<p> DNA origami is a powerful method to construct DNA nanostructures. It requires long, single-stranded DNAs. The preparation of such long DNA strands is often quite tedious and has a limited production yield. In contrast, duplex DNAs can be easily prepared via enzymatic reactions in large quantities. Thus, we ask a question: can we design DNA nanostructures in such a way that the two complementary strands can simultaneously fold into the designed structures in the same solution instead of hybridizing with each other to form a DNA duplex? By engineering DNA interaction kinetics, herein, we are able to provide multiple examples to concretely demonstrate a positive answer to this question. The resulting DNA nanostructures have been thoroughly characterized by electrophoresis and atomic force microscopy imaging. The reported strategy is compatible with the DNA cloning method; thus, would provide a convenient way for large-scale production of the designed DNA nanostructures. </p>

<p>   Organic electronics has been a highly researched field owing to the low cost, biocompatibility, mechanical flexibility, and superior performance relative to their inorganic counterparts in some applications. Significant advancement has been achieved across various device platforms including organic light-emitting diodes (OLEDs), organic field effect transistors (OFETs), and organic solar cells, for instance. Recently, soft materials that can conduct both charge and ions simultaneously (i.e., organic mixed conductors) have been a major catalyst in the fields of biosensors and energy storage. Extensive research efforts in the organic electronics field are being invested to establish the relevant structure-property relationships to design and develop higher performing organic mixed conductors. Simultaneously, these materials are utilized in developing prototype biosensors with the aim of superior performance, lower cost, and better patient comfort and outcomes than currently available technologies. Following suit, this dissertation is dedicated to furthering organic electronics on both fundamental and applied fronts. Specifically, this work examines a novel class of redox-active macromolecules, radical polymers, as the organic electrochemical transistor (OECT) active layer. In addition, wearable ocular biosensors utilizing soft materials to realize design innovation are presented.</p> <p>   For the first part of the present dissertation, radical polymer-based blends are evaluated for mixed electron and ion conduction in OECTs. Traditional macromolecular design motifs for OECT active layer materials have been a closed-shell macromolecular backbone for electron conduction with charge-neutral hydrophilic side chains (e.g., triethylene glycol) for ion conduction. When poly(4-glycidyloxy-2,2,6,6-tetramethylpiperidine-1-oxyl) (PTEO) is blended with poly(3-hexylthiophene) (P3HT), 2,2,6,6-tetramethylpiperidin-N-oxy (TEMPO) radicals in PTEO act as an independent voltage regulator that modulates the ionic and hence electronic transport of the OECT devices. Electrochemical analysis of the blend films reveals that the ionic transport and hence electrochemical doping of the P3HT phase occur when the applied bias matches the onset oxidation potential of TEMPO radicals in PTEO even though that of P3HT is lower than that of TEMPO oxidation. By optimizing the blend ratio, figure-of-merit (i.e., μC*) values over 150 F V–1 cm–1 s–1 at loadings as low as 5% PTEO (by weight) are achieved, placing the performance on the same order as top-performing conjugated polymers despite the mediocre performance of pristine P3HT (<10 F V–1 cm–1 s–1). These findings suggest that introduction of open-shell moieties in the OECT active layer as a secondary redox-active species may significantly improve OECT performance metrics and offer a new paradigm for future macromolecular designs.</p> <p>   In the second part of the dissertation, novel design strategies for wearable ocular electroretinography (ERG) sensors are presented. Typically, wearable sensors are custom-made contact lenses fabricated in a bottom-up fashion where the pre-fabricated sensor component is either embedded in the contact lens body or sandwiched between two. The present work instead utilizes commercially available contact lenses, and the corneal electrode is integrated via electropolymerization of poly(3,4-ethylenedioxythiophene):iron(III) p-toluenesulfonate (PEDOT:Tos) on the lens surface. Electrochemical analysis of the PEDOT:Tos reveals that the measured impedance is several orders of magnitude lower than that of noble metals (e.g., Au) used as the working electrode in commercial electrodes. The mechanical and chemical stability along with the soft form factor of the present design strategy enables high-fidelity recording of ERG signals in human subjects without the need for topical anesthesia.</p> <p>   Following the similar strategy, a new seamless wearable ocular sensor integration strategy utilizing polydopamine (PDA) conformal coating is demonstrated. In this work, we utilize its strong adhesive property originating from the van der Waals interactions between catechol moieties of PDA and various hydrophilic functional groups (e.g., hydroxy, ether, etc.) already present in commercial contact lens materials. The facile integration demonstrates high peeling strength (> 55 J m-2), chemical and mechanical stability. A series of <em>in vivo</em> assessments demonstrates high accuracy, reliability, and user comfort of the fabricated wearable sensor in both animal and human subjects. The findings suggest that the PDA-assisted integration strategy may be applied in designing various future-generation wearable ocular electrophysiological sensors.</p>

