Nucleic acid aptamers are "short single-stranded DNA- or RNA-based oligonucleotides that can selectively bind to small molecular ligands or protein targets with high affinity and specificity, when folded into their unique three-dimensional structure" (1). Aptamers have shown promising ability for detection in the subnanomolar range of nucleic acid targets with specificity down to single nucleotide variations (2). The selectivity, low limit of detection, and cost-effectiveness make these nucleic acid aptamers optimal bio-sensors. Previous work by our group has been done to optimize the signal of the dapoxyl-binding aptamer (DAP), which is a light-up aptamer. Here, we propose to organize this aptamer into a split-aptamer system and determine the limit of detection and selectivity for a target gene in Mycobacterium tuberculosis.

Thesis advisor: Jia Niu / Thesis advisor: Abhishek Chatterjee / The functions of natural nucleic acids such as DNA and RNA have transcended from serving as the primary information carrier in cells and have emerged as a new class of functional material with applications encompassing medicine, diagnosis, and research tools. While the vulnerability of natural nucleic acids to nuclease degradation as well as the lack of chemical functionality have imposed a significant constraint on their ever-expanding applications, scientists have put in the effort to develop new classes of synthetic nucleic acids (XNAs) to overcome current limitations. In this dissertation, we will describe the development of a novel XNA oligonucleotide structure, the “click handle-modified FANA” (cmFANA), as the next-generation nucleic acid-based biopolymer that is capable of post-polymerization functionalization and evolution. In this dissertation, we divide our graduate research into three chapters: the development of the essential building block for cmFANA and the synthesis of cmFANA oligonucleotide as Chapter 1; the evolution and application of cmFANA as a sugar-presenting affinity reagent that targets disease-related Carbohydrate-Binding Proteins (CBPs) as Chapter 2; and other collaboration projects as Chapter 3. Together, we described a highly potential XNA structure that goes beyond established impressions of nucleic acids and carries the ability to be a versatile platform technology. / Thesis (PhD) — Boston College, 2023. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Advances in our ability to detect biological targets relevant to human health have come from the engineering of biological molecules into assemblies capable of performing target-induced signal generation. Such assemblies, known as biosensors, are composed of a molecular recognition element (MRE) and a signal generating transduction element. One MRE class that has received great attention in recent years is functional nucleic acids, which include DNA aptamers and DNAzymes. Since 1990, a large number of functional nucleic acids have been reported. However, broad commercial use of functional nucleic acids in applications that benefit human health is sparse. The goal of this thesis is to expand the usefulness of functional nucleic acids. The thesis is made of four projects. In the first project I developed a simple colorimetric biosensor for the detection of a toxic metal ion using a reported RNA-cleaving DNAzyme coupled with urease as the signal reporter. This is followed by a project where I developed a highly effective method for the synthesis and purification of the DNA-urease conjugate needed for the biosensor. I then turned my attention to the search for high-affinity DNA aptamers that bind VEGF-165, an important human protein found to be relevant in the progression of cancers. Given that VEGF-165 is a homodimeric protein, in my third project I looked into the suitability of reported DNA aptamers for this protein for the creation of dimeric aptamers with higher binding affinity. I examined multiple factors that may affect the successful engineering of dimeric aptamers and determined that none of the existing aptamers are compatible for creating a productive dimeric aptamer. With this finding, I made an effort to create our own aptamers for this protein target. I was able to isolate a new aptamer that appears to be an excellent candidate for creating a higher affinity DNA aptamer. Overall, my work adds to our increasing appreciation of the functional capability demonstrated by single-stranded DNA molecules. More importantly, I hope the methods I have developed and new functional DNA molecules I have generated in this thesis will continue to drive the development of the functional nucleic acid field and contribute to the health research community’s efforts to increase human longevity. / Thesis / Doctor of Philosophy (PhD)

Aptamers are nucleic acid ligands that bind to a specific target molecule. They are discovered by in-vitro selection, whereby binding sequences are selected from a large library of random sequences through iterative affinity steps. Aptamers are used as molecular recognition elements in aptamer-based, as such, creating aptamers with high affinity and specificity to their targets is important to the field. Ligands with two binding sites have been reported to have enhanced binding affinity than ligands with one binding site. To improve the quality of aptamers for downstream applications, multidomain selection is proposed as a new method for selecting aptamers compatible with dimerization. Here, we applied the multidomain selection approach to Fusobacterium nucleatum DnaK and produced aptamers that target the N-terminal domain (NTD) and the C-terminal domain (CTD) of DnaK. The top aptamer for DnaK-NTD had a Kd of 59.7 nM, and for DnaK-CTD had a Kd of 202.0 nM. However, the aptamers did not bind to the full-length DnaK and could not be dimerized. Multiple-site binding offers greater flexibility in the design of detection systems, which could provide higher selectivity and sensitivity than aptamers found through standard approaches. Validation of a method to discover aptamers compatible with dimerization would result in the development of a targeted approach to discover high-quality aptamers for bacterial proteins that can be used in bacteria-detection techniques. / Thesis / Master of Science (MSc)

