Over the past decade, solid-state nanopores have emerged as a versatile tool for the detection and characterization of single molecules, showing great promise in the field of personalized medicine as diagnostic and genotyping platforms. While solid-state nanopores offer increased durability and functionality over a wider range of experimental conditions compared to their biological counterparts, reliable fabrication of low-noise solid-state nanopores remains a challenge. In this thesis, a methodology for treating nanopores using high electric fields in an automated fashion by applying short (0.1-2 s) pulses of 6-10 V is presented which drastically improves the yield of nanopores that can be used for molecular recognition studies. In particular, this technique allows for sub-nanometer control over nanopore size under experimental conditions, facilitates complete wetting of nanopores, reduces noise by up to three orders of magnitude and rejuvenates used pores for further experimentation. This improvement in fabrication yield (over 90%) ultimately makes nanopore-based sensing more efficient, cost-effective and accessible. Tuning size using high electric fields facilitates nanopore fabrication and improves functionality for single-molecule experiments. Here, the use of nanopores for the detection of DNA-protein complexes is examined. As proof-of-concept, neutravidin bound to double-stranded DNA is used as a model complex. The creation of the DNA-neutravidin complex using polymerase chain reaction with biotinylated primers and subsequent purification and multiplex creation is discussed. Finally, an outlook for extending this scheme for the identification of proteins in a sample based on translocation signatures is presented which could be implemented in a portable lab-on-a-chip device for the rapid detection of disease biomarkers.

The work presented here has a multidisciplinary character, having as a common factor the characterization of self-assembled nanostructures through force spectroscopy. Exploring AFM as a tool for characterizing self-assembly and interaction forces in soft matter nanostructures, three different Bio and nonbiological systems where investigated, all of them share the common characteristic of being soft matter molecular structures at the nanoscale. The studied systems in question are: a) Polyelectrolyte – lipid nanocomposites. Single polyelectrolyte adsorption-desorption from supported lipid bilayers, b) Polyelectrolyte brushes and c) Virus-Like particles (VLPs). The scientific interest and industrial applications for each of these different nanostructures is broad, and their potential uses in the near future ranges from smart nanocontainers for drug and gene delivery, surface platforms for molecular recognition to the development of new nanodevices with ultrasensitive external stimuli responsiveness. These nano-structures are constructed following assembly of smaller subunits and belong to representative examples of soft matter in modern nanotechnology. The stability, behavior, properties and long term durability of these self-organized structures depends strongly on the environmental conditions to which they are exposed since their building mechanism is a balance between attractive noncovalent interactions and momentum transmitted collisions due Brownian motion of the solvent molecules. For example a set of long chain molecules firmly attached to one end to a surface will alter their conformation as the space between them is reduced or the environmental conditions are modified (i.e. ionic strength, pH or temperature). For a highly packed condition, this fuzzy surface known as a polyelectrolyte brush will then behave as a responsive material with tunable responsiveness. Thus the objective in the present case was to investigate the change in morphology and the mechanical response of a polyelectrolyte brush to external forces by application of AFM nanoindentations under different ionic strength conditions. The degree of penetration of the AFM tip through the brush will provide insights into the forces exerted by the brush against the tip. Compressions on the brush should aid to characterize its changes in compressibility for different salt concentrations. For the second chosen system, the interaction between two assembled interfaces was investigated at the single molecular level. A multilayered film formed by the consecutive assembly of oppositely charged polyelectrolytes and subsequently coated with a lipid membrane represents a fascinating soft composite material resembling more than a few structural components emerging in living organisms. The fluid bilayer, thus provide a biocompatible interface where additional functionalities can further be integrated (fusion peptides for instance). The smooth polymer cushion confers not only structural flexibility but also adaptability of the chosen substrate properties to be coated. This type of interface could be useful in the development of novel molecular biosensors with single molecule recognition capacities or in the fabrication of assays against pathogenic agents. The aim of this project was to study the molecular binding mechanism between the last polyelectrolyte layer and the lipid head group of the lower lipid leaflet. Understanding this adsorption mechanism between both interfaces, should likewise contribute to improve the fabrication of lipid coated polymeric nano/micro capsules with targeting properties. For example this could be critical in the field of nonviral gene therapy, where the improvement in the design of condensates of nucleic acids and other polymers with lipids (lipoplexes) are of main interest for its posterior use as delivery vectors. Finally, viral capsids were investigated. These naturally occurring assembled nanocontainers within living organisms stand for a remarkable example of nature’s morphological designs. These structures self-assemble from a small number of different proteins occurring in identical copies. The capsid as a self-assembled structure carries multiple functions: compaction of the genome, protection against external chemical threats, target recognition, structural support and finally facilitating the release of the genome into the host cell. It is highly interesting how these different functions are organized within the capsid which consists, for example, in the case of the norovirus of 180 identical copies of one single protein. Therefore, the mechanical stability and elastic properties of virus-like particles of Rubella and Norovirus were investigated by external application of loading forces with an AFM tip. The measurements were performed under conditions relevant for the virus infection mechanism. The applied compressions on these protein shells at pH values mimicking the virus life cycle will aid to learn about possible internal transitions among proteins which may be important for switching between the various functions of the capsid. The choice of two unrelated viral systems with different entry pathways into the cell and with different morphological architectures is expected to reveal crucial information about the stability and mechanical resistance to deformation of these empty membrane-coated and bare viral capsids. This last might provide clues on the stage of particle disassembly and cargo release during the final step of the infection process.

