The work presented herein focuses on the synthesis and characterization of new cyanide bridged molecular magnetic materials that form discrete molecules as well as three dimensional networks. This research is inspired by the recognition that the Prussian blue (PB) family exhibits a wide range of interesting magnetic properties such as photomagnetism, spin crossover, and high TC magnets owing to the presence of the cyanide bridge that promotes magnetic communication between adjacent metal spins. An underexplored facet of this research is the systematic development of the topic with anisotropic metal ions research that was undertaken as part of this dissertation. The resulting discoveries are materials that exhibit a wide range of bistable magnetic properties, including photomagnetism, long range magnetic ordering, SMM, and exchange-biased SMM behavior. New Prussian Blue analogs are presented in Chapter II of this thesis that are based on the nearly unexplored hexacyanoosmate(III) ion. A family of CoII PB derivatives of OsIII were found to exhibit photomagnetic and charge transfer induced spin transition (CTIST) behavior and a study of alkali metal cation dependence revealed marked differences in both the photomagnetic and CTIST properties, with the highest ordering temperature being observed for the K+ analog which exhibits a TC of 28.5 K. The phenomenon of linkage isomerism reported for PB analogs and other molecular materials that incorporate the [Cr(CN)6]3- ion wherein the CN ligand reverses its binding mode between the two metal centers was studied in detail as described in Chapter III. Small molecule models that incorporate [Cr(CN)6]3- and CoII ions were investigated by single crystal X-ray crystallography, magnetism, and solution IR studies and the data led to useful mechanistic information about the nature of the cyanide reversal process. The use of the anisotropic hexacyanoosmate(III) anion to form a trinuclear species with MnIII was undertaken in the study described in Chapter IV. The first SMM based on the hexacyanoosmate(III) ion was discovered and found to exhibit a very rare exchange biased SMM phenomena in one of its crystal forms. In Chapter V new building blocks with the pentadentate MPPA ligand are described which are ideally suited for the preparation of a range of model compounds of the dinuclear and trinuclear variety.

We have constructed a single molecule detection system with the capability to simultaneously measure many parameters, including transient fluorescence intensity, fluorescence lifetime, and photon anti-bunching behavior via the Hanbury Brown-Twiss photon-correlation technique. In addition, we apply the system to study the single DiI (1, 1 '- dioctadecyl- 3, 3 , 3 ', 3 ' - tetramethylindocarbocyanine perchlorate) molecule, to characterize the photo-physical behaviors. Cyanine dyes are the molecules that constitute of two nitrogen centers, one of which is positive charged, and is linked by a conjugated chain with odd number of carbon atoms to the other nitrogen center. Cyanine dyes are interested in the photo sensitization, optical recording media, nonlinear optics, laser dyes, and many interesting photophysical and photochemical behaviors. Among them, DiI plays an important role in single molecule fluorescence investigations. The high photo-stability, good QE, and low inter-system crossing rates, make it a pioneer for the widely investigations in single molecule studies. Our experimental goal is to understand the characteristic of the monitored single molecule by the measuring photo-physical parameters. Our results include the typical behaviors in DiI molecules: clear on-off blinking, fluorescence anti-bunching, one-step photo-bleaching, and consistent fluorescence polarization orientation. In addition, we also observed some change during measurement, which indicates the corresponding change of structure. Few molecules also exhibit non-zero probability around the zero delay time, which indicates the simultaneous existence of more than one quantum emitters in the detected region. These results demonstrate that the parameters are essential for understanding and characterizing the observed molecules in single molecule level.