Gegenstand dieser Arbeit ist die Herstellung funktioneller Polymerpartikel und deren Nutzung für biomedizinische Applikationen. Die Anwendungsgebiete der resultierenden Hybridmaterialien reichen vom Einsatz als Kontrastmittel in bildgebenden Verfahren der medizinischen Diagnostik über die Verwendung als Antimikrobium bis hin zum Einsatz als „Werkzeug“ zur Zellisolierung und aktivierung. Dazu wurden kompakte Latexpartikel und sensitive, poröse Mikrogelpartikel mittels emulgatorfreier Heterophasenpolymerisation synthetisiert. Als funktionelles Monomer wurde Glycidylmethacrylat verwendet, über dessen reaktive Epoxygruppen anschließend weitere Moleküle angebunden werden können. Die Funktionalisierung der Polymerpartikel erfolgte einerseits mit anorganischen Nanopartikeln (dotierte Lanthanfluorid-Nanopartikel, Gold- und Silbernanopartikel) und andererseits mit Biomolekülen wie Nukleotiden und Antikörpern. Einige Verwendungsgebiete, wie die Stimulierung von Memory-T-Zellen mit Antikörper-Polymer-Konjugaten oder der Einsatz der Silberkomposite aufgrund ihrer antimikrobiellen Wirkung, wurden näher untersucht. / The aim of this work was the synthesis of functional polymeric particles and their use for biomedical purposes. The application areas of the resulting hybrid materials range from contrast agents in medical diagnostics and usage due to antimicrobial properties to “tools” for cell isolation and activation. Compact core-shell particles and porous microgel particles were prepared by surfactant-free heterophase polymerization in water. All particles contain glycidyl methacrylate whose epoxy groups are capable to bind other molecules covalently. On the one hand, polymeric particles were functionalized with inorganic nanoparticles (doped lanthanum fluoride nanoparticles, gold and silver nanopariticles) and on the other hand with biomolecules such as nucleotides and antibodies. Selected application fields like the stimulation of memory T-cells with polymer-antibody-conjugates or the use of the silver composites due to their antimicrobial activity were investigated in detail.

The aim of this work was to functionalize silicon dioxide surfaces with biochemical molecules in such a way that biorecognition of target molecules in solution will be possible. By introducing a tool set of different molecules and characterization methods, a more universal approach towards various biosensor setups is presented. This includes on the one hand preparation of the biosensor surfaces to allow further molecule attachment via their reactive functional groups. Secondly, the selection of chemical molecules providing suitable counterparts for abundant functional groups of potential receptors is discussed. Two detection schemes are introduced – based on an antibody to detect the antibiotic amoxicillin and aptamers to detect thrombin. The antibody was implemented in an inverse competition assay to probe such small target molecules. Antibiotic residues are often present in wastewater. Aptamers, so-called artificial antibodies, were selected as they provide many advantages over antibodies. As a model system, two different thrombin binding aptamers were chosen which allowed to perform sandwich assays as well. The protein thrombin plays an important role in the blood coagulation cascade. To probe the individual modification steps, different techniques for analysis were applied. Surface micropatterning was introduced to improve recognition of modified areas and fluorescence-to-background ratios resulting in a thrombin detection limit down to 20 pM. One important goal was the integration in ion-sensitive field-effect transistor devices. Aptamers are small in size which might enable a higher sensitivity of these devices compared to the use of antibodies because of the Debye layer thickness. As a final step, first measurements towards silicon nanowire based field-effect transistor biosensors were carried out on devices with bottom-up and top-down fabricated nanowires using both proposed receptor-analyte combinations. The potential of these devices as portable sensors for real-time and label-free biosensing is demonstrated. / Ziel dieser Arbeit war es Siliziumdioxidoberflächen so mit biochemischen Molekülen zu funktional- isieren, dass die biologisch spezifische Erkennung von Zielmolekülen in Lösung möglich wird. Hier wird eine Auswahl an geeigneten Molekülen und Charakterisierungsmethoden für einen vielseitigen Ansatz gezeigt, der auf verschiedene Biosensorsysteme anwendbar ist. Das beinhaltet zum Einen die Präparation der Biosensoroberflächen, so dass die Moleküle über reaktive funktionelle Gruppen angebunden werden können. Als zweites ist die Auswahl der chemischen Moleküle wichtig, da diese die passenden Gegenstücke zu potentiellen funktionellen Gruppen der Rezeptoren darstellen. Zwei verschiedene Detektionsvarianten werden eingeführt – Antikörper gegen das Antibiotikum Amoxicillin und Aptamere gegen Thrombin. Der Antikörper wurde in einen inversen Wettbewerbsassay integriert um einen solch kleinen Ana- lyten detektieren zu können. Rückstände von Antibiotika sind häufig in Abwässern zu finden. Ap- tamere, sogenannte künstliche Antikörper, weisen gegenüber Antikörpern viele Vorteile auf. Als ein Modellsystem wurden zwei unterschiedliche Thrombin bindende Aptamere verwendet, was auch die Durchführung von Sandwich Assays ermöglichte. Das Protein Thrombin spielt eine wichtige Rolle bei der Blutgerinnung. Um die einzelnen Modifikationsschritte zu untersuchen, wurden verschiedene Charakterisierungsmethoden angewendet. Die Mikrostrukturierung der Funktionalisierung erleichterte die Erkennung der modifizierten Flächen und verbesserte das Fluoreszenz-zu-Hintergrund Verhältnis. Das führte zu einer Detektionsgrenze von 20 pM für Thrombin. Ein wichtiges Ziel dieser Arbeit war die Integration der Funktionalisierung in einen ionen-sensitiven Feldeffekttransistor. Die kleinen Aptamere könnten dabei aufgrund der geringen Debye-Schichtdicke bei diesen Sensoren eine höhere Sensitivität als mit Antikörpern ermöglichen. Zuletzt wurden erste Messungen hin zu Silizium Nanodraht basierten Feldeffekttransistor Biosen- soren mit beiden untersuchten Rezeptor-Analyt-Kombinationen durchgeführt. Sowohl die Chips mit bottom-up als auch mit top-down gewachsenen Nanodrähten zeigen dabei ihr Potential als handliche Sensoren zur markerfreien Detektion in Echtzeit.

