Single molecule force spectroscopy is an important technique to determine the interaction forces between biomolecules. Atomic force microscopy (AFM) is one of the tools used for this purpose. So far, AFMs usually use cantilevers as the force sensors and piezoelectrics as the actuators which may have some drawbacks in terms of speed and noise. In this research, a micromachined membrane actuator was used in two important types of experiments, namely the single molecule pulling and force-clamp based force spectroscopy. These two methods permit a more direct way of probing the forces of biomolecules, giving a detailed insight into binding potentials, and allowing the detection of discrete unbinding forces. To improve the quality of the experiments there is a need for high force resolution, high time resolution and increase in the throughput. This research focuses on using the combination of AFM and membrane based probe structures that have electrostatic actuation capability. The membrane actuators are characterized for range, dynamics, and noise to illustrate their adequacy for these experiments and to show that the complexity they introduce does not affect the noise level in the system. The control system described in this thesis utilizes the novel membrane actuator structures and integrates it into the current AFM setup. This is a very useful tool which can be implemented on any AFM without changing its mechanical architecture. To perform an experiment, all that is needed is to place the membrane actuator on the AFM stage, under the imagining head, and run the control system, which was implemented using LabVIEW. The system allows the user to maintain a precise and continuous control of the force. This was demonstrated by performing a life time experiment using biomolecules. Moreover, by slightly modifying the control scheme, the system allows us to linearize the membrane motion, which is inherently non-linear. The feasibility of using this control system for a variety of loading rate experiments are also demonstrated.

Integrins are heterodimers that mediate cell adhesion in many physiological processes. Binding of integrins to ligands provides anchorage and signals for the cell. However, how force regulates integrin/ligand dissociation is unclear. Atomic force microscopy was used to measure the force dependence of lifetimes of single bonds between a FN fragment and integrin α₅β₁. First, lifetime-force relationships demonstrated that force prolonged bond lifetimes in the 10-30 pN range, a behavior called catch bonds. Changing divalent cations from Ca²⁺/Mg²⁺ to Mg²⁺/EGTA and to Mn²⁺ caused more pronounced catch bonds. A truncated α₅β₁ construct containing the headpiece but not the legs (trα₅β₁-Fc) formed much longer-lived catch bonds in the same force range. Bindings of two activating mAbs, 12G10 and TS2/16, left shift the catch bond and converted catch bonds to slip bonds, respectively. Catch bonds may provide a mechanical mechanism for the cell to regulate adhesion by applying different forces. Second, FNIII₇₋₁₀/α₅β₁-Fc/GG-7 bond was stretched to ~ 30 pN and then relaxed to ~ 7 pN at which the bond's lifetime was measured. The strong bond state induced by the 30 pN stretching stayed stable even after the force was reduced to 7 pN. In other words, lower the force would not weaken FNIII₇₋₁₀/α₅β₁-Fc bond once it had been stretched. Similar behaviors were observed for FNIII₇₋₁₀/trα₅β₁-Fc and FNIII₇₋₁₀/mα₅β₁interactions. In addition, the efficiency of the force to induce such a strong bond state for FNIII₇₋₁₀/α₅β₁-Fc interaction in 2 mM Mg²⁺/EGTA condition was characterized. The probability of force to induce the strong bond state increased as force increased and when the force reached 26 pN, all bonds were transit to the strong state. Moreover, reversible unbending of α₅β₁binding with FNIII₇₋₁₀ under mechanical force were observed, which proved that integrin bending and unbending was dynamic. Importantly, integrin could restore bent conformation even when engaged with its ligand, providing a mechanism for mechanotransduction. Third, structural changes of α₅β₁under force were observed. The structural changes did not change the trend of lifetime-force relationships of FNIII₇₋₁₀/α₅β₁/GG-7 bond. Moreover, the lifetime for the structural changes to occur and molecular length changes caused by them were characterized.