Clusters of metal ions that possess large numbers of magnetically coupled unpaired electrons have attracted much interest in recent years due to their fascinating magnetic behavior. With an appreciable component of magnetic anisotropy, these large-spin paramagnetic molecules can exhibit an energy barrier to inversion of their magnetic dipole, leading to spontaneous magnetization and magnetic hysteresis below a critical temperature. Since this behavior is a property of an individual clusters rather than a collection of molecules, this phenomenon has been dubbed ??Single Molecule Magnetism??. Our approach to the study of new high-spin systems has been to exert a measure of synthetic control in the preparation of clusters. Specifically we are employing highly anisotropic metal ions with the anticipation that these ions would engender large overall magnetic anisotropy in the resulting clusters. The first step in this process was the development of the chemistry of two new d5 ReII (S = ??) complexes, namely [ReII(triphos)(CH3CN)3][PF6]2 and [Et4N][ReII(triphos)(CN)3]. The magnetic, optical and electrochemical properties were studied and theoretical models were developed to describe the origin of the large temperature independent paramagnetism that was observed. Next, we successfully employed transition metal cyanide chemistry using the ReII building blocks to prepare a family of isostructural, cubic clusters of the general formula {[MCl]4[Re(triphos)(CN)3]4} M = Mn, Fe, Co, Ni, Cu, Zn whose 3d ions adopt local tetrahedral geometries. Within the clusters, magnetic exchange is observed between the paramagnetic ions, which has been modeled using an Ising exchange model to account for the dominating anisotropy of the ReII ion. Despite the high pseudo-symmetry of the clusters (Td), this work has yielded a rare example of a metal-cyanide single molecule magnet, {[MCl]4[Re(triphos)(CN)3]4} with an S = 8 ground state, D = -0.39 cm-1 and an effective energy barrier for magnetization reversal of Ueff = 8.8 cm-1. The elucidation of this family of isostructural clusters has also allowed us to pursue fundamental work on the structure/property relationships of the exotic, paramagnetic ReII ion. As the clusters are soluble, stable compounds, the future of this chemistry lies in the development of a true building-block approach to ??super-clusters?? that exhibit very high ground state spin values.

We have engineered a mutant of HIV Reverse Transcriptase that can be fluorescently labeled by covalent attachment of the environmentally sensitive fluorophore 7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl)coumarin (MDCC). The result is a polymerase that is kinetically indistinguishable from the wild-type enzyme, but provides a signal to monitor changes in enzyme structure that result from conformational changes induced by substrate binding. Using this system, we have expanded the kinetic model governing nucleotide binding to include an enzymatic isomerization following initial nucleotide binding. In doing so, we define the role of induced-fit in nucleotide specificity and mismatch discrimination. Additionally, we have characterized the kinetics governing the specificity and discrimination of several widely administered Nucleotide Reverse Transcriptase Inhibitors (NRTI’s) used to combat HIV infection including 3TC (Lamivudine), FTC (Emtricitabine), and AZT (Zidovudine) for the wild-type polymerase and mutants with clinical resistance to these compounds. Our findings resolve the apparent tighter binding of these inhibitor compounds compared to the correct nucleotide by showing that the affinity for the correct nucleotide is stronger than the inhibitors. The apparent weaker binding of the correct nucleotide is a result of a incomplete interpretation of binding data that fails to account for the importance of the reverse rate of the conformational change. The apparent Kd (Kd,app) measurements for correct nucleotide estimates Km rather than Kd because nucleotide binding does not reach equilibrium. The conformationally sensitive enzyme has also been used to characterize the kinetics governing DNA association. We show that DNA binding is governed by a two-step process where a fast initial association is followed by a second, slow isomerization that is off the pathway for nucleotide binding and incorporation. Finally, we have implemented single molecule techniques using fluorophore labeled nucleotides to study the effects of AZT incorporation on the DNA translocation dynamics of the polymerase. We find that primer termination with AZT results in DNA that fails to translocate, therefore occluding the next nucleotide from binding. This shift in translocation equilibrium exposes the newly formed phosphodiester bond to ATP- or pyrophosphate-mediated AZT excision; thereby rescuing productive polymerization. This finding represents the first kinetic measurement of DNA translocation by a polymerase. / text

Dynamics between organic molecules and surface enhanced Raman scattering (SERS) hot spots are extracted from far-field optical images by two experimental methods presented in this thesis: orientational imaging and super-resolution optical imaging. We introduce SERS orientational imaging as an all-optical technique able to determine the three-dimensional orientations of SERS-active Ag nanoparticle dimers. This is accomplished by observing lobe positions in SERS emission patterns formed by the directional polarization of SERS emission along the longitudinal axis of the dimer. We further extend this technique to discriminate nanoparticle dimers from higher order aggregates by observing the wavelength-dependence of SERS emission patterns, which are unchanged in nanoparticle dimers, but show differences in higher order aggregates involving two or more nanoparticle junctions. Dynamic fluctuations in the SERS emission pattern lobes are observed in aggregates labeled with low dye concentrations, as molecules diffuse into regions of higher electromagnetic enhancement in multiple nanoparticle junctions. In order to investigate these dynamic interactions between single organic molecules and nanoparticle hot spots we present the first super-resolution optical images of single-molecule SERS (SM-SERS), introducing super-resolution imaging as a powerful new tool for SM-SERS studies. Mapping the dynamic movement of SM-SERS centroid positions with +/- 5 nm resolution reveals the position-dependent SERS intensity as the centroid samples different positions in space. We have proposed that the diffusion of the SERS centroid is due to diffusion of a single molecule on the surface of the nanoparticle, which leads to changes in coupling between the scattering dipole and the optical near field of the nanoparticle. Finally, we combine an isotope-edited bi-analyte SERS spectral approach with super-resolution optical imaging and atomic force microscopy (AFM) structural analysis for a more complete picture of molecular dynamics in SERS hot spots. We demonstrate the ability to observe multiple molecule dynamics in a single hot spot and show that in addition to the single-molecule regime, a "few" molecule regime is able to report on position-dependent SERS intensities in a hot spot. Furthermore, we are able to identify multiple local hot spots in single nanoparticle aggregates. / text

