I present two applications of fluorescence spectroscopy in biophysics. The first is an instrument, the anti-Brownian electrokinetic (ABEL) trap, which is capable of trapping individual small molecules in aqueous solution at room temperature. The second is an investigation of the bending mechanics of double-stranded DNA using a novel DNA structure called a "molecular vise". Both projects take advantage of the sensitivity and specificity of fluorescence spectroscopy, and both benefit from the interplay of experimental work with theoretical and computational modeling. The ABEL trap uses fluorescence microscopy to track a freely diffusing particle, and applies real-time electrokinetic feedback forces to oppose observed motion. Small molecules are difficult to trap because they diffuse quickly and because their fluorescence emission is typically weak. I describe the experimental and algorithmic approaches that enabled small-molecule fluorophores to be trapped at room temperature. I additionally derive and discuss the theory of the molecules' behavior in the trap; this mathematical work informed the design of the trapping algorithm and additionally enabled trapped molecules to be distinguished on the basis of their diffusion coefficient and electrokinetic mobility. Molecular vises are DNA hairpins that use the free energy of hybridization to exert a compressive force on a sub-persistence length segment of double-stranded DNA. In response to the applied force, this "target strand" may either remain straight or bend, depending on its flexibility and length. Experimentally, the conformation can be monitored via Förster resonance energy transfer (FRET) between appended fluorophores. The experimental results quantitatively matched the predictions of the classic wormlike chain (WLC) model of DNA elasticity at low-to-moderate salt concentrations. Higher ionic strength induced an apparent softening of the DNA which was best accounted for by a high-curvature "kinked" state. The molecular vise is exquisitely sensitive to the sequence-dependent linear and nonlinear elastic properties of dsDNA and provides a platform for studying the effects of chemical modifications and small-molecule or protein binding on these properties.

My research has demonstrated the feasibility of the experimental methodologies for proton-sensitive molecular probes of proton transport at the single-molecule level where a single molecule fluorescence spectral shift was observed in poly acrylamide gel (PAAG) matrix after the addition of HCl with a grating spectrometer. Proton-sensitive molecular probes are employed for observing variations of photophysical properties as protons from acid sources transport and react with the reporter molecules such as Coumarin 6 where it has two different protonated states and then shows distinguished emission spectrum. As well, in order to understand the fluorescence properties of neutral and protonated Coumarin 6 in each emission spectrum region, dual-channel detection experiment was built where those fluorescence emission spectrum are allowed to be separated into each optical detection channel. The two-color detection will provide us with the understanding of the heterogeneities indicative of the interaction of pH-responsive probe with its environment. Based on those methodologies and results, this research will lead to investigate how proton transfer kinetics and dynamics are influenced by the geometric arrangements such as inter-functional group spacing, alignment, and flexibility in single macromolecular scaffolds which will suggest the development for future fuel cell and better understanding of biological process.

No description available.

Metalloporphyrin aggregation is critical for triplet-triplet annihilation (TTA) to occur. In order to maximize the efficiency of TTA, to use as a mechanism of photon upconversion in dye-sensitized solar cells, it is important to understand the phenomenon of absorber aggregation. The aggregation of ZnTPP in polymer films was investigated by fluorescence anisotropy and total internal reflection fluorescence microscopy (TIRFM). Single molecule spectroscopy (SMS) and spectromicroscopy were the techniques used to study single molecules and multimolecular aggregates of ZnTPP/ZnTPPS in polymer films/adsorbed on glass substrates.<p> Fluorescence anisotropy measurements consistently showed depolarized emission from films most concentrated with ZnTPP. This observation was likely a result of energy transfer in and among porphyrin aggregates. Fluorescence intensity decays were also obtained and they illustrated a pattern of decreased fluorescence lifetime (i.e. faster decays) as the concentration of porphyrin in the film increased. These results are consistent with the formation of aggregates, and their increased presence in more concentrated films. The formation of these aggregates quenches the fluorophores fluorescence, resulting in the observed shorter fluorescence lifetimes. <p> TIRFM was performed to study the structure of these polymer films doped with ZnTPP. It was determined that these films consisted of discrete domains and thus lacked homogeneity, and the presence of aggregates was clearly visible. Time-resolved TIRFM measurements were also performed but no interesting results were collected.<p> SMS and spectromicroscopy were the final techniques employed to study porphyrin aggregation. Preliminary measurements were performed with polymer films doped with ZnTPP, and the single step decay time trajectories collected indicated that single molecules were being studied. Furthermore, emission spectra of these molecules were collected and they were similar to those obtained for a bulk measurement, but the bands were slightly shifted in comparison. These measurements were repeated with ZnTPPS adsorbed to glass substrates. Two different patterns of decay trajectories were measured: (i) single step decays corresponding to single ZnTPPS molecules and (ii) multi step/complex decays representative of multimolecular aggregates. Emission spectra were also collected for the multimolecular aggregates, and they were consistent with those of an ensemble measurement but slightly blue-shifted. Such a shift is common when studying aggregates on such a highly polar surface. Thus, these results demonstrate that ZnTPPS aggregates form even at concentrations as low as 10-8 M, and can be studied using SMS despite their weak fluorescence emission.

