Nucleases are integral to all DNA processing pathways. The exact nature of substrate recognition and enzymatic specificity in structure-specific nucleases that are involved in DNA replication, repair and recombination has been under intensive debate. The nucleases that rely on the contours of their substrates, such as 5’ nucleases, hold a distinctive place in this debate. How this seemingly blind recognition takes place with immense discrimination is a thought-provoking question. Pertinent to this question is the observation that even minor variations in the substrate provoke extreme catalytic variance. Increasing structural evidence from 5’ nucleases and other structure-specific nuclease families suggest a common theme of substrate recognition involving distortion of the substrate to orient it for catalysis and protein ordering to assemble active sites. Using three single-molecule (sm)FRET approaches of temporal resolution from milliseconds to sub-milliseconds, along with various supporting techniques, I decoded a highly sophisticated mechanism that show how DNA bending and protein ordering control the catalytic selectivity in the prototypic system human Flap Endonuclease 1 (FEN1). Our results are consistent with a mutual induced-fit mechanism, with the protein bending the DNA and the DNA inducing a protein-conformational change, as opposed to functional or conformational selection mechanism. Furthermore, we show that FEN1 incision on the cognate substrate occurs with high efficiency and without missed opportunity. However, when FEN1 encounters substrates that vary in their physical attributes to the cognate substrate, cleavage happens after multiple trials During the course of my work on FEN1, I found a novel photophysical phenomena of protein-induced fluorescence quenching (PIFQ) of cyanine dyes, which is the opposite phenomenon of the well-known protein-induced fluorescence enhancement (PIFE). Our observation and characterization of PIFQ led us to further investigate the general mechanism of fluorescence modulation and how the initial fluorescence state of the DNA-dye complex plays a fundamental role in setting up the stage for the subsequent modulation by protein binding. Within this paradigm, we propose that enhancement and quenching of fluorescence upon protein binding are simply two different faces of the same process. Our observations and correlations eliminate the current inconvenient arbitrary nature of fluorescence modulation experimental design.

Single-molecule DNA flow-stretching assays have been a powerful approach to study various aspects on the mechanism of DNA replication for more than a decade. This technique depends on flow-induced force on a bead attached to a surface-tethered DNA. The difference in the elastic property between double-strand DNA (long) and single-strand DNA (short) at low regime force allows the observation of the beads motion when the dsDNA is converted to ssDNA by the replisome machinery during DNA replication. Here, I aim to develop an assay to track in real-time the encounter of the bacteriophage T7 replisome with abasic lesion site inserted on the leading strand template. I optimized methods to construct the DNA substrate that contains the abasic site and established the T7 leading strand synthesis at the single molecule level. I also optimized various control experiments to remove any interference from the nonspecific interactions of the DNA with the surface. My work established the foundation to image the encounter of the T7 replisome with abasic site and to characterize how the interactions between the helicase and the polymerase could influence the polymerase proofreading ability and its direct bypass of this highly common DNA damage type.

La localisation d’ARNm a été découverte en 1983 dans les ovocytes et les embryons des ascidies. Depuis, plusieurs exemples d'ARN localisés ont été trouvés dans de nombreux organismes, y compris les plantes, les levures, les champignons, les insectes, les poissons et les mammifères. Les ARNm localisés contribuent à de nombreuses fonctions biologiques, telles que le développement embryonnaire, la division cellulaire asymétrique, la migration cellulaire, la signalisation, la plasticité neuronale et plein d’autres ...Jusqu'à présent, quelques études ont analysé la localisation d’ARNm de manière systématique. Trois d'entre eux ont été effectués chez la drosophile pendant l'embryogenèse, l'oogenèse ou le stade larvaire et ont analysé environ 16000 ARN au total. Les deux autres études ont été réalisées dans des cellules de mammifères et ont analysé près de 1000 ARNm chacune. Ces études ont montré l'importance de la localisation d’ARNm dans les cellules humaines et son implication dans différents processus biologiques. L'objectif de ma thèse était donc d'augmenter le débit des techniques FISH à l’échelle de molécule unique (smFISH) et d'étudier la localisation d’ARNm dans les cellules HeLa de manière systématique.Une limitation de smFISH est le coût de sondes fluorescentes, qui limite le nombre d'ARNm qui peut être analysé. Par conséquent, j'ai développé un protocole alternatif dans lequel des sondes pour de nombreux gènes ont été synthétisées comme un pool d'oligonucléotides (40 par gène en moyenne, plus de 12000 au total). Les sondes spécifiques d’un ARNm donné ont ensuite été amplifiées par PCR et converties en simple brin par transcription in vitro. J'ai généré un protocole complet, à partir de la conception de la sonde et jusqu'à l'acquisition de l'image. Je me suis intéressé à l’étude des ARNm du cycle cellulaire. En effet, les gènes du