Gene regulation is vital to the success of all living organisms. Understanding this complex process is crucial to our knowledge of how cells function and how in some cases they can lead to debilitating or even fatal disease. In this thesis I focus on a set of DNA-binding proteins known as transcription factors (TFs), proteins fundamental to the process of gene regulation at the level of transcription. I develop assays and techniques for the detection and quantitation of TFs in vitro and in vivo as well as a method for TF encapsulation and release. The advantages of the TF detection assays in this thesis are made possible through the use of single-molecule (sm) fluorescence. This methodology enables detection of individually labeled molecules allowing discrimination of sample heterogeneities inaccessible with ensemble techniques. Here I present two different TF assays based on two sm observables: relative probe stoichiometry and Förster resonance energy transfer (FRET). The first assay design, based on stoichiometry, detects TFs using TF-dependent coincidence of two distinctly labelled DNA ‘half-sites’. I demonstrate sensitive detection (~ pM) in solution and on surfaces, multiplexed detection of multiple TFs, and detection in cell lysates. A kinetic model of the system is also developed, verified experimentally and used to quantify TF concentrations without the need for a calibration curve. The second assay design, based on FRET, is a novel approach to TF detection using TFmediated DNA bending. TFs are detected by bending the sensor and monitored with FRET at the single-molecule or ensemble level. I demonstrate TF detection in purifed form and expressed in cell lysates. As this sensor was designed for use in vivo, methods to hinder nuclease degradation are explored. For TF detection in vivo, I describe a successful strategy to internalise fluorescently labeled molecules into live E.coli. Viability and internalisation efficiency are characterised and ensemble measurements with FRET standards are demonstrated. Importantly, sm FRET measurements in vivo are achieved opening many exciting possibilities. The FRET based TF sensor is then internalised as a step towards real-time in vivo monitoring of TF concentrations. Finally a system based on DNA nanotechnology is presented for the non-covalent encapsulation and release of TFs. Such a system could be delivered into a cell to alter levels of gene expression using external stimuli as inputs. We believe these tools will generate valuable information in the study of prokaryotic gene expression as well as providing a potential commercial avenue towards diagnostics.

With the increased usage and production of engineered nanoparticles (ENPs), entry into the environment and hence contact with plant root systems is inevitable. Nano zinc oxide (nZnO) is widely used in commercial products, such as sunscreens, paints and coatings due to its high antimicrobial properties and wide electrical band-gap. Disposal down drains and into greywater leads to particle entry into the environment via waste water systems. Here, ENPs could potentially interact with plant root systems, which may lead to uptake, translocation and accumulation within plant tissues, and in the case of edible crops have consequences on human health. This study aimed to identify mechanisms of toxicity by employing whole-cell biosensors in conjunction with model bacteria and plant species. Furthermore, zeta potential (ZP), particle size, reactive oxygen species (ROS) release and solubility of the particles were determined and linked to both plant and bacterial toxicity. In Escherichia coli bacteria, it was demonstrated that growth inhibition from nano-scale ZnO treatment was similar to that from the bulk-scale ZnO and ionic zinc treatments, with the concentrations leading to 50 % inhibition (IC50) demonstrated to be 251, 282 and 298 mg/L for bulk, nano-scale and ZnSO4, respectively. It was demonstrated that the mode of nZnO toxicity in E. coli was bacteriostatic rather than bacteriotoxic. In barley plants, biomass was negatively impacted by up to 50 %, and significantly more zinc was able to enter root tissues as a result of hydroponic nZnO treatment, with 47 mg/L zinc detected in root tissues after 7 days treatment with 500 mg/L nZnO. Comparison of particle characteristics revealed that ROS, solubility, ZP, size and concentration were involved in toxicity, with ZP (charge) identified as a key parameter in both plant and bacterial toxicity.