<p dir="ltr">Methods of protein engineering and mutation to achieve selective and designed enzymatic function are often challenged by issues with foldamer stability. Molecular nanocages present an exciting new opportunity for biomimetic-defined cavities capable of biomolecule recognition and catalysis. While many different types of molecular cages exist, covalent organic molecular cages offer great flexibility and control over the design of the cage. Furthermore, the covalent linkages provide a robust framework resistant to degradation and stable in many chemical environments. Lastly, covalent organic cages may be designed for the precise placement of functional groups, including group placement inside the cage cavity for molecular recognition and binding. I report our recent advances in developing new synthetic methods for robust organic molecular cages with well-defined cavities and tunable functions for artificial enzyme catalysis and recognition. The basic design philosophy for such protein-mimetic structures will be introduced for the scalable synthesis of these macromolecules. Herein, we report two approaches to a [8+12] triazine-linked organic cage and a similar [8+12] triazine and boroxine-linked cage. While our first approach attempts a kinetically controlled tethered cage formation, our second method relies on the principles of dynamic covalent chemistry in the thermodynamically controlled self-assembly of the final cage structure.</p>

<p dir="ltr">Water molecules present an obstacle between most synthetic adhesives and surfaces, limiting molecular contact between the glue and substrates. Water can also hydrolyze or swell bulk adhesives, weakening cohesive strength. Nature has solved these challenges for millennia. Marine mussels’ ability to adhere well to wet surfaces stems from an uncommon amino acid, 3,4-dihydroxyphenylalanine (Dopa). The amino acid Dopa contains a catechol moiety that contributes to adhesion and cohesion through hydrogen bonding, metal coordination, and oxidative cross-linking. Hence, biomimetic systems often incorporate catechol groups to provide strong adhesion in both dry and wet environments. In addition to Dopa, mussel adhesive proteins are rich in cationic amino acids lysine and arginine. Previous studies have suggested that cations could displace surface-bound ions, enhancing surface adhesion. However, adhesion performance varied between systems, with no agreement on whether cations are advantageous or disadvantageous. A clear picture of how cations influence underwater adhesion has yet to emerge; therefore, this thesis aims to systematically study these effects.</p><p dir="ltr">In Chapter 2, the synthesis of catechol-containing biomimetic polymers with varying amounts of quaternary ammoniums is presented. Quaternary ammoniums, unlike protonated primary amines, contain non-reactive cations and were used to isolate effects from only charges on adhesion. In Chapter 3, differences between reactive primary amines and quaternary ammoniums were investigated. Structure-function studies have shown how cations influence bulk cohesion versus surface adhesion in dry, under deionized water, and under salt water. The roles of cations in adhesion were complex, with both cohesive and surface bonding relevant in different ways, sometimes even working in opposite directions.</p><p dir="ltr">Furthermore, a styrene-based catechol-containing polymer with excellent underwater adhesion performance is ready to enter the market, but several barriers hinder its industrial implementation. In Chapter 4, new synthetic strategies were developed to scale up and reduce the cost of producing p[vinylcatechol-<i>co-</i>styrene], which are essential for commercialization. This was achieved by selecting cheaper starting materials, switching from anionic to suspension polymerization, and optimizing deprotection reaction conditions. This change also improved adhesion in both dry and underwater conditions. This work is presented as part of our effort to advance the design of adhesives that function in challenging environments.</p>