Micro-pollutants such as 17β-estradiol (E2) have been detected in different water resources and their negative effects on the environment and organisms have been demonstrated. It is essential to confirm the presence of micro-pollutants in different environments by biosensors and to remove these compounds. In this thesis, E2-binding target structures were used to investigate the underlying binding properties. E2-binding protein, DNA-, and PNA-aptamere (peptide nucleic acid) structures were used as targets to determine physicochemical interactions. The protein dataset consist of 35 publicly accessible three-dimensional structures of E2-protein complexes, from which six representative binding sites could be selected. There is no three-dimensional structure information for an E2-specific DNA aptamer, thus it was modeled using a coarse-grained modeling method. Using sequence information additional DNA aptamers were modeled. The E2 ligand was positioned close to the potential binding area of the aptamer structures, the underlying complexes were investigated by a molecular dynamics simulation, and the interactions were examined by an interaction profiler tool for each time step. A PNA generator was developed that can convert DNA and RNA in silico to more robust, but chemically equivalent PNA. This generator was used to transform the E2-specific DNA aptamer into PNA for binding studies with E2. All formed complexes were investigated with respect to the following non-covalent interaction types: hydrogen bonds, water-mediated hydrogen bonds, π-stacking, and hydrophobic interactions. Ten functional groups could be derived which formed the conserved interactions to E2. The study contributes to the understanding of the behavior of ligands that bind through different target structures in an aqueous solution and to the identification of binding specific interaction partners. The results of this thesis can be used to design novel synthetic receptor and filter systems.