Systemic administration of adenovirus type 5 (Ad5) vectors for the treatment of cancer is limited by poor circulation kinetics and inefficient uptake from the bloodstream into tumours. This study reports a novel method for linkage of highly-PEGylated gold nanoparticles (AuPEG) to Ad5 by a single reduction cleavable bond. The resulting ‘dandelion’ structure provides very effective steric shielding with only minimal and reversible modification of the Ad5 capsid. This ablates in vitro cell infection, improves protection against the binding of antibodies, and enhances in vivo circulation kinetics. Focused ultrasound is a promising technology for the non-invasive, targeted treatment of cancer. In the context of drug delivery, cavitational energy generated upon exposure of ultrasound contrast agents to focused ultrasound can be used as a powerful stimulus to move therapeutics over distances of hundreds of microns away from blood vessels. In addition to providing a platform for effective stealthing, conjugation of AuPEG to Ad5 also increases the effective density of Ad5. This increase in density imparts a second major advantage on the strategy, observed for the first time in the present study: denser particles are transported significantly farther by cavitation-induced microstreaming than identically-sized particles of lower density. Specifically, in in vitro tests using a tumour-mimicking flow-channel phantom model and in in vivo experiments using tumour bearing mice, Ad5–AuPEG was delivered farther from vessels in response to ultrasound induced cavitation than either naked Ad5 or polymer-coated Ad5. The enhancements in stealthing and improvements in response to ultrasound provided by this strategy enabled up to 12% (S.D. 0.97) of the injected dose to be deposited in the tumour, compared to just 0.12% (S.D. 0.05) for Ad5 without ultrasound (p < 0.001). Consequently, in a survival study, mice treated with Ad5–AuPEG with focussed ultrasound had the slowest tumour growth and longest survival rate when compared to mice treated with Ad5 alone, Ad5–AuPEG alone, or Ad5 with focussed ultrasound. These results provide compelling evidence that the combination of focussed ultrasound with density-augmented stealthed Ad5 results in improved delivery to tumours and therapeutic efficacy. This combination of ultrasound with particle modification for optimal cavitation-mediated delivery has the potential to be applied to a broad range of anti-cancer nano-medicines and therapeutics to augment their bio-availability for improved cancer treatment.

This thesis forms part of an ongoing project in the DNA Group to build and operate a synthetic ribosome. We present two synthetic ribosome designs that can be combined with DNA-templated chemistry to generate libraries of functional synthetic small molecules. In Chapter 2 we use the DNA strand displacement technique to construct a mechanism that is capable of moving along a DNA track. We explore ways to control the speed and the driving force of the mechanism, and present a mathematical model of the system. We discuss the ability of the design to incorporate chemically-functionalised DNA strands. In Chapter 3 we use a 2D DNA origami tile as the basis of the synthetic ribosome mechanism. Functionalised DNA strands are arranged on the surface of the tile, and we demonstrate the ability to template reactions between the strands, and discuss the possibility of creating a library of distinct chemical products from a single origami tile.

This thesis describes my investigations into the principles underlying self-assembly of DNA origami nanostructures and discusses how these principles may be applied. To study the origami folding process I designed, synthesized and characterized a polymorphic tile, which could adopt various shapes. The distribution of tile shapes provided new insights into assembly. The origami tiles I studied were based on scaffolds derived from customized plasmids, which I prepared using recombinant DNA technology. I developed a technique to monitor incorporation of individual staples in real time using fluorescence, measuring small differences in staple binding temperatures (~0.5-5 °C). I examined the tiles using Atomic Force Microscopy and I found that a remarkably high proportion of polymorphic tiles folded well, which suggests that there are assembly <b>pathways</b>, arising from strong cooperation between staples. In order to analyse the tile shapes quantitatively, I developed a specialized image processing technique. For validation of the method, I generated and analysed simulated data, and the results confirmed that I could measure individual tile parameters with sub-pixel resolution. I studied eleven variants of the polymorphic tile, and I proved that minor staple modifications can be used to change the folding pathway dramatically. The strength of cooperation between staples affects their behaviour, which is also influenced by their length and base sequences. Paired staples are particularly significant in assembly, and there are clear parallels with protein folding. I describe in an Appendix how I applied origami assembly principles in the development of my concept for an autonomous rotary nanomotor utilizing the sequential opening of DNA hairpins (already used for linear motors). This device represents an advance over non-autonomous rotary motors and I have simulated its performance. In this thesis I have answered important questions about DNA origami assembly, and my findings could enable the development of more sophisticated DNA nanostructures for specific purposes.

