In this thesis, I describe the first exploratory experimental efforts probing light-matter interactions of chiral systems at the single molecule level. The dissymmetric single molecule chiroptical response in both excitation and emission polarization has been studied for different diastereomeric forms of bridged triarylamine helicenes. Fluorescence excitation circular dichroism (FECD), measuring the dissymmetric absorption with respect to excitation polarization, reports on the response to excitation polarization. The magnitude and distribution of chiroptical single molecule responses suggest both surface and orientation effects play a significant role. Computational modeling done to calculate the dissymmetry for specific orientations supports orientational dependence. Using a defocused imaging technique, which can be used to obtain orientation information for linear dipoles, emission patterns were obtained that lacked bilateral symmetry. These emission patterns were simulated using a semi-classical model that closely approximated the lack of bilateral symmetry. Refinement of the model and additional experiments using oriented molecules will allow for direct correlation of orientation and dissymmetry which is important for understanding the heterogeneities in the single molecule responses. In addition, dissymmetry in emission polarization has been studied using a novel imaging technique resolving polarization components on a frame-by-frame basis. The research into the intersection of single molecule spectroscopy and chiroptics has given new insight into the role of solvation and local environment in chiroptical interactions and may be useful for understand chiral-based photonics and advancing new technologies.

Yes / We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.

This thesis is a report of the work I have done over the last five years to study thermodynamic and kinetic aspects of single-molecule behavior in the condensed phase. It is concerned specifically with the development of analytically tractable models of various phenomena that have been observed in experiments on such single-molecule systems as colloids, double-stranded DNA, multi-unit proteins, and enzymes. In fluid environments, the energetics, spatial conformations, and chemical reactivity of these systems undergo fluctuations that can be characterized experimentally in terms of time correlation functions, survival probabilities, mean first passage times, and related statistical parameters. The thesis shows how many of these quantities can be calculated in closed form from a model based on simple Brownian motion, or generalizations of it involving fractional calculus. The theoretical results obtained here have been shown to agree qualitatively or quantitatively with a range of experimental data. The thesis therefore demonstrates the effectiveness of Brownian motion concepts as a paradigm of stochasticity in biological processes.

The force-induced activation of adhesive proteins such as von Willebrand Factor (VWF), which experience high hydrodynamic forces, is essential in initiating platelet adhesion. The importance of the mechanical force induced functional change is manifested in the multimeric VWF’s crucial role in blood coagulation, when high fluid shear stress activates pVWF multimers to bind platelets. Here we showed that a pathological level of high shear flow exposure of pVWF multimers results in domain conformational changes, and the subsequent shifts in the unfolding force allow us to use force as a marker to track the dynamic states of multimeric VWF. We found that shear-activated pVWF multimers (spVWF) are more resistant to mechanical unfolding than non-sheared pVWF multimers, as indicated in the higher peak unfolding force. These results provide insight into the mechanism of shear-induced activation of pVWF multimers.

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Molecular motor proteins are responsible for the long range transport of vesicles and organelles inside living cells. A small number of motor types transport thousands of distinct cargoes to various regions in the cell at the same time. This requires that intracellular transport be tightly regulated, yet the details of how motor regulators and cofactors tune motor function remain unknown in most cases. In-vitro studies at the single motor level have been instrumental in understanding the function of individual motors. In this thesis work I developed the methodology to extend in-vitro experiments to interrogate motor regulation at the single molecule level. I describe my modifications to the microscope setup as well as the acquisition cycle that made this possible. By combining differential interference contrast microscopy with single molecule fluorescence imaging and optical trapping I was able to manipulate and image the cargo while imaging a fluorescently-labeled regulator binding at the site of the motors. I used lipid droplets purified from Drosophila embryos as cargoes. Lipid droplets are carried by the opposite polarity microtubule motors kinesin and dynein in the embryos, and bind specifically to microtubules in-vitro. In the presence of ATP they exhibit long-range and short-range motility. For this proof-of-principle experiment I used fluorescently labeled AMPPNP, a non-hydrolysable analogue of ATP which binds to the motor domain of kinesin when microtubule-bound, to image the binding of the nucleotide to the motor and demonstrate the activity of the motors. While a large fraction of microtubule-bound droplets co-localized with a fluorescent AMPPNP molecule, non-specific binding of the nucleotide to the microscope slide surface prevented confirming the specificity of the colocalization events. Nevertheless, these data demonstrate the ability of the methodology to capture, in real time, the process of a regulator binding the motor at the single molecule level. / text