Gene regulation mediated by transcription factors (TFs) is essential for all organisms. The functionality of TFs can largely be described by the fraction of time they occupy their regulatory binding sites on the chromosome. DNA-binding proteins have been shown to find their targets through facilitated diffusion in vitro. In its simplest form this means that the protein combines a random 3D search in the cytoplasm with 1D sliding along DNA. This has been proposed to speed up target location. It is difficult to mimic the in vivo conditions for gene regulation in biochemistry experiments; i.e. the ionic strength, chromosomal structure, and the presence of other DNA-binding macromolecules.    In this thesis single molecule imaging assays for live cell measurements were developed to study the kinetics of the Escherichia coli transcription factor LacI. The low copy number LacI, in fusion with a fluorescent protein (Venus) is detected as a localized near-diffraction limited spot when being DNA-bound for longer than the exposure time. An allosteric inducer is used to control binding and release. Using this method we can measure the time it takes for LacI to bind to different operator sequences. We then extend the assay and show that LacI slides in to and out from the operator site, and that it is obstructed by another DNA-binding protein positioned next to its target. We present a new model where LacI redundantly passes over the operator many times before binding.    By combining experiments with molecular dynamics simulations we can characterize the details of non-specific DNA-binding. In particular, we validate long-standing assumptions that the non-specific association is diffusion-controlled. In addition it is seen that the non-specifically bound protein diffuses along DNA in a helical path.    Using microfluidics we design a chase assay to measure in vivo dissociation rates for the LacI-Venus dimer. Based on the comparison of these rates with association rates and equilibrium binding data we suggest that there might be a short time following TF dissociation when transcription initiation is silenced. This implies that the fraction of time the operator is occupied is not enough to describe the regulatory range of the promoter.

Common to molecular electronics studies, nanoscale break junctions created through electromigration also naturally produce electroluminescent arrays of individual gold nanoclusters spanning the electrodes. Due to inelastic electron tunneling into cluster electronic energy levels, these several-atom nanoclusters (Au~18-22) exhibit bright, field-dependent, antibunched emission in the near infrared (650800 nm), acting as room-temperature electrically driven single-photon sources. AC electrical excitation with time-stamping of photon arrival times enables fast and local tracking of electrode-nanocluster coupling dynamics demonstrating that charge injection to the clusters is directly modulated by dynamic coupling to individual electrodes. The electrode-nanocluster coupling rate fluctuates by nearly an order of magnitude and, due to the asymmetry of the electromigration process, exhibits preferential charge injection from the anode. Directly reporting on (and often facilitating) nanoscale charge transport, time-tagged single-molecule electroluminescence reveals a significant mechanism for nanoscale charge transport in nanoscale gold break junctions, and offers direct readout of the electrode-molecule interactions that can be correlated with current flow. Single-molecule electroluminescence techniques for characterization of electrode heterogeneity and dynamics as well as implications for future research are discussed.