La nanotechnologie possède la potentialité d’améliorer la sécurité, les procédés, l’emballage alimentaire et le concept d’ingrédient fonctionnel. La nano-encapsulation d’agents actifs, est un concept innovant permettant de protéger les agents actifs d’une dégradation éventuelle pendant le procédé de fabrication de l’aliment et son stockage. Le principal objectif de ce travail est de développer et d’optimiser une méthode de marquage fluorescent afin d’effectuer des études de transfert dans différents films de bio-polymères et dans l’aliment et de nano-encapsuler la nisine. La nano-encapsulation de la nisine dans différents nano-liposomes par micro-fluidisation (CCDS) est une technique innovante pour la fabrication de nano-systèmes de re-largage. L’incorporation de nisine sous forme de nano-émulsion est une méthode efficace de contrôle des flores pathogènes sans altérer les caractéristiques des films d’HPMC. La nisine Z a été marquée par un composé fluorescent, et a une masse moléculaire de 3713,3. Des études en microscopie confocale ont permis de démontrer que l’interaction de la nisine avec les membranes bactériennes se situait au niveau de site de division de la cellule. L’HPMC, le chitosane, le caséinate et l’acide poly-lactique agissent comme des réservoirs et libèrent progressivement la nisine afin d’obtenir un effet inhibiteur durable. Le choix du biopolymère affecte la biodispinibilité du composé à la surface et à l’intérieur de l’aliment. La prochaine révolution concernant la sécurité alimentaire par l’emballage mettra en avant le dernier concept technologique « 3-BIOs » qui se réfère aux notions Bioactif - Biodégradable - Bionanocomposite / Food nanotechnology has the potential to improve food safety and bio-security, food processing, food packaging and functional ingredients. Nano-encapsulation of active agents is an innovative concept to protect them against possible denaturation during processing and storage. The overall objective of the present work was to optimize and develop fluorescent labeling and encapsulation of nisin for molecular transfer study in different packaging based on biopolymers and in the food. Nanoencapsulation of nisin in different nanoliposomes by using continuous cell disruption system (CCDS) has provided an innovative method for nano-delivery systems fabrication. Incorporation of nisin in nano-emulsion form (encapsulated and free) can possibly be an effective approach to control pathogen without compromising the basic physico-chemical attributes of composite HPMC coatings. The fluorescently labeled nisin Z prepared had a molecular weight of 3717.3 Da. Confocal microscopic studies demonstrated the interaction of nisin with the bacterial membranes at the cell-division sites as possible mechanism of action against food borne pathogen. HPMC, CTS, SC and PLA packaging bio-membranes act as a reservoir and progressively release nisin to sustain a constant inhibitory effect. Choice of biopolymer is significant in providing requisite bioavailability of antimicrobial compounds at exterior surface and inside the food system. Based on the present study results, the emerging revolution concerning food safety through packaging possibly will rely on « 3-BIOs » blend with nanotechnology, which refers to Bioactive, Biodegradable and Bio-nanocomposite