<p dir="ltr">The recent COVID-19 pandemic has emphasized the risk of respiratory infections leading to acute respiratory distress syndrome (ARDS). A significant factor contributing to poor ARDS outcomes is the impairment of lung surfactant due to infiltrating surface-active proteins and phospholipases during lung inflammation. Lung surfactant's vital role in stabilizing alveoli by reducing air-water interfacial tension becomes evident as its dysfunction severely compromises respiratory function. Although lung surfactant (LS) replacement therapy effectively addresses neonatal LS deficiencies, its efficacy in ARDS treatment for adults remains limited. The challenge lies in the chemical similarity between current animal-extracted surfactants and human lung surfactant which are both phospholipid-based. To address this issue, this dissertation outlines a transformative "polymer lung surfactant (PLS)" designed to overcome the limitations of conventional exogenous surfactants in treating ARDS.</p><p dir="ltr">Firstly, a formulation method, referred to as equilibration-nanoprecipitation (ENP), is established which achieves reproducibility, controls sizing, and limits dispersity of the PLS formulation consisting of block copolymer (BCP) kinetically "frozen" micelles/nanoparticles suspended in water. The method uses a two-step approach of 1) equilibrating the BCP nanoparticles in a water/co-solvent mixture and 2) removing co-solvent using dialysis against a large water reservoir. Comparison of ENP with a conventional solvent-exchange technique through experimental and computational analysis yields further insights into ENP's advantages.</p><p dir="ltr">Next, various studies are highlighted which provide fundamental characterizations of the air-water surface behavior and physical properties of BCP nanoparticles in water. The air-water surface properties of block copolymers have been studied extensively when spread as free chains in organic solvent; however, little was previously known about air-water interfacial behavior of water-spread polymer nanoparticles. The studies address such topics as the effect of nanoparticle size, effect of nanoparticle core chemistry, and the effect of temperature on surface-mechanical behavior. Insights into nanoparticle molecular structure at the interface are provided through X-ray reflectivity and grazing incidence X-ray diffraction. The effect of temperature is further characterized by developing novel NMR and Langmuir trough methods to determine the physical state (glassy vs rubbery) of the core domain in the nanoconfined state at temperatures above and below physiologic temperature.</p><p dir="ltr">Lastly, <i>in vivo </i>studies are presented which demonstrate the detailed and promising proof-of-concept results on the efficacy of the PLS technology in mouse models of lung injury. The PLS therapy not only improves biomechanical function of the lung, but it also significantly lowers the extent of lung injury as shown by histological analysis and inflammatory marker measurements. An additional <i>in vivo </i>study is presented which highlights challenges in the delivery of the liquid PLS suspension to the lungs. The <i>in vivo </i>studies ultimately provide solid motivation for continued research into the development of the PLS therapy.</p><p dir="ltr">Given the promising potential of the PLS technology shown in the <i>in vivo</i> studies, the materials characterizations shared in this presentation offer valuable insights into the design of a novel PLS therapy. From these insights, key design parameters such as nanoparticle size characteristics, core chemistry, and core molecular weight can be chosen to produce the most desirable material properties. Overall, this dissertation furthers the progress of PLS therapeutic development and will hopefully ultimately contribute to improved health outcomes in patients suffering from ARDS.</p>