Metalloporphyrin aggregation is critical for triplet-triplet annihilation (TTA) to occur. In order to maximize the efficiency of TTA, to use as a mechanism of photon upconversion in dye-sensitized solar cells, it is important to understand the phenomenon of absorber aggregation. The aggregation of ZnTPP in polymer films was investigated by fluorescence anisotropy and total internal reflection fluorescence microscopy (TIRFM). Single molecule spectroscopy (SMS) and spectromicroscopy were the techniques used to study single molecules and multimolecular aggregates of ZnTPP/ZnTPPS in polymer films/adsorbed on glass substrates.<p> Fluorescence anisotropy measurements consistently showed depolarized emission from films most concentrated with ZnTPP. This observation was likely a result of energy transfer in and among porphyrin aggregates. Fluorescence intensity decays were also obtained and they illustrated a pattern of decreased fluorescence lifetime (i.e. faster decays) as the concentration of porphyrin in the film increased. These results are consistent with the formation of aggregates, and their increased presence in more concentrated films. The formation of these aggregates quenches the fluorophores fluorescence, resulting in the observed shorter fluorescence lifetimes. <p> TIRFM was performed to study the structure of these polymer films doped with ZnTPP. It was determined that these films consisted of discrete domains and thus lacked homogeneity, and the presence of aggregates was clearly visible. Time-resolved TIRFM measurements were also performed but no interesting results were collected.<p> SMS and spectromicroscopy were the final techniques employed to study porphyrin aggregation. Preliminary measurements were performed with polymer films doped with ZnTPP, and the single step decay time trajectories collected indicated that single molecules were being studied. Furthermore, emission spectra of these molecules were collected and they were similar to those obtained for a bulk measurement, but the bands were slightly shifted in comparison. These measurements were repeated with ZnTPPS adsorbed to glass substrates. Two different patterns of decay trajectories were measured: (i) single step decays corresponding to single ZnTPPS molecules and (ii) multi step/complex decays representative of multimolecular aggregates. Emission spectra were also collected for the multimolecular aggregates, and they were consistent with those of an ensemble measurement but slightly blue-shifted. Such a shift is common when studying aggregates on such a highly polar surface. Thus, these results demonstrate that ZnTPPS aggregates form even at concentrations as low as 10-8 M, and can be studied using SMS despite their weak fluorescence emission.

Morphology is the origin of life and function. Defining and designing morphology, understanding the relationship between morphology and function, is an essential theme in a number of research areas. In conjugated polymer research, the major obstacles to achieving these goals are the heterogeneity and complexity of conjugated polymer films. In the study presented in this dissertation, various single molecule spectroscopy techniques were used as an approach to minimize the complexity of these problems. By using excitation polarization spectroscopy, it was discovered that single chains of poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) assume a highly ordered rod conformation despite the fact that the morphology of bulk films is known to be amorphous. The comparison of results from experiments and a coarse grained bead-on-a-chain simulation suggested that single chains have the ability to use a thermally induced defect to maximize [pi]-[pi] stacking and adopt a rod conformation as a stable conformation. Bias-induced centroid spectroscopy (BIC) on highly ordered single chains demonstrated that the energy transfer scale could be an order of magnitude larger than the value typically measured for bulk films. It was further demonstrated that such an extraordinary long energy transfer was not a unique property of single chains but was also observed in aggregates as long as the morphology was ordered. These studies were extended to another model compound poly(3-hexylthiophene) (P3HT) to generalize the mechanism of morphology formation and the structure-property relationship. For P3HT, it was shown that side-chains were a very important factor in determining single chain conformation, while the conformation of MEH-PPV was not affected by side-chains. By controlling the side-chains, both ordered and disordered P3HT chains were obtained. The comparison of results from experiments and an energy transfer model simulation quantified that energy transfer was at least twice as efficient in ordered chains as in disordered chains. In aggregates, the difference between the energy transfer efficiency of ordered and disordered morphology was even larger than that in the case of single chains. These results could suggest that there is a very fast energy transfer mechanism that occurs through interchain interactions when chains are packed in ordered fashion. / text