The aim of this work was to functionalize silicon dioxide surfaces with biochemical molecules in such a way that biorecognition of target molecules in solution will be possible. By introducing a tool set of different molecules and characterization methods, a more universal approach towards various biosensor setups is presented. This includes on the one hand preparation of the biosensor surfaces to allow further molecule attachment via their reactive functional groups. Secondly, the selection of chemical molecules providing suitable counterparts for abundant functional groups of potential receptors is discussed. Two detection schemes are introduced – based on an antibody to detect the antibiotic amoxicillin and aptamers to detect thrombin. The antibody was implemented in an inverse competition assay to probe such small target molecules. Antibiotic residues are often present in wastewater. Aptamers, so-called artificial antibodies, were selected as they provide many advantages over antibodies. As a model system, two different thrombin binding aptamers were chosen which allowed to perform sandwich assays as well. The protein thrombin plays an important role in the blood coagulation cascade. To probe the individual modification steps, different techniques for analysis were applied. Surface micropatterning was introduced to improve recognition of modified areas and fluorescence-to-background ratios resulting in a thrombin detection limit down to 20 pM. One important goal was the integration in ion-sensitive field-effect transistor devices. Aptamers are small in size which might enable a higher sensitivity of these devices compared to the use of antibodies because of the Debye layer thickness. As a final step, first measurements towards silicon nanowire based field-effect transistor biosensors were carried out on devices with bottom-up and top-down fabricated nanowires using both proposed receptor-analyte combinations. The potential of these devices as portable sensors for real-time and label-free biosensing is demonstrated. / Ziel dieser Arbeit war es Siliziumdioxidoberflächen so mit biochemischen Molekülen zu funktional- isieren, dass die biologisch spezifische Erkennung von Zielmolekülen in Lösung möglich wird. Hier wird eine Auswahl an geeigneten Molekülen und Charakterisierungsmethoden für einen vielseitigen Ansatz gezeigt, der auf verschiedene Biosensorsysteme anwendbar ist. Das beinhaltet zum Einen die Präparation der Biosensoroberflächen, so dass die Moleküle über reaktive funktionelle Gruppen angebunden werden können. Als zweites ist die Auswahl der chemischen Moleküle wichtig, da diese die passenden Gegenstücke zu potentiellen funktionellen Gruppen der Rezeptoren darstellen. Zwei verschiedene Detektionsvarianten werden eingeführt – Antikörper gegen das Antibiotikum Amoxicillin und Aptamere gegen Thrombin. Der Antikörper wurde in einen inversen Wettbewerbsassay integriert um einen solch kleinen Ana- lyten detektieren zu können. Rückstände von Antibiotika sind häufig in Abwässern zu finden. Ap- tamere, sogenannte künstliche Antikörper, weisen gegenüber Antikörpern viele Vorteile auf. Als ein Modellsystem wurden zwei unterschiedliche Thrombin bindende Aptamere verwendet, was auch die Durchführung von Sandwich Assays ermöglichte. Das Protein Thrombin spielt eine wichtige Rolle bei der Blutgerinnung. Um die einzelnen Modifikationsschritte zu untersuchen, wurden verschiedene Charakterisierungsmethoden angewendet. Die Mikrostrukturierung der Funktionalisierung erleichterte die Erkennung der modifizierten Flächen und verbesserte das Fluoreszenz-zu-Hintergrund Verhältnis. Das führte zu einer Detektionsgrenze von 20 pM für Thrombin. Ein wichtiges Ziel dieser Arbeit war die Integration der Funktionalisierung in einen ionen-sensitiven Feldeffekttransistor. Die kleinen Aptamere könnten dabei aufgrund der geringen Debye-Schichtdicke bei diesen Sensoren eine höhere Sensitivität als mit Antikörpern ermöglichen. Zuletzt wurden erste Messungen hin zu Silizium Nanodraht basierten Feldeffekttransistor Biosen- soren mit beiden untersuchten Rezeptor-Analyt-Kombinationen durchgeführt. Sowohl die Chips mit bottom-up als auch mit top-down gewachsenen Nanodrähten zeigen dabei ihr Potential als handliche Sensoren zur markerfreien Detektion in Echtzeit.

Gegenstand dieser Arbeit ist die Herstellung funktioneller Polymerpartikel und deren Nutzung für biomedizinische Applikationen. Die Anwendungsgebiete der resultierenden Hybridmaterialien reichen vom Einsatz als Kontrastmittel in bildgebenden Verfahren der medizinischen Diagnostik über die Verwendung als Antimikrobium bis hin zum Einsatz als „Werkzeug“ zur Zellisolierung und aktivierung. Dazu wurden kompakte Latexpartikel und sensitive, poröse Mikrogelpartikel mittels emulgatorfreier Heterophasenpolymerisation synthetisiert. Als funktionelles Monomer wurde Glycidylmethacrylat verwendet, über dessen reaktive Epoxygruppen anschließend weitere Moleküle angebunden werden können. Die Funktionalisierung der Polymerpartikel erfolgte einerseits mit anorganischen Nanopartikeln (dotierte Lanthanfluorid-Nanopartikel, Gold- und Silbernanopartikel) und andererseits mit Biomolekülen wie Nukleotiden und Antikörpern. Einige Verwendungsgebiete, wie die Stimulierung von Memory-T-Zellen mit Antikörper-Polymer-Konjugaten oder der Einsatz der Silberkomposite aufgrund ihrer antimikrobiellen Wirkung, wurden näher untersucht. / The aim of this work was the synthesis of functional polymeric particles and their use for biomedical purposes. The application areas of the resulting hybrid materials range from contrast agents in medical diagnostics and usage due to antimicrobial properties to “tools” for cell isolation and activation. Compact core-shell particles and porous microgel particles were prepared by surfactant-free heterophase polymerization in water. All particles contain glycidyl methacrylate whose epoxy groups are capable to bind other molecules covalently. On the one hand, polymeric particles were functionalized with inorganic nanoparticles (doped lanthanum fluoride nanoparticles, gold and silver nanopariticles) and on the other hand with biomolecules such as nucleotides and antibodies. Selected application fields like the stimulation of memory T-cells with polymer-antibody-conjugates or the use of the silver composites due to their antimicrobial activity were investigated in detail.

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