cycle cellulaire ont été largement étudiés au niveau de la protéine, mais on sait peu de choses sur la localisation de leurs ARNm. Pendant la mitose, les cellules subissent d'importantes modifications morphologiques et la traduction locale pourrait être un moyen d'atteindre la localisation des protéines. Le screening sur ces ARNm est en cours.Parallèlement à ces expériences, j'ai réalisé des expériences de smFISH sur 100 gènes choisis au hasard et 50 régulateurs de la transition G2/M du cycle cellulaire, en utilisant un protocole de smFISH classique. Dans cette configuration, on disposait d'une collection de lignées cellulaires HeLa, dans laquelle chaque cellule contient un chromosome artificiel bactérien avec le gène d'intérêt marqué au GFP. Par conséquent, en utilisant des sondes qui s'hybridaient à la séquence GFP, je pourrais utiliser le même ensemble de sondes marquées pour étudier la localisation de tous les ARNm. Un autre avantage est que la localisation des protéines pourrait être évaluée simultanément. Mes résultats indiquent que 4 ARNm ont montré une localisation spécifique lors du screening de 100 gènes choisis d’une manière aléatoire et 15 ARNm parmi les 54 régulateurs de la transition G2 / M. Ces ARNm appartiennent à cinq classes de localisation: "blobs", qui sont des agrégats d'ARNm cytoplasmiques; «clusters», qui sont des zones de concentration locale élevée d'ARNm, mais où une molécule unique d’ARNm peut encore être résolu; «nuclear membrane », où les ARNm se concentrent autour de l'enveloppe nucléaire; "spindle", qui sont des ARNm accumulés sur l'appareil de division mitotique, “spots" qui sont des agrégats d'ARNm cytoplasmiques où une molécule unique d’ARNm ne peut pas être résolu, et qui sont plus grands que les blobs. La colocalisation entre l'ARNm et la GFP, qui suggère une traduction locale, n'a été trouvée que pour 1 ARNm.Ces screenings aléatoires et ciblés effectués à petite échelle montrent une fréquence et une diversité inattendues dans les modèles de localisation d’ARNm. Cela ouvre la voie pour effectuer des screenings à plus grande échelle. / MRNA localization was discovered in 1983 in ascidian oocytes and early embryos. Since then many examples of localized RNAs have been found in many organisms, including plants, yeast, fungi, insects, fish and mammals. Localized mRNAs contribute to many biological functions, such as embryonic patterning, asymmetric cell division, cell migration, signaling, neuronal plasticity and others…Until now, only few studies analyzed RNA localization in a systematic manner. Three of them were done in Drosophila, during embryogenesis, oogenesis or larval stage and analyzed around 16000 mRNAs in total. The two other studies were done in mammalian cells and analyzed nearly 1000 mRNAs each. These studies opened a door and raised questions regarding the importance of mRNA localization in human cells and its implication in different biological processes. The goal of my thesis was thus to increase the throughput of single molecule FISH techniques (smFISH) and to study mRNA localization in HeLa cells in a systematic manner.One limitation in smFISH is the cost of the fluorescent oligonucleotide probes, which limits the number of mRNAs that can be analyzed. Therefore, I developed an alternative protocol in which probes for many genes were synthesized as a pool of oligonucleotides (40 per gene in average, more than 12000 in total). Gene-specific probes were then amplified by PCR and converted into single strand by in vitro transcription. I generated a complete protocol, starting from probe design and up to image acquisition. I was interested in studying cell cycle genes. Indeed, cell cycle genes have been extensively studied at the protein level but little is known concerning the localization of their mRNAs. During mitosis, cells go through important morphological modifications and local translation could be a mean of achieving protein localization. This screen is ongoing.In parallel to these experiments, I performed a smFISH based screen on 100 randomly chosen genes and 50 regulators of the G2/M transition of the cell cycle, using a traditional smFISH protocol. In this set-up, I took advantage of a library of HeLa cell lines, in which each cell line contains a bacterial artificial chromosome with the gene of interest tagged with GFP. Therefore, using oligonucleotides hybridizing to the GFP sequence, I could use the same probe set to study the localization of all the tagged mRNAs. A further advantage is that protein localization could be assessed simultaneously. My results indicate that two mRNAs showed a specific localization when screening 100 random genes, and 16 mRNAs among the 50 regulators of the G2/M transition. These mRNAs belong to five localization classes: "blobs", which are cytoplasmic mRNA aggregates; "clusters", which are areas of high local mRNA concentration but where individual mRNA can still be resolved; "nuclear envelope", where mRNAs concentrate around the nuclear envelope; "spindle", which are mRNAs accumulating on the cell division apparatus during mitosis, “spots" which are cytoplasmic mRNA aggregates where individual mRNA can’t be resolved and are bigger than blobs. Interestingly, colocalization between mRNA and GFP, which suggests local translation, was only found for 1 mRNA.These random and targeted screens performed at small-scale show an unexpected frequency and diversity in mRNA localization patterns, therefore pointing to new functions related to this process. This will stimulate future studies aiming at performing screenings at a higher scale.