Photophysical characterization of several species of fluorescent silver nanoclusters, encapsulated in oligonucleotide scaffolds, was achieved at the bulk and single molecule level. These studies reveal the presence of a short-lived microsecond blinking component which leads to higher emission rates than exhibited by common organic dyes. This dark state was found to be photo-accessible with a very efficient depopulation transition leading to repopulation of the emissive state. Secondary excitation on resonance with this transition significantly shortens the residence time in the dark state giving rise to as much as 5-fold fluorescence enhancement. Manipulation of the secondary laser can be used to impose a regularly modulated waveform onto the fluorescent signal. Signal processing techniques can be employed to extract the modulated signal from large backgrounds, leading to drastically improved sensitivity. This new imaging concept can be extended, beyond Ag nanoclusters, to common organic fluorophores that demonstrate large dark state quantum yields. These fluorophores simultaneously illustrate the utility of this technique and help to define a general set of parameters for engineering ideal dyes for modulated signal extraction. Ideally suited for fluorescence enhancement, FRET pairs can be used to engineer a wide range of modulatable systems, based on detecting donor emission in the presence of a laser directly exciting the acceptor. The utility of Ag nanoclusters, organic dyes, and FRET systems for improved sensitivity are investigated in this work.

Conventional kinesin (kinesin-1) transports membrane-bounded cargos such as mitochondria and vesicles along microtubules. In vivo it is likely that several kinesins move a single organelle and it is important that they operate in a coordinated fashion so that they do not interfere with each other. Evidence for coordination comes from in vitro assays, which show that the gliding speed of a microtubule driven by many kinesins is as high as one driven by just a single kinesin molecule. Coordination is thought to be facilitated by flexible domains so that when one motor is bound another can work irrespectively of their orientations. The tail of kinesin-1 is predicted to be composed of a coiled-coil with two main breaks, the “swivel” (380-442 Dm numbering) and the hinge (560-624). The rotational Brownian motion of microtubules attached to a glass surface by single kinesin molecules was analyzed and measured the torsion elasticity constant. The deletion of the hinge and subsequent tail domains increase the stiffness of the motor (8±1 kBT/rad) compared to the full length (0.06±0.01 kBT/rad measured previously), but does not impair motor cooperation (700±16nm/s vs. full length 756±55nm/s - speed in high motor density motility assays). Removal of the swivel domain generates a stiff construct (7±1 kBT/rad), which is fully functional at single molecule (657±63nm/s), but it cannot work in large numbers (151±46nm/s). Due to the similar value of flexibility for both short construct (8±11 kBT/rad vs 7±1 1 kBT/rad) and their different behavior at high density (700±16 nm/s vs. 151±46 nm/s) a new hypothesis is presented, the swivel might have a strain dependent conformation. Using Circular Dichroism and Fluorescence the secondary structure of this tail region was studied. The central part of the swivel is dimeric α-helical and it is surrounded by random coils, thereby named helix-coil (HC) region. Furthermore, an experimental set-up is developed to exert a torque on individual kinesin molecules using hydrodynamic flow. The results obtained suggest for the first time the possibility that a structural element within the kinesin tail (HC region) has a force-dependent conformation and that this allows motor cooperation.

Thesis (Ph.D.)--York University, 2007. Graduate Programme in Chemistry. / Typescript. Includes bibliographical references. Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:NR39012

In recent years Crowdsourced, or Volunteered, Geographic Information (CGI, VGI), has emerged as a large, up-to-date and easily accessible data source. Primarily attributable to the rise of the Geoweb and widespread use of location enabled technologies, this environment of widespread innovation has repositioned the role of consumers of spatial information. Collaborative and participatory web environments have led to a democratisation of the global mapping process, and resulted in a paradigm shift to the consumer of geographic data also acting as a data producer. With such a large and diverse group of participants actively mapping the globe, the resulting flood of information has become increasingly attractive to authoritative mapping agencies, in order to augment their own spatial data supply chains. The use of CGI would allow these agencies to undertake continuous improvement of their own data and products, adding a dimension of currency that has previously been unattainable due to high associated costs. CGI, however, through its diversity of authorship, presents a quality assurance risk to these agencies should it be included in their authoritative products. Until now, this risk has been insurmountable, with CGI remaining a “Pandora’s Box” which many agencies are reluctant to open. This research presents an algorithmic model that overcomes these issues, by quantifying trust in CGI in order to assess its implied quality. Labeled “VGTrust”, this model assesses information about a data author, its spatial trust, as well as its temporal trust, in order to produce an overall metric that is easy to understand and interpret. The VGTrust model will allow mapping agencies to harness CGI to augment existing datasets, or create new ones, thereby facilitating a targeted quality assurance process and minimizing risk to authoritativeness. This research proposes VGTrust in theory, on the basis of existing examinations of trust issues with CGI. Furthermore, a facilitated case study, “Building Our Footprints” is presented, where VGTrust is deployed to facilitate the capture of a building footprint dataset, the results of which revealing the veracity of the model as a measure to assess trust for these data. Finally, a data structure is proposed in the form of a “geo-molecule”, which allows the full spectrum of trust indicators to be stored a data structure at feature level, allowing the transitivity of this information to travel with each feature following creation. By overcoming the trust issues inherent in CGI, this research will allow the integration of crowdsourced and authoritative data, thereby leveraging the power of the crowd for productive and innovative re-use.