<p dir="ltr">DNA sequence design requires the ability to identify possible tertiary structural defects, secondary structure disruptions, and self-complimentary stretches that will disallow your complimentary strands to come together to form the desired duplex design. However, there is a need for those self-complimentary stretches, especially when designed with the intent for this to homo-oligomerize into the desired building block. With the programmability of nucleic acid hybridization, there is an expanding field wherein this specific, self-complimentary design feature can give new possibility of fine-tuning DNA self-assembly (Chapter 1) or overcome a previously thought limit of DNA ligation (Chapter 2).</p><p dir="ltr">The first chapter will closely look at the branched kissing loop interaction. This interaction was studied as a homo-polymerizable DNA building block that is topologically closed. As such, this paranemic motif has increased stability due to the Watson-Crick base pairing being “protected” by a 3-base adenine branch which close the loop of the sticky-end, meaning no free ends in the binding region. With this, herein we report that the intended higher-level structure could influence the lower-level building block formation. In DNA nanotechnology, this could mean the final higher-level structure would allow for fine-tuning as this would dictate the building blocks that fill in the defected parts of the higher-level structure.</p><p dir="ltr">The second chapter looks at the more finite than broad picture. Whilst the first chapter focusses on the impact the microscale has on the nanoscale through a homo-polymerizable design, the second chapter focusses on the ability to break barriers with homo-polymerizable design. In this chapter, we prove that with our splint strand design, when improved with a hairpin loop on the terminal ends, we can ligate DNA strands enzymatically as short as 16 nucleotides with an efficiency of 97% at high concentrations (100 uM). These hairpins allow for a stable, robust splint strand as they are a self-complimentary region which will maintain its shape throughout the process of joining together the 5’ and 3’ ends of the target strand.</p><p dir="ltr">Overall, this dissertation hopes to prove that homo-polymerizable DNA sequence designs are helping expand upon the DNA nanotechnology toolbox by introducing new possibilities for nanoscale design, as well as push past previously held boundaries through necessary added stability afforded by the self-complimentary strands.</p>

Résumé indisponible / This PhD work is dedicated to investigate potentialities of phthalocyanines materials to realize a Quartz Crystal Microbalance (QCM) sensor for Benzene, Toluene and Xylenes (BTX) detection in air. The goal is to develop a sensor-microsystem capable of measuring BTX concentrations quantitatively below the environmental guidelines with sufficient accuracy. To achieve these objectives, our strategies mainly focused on experimental works encompassing sensors realization, sensing material characterizations, development of gas-testing facility and sensor testing for different target gases. One of the main aims is to identify most appropriate phthalocyanine material for sensor development. After comparative sensing studies, tert-butyl-copper phthalocyanine based QCM device is found as most sensitive and detail metrological characteristics are further investigated. Results show repeatable, reversible and high magnitude of response, low response and recovery times, sub-ppm range detection limit, high resolutions and combined selectivity of BTX gases among common atmospheric pollutants. Special focus is given to understand the gas/material interactions which are achieved by (a) XRD and SEM characterizations of sensing layers, (b) formalization of a two-step adsorption model and (c) assessing extent of diffusion of target gas in sensing layer. At last, possible ageing of sensor and suitable storage conditions to prevent such effect are investigated.

<p> In an era of advancing printed electronics, solution-processable organic semiconductors continue to make significant strides in electronic and optoelectronic applications. Electrochromic (EC) technology, which encompass reversible optical modulation under electrochemical biasing, has progressed rapidly over the past half-century and developed into niche commercial-scale devices for auto-tinting glasses as well as low-power, non-emissive displays. To utilize the advantages of organic electrochromic materials in next-generation devices, it is imperative to understand their fundamental material properties, interactions with other device components, and the underlying electrochemistry that governs the overall optical and electrochemical response of the complete electrochromic device. This dissertation presents a discussion on the synergistic role of organic electrochromes, charge-balancing layers and electrolytes in determining two key performance metrics, namely the optical contrast and operational stability, of an electrochromic device (ECD). The absorption features of colored-to-transmissive switching conjugated polymers have been investigated by exploring material design strategies in conjunction with analytical approaches to optimize and enhance the optical contrast. In parallel, transmissive redox-active radical polymer counter electrodes have been developed as compatible charge-balancing layers and integrated into devices by pairing with electrochromic polymers (ECPs) to achieve stable and high-contrast optical modulation. Electrochemical activity of both conjugated and radical polymer electrodes in different ionic and solvent environments have been further examined to understand material-electrolyte interactions governing mixed ionic-electronic conduction. Finally, a small molecular approach to realizing transparent-to-colored electrochromism is discussed, where distinct substituent-induced degradation pathways of conjugated radical cations were revealed. Overall, this research aims to assist future development of robust, ultra-high contrast organic electrochromic platforms.  </p>

