Ian (Committee member) / Li, Jian (Committee member) / Arizona State University (Publisher)
Created2023
Description
Proteins are among the important macromolecules in living systems, with diverse biological functions and properties that make them greatly interesting to study in both structure and function. The chemical synthesis of proteins allows researchers to incorporate a wide variety of post-translation modifications that can diversify protein functions. It also allows the incorporation of many noncanonical amino acids that enable the study of protein structure and function, as well as the control of their activity in living cells. The work presented in this dissertation focuses on two DNA-templated chemical synthesis approaches for the synthesis of proteins: i) DNA-templated native chemical ligation (NCL), and ii) DNA-templated click chemistry. NCL and its extended version has been used as a powerful tool to obtain proteins; however, it still struggles to make longer proteins due to aggregation and poor yield. To address these issues, a DNA-templated approach is being developed where two peptide fragments are brought into proximity by an oligonucleotide to facilitate the NCL reaction. The sequential ligation of the peptide fragments will result in full-length proteins with increased yield and improved solubility. This research involves synthesis of small molecule auxiliaries, thioester peptides, DNA-peptide conjugates, and ligation of peptides through NCL. This method has the potential to be applied to synthesize large hydrophobic proteins.
A DNA-templated click chemistry method was also reported where duplex DNA was utilized as a template for enhancing the copper click reaction between peptide fragments into functional mini-proteins. As a proof of principle, peptide fragments were synthesized with click functional groups and conjugated with distinct DNA handles through a disulfide exchange bioconjugation reaction. The DNA-peptide conjugates were assembled with the template to bring the two peptides into proximity and enhance the effective molarities of the functional groups. The peptides were coupled efficiently using a copper click reaction. The designed DNA-templated method is being implemented to synthesize a designed mini-protein (called LCB1), which can bind tightly to the spike protein of SARS-CoV-2 and inhibit its interaction with the human angiotensin-converting enzyme 2 (ACE2) receptor. This method allows researchers to introduce multiple non-natural amino acids in the protein and has the potential to extend to larger proteins, synthetic polymers, and DNA-peptide biomaterials.
ContributorsAl-Amin, Md (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Gould, Ian (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2024
Description
Organic compounds are influenced by hydrothermal conditions in both marine and terrestrial environments. Sedimentary organic reservoirs make up the largest share of organic carbon in the carbon cycle, leading to petroleum generation and to chemoautotrophic microbial communities. There have been numerous studies on the reactivity of organic compounds in water at elevated temperatures, but these studies rarely explore the consequences of inorganic solutes in hydrothermal fluids. The experiments in this thesis explore new reaction pathways of organic compounds mediated by aqueous and solid phase metals, mainly Earth-abundant copper. These experiments show that copper species have the potential to oxidize benzene and toluene, which are typically viewed as unreactive. These pathways add to the growing list of known organic transformations that are possible in natural hydrothermal systems. In addition to the characterization of reactions in natural systems, there has been recent interest in using hydrothermal conditions to facilitate organic transformations that would be useful in an applied, industrial or synthetic setting. This thesis identifies two sets of conditions that may serve as alternatives to commonplace industrial processes. The first process is the oxidation of benzene with copper to form phenol and chlorobenzene. The second is the copper mediated dehalogenation of aryl halides. Both of these processes apply the concepts of geomimicry by carrying out organic reactions under Earth-like conditions. Only water and copper are needed to implement these processes and there is no need for exotic catalysts or toxic reagents.