Rotaviruses are the single most common cause of fatal and severe childhood diarrhoeal illness worldwide (>125 million cases annually). Rotavirus shares structural and functional features with many viruses, such as the presence of segmented double-stranded RNA genomes selectively and tightly packed with a conserved number of transcription complexes in icosahedral capsids. Nascent transcripts exit the capsid through 12 channels, but it is unknown whether these channels specialise in specific transcripts or simply act as general exit conduits; a detailed description of this process is needed for understanding viral replication and genomic organisation. To test these opposing models, a novel single-molecule assay was developed for the capture and identification (CID) of newly synthesised specific RNA transcripts. CID combines the hybridisation of transcripts with biotinylated and FRET compatible labelled ssDNAs with the implementation of recent developments in single molecule fluorescence such as alternating laser excitation (ALEX) and total internal reflection fluorescence (TIRF) microscopy. CID identifies and quantifies specific transcripts of rotavirus based on a FRET/Stoichiometry (E*/S) value of the hybridised labelled probes. I used CID to pull down the capsid on the surface slide and identify partially extruded transcripts of three different segments 2, 6 and 11. The findings presented in this thesis support a model in which each channel specialises in extruding transcripts of a specific segment, that in turn is linked to a single transcription complex. The method can be extended to study other transcription systems including E.coli, and can be further developed as a potential diagnostic tool.

The effect of pressure on a number of magnetically interesting compounds such as single-molecule magnets and dimeric copper and manganese molecules has been investigated to probe the validity of ambient magneto-structural correlations. The first chapter is an introduction to the equipment and methodologies that have been adopted to carry out the experimental high-pressure work. The second chapter reports the first combined high-pressure single crystal X-ray diffraction and high pressure magnetism study of four single-molecule magnets (SMMs). At 1.5 GPa the structures [Mn6O2(Et-sao)6(O2CPh(Me)2)2(EtOH)6] (1) – an SMM with a record effective anisotropy barrier of ~86 K – and [Mn6O2(Etsao) 6(O2C-naphth)2(EtOH)4(H2O)2] (2) both undergo significant structural distortions of their metallic skeletons which has a direct effect upon the observed magnetic response. Up to 1.5 GPa pressure the effect is to flatten the Mn-N-O-Mn torsion angles weakening the magnetic exchange between the metal centres. In both compounds one pairwise interaction switches from ferro- to antiferromagnetic, with the Jahn-Teller (JT) axes compressing (on average) and re-aligning differently with respect to the plane of the three metal centres. High pressure dc χMT plots display a gradual decrease in the low temperature peak value and slope, simulations showing a decrease in |J| with increasing pressure with a second antiferromagnetic J value required to simulate the data. The “ground states” change from S = 12 to S = 11 for 1 and to S = 10 for 2. Magnetisation data for both 1 and 2 suggest a small decrease in |D|, while out-of-phase (χM //) ac data show a large decrease in the effective energy barrier for magnetisation reversal. The third SMM is the complex [Mn3(Hcht)2(bpy)4](ClO4)3·Et2O·2MeCN (3·Et2O·2MeCN) that at 0.16 GPa loses all associated solvent in the crystal lattice, becoming 3. At higher pressures structural distortions occur changing the distances between the metal centres and the bridging oxygen atoms making |J| between the manganese ions weaker. No significant variations are observed in the JT axis of the only MnIII present in the structure. Highpressure dc χMT plots display a gradual decrease in the low temperature peak value and slope. Simulations show a decrease in J with increasing pressure although the ground state is preserved. Magnetisation data do not show any change in |D|. The fourth SMM, [(tacn)6Fe8O2(OH)12](ClO4)3.9Br4.1⋅6H2O, (4) is the largest inorganic compound ever studied at high-pressure. Up to 2.0 GPa the conformation of the complex remains largely unaffected, with the counter ions and water molecules moving around to accommodate a compression of the unit cell volume. High pressure magnetic susceptibility data collected up to 0.93 GPa confirm minimal changes in the intra-molecular exchange interactions. The third chapter focuses on three hydroxo-bridged CuII dimers: [Cu2(OH)2(H2O)2(tmen)2](ClO4)2 (5), [Cu2(OH)2(tben)2](ClO4)2 (6) and [Cu2(OH)2(bpy)2](BF4)2 (7) have been structurally determined up to 2.5, 0.9 and 4.7 GPa, respectively. 6 and 7 have never been reported before. Pressure imposes important distortions in the structures of all three complexes, particularly on the bond distances and angles between the metal centres and the bridging hydroxo groups. 5 undergoes a phase transition between 1.2 and 2.5 GPa caused by the loss of a coordinated water molecule. This leads to a loss of symmetry and dramatic changes in the molecular structure of the complex. The structural changes are manifested in different magnetic behaviours of the complexes as seen in dc susceptibility measurements up to ~0.9 GPa: J becomes less antiferromagnetic in 5 and 6 and more ferromagnetic in 7. The fourth chapter shows the compression of two oxo-bridged MnII/MnIII mixed valence dimers: [Mn2O2(bpy)4](ClO4)3⋅3CH3CN, (8) has been squeezed up to 2.0 GPa whilst [Mn2O2(bpy)4](PF6)3⋅2CH3CN⋅1H2O, (9) could be measured crystallographically up to 4.55 GPa. 9 has never been reported before, while 8 has been reported in a different crystallographic space group. The application of pressure imposes significant alterations in the structures of both complexes. In particular, in 8 the Mn-Mn separation is reduced by the contraction of some of the Mn-O bond distances, 9 shows essentially analogous behaviour: the Mn-Mn distance and nearly all the Mn-N bonds shrink significantly. The magnetic behaviour of the complexes has been measured up to 0.87 GPa for 8 and 0.84 GPa for 9, but neither display any significant differences with respect to their ambient data.