For polymers near the glass transition, the dynamics in some regions can be orders of magnitude different compared with the dynamics in other regions only a few nanometers away, so called spatial heterogeneity [1]. In this thesis, single molecule fluorescence microscopy as a powerful tool, was applied to study the spatially heterogeneous dynamics, both orientational and translational, within the polymer matrix near the glass transition temperature. With our total internal reflection fluorescence microscopy (TIRFM) methods, many individual fluorescent dye molecules embedded in the poly (isopropyl acrylate) (PIPA) thin films can be simultaneously excited. Their emission patterns are analyzed using our orientation determination methods [2] to give the true 3D orientational trajectories of the individual molecules. At Tg < T < 1.2 Tg, single molecule tracking was used to study the dye molecules translational diffusion. Results show that, below 1.1 Tg, the probe molecules are in the confined flow region [3]; at T > 1.1 Tg, the diffusion follows normal diffusion model; at T = 1.2 Tg, although the statistical results shows that normal random walk behavior is followed, the individual molecules still show different diffusion behaviors, clear evidence of the spatial heterogeneity that still exists at this temperature. The second part of this thesis is a development of the 3-detector method to determine the 3D orientation of single molecules [4]. This method is based on the work proposed by Fourkas [4] in 2001. Results utilizing this experimental setup are compared with our emission pattern fitting methods. The results show that, with a little bit higher error range (10º in θ, 20º in φ), the 3-detector method can give agreeable orientation fittings, further more, with higher time resolution of < 10 ms. This 3-detector method is useful and can be applied to study the fast orientation dynamics in different systems.

This dissertation focuses on three separate studies. First, magnetization of the Mn12- acetate was studied by low temperature hysteresis loops and DC magnetization data on magnetically aligned Mn12-acetate micro-crystals. Secondly, Mn12-acetate thin films were fabricated and characterized by AFM and STM. Finally, magnetization of the film material was also studied. Enhanced alignment of Mn12-acetate micro-crystals as compared to prior studies was verified by observation of several sharp steps in low temperature hysteresis loops. It was found that ~ 0.5 T is sufficient to orient the micro-crystals in an organic solvent to a degree comparable to a single crystal. The degree of the alignment was controlled by varying the magnetic field at room temperature and during the cooling process. Subsequently, low temperature hysteresis loops and DC magnetizations were measured for each prepared orientation state of a sample. The high temperature magnetic anisotropy responsible for the alignment could not be measured, possibly due to its small magnitude. Mn12-acetate was deposited onto Si/SiO2 by a solution evaporation method. Atomic force microscopy studies revealed that 2 nm thick films of molecular level smoothness were formed. Mn12-acetate was also deposited onto a Highly Ordered Pyrolytic Graphite (HOPG) surface for scanning tunneling microscopy (STM) studies. A self-assembled triangular lattice was observed in the Mn12-acetate thin films by STM at room temperature under ambient conditions. These STM images show typical center to center intermolecular separations of about 6.3 nm and height corrugation of less than 0.5 nm. Magnetization measurements were not successful in Mn12-acetate thin films due to the small amount of material in the film and the large background signal from the substrate. Therefore, a sample for the magnetization measurements, called “film material”, was made by evaporating a dilute solution of Mn12-acetate powder in acetonitrile. Significant changes in magnetic properties of the film material were observed from magnetization measurements. The blocking temperature of the film material was found to increase to TB > 10 K at low magnetic fields.