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

Telomerase and telomere play crucial roles in the maintenance of genomic stability. Through its ability to extend chromosome ends with G-rich telomeric sequence, telomerase solves the end-replication problem of linear chromosomes and allows complete replication of the genetic information. Telomere along with its protein partners solves the end-protection problem and guards the chromosome ends against aberrant DNA damage response. In this thesis, I present two single-molecule fluorescence-based studies that determined the functional structure of telomerase RNA within active telomerase holoenzyme and probed the structure of telomere and its dependence on telomere binding proteins. In the first study, we developed a single-molecule Förster resonance energy transfer (FRET) assay to interrogate the structure of telomerase RNA within active telomerase enzymes. In this assay, oligonucleotide hybridization was used to probe the primer-extension activity of individual telomerase enzymes with single nucleotide sensitivity. FRET signals from individual enzyme molecules during active binding events were then used to determine the organization of telomerase RNA within active telomerase. Using this assay, we have identified an active conformation of telomerase in which the conserved telomerase RNA pseudoknot is properly folded. In the second study, we used super-resolution fluorescence technique STochastic Optical Reconstruction Microscopy (STORM) to probe the structure of mammalian telomere. We showed that previously described telomere loop structures are detected by STORM imaging. Removal of telomere-binding protein TRF2 significantly reduces the fraction of telomeres found in loops. Furthermore, this reduction of telomere loops occurs in the absence of ATM-dependent DNA damage signaling and non-homologous end joining mediated chromosome fusion, suggesting a direct role of TRF2 in the formation or maintenance of telomere loops.

DNA replication is a fundamental cellular process. However, the structure and dynamics of the eukaryotic DNA replication machinery remain poorly understood. A soluble extract system prepared from Xenopus eggs recapitulates eukaryotic DNA replication outside of a cell on a variety of DNA templates. This system has been used to reveal many aspects of DNA replication using a variety of ensemble biochemical techniques. Single-molecule fluorescence imaging is a powerful tool to dissect biochemical mechanisms. By immobilizing or confining a substrate, its interaction with individual, soluble, fluorescently-labeled reactants can be imaged over time and without the need for synchrony. These molecular movies reveal binding parameters of the reactant and any population heterogeneity. Moreover, if the experiments are imaged in wide-field format, the location or motion of the labeled species along the substrate can be followed with nanometer accuracy. This dissertation describes the use and development of novel single-molecule fluorescence imaging techniques to study eukaryotic DNA replication. A biophysical characterization of a replication fork protein, PCNA, revealed both helical and non-helical sliding modes along DNA. Previous experiments demonstrate that the egg extracts efficiently replicate surface-immobilized linear DNA. This finding suggested replication of DNA could be followed as motion of the replication fork along the extended DNA. However, individual proteins bound at the replication fork could not be visualized in the wide-field due to the background from the high concentration of the fluorescent protein needed to compete with the extract’s endogenous protein. To overcome this concentration barrier, I have developed a wide-field technique that enables sensitive detection of single molecules at micromolar concentrations of the labeled protein of interest. The acronym for this method, PhADE, denotes three essential steps: (1) Localized PhotoActivation of fluorescence at the immobilized substrate, (2) Diffusion of unbound fluorescent molecules to reduce the background and (3) Excitation and imaging of the substrate-bound molecules. PhADE imaging of flap endonuclease I (Fen1) during replication revealed the time-evolved pattern of replication initiation, elongation and termination and the kinetics of Fen1 exchange during Okazaki fragment maturation. In the future, PhADE will enable the elucidation of the dynamic events at the eukaryotic DNA replication fork. PhADE will also be broadly applicable to the investigation of other complex biochemical process and low affinity interactions. It will be especially useful to those researchers wishing to correlate motion with binding events.

Advances in optical imaging techniques have allowed quantitative studies of many biological systems. This dissertation elaborates on our efforts in both developing novel imaging modalities based on detection of optical absorption and applying high-sensitivity fluorescence microscopy to the study of biology. / Chemistry and Chemical Biology

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