Nanoaperture optical tweezers are emerging as useful tools for the detection and identification of biological molecules and their interactions at the single molecule level. Nanoaperture optical tweezers provide a low-cost, scalable, straight-forward, high-speed platform for single molecule studies without the need to use tethers or labeling. This thesis gives a general description of conventional optical tweezers and how they are limited in terms of their capability to trapping biological molecules. It also looks at nanoaperture-based optical tweezers which have been suggested to overcome the limitations of conventional optical tweezers. The thesis then focuses on the double nanohole optical tweezer as a tool for trapping biological molecules and studying their behaviour and interactions with other molecules. The double nanohole aperture trap integrated with microfluidic channels has been used to detect single protein binding. In that experiment a double-syringe pump was used to deliver biotin-coated polystyrene particles to the double nanohole trapping site. Once stable trapping of biotin-coated polystyrene particle was achieved, the double-syringe pump was used to flow in streptavidin solution to the trapping site and binding was detected by measuring the transmission through the double nanohole aperture. In addition, the double nanohole optical tweezer has been used to observe the real-time dynamic variations in protein-small molecule interaction (PSMI) with the primary focus on the effect of single and multiple binding events on the dynamics of the protein in the trap. Time traces of the bare form of the streptavidin showed slower timescale dynamics as compared to the biotinylated forms of the protein. Furthermore, the double nanohole aperture tweezer has been used to study the real-time binding kinetics of PSMIs and to determine their disassociation constants. The interaction of blood protein human serum albumin (HSA) with tolbutamide and phenytoin was considered in that study. The dissociation constants of the interaction of HSA with tolbutamide and phenytoin obtained using our technique were in good agreement with the values reported in the literature. These results would open up new windows for studying real-time binding kinetics of protein-small molecule interactions in a label-free, free-solution environment, which will be of interest to future studies including drug discovery. / Graduate

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