Indiana University-Purdue University Indianapolis (IUPUI) / The human aldehyde dehydrogenase (ALDH) superfamily consists of 19 isoenzymes that are critical for normal physiology as well as the removal of toxic aldehydes. Members of the ALDH1/2 family have vital roles in cell signaling during early development, ethanol metabolism, and the removal of aldehydes derived from oxidative stress. We sought to develop selective compounds toward ALDH2 to help determine its individual contribution to biological function, as many of the ALDH1/2 family possess overlapping substrate preferences. A high-throughput screen of over 100,000 compounds uncovered a class of aromatic lactones which inhibit the ALDH1/2 enzyme family. The lactones were then characterized using a combination of enzyme kinetics, X-ray crystallography, and cell culture experiments. We found that many of the lactones are over ten times more potent toward ALDH2 than daidzin, a previously described ALDH2 inhibitor. Our ability to produce many more ALDH isoenzymes allowed us to determine that daidzin is not as selective as previously believed, inhibiting ALDH2, ALDH1B1, and ALDH1A2 with equal potency. This inhibition pattern was seen with several of the aromatic lactones as well. Structural studies show that many of the lactones bind between key aromatic residues in the ALDH1/2 enzyme substrate-binding sites. One lactone in particular mimics the position of an aldehyde substrate and alters the position of the catalytic cysteine to interfere with the productive binding of NAD+ for enzyme catalysis. Further characterization of related compounds led to the realization that the mechanism of inhibition, potency, and selectivity differs amongst the lactones based off the substituents on the aromatic scaffold and its precise binding location. Two of these compounds were found to be selective for one of the ALDH1/2 family members, BUC22, selective for ALDH1A1, and BUC27, selective for ALDH2. BUC22 demonstrates ten-fold selectivity for ALDH1A1 over ALDH1A2 and does not inhibit the remaining ALDH1/2 enzymes. Additionally, treatment with BUC22 led to decreased growth of triple-negative breast cancer cells in culture. BUC27 inhibits ALDH2 with the same potency as daidzin. Both BUC22 and BUC27 could be further developed to use as chemical tools to better understand the functional roles of ALDH1A1 and ALDH2 in biological systems.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20396号 / 工博第4333号 / 新制||工||1671(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 村田 靖次郎, 教授 辻 康之, 教授 中村 正治 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第21116号 / 工博第4480号 / 新制||工||1696(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 辻 康之, 教授 大江 浩一, 教授 松田 建児 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

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The incorporation of molecules as low-cost and stable structures in electronic circuits is a promising strategy to miniaturize electronic components. Although single-molecule electronics is still at an early phase, the investigation of charge transport through single molecules is fundamentally important to understand the relevant scientific concepts and technological applications. In this dissertation, we measured and modulated the charge transport perpendicular to the plane of small benzene derivatives. In contrast to the conventional strategy to link molecules to electrodes via anchoring groups, we used the electrode potential to control the geometry of molecules and to form the junctions through π-system-metal electrode interactions. Using a combination of electrochemical STM (EC-STM) imaging and STM-BJ methods, the measurement of charge transport through single, flat oriented tetrafluoroterephthalic acid (TFTPA) molecules on an electrified Au (111) electrode showed that, at potentials below the potential of zero-charge (pzc) of Au(111), the molecules lie flat on the electrode and form highly ordered structures. The conductance of TFTPA, along the axis perpendicular to the benzene plane, is 0.24 ± 0.04 G0, consistent with reports for other molecules oriented flat in the junction. The configuration dependent conductivity has been confirmed by first-principles non-equilibrium Green’s function computation performed by Professor John Perdew and Dr. Haowei Peng at Temple University. Hence, the electrochemical surface potential can be employed to control the orientation of molecules to access a new charge transport measurement axis. Building on our previous results (Chapter 3), we studied charge transport through two fundamentally important