Single-molecule fluorescence spectroscopy techniques such as Fluorescence Correlation Spectroscopy (FCS) and single-molecule Förster Resonance Energy Transfer (smFRET) not only possess an unprecedented high sensitivity but also have high temporal and spatial resolution. Therefore, they have an immense potential both in investigation of fundamental biological principles and in clinical applications. FCS analyses are based on both theoretical approximations of the beam geometry and assumptions of the underlying molecular processes. To address the accuracy of analysis, firstly the experimental conditions that should be fulfilled in order to obtain reliable physical parameters are discussed and the input parameters are carefully controlled accordingly to demonstrate the performance of FCS measurements on our home-built confocal multiparameter photon-counting microscope in several in vitro and in-vivo applications. Secondly, we performed a comprehensive FCS analysis of rhodamine family of dyes to evaluate the validity of assigning the correlation relaxation times to the time constant of conformational dynamics of biomolecules. While it is the common approach in literature our data suggests that conformational dynamics mainly appear in the correlation curve via modulation of the dark states of the fluorophores. The size and shape of the folded, unfolded and chemically-denatured states of the N-terminal Src-homology-3 of downstream of receptor kinases (DrkN SH3) were investigated by FCS and smFRET burst experiments. Based on the data, we conclude that a considerable sub-population of the denatured protein is in a closed loop state which is most likely formed by cooperative hydrogen bonds, salt bridges and nonpolar contacts. As a clinical application, we developed and characterized an ultrasensitive capillary electrophoresis method on our multiparameter confocal microscope. This allowed us to perform Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with about 500 times better sensivity than a commercial instrument. Quite remarkably, we were able to analyze samples of cell lysate down to the contents of a single cell.

Single-molecule fluorescence spectroscopy techniques such as Fluorescence Correlation Spectroscopy (FCS) and single-molecule Förster Resonance Energy Transfer (smFRET) not only possess an unprecedented high sensitivity but also have high temporal and spatial resolution. Therefore, they have an immense potential both in investigation of fundamental biological principles and in clinical applications. FCS analyses are based on both theoretical approximations of the beam geometry and assumptions of the underlying molecular processes. To address the accuracy of analysis, firstly the experimental conditions that should be fulfilled in order to obtain reliable physical parameters are discussed and the input parameters are carefully controlled accordingly to demonstrate the performance of FCS measurements on our home-built confocal multiparameter photon-counting microscope in several in vitro and in-vivo applications. Secondly, we performed a comprehensive FCS analysis of rhodamine family of dyes to evaluate the validity of assigning the correlation relaxation times to the time constant of conformational dynamics of biomolecules. While it is the common approach in literature our data suggests that conformational dynamics mainly appear in the correlation curve via modulation of the dark states of the fluorophores. The size and shape of the folded, unfolded and chemically-denatured states of the N-terminal Src-homology-3 of downstream of receptor kinases (DrkN SH3) were investigated by FCS and smFRET burst experiments. Based on the data, we conclude that a considerable sub-population of the denatured protein is in a closed loop state which is most likely formed by cooperative hydrogen bonds, salt bridges and nonpolar contacts. As a clinical application, we developed and characterized an ultrasensitive capillary electrophoresis method on our multiparameter confocal microscope. This allowed us to perform Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with about 500 times better sensivity than a commercial instrument. Quite remarkably, we were able to analyze samples of cell lysate down to the contents of a single cell.

No description available.

Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / The preparation of mesoporous/macroporous silica materials and polarity gradient thin film are introduced in this thesis. These porous silica materials and gradient materials have the potential applications as stationary phases for chemical separations, as materials for combinatorial catalysis and as absorbent/adsorbent layers for use in chemical or biological sensors. Single molecule spectroscopy is used to probe the chemical interaction between single dye molecule and porous silica matrix. Bulk fluorescence spectroscopy is used to investigate the properties of gradient film. In Chapter one, the applications of single molecule spectroscopic methods to sol-gel silica materials are reviewed, which covers a subset of the recent literature in this area and provided salient examples of the new information that can be obtained by single molecule studies. In Chapter two, both the sample preparation and experiment setup are covered. In Chapter three, the preparation of mesoporous silica film is presented. Single molecule spectroscopy is used to probe the mass transport and molecule-matrix interactions in mesoporous thin-film systems. Three different dyes of varying size, charge, and hydrophilicity are used. Silica films with/without surfactant or containing different kind surfactant are studied. The results provide new information on mass transport through the films, evidence of reversible surface adsorption, and quantitative information on variations in these phenomena with film hydration. In Chapter four, a new model describing how to explore the actual dye concentration in single molecule experiment with considering the molecule orientation is presented, which is verified to be correct by both experimental and simulated data. In Chapter five, the growth process of Methylsilsesquioxane (MSQ) particle is studied by single molecule spectroscopy, in which, the MSQ particle is treated as “native” dye molecule. In Chapter six, silica films incorporating polarity gradients are produced by using “infusion-withdrawal dip-coating” method. The gradient film is characterized by bulk fluorescence spectroscopy, water contact angle and FTIR. In Chapter seven, a brief conclusion is drawn and future directions are presented.