<p>Inducible Heat shock protein (Hsp70i) is a protein chaperone that is utilized during tumorigenesis and viral infections for efficient propagation. Overexpression of Hsp70i is observed in a wide spectrum of human tumors, and this overexpression correlates with metastasis, poor outcomes, and resistance to chemotherapy in patients. Hsp70i aids in cancer cell propagation through regulation of anti-apoptotic and cell survival pathways. Furthermore, Hsp70i is induced following infection for several viruses and aids viral propagation, in part through regulation of anti-apoptotic pathways as well as promoting the folding of newly synthesized proteins. Due to the parallel role of Hsp70i in both cancer and viral pathogenesis, identification of small-molecule inhibitors selective for Hsp70i could provide tools for the development of novel therapeutics and further elucidate the role of Hsp70i in both cancer and viral infections.</p><p>To date, few Hsp70 inhibitors have been identified and characterized, and their efficacy in clinical settings is unknown. Through the fluorescence-linked enzyme chemoproteomic strategy (FLECS) screen, an allosteric inhibitor selective for Hsp70i was identified, called HS-72. We show that HS-72 is highly selective for Hsp70i, over the broader purinome and other Hsp70 family members, in particular the closely related constitutively active Hsp70 family member, Hsc70. Additionally, HS-72 acts as an allosteric inhibitor to induce a conformational change and inhibit Hsp70i activity. HS-72 displays hallmarks of Hsp70i inhibition in vitro by promoting Hsp70i substrate protein degradation, protein aggregation, and selective growth inhibition of cancer cells. In wild type mice HS-72 is well tolerated and a limited PK study shows HS-72 is bioavailable. Furthermore, in a MMTV-neu breast cancer mouse model, HS-72 shows efficacy to inhibit tumor growth and promote survival.</p><p>Due to the similar utilization of Hsp70i in cancer and viral pathogenesis, this suggests the potential for HS-72 as an antiviral agent. Dengue virus (DENV) is of great public health importance due to estimates of up to 400 million infections per year, coupled with the geographic distribution of the virus, which is now endemic in over 100 countries worldwide. There is also a pressing need for DENV interventions, owing to the lack of approved vaccines or antiviral therapies. DENV is reliant on host factors throughout the viral life cycle and Hsp70i has been implicated as a host factor in DENV pathogenesis. Additionally, the complete role of Hsp70i in DENV pathogenesis remains to be elucidated, highlighting a unique opportunity to use HS-72 as a tool to specifically probe Hsp70i function. In monocytes, Hsp70i is expressed at low levels preceding DENV infection, but Hsp70i expression is induced upon DENV infection. Furthermore, inducing Hsp70i expression prior to infection, correlates with an increase in DENV infection. Targeting Hsp70i with HS-72, results in a dose dependent reduction in DENV infected monocytes, while cell viability was maintained, through inhibiting the entry stage of the viral life cycle. Following infection, Hsp70i localizes to the cell surface and interacts with the DENV receptor complex to mediate viral entry. While, HS-72 treatment results in a disruption of the interaction of Hsp70i with the DENV receptor complex, yielding a reduction in infected cells. </p><p>Collectively this work further supports Hsp70i as an anticancer and anti-dengue virus target, and identifies HS-72, a chemical scaffold that is amenable to resynthesis and iteration, as an ideal starting point for a new generation of therapeutics targeting Hsp70i.</p> / Dissertation