ContributorsLoescher, Grant (Author) / Shock, Everett (Thesis advisor) / Hartnett, Hilairy (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2020
Description
Fluorescence spectroscopy has been a vital technique in biophysics due to its high sensitivity and specificity. While the recent development of single-molecule (SM) techniques has furthered the molecular-level understanding of complicated biological systems, the full potential of these techniques hinges on the development and selection of fluorescent probes with customized photophysical properties. Red region probes are inherently desirable as background noise from typical biological systems tends to be at its minimum in this spectral region. The first part of this work studies the photophysical properties of red cyanine dyes to access their usefulness for particular SM applications.Protein-induced fluorescence enhancement (PIFE) based approaches are increasingly being used to investigate DNA-protein interactions at the SM level. However, a key limitation remains the absence of good red PIFE probes. This work investigates the photophysical properties of a red hemicyanine dye (Dy-630) as a potential PIFE probe. Results shed light on optimal design principles for ideal probes for PIFE applications, opening new avenues for the technique’s broad applicability in biophysical studies.
Further, the photophysical behavior of two novel cyanine fluorophores in the far-red (rigidized pentacyanine) and near-Infrared (IR) (rigidized heptacyanine) region are studied. Both probes are designed to eliminate a photoisomerization caused non-radiative pathway by rigidization of the cyanine backbone. The rigidized pentacyanine was found to have desired photophysical properties and improved quantum yield, vital for application in super-resolution imaging. For rigidized heptacyanine, in contrast to the prior project, it was found that photoisomerization does not contribute significantly to the deactivation pathway. Thus, this work clarifies the role of photoisomerization on heptamethine cyanine scaffold and will enable future efforts to optimize NIR dyes for diverse applications.
The second part of this work aims to answer the fundamental question of how the physics of DNA can impact its biology. To this end, interlinkage between the flexibility of local sequence context and the efficiency of uracil removal by Uracil-DNA glycosylase (UDG) protein is investigated using fluorescent base analogue, 2-Aminopurine (2-AP).
In summary, this work focuses on photophysical investigations, the understanding of which is vital for the selection and development of fluorescent probes for biophysical studies.
ContributorsKumari, Nikita (Author) / Levitus, Marcia (Thesis advisor) / Gould, Ian (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2021
Description
Since the conception of DNA nanotechnology, the field has evolved towards the development of complex, dynamic 3D structures. The predictability of Watson-Crick base pairing makes DNA an unparalleled building block, and enables exceptional programmability in nanostructure shape and size. The work presented in this dissertation focuses on expanding two facets of the field: (1) introducing functionality through the incorporation of peptides to create DNA-peptide hybrid materials, and (2) the development of self-assembling DNA crystal lattices for scaffolding biomolecules. DNA nanostructures have long been proposed as drug delivery vehicles; however, they are not biocompatible because of their low stability in low salt environments and entrapment within the endosome. To address these issues, a functionalized peptide coating was designed to act as a counterion to a six-helix bundle, while simultaneously displaying numerous copies of an endosomal escape peptide to enable cytosolic delivery. This functionalized peptide coating creates a DNA-peptide hybrid material, but does not allow specific positioning or orientation of the peptides. The ability to control those aspects required the synthesis of DNA-peptide or DNA-peptide-DNA conjugates that can be incorporated into the nanostructure. The approach was utilized to produce a synbody where three peptides that bind transferrin with micromolar affinity, which were presented for multivalent binding to optimize affinity. Additionally, two DNA handle was attached to an enzymatically cleavable peptide to link two unique nanostructures. The second DNA handle was also used to constrain the peptide in a cyclic fashion to mimic the cell-adhesive conformations of RGD and PHSRN in fibronectin.
The original goal of DNA nanotechnology was to use a crystalline lattice made of DNA to host proteins for their structural determination using X-ray crystallography. The work presented here takes significant steps towards achieving this goal, including elucidating design rules to control cavity size within the scaffold for accommodating guest molecules of unique sizes, approaches to improve the atomic detail of the scaffold, and strategies to modulate the symmetry of each unique lattice. Finally, this work surveys methodologies towards the incorporation of several guest molecules, with promising preliminary results that constitute a significant advancement towards the ultimate goal of the field.
ContributorsMacCulloch, Tara Lynn (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Borges, Chad (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2021