>Magister Scientiae - MSc / Nanotechnology has emerged as an elementary division of modern science and stemmed directly from green chemistry twelve basic concepts, it receives global attention due to its unique character and ample applications. It also has great potential to mitigate the challenges they face in various fields, especially medical sector. Nanodrugs are increasingly considered as a potential candidate to carry therapeutic agents safely into a targeted compartment in an organ, particular tissue or cell. In this study, twenty (20) Libyan plants were selected and evaluated for their potential to synthesis gold and silver nanoparticles. The screening of the different plant extracts was performed using 96 well plate method at 25 °C and 70 °C. The NPs formation was confirmed and characterized using UV- Vis, DLS, HR-TEM and EDX. A well-defined NPs were obtained at high temperature (70 °C). The Au NPs had an average diameter of 92 nm at 25 °C and 66 nm at 70 °C. The zeta potential values were observed to be negative (-14 to -24) and indicate the stability of the Au NPs. The HR-TEM showed polydispersity, which decreased at higher temperature (70 °C). The stability of Au NPs in nutrient broth prior was conducted as well. All the Au NPs under study showed stability, only minimal changes in the UV-Vis spectra can be observed. Two plant extract viz Pistacia atlantica, Junipers phoenicea showed consistent results and forming stable and smaller NPs compared to others, both of the plant extracts and the corresponding NPs were tested against Streptococcus mutans and showed MIC value ~ 49 g/mL. In case of silver NPs, two plant extracts viz J. phoenicea, Rosmarinus officinalis, showed superior results than the others; both plants produced stable and small Ag NPs. The antibacterial activity against S. mutans demonstrated MIC valus ~ 50 g/mL. The synthesised NPs showed a promising bioactivity for developments of new antibacterial agents against S. mutans strains. Dose-dependent activity was observed for the tested NPs.

Understanding the factors influencing the ET characteristics of redox proteins confined at an electrochemical interface is of fundamental importance from both pure (fundamental science) and applied (biosensory) perspectives. This thesis reports on progress made in the emerging field of coupled electrochemical characterization and optical imaging in moving the analysis of redox-active films to molecular scales. More specifically the combination of cyclic voltammetry and wide-field Total Internal Reflection (TIRF) microscopy, here named ‘Fluorescent Cyclic Voltammetry’ (FCV), was applied to monitoring the response of surface-confined redox active proteins at submonolayer concentrations. The combined submicrometre spatial resolution and photon capture efficiency of an inverted TIRF configuration enabled the redox reactions of localized populations of proteins to be directly imaged at scales down to a few hundreds of molecules. This represents a 6-9 orders of magnitude enhancement in sensitivity with respect to classical current signals observed in bioelectrochemical analysis. Importantly, measurements of redox potentials at this scale could be achieved from both natural and artificially designed bioelectrochemical fluorescent switches and shed fundamental light on the thermodynamic and kinetic dispersion within a population of surface confined metalloproteins. The first three chapters of this thesis provide an overview of the relevant literature and a theoretical background to both the rapidly expanding fields of electroactive monolayers bioelectrochemistry and TIRF imaging. The initial design and construction of a robust electrochemically and optically addressable fluorescent switch, crucial to the applicability of FCV is reported in chapter 5. The generation of optically transparent, and chemically modifiable electrode surfaces suitable for FCV are also described. Chapter 6 describes the response of the surface confined azurin-based switch. Analysis of the spatially-resolved redox reaction of zeptomole samples in various conditions enables the mapping of thermodynamic dispersion across the sampled areas. In chapter 7 the newly developed FCV detection method was extended to investigate more complex bioelectrochemical systems containing multiple electron transferring redox centres and responding optically at different wavelengths. This approach provides a platform for spectral resolution of different electrochemical processes on the same sample. Finally in chapter 8 an electrochemical procedure is proposed for investigating the kinetic response of redox proteins using a fundamentally new methodology based on interfacial capacitance. In using variations in the surface chemistry to tune the rate of electron transfer, the approach was shown to be a robust and facile means of characterising redox active films in considerably more detail than possible through standard electrochemical methodologies. Ultimately, it can be applied to probe dispersion within protein populations and represents a powerful means of analysing molecular films more generally.