molecules, tetracyanoquinodimethane (TCNQ) and tetrafluorotetracyanoquinodimethane (F4TCNQ) to determine the effect of molecule-electrode binding while maintaining the same core molecular structure. The findings show that on the negatively charged Au(111), the flat-oriented TCNQ and F4TCNQ molecules exhibit similar but high conductance of ~ 0.22 ± 0.01 G0 and 0.24 ± 0.01 G0, respectively. In addition to the high conductance, two peaks at 0.02 G0, and 0.05 G0 were detected for both molecules, assigned to the bidentate-bidentate and monodentate-bidentate configurations. Density functional theory (DFT) and non-equilibrium Green’s function (NEGF) calculations were performed by Professor Manuel Smeu and Dr. Stuart Shepard at Binghamton University to determine the conductance of four distinct molecular configurations. The results show how the orientation of molecules in the junction and the molecule-electrode denticity influence the molecular orbital offsets relative to the Fermi level and the consequent charge transport. The electronic structure and charge transport through single molecules can be modulated using various functional groups. Interestingly, our previous findings (Chapters 3, and 4) showed that the conductance perpendicular to the plane of TFTPA and TCNQ/F4TCNQ was similar to the parent molecules (TPA and TCNQ). Thus, it appeared that fluorination did not significantly change charge transport properties perpendicular to the molecular plane. Building on our previous studies, we measured the conductance through mesitylene substituted with electron-withdrawing groups (e.g., NO2, Br) or with electron-donating groups (e.g., CH3) to determine if other groups might impact conductance. Our results showed that the conductance perpendicular to the molecular plane increases by introducing electron-withdrawing groups and decreases as electron-donating groups are introduced to the mesitylene molecule. Density functional theory (DFT) and non-equilibrium Green’s function (NEGF) calculations were performed to rationalize our experimental findings (By Professor Smeu and Dr. Stuart Shepard). We demonstrated that the changes in the conductance perpendicular to the molecular plane correlate well with the Hammett constant of the corresponding functional groups, indicating the importance of the nature and strength of chemical substituents on the degree of conductance modulations at least for mesitylene derivatives. Following up on the modulation of charge transport through the intrinsic properties of molecules, we investigated the effect of solvent polarity on conductance of single molecules. Particularly, we focused on charge transport through dimethylaminobenzonitrile (DMABN), a molecule that shows unique behavior, such as noticeable bulk electronic modulations in response to the physical properties of the solvents in which the molecule is immersed, e.g., dual fluorescence in polar environment, due to the stabilized intramolecular charge transfer (TICT) state. Our charge transport results show that the conductance of DMABN in a polar solvent (acidified water) is ~ten times higher than the value observed in toluene (nonpolar solvent). The conductance of a molecule with no TICT properties shows no solvent polarity-dependent conductance, indicating that the intrinsic properties of DMABN (i.e., the TICT effect) play a critical role in the enhanced conductivity in the polar solvent. Molecular dynamics calculations (performed by Professor Manuel Smeu, and Dr. Stuart Shepard) suggest that the DMABN molecule can undergo internal rotation in the junction in polar solvents, result in a higher conductance compare to the planar geometry. Our results demonstrate that molecules exhibiting TICT properties can be promising candidates to design molecular devices with sensing and switching functionalities. The findings of this dissertation, in combination with the calculations (via collaboration with computational experts), show that the intrinsic and extrinsic properties of junctions, e.g., the geometry of molecule within the junction, the charge transport axis, the molecule-electrode binding, the characteristics and electronic structure of the molecules investigated, and the physical properties of the environment, influence charge transport through single molecules. This fundamental understanding and the ability to control charge transport through single molecules may allow the design of practical devices, e.g., large-scale molecular architectures and circuits, molecular switches, and sensors. / Chemistry

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