Over the past few decades, RNA has emerged as much more than just an intermediary in biology’s central dogma. RNA is now known to play a variety of catalytic, regulatory and defensive roles in living systems as demonstrated through the discoveries of ribozymes, riboswitches, microRNAs, small interfering RNAs, Piwi-interacting RNAs, small nuclear RNAs, clusters of regularly interspaced short palindromic repeat RNAs and long non-coding RNAs. In contrast to the functional diversity of RNA, the chemical diversity has remained primarily limited to canonical polyribonucleotides, the 5’ cap on mRNAs in eukaryotes, modified nucleotides and 3’-aminoacylated tRNAs. This disparity coupled with the powerful functional properties of small molecule-nucleic acid conjugates led us to speculate that novel small molecule-RNA conjugates existed in modern cells, either as evolutionary fossils or as RNAs whose functions are enabled by the small molecule moieties. We developed and applied a nuclease-based screen coupled with high-resolution liquid chromatography/mass spectrometry analysis to detect novel small molecule-RNA conjugates, broadly and sensitively. We discovered NAD-linked RNA in two types of bacteria and further characterized the small molecule and RNA in Escherichia coli. The NAD modification is found on the 5’ end of RNAs between 30 and 120 nucleotides long, and is surprisingly abundant at around 3,000 copies per cell. Subsequent experiments to characterize further NAD-linked RNA have been undertaken, including sequencing the RNAs to which NAD is attached and elucidating the biological functions of the small molecule-RNA conjugate. The development and application of a screen to detect novel nucleotide modifications that is independent of structure or biological context has the potential to increase our understanding of the functional and chemical diversity of RNA. The discovery and biological characterization of NAD-linked RNA can provide new examples of RNA biology and offer insight into the RNA world.

The studies discussed in this thesis unify experimental and theoretical techniques, both established and novel, in investigating the problem of how a protein that binds specific sites on DNA translocates to, recognizes, and stably binds to its target site or sites. The thesis is organized into two parts. Part I outlines the history of the problem and the theory and experiments that have addressed the problem and presents an apparent incompatibility between efficient search and stable, specific binding. To address this problem, we elaborate a model of protein-DNA interaction in which the protein may bind DNA in either a search (S) mode or a recognition (R) mode. The former is characterized by zero or weak sequence-dependence in the binding energy, while the latter is highly sequence-dependent. The protein undergoes a random walk along the DNA in the S mode, and if it encounters its target site, must undergo a conformational transition into the R mode. The model resolves the apparent paradox, and accounts for the observed speed, specificity, and stability in protein-DNA interactions. The model shows internal agreement as regards theoretical and simulated results, as well as external agreement with experimental measurements. Part II reports on research that has tested the applicability of the two-mode model to the tumor suppressor transcription factor p53. It describes in greater depth the experimental techniques and findings up to the present work, and introduces the techniques and biological system used in our research. We employ single-molecule optical microscopy in two projects to study the diffusional kinetics of p53 on DNA. The first project measures the diffusion coefficient of p53 and determines that the protein satisfies a number of requirements for the validity of the two-mode model and for efficient target localization. The second project examines the sequence-dependence in p53's sliding kinetics, and explicitly models the energy landscape it experiences on DNA and relates features of the landscape to observed local variation in diffusion coefficient. The thesis closes with proposed extensions and complements to the projects, and a discussion of the implications of our work and its relation to recent developments in the field.

Gene expression is a fundamental process in the cell and is made up of two parts – the information flow from DNA to RNA, and from RNA to protein. Here, we examined specific sub-processes in Escherichia coli gene expression using newly available tools that permit genome-wide analysis. We begin our studies measuring mRNA and protein abundances in single cells by single-molecule fluorescence microscopy, and then focus our attention to studying RNA generation and degradation by high throughput sequencing. The details of the dynamics of gene expression can be observed from fluctuations in mRNA and protein copy numbers in a cell over time, or the variations in copy numbers in an isogenic cell population. We constructed a yellow fluorescent fusion protein library in E. coli and measured protein and mRNA abundances in single cells. At below ten proteins per cell, a simple model of gene expression is sufficient to explain the observed distributions. At higher expression levels, the distributions are dominated by extrinsic noise, which is the systematic heterogeneity between cells. Unlike proteins which can be stable over many hours, mRNA is made and degraded on the order of minutes in E. coli. To measure the dynamics of RNA generation and degradation, we developed a protocol using high throughput sequencing to measure steady-state RNA abundances, RNA polymerase elongation rates and RNA degradation rates simultaneously with high nucleotide-resolution genome-wide. Our data shows that RNA has similar lifetime at all positions throughout the length of the transcript. We also find that our polymerase elongation rates measured in vivo on a chromosome are generally slower than rates measured on plasmids by other groups. Studying nascent RNA will allow further understanding of RNA generation and degradation. To this end, we have developed a labeling protocol with a nucleoside analog that is compatible with high throughput sequencing.