Tumour-associated vasculature provides an accessible target for systemic gene therapy using targeted adenoviruses. The aim of this thesis is to develop strategies for targeting adenovirus infection to tumour-associated endothelium. Adenovirus expressing luciferase (Adluc) was coated with an amino-reactive polymer based on poly [N-(2-hydroxypropyl) methacrylamide] [pHPMA] to ablate normal infection pathways¬. This was a pre-requisite to redirecting virus tropism to infect endothelial cells via specific receptors. Direct attachment to the pHPMA-adenovirus (pcAdluc) of ligands including vascular endothelial growth factor (VEGF165) and a monoclonal antibody (RAFL) recognising VEGF receptor 2 (VEGFR-2) retargeted infectivity to VEGFR-2-positive endothelial cells and not to receptor-negative cells. Specificity of transduction in vitro was shown by competition with excess antibody. In vivo however, the VEGF165-retargeted virus failed to transduce tumour-associated endothelia following systemic administration. Similarly, direct linkage of a monoclonal antibody against E-Selectin (MHES) demonstrated E-Selectin-specific transduction of tumour necrosis factor-α (TNF-α)-activated endothelial cells, although overall levels of infection were not increased compared to unmodified Adluc. A two-component targeting system using protein A or protein G as ‘bridging’ agents was developed to ensure the required orientation of targeting antibodies. Using this system MHES mediated greater transduction of TNF-α-activated endothelial cells than Adluc. Conjugation using protein A also gave non-specific effects which were not seen with protein G. Whereas the unmodified Adluc virus failed to transduce TNF-α-activated endothelium in an umbilical vein model ex vivo, the MHES-protein G-pHPMA-adenovirus (MHES-StrepGpcAdluc) mediated good transduction. Similarly, StrepGpcAdluc retargeted with a chimeric P-Selectin Glycoprotein Ligand-1 (PSGL-1)-Fc fusion protein, showed good circulation kinetics and significant uptake into HepG2 xenografts following intravenous administration. Histological studies suggested selective targeting to tumour-associated endothelial cells. Overall these findings support the assertion that tumour-associated vasculature is an accessible target for systemic gene delivery, and the use of protein G as bridging agent facilitates rapid screening of Fc-bearing ligands for retargeting pcAd infection to tumour-associated endothelium.

Peptide fusion tags are fundamental for the identification, detection, and capture of proteins in biological assays. Commonly used peptide fusion tags rely on temporary non-covalent interactions for binding, which can put constraints on assay sensitivity. Here, peptide fusion tags were developed that could specifically interact with protein binding partners via spontaneous and irreversible isopeptide bond formation. To develop covalently interacting peptide-protein pairs, outer-membrane proteins from Gram-positive bacteria that form autocatalyzed intramolecular isopeptide bonds were dissected to generate a short peptide fragment and a protein binding partner. Initially, the major pilin subunit Spy0128 from Streptococcus pyogenes was split to develop the 16 residue isopeptag peptide and the 31 kDa pilin-C protein partner. The isopeptag:pilin-C pair were able to react via spontaneous isopeptide bond formation between an Asn residue in isopeptag and a Lys residue in pilin-C without the requirement for any accessory factors, and with a yield of 60% after a 72 hr reaction. Reconstitution between the isopeptag:pilin-C pair was robust and occurred under all biologically relevant conditions tested, and also in the complex environment of a bacterial cytosol and on the surface of mammalian cells. A similar approach was also used to dissect the small CnaB2 domain that is part of the large FbaB fibronectin-binding protein from S. pyogenes. This led to the development of a more efficient peptide-protein pair, which was rationally modified to generate the highly optimized SpyTag:SpyCatcher pair. SpyTag is a 13 amino acid peptide with a reactive Asp that forms a spontaneous intermolecular isopeptide bond with a Lys present in the 12 kDa SpyCatcher binding partner. In a reaction with SpyTag, over 40% of SpyCatcher was depleted after 1 min and SpyCatcher could no longer be detected after 2 hr. The SpyTag and SpyCatcher reaction did not require any accessory factors and proceeded efficiently at a range of biologically relevant temperatures, pH values, concentrations, buffer compositions, and in the presence of commonly used detergents. The SpyTag:SpyCatcher technology was also used for specific cell surface labelling on mammalian cell membranes. SpyTag and SpyCatcher are both composed of the regular 20 amino acids and can therefore be genetically encoded as fusion constructs for a variety of in vitro and in vivo applications. Potential applications of the SpyTag:SpyCatcher technology include specific cell surface labelling, the development of novel protein architectures, and the covalent and irreversible capture of target proteins in biological assays.