The cyanide ligand has frequently been used to prepare clusters with novel magnetic properties due to its ability to provide an efficient pathway for superexchange between metal centers that are bound in an end-to-end fashion. One of the common synthetic approaches in this chemistry is to design suitable cyanide containing precursors and then to react such building blocks with metal complexes consisting of accessible sites. The triphos ligand (triphos: 1,1,1-tris(diphenylphosphinomethyl)ethane) has been employed in this vein to prepare metal complexes, one of which is a five coordinate paramagnetic complex (S = 1/2) with a square pyramidal metal center, [CoII(triphos)(CN)2]. A family of molecular squares, [{MIICl2}2{CoII(triphos)(CN)2}2] (M= Mn (2), Fe (3), Co (4), Ni (5), and Zn (6)), has been synthesized by the reaction of CoII(triphos)(CN)2 and MCl2 (M= Mn, Co, Ni, Zn) or Fe4Cl8(THF)6 in CH2Cl2/EtOH mixture. A series of cyanide-bridged trinuclear complexes, {[Co(triphos)(CN)2]2 [M(MeOH)4]}(ClO4)2 ( M = Mn (7), Fe (8), Co (9), and Ni (10)) and tetranuclear complexes, {[Co(triphos)(CN)2]2[M(MeOH)4]2}(ClO4)4 ([Co2M2] M = Mn (11) and Ni (12)) have been synthesized in a similar fashion by the reaction of CoII(triphos)(CN)2 and M(ClO4)2.6H2O (M= Mn, Fe, Co, Ni) in methanol. The trinuclear compounds (7-9), and tetranuclear complexes (2-6, 11, 12), are characterized by antiferromagnetic coupling between metal centers while magnetic behavior of 10 indicates the presence of ferromagnetic interactions between the paramagnetic metal centers. Interactions between magnetic orbitals of Co(II) and M(II) ions were also investigated by means of the density functional theoretical (DFT) calculations. Another triphos containing building block, [(triphos)Re(CN)3] anion (13), has been employed to prepare derivatives of a cubic SMM cluster with four octahedral Re(II) ions and four tetrahedral Mn(II) sites bridging through cyanide ligand. The reactions of Re(II) precursor with MnI2 and solvated Mn(II) ions resulting in derivatives of Re4Mn4 cube with different ligands attached to the Mn center other than the chloride atom were reported. Our efforts on linking these cubes using organo cyanide ligands such as dicyanamide (dca) and 7,7,8,8-tetracyanoquinodimethane (TCNQ) to form extended networks were also discussed.

The work presented herein describes efforts to synthesize and characterize cyanide-bridged molecular compounds with high-spin ground states. This investigation focused primarily on the assembly of hexacyanometallate units with convergent cationic metal complexes that are coordinated to capping ligands. In this manner, a family of related compounds was developed that serve as models for understanding the role of magnetic exchange interactions and anisotropy in nanomagnetic materials. The work presented in Chapter II describes the successful incorporation of the [Fe(CN)6]3- building block into planar geometries with nuclearities ranging from three to ten metal centers. In Chapter III, this methodology was optimized to yield two pentanuclear FeIII/NiII clusters, namely, the trigonal bipyramidal unit, {[Ni(tmphen)2]3[Fe(CN)6]2}, and the extended square, {[Ni(bpy)2(H2O)][Ni(bpy)2]2-[Fe(CN)6]2}. Magnetic measurements on pure phases of these samples revealed that each system exhibits ferromagnetic coupling between the L.S. FeIII and NiII centers, but neither exhibits slow paramagnetic relaxation effects down to T=2K. In Chapter IV, this chemistry was extended to the [Mn(CN)6]3-building block in order to increase magnetic exchange coupling and anisotropy in this cluster type, efforts that resulted in the isolation of the molecule, {[Mn(tmphen)2]3[Mn(CN)6]2}. This cluster exhibits intramolecular antiferromagnetic exchange interactions between the Mn centers which lead to an S=11/2 ground state and a negative ZFS value (D=-0.348 cm-1), parameters that support the experimental observation of Single-Molecule Magnet (SMM) behavior at low temperatures. A detailed investigation of the physical and structural properties of {[Co(tmphen)2]3[Fe(CN)6]2} in Chapters V and VI led to the realization that the cluster exhibits sensitivity to temperature and humidity. The molecule exists in three different electronic isomeric forms in the solid state and undergoes a charge-transfer induced spin-transition (CTIST) under the influence of temperature. The results presented in Chapter VI describe the behavior of this same cluster in solution, the highlight of which is the discovery that water reacts with the cluster to form a fourth electronic isomer. Finally, it is described in Chapter VII that this Co/Fe trigonal bipyramidal unit can be used as a building block for systematically incorporating three metal types into a family of 1-D chain and cluster compounds.

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.