This diploma thesis deals with selection, design and creation of new education materials for high school teacher supporting webpage www.studiumchemie.cz. The selection of the proper theme was done on the basis of research and evaluation of recent materials on the mentioned webpage and materials created at the Department of chemical education of Faculty of Science of Charles University in Prague. Preliminarily, the themes of synthetic macromolecular materials and new materials were selected. The convenience of the selected themes was confirmed by research and evaluation concerned to the preliminarily selected theme of recent high school textbooks and webpages. Consequently, educational materials in the form of PowerPoint presentations, websites, worksheets, tests, games and experiments focused on the themes of synthetic macromolecular substances and new materials were created. Materials were processed in accordance with the Framework Education Programme for Secondary General Education (Grammar Schools) as well as in accordance with the requirements of the Catalogue of graduation exam requirements from chemistry. The PowerPoint presentation and the webpage on synthetic macromolecular materials were roughly evaluated by group of teachers and the results of the evaluation are also part of the thesis....

<p> </p> <p>Learning about ‘behavior’ has always been at the heart of my research endeavors. While my undergraduate work in evolution and ecology exposed me to the science behind why a behavior exists, in my graduate work, I intended to explore how to use something’s behavior to widen its applicability. In this thesis, <em>I will present three works that utilize some of the fundamental</em></p> <p><em>behaviors (i.e., properties) of elastin-like polypeptides (ELP) to improve existing protein purification methods or explore their applicability in bladder cancer imaging and immunotherapy. </em></p> <p>Bladder cancer has high recurrence rates (60-70 % annually) that necessitate multiple follow-up therapies making it one of the costliest cancers per patient. In this work, we have attempted to address two leading causes of the recurrence. First is a low sensitivity (62-84 %) and variable specificity (43-95 %) of white light cystoscopy used to diagnose and remove tumors. We aimed to address the heart of this problem, i.e., the non-specific mode of detection using white light. Only the trained eyes can discern abnormal from normal-appearing tissues even then, leaving up to 45% of tumors unresected to colonize and spread. <em>We developed and characterized near infrared dye-peptide-ligand conjugates (NIR-ELP-ligand) that undergo receptor-mediated binding and internalization to human bladder cancer cells in vitro and tissues ex vivo.</em> By using a molecular target-based probe in combination with NIR imaging, we can aid in improving the detection limit via selective binding to the tumor and reduction in background autofluorescence.</p> <p>Bacillus-Calmette Guérin (BCG) instillation in the bladder is the gold-standard</p> <p>immunotherapy used after surgical removal of bladder tumors. This was approved as a response to the inefficiency of surgery alone in improving cancer status. It has succeeded by reducing the recurrence rate to 30-50 %. But it comes with the complications of putting a live mycobacterium</p> <p>in the human body and giving a patient a urinary tract infection right after surgical tumor resection. <em>Thus, we aimed to deliver nucleic acid as immunotherapeutic cargo in a selective manner to elicit robust anti-tumor immune responses while minimizing the side effects due to its carrier.</em> Towards</p> <p>this goal, we have developed a highly modular and adaptable ELP-ligand fusion protein-based nucleic acid delivery carrier targeted toward bladder cancer. Before developing targeted peptide-based cancer imaging and nucleic acid delivery modalities, we addressed the Achilles heel of peptide-based approaches. The peptide and protein industry suffers</p> <p>through complex, time-consuming, inconsistent, and low-yielding purification methods. <em>We have developed a scalable, facile, and reproducible protein purification method that delivers ELP and ELP fusion proteins free of host cell proteins and nucleic acids and has low lipopolysaccharide</em></p> <p><em>content in just 3 h starting from a bacterial pellet. </em>Thus, for a coherent narrative, the thesis is structured as follows:</p> <p>1. Introduction</p> <p>2. ELP as a protein purification tag: Development of a rapid purification method for ELPs and ELP fusion proteins.</p> <p>3. ELP as a cancer imaging agent: Development of NIR-ELP-Ligand imaging probe targeting bladder cancer.</p> <p>4. ELP as a drug delivery agent: Utilizing ELP-ligand fusion protein in the formulation of targeted nucleic acid delivery carrier to bladder cancer.</p>