abstract: Fluorescence spectroscopy is a popular technique that has been particularly useful in probing biological systems, especially with the invention of single molecule fluorescence. For example, Förster resonance energy transfer (FRET) is one tool that has been helpful in probing distances and conformational changes in biomolecules. In this work, important properties necessary in the quantification of FRET were investigated while FRET was also applied to gain insight into the dynamics of biological molecules. In particular, dynamics of damaged DNA was investigated. While damages in DNA are known to affect DNA structure, what remains unclear is how the presence of a lesion, or multiple lesions, affects the flexibility of DNA, especially in relation to damage recognition by repair enzymes. DNA conformational dynamics was probed by combining FRET and fluorescence anisotropy along with biochemical assays. The focus of this work was to investigate the relationship between dynamics and enzymatic repair. In addition, to properly quantify fluorescence and FRET data, photophysical phenomena of fluorophores, such as blinking, needs to be understood. The triplet formation of the single molecule dye TAMRA and the photoisomerization yield of two different modifications of the single molecule cyanine dye Cy3 were examined spectroscopically to aid in accurate data interpretation. The combination of the biophysical and physiochemical studies illustrates how fluorescence spectroscopy can be used to answer biological questions. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2015

abstract: Quiescin sulfhydryl oxidase 1 (QSOX1) is a highly conserved disulfide bond-generating enzyme that represents the ancient fusion of two major thiol-disulfide oxidoreductase gene families: thioredoxin and ERV. QSOX1 was first linked with cancer after being identified as overexpressed in pancreatic ductal adenocarcinoma (but not in adjacent normal ductal epithelia, infiltrating lymphocytes, or chronic pancreatitis). QSOX1 overexpression has been confirmed in a number of other histological tumor types, such as breast, lung, kidney, prostate, and others. Expression of QSOX1 supports a proliferative and invasive phenotype in tumor cells, and its enzymatic activity is critical for promoting an invasive phenotype. An in vivo tumor growth study utilizing the pancreatic tumor cell line MIAPaCa-2 containing a QSOX1-silencing shRNA construct revealed that QSOX1 expression supports a proliferative phenotype. These preliminary studies suggest that suppressing the enzymatic activity of QSOX1 could represent a novel therapeutic strategy to inhibit proliferation and invasion of malignant neoplasms. The goal of this research was to identify and characterize biologically active small molecule inhibitors for QSOX1. Chemical inhibition of QSOX1 enzymatic activity was hypothesized to reduce growth and invasion of tumor cells. Recombinant QSOX1 was screened against libraries of small molecules using an enzymatic activity assay to identify potential QSOX1 inhibitors. Two lead QSOX1 inhibitors were confirmed, 2-phenyl-1, 2-benzisoselenazol-3-one (ebselen), and 3-methoxy-n-[4-(1 pyrrolidinyl)phenyl]benzamide. The biological activity of these compounds is consistent with QSOX1 knockdown in tumor cell lines, reducing growth and invasion in vitro. Treatment of tumor cells with these compounds also resulted in specific ECM defects, a phenotype associated with QSOX1 knockdown. Additionally, these compounds were shown to be active in pancreatic and renal cancer xenografts, reducing tumor growth with daily treatment. For ebselen, the molecular mechanism of inhibition was determined using a combination of biochemical and mass spectrometric techniques. The results obtained in these studies provide proof-of-principle that targeting QSOX1 enzymatic activity with chemical compounds represents a novel potential therapeutic avenue worthy of further investigation in cancer. Additionally, the utility of these small molecules as chemical probes will yield future insight into the general biology of QSOX1, including the identification of novel substrates of QSOX1. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2015

abstract: Studying charge transport through single molecules is of great importance for unravelling charge transport mechanisms, investigating fundamentals of chemistry, and developing functional building blocks in molecular electronics. First, a study of the thermoelectric effect in single DNA molecules is reported. By varying the molecular length and sequence, the charge transport in DNA was tuned to either a hopping- or tunneling-dominated regimes. In the hopping regime, the thermoelectric effect is small and insensitive to the molecular length. Meanwhile, in the tunneling regime, the thermoelectric effect is large and sensitive to the length. These findings indicate that by varying its sequence and length, the thermoelectric effect in DNA can be controlled. The experimental results are then described in terms of hopping and tunneling charge transport models. Then, I showed that the electron transfer reaction of a single ferrocene molecule can be controlled with a mechanical force. I monitor the redox state of the molecule from its characteristic conductance, detect the switching events of the molecule from reduced to oxidized states with the force, and determine a negative shift of ~34 mV in the redox potential under force. The theoretical modeling is in good agreement with the observations, and reveals the role of the coupling between the electronic states and structure of the molecule. Finally, conclusions and perspectives were discussed to point out the implications of the above works and future studies that can be performed based on the findings. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2017

abstract: Acute Myeloid Leukemia (AML) is a disease that occurs when genomic changes alter expression of key genes in myeloid blood cells. These changes cause them to resume an undifferentiated state, proliferate, and maintain growth throughout the body. AML is commonly treated with chemotherapy, but recent efforts to reduce therapy toxicity have focused on drugs that specifically target and inhibit protein products of the cancer’s aberrantly expressed genes. This method has proved difficult for some proteins because of structural challenges or mutations that confer resistance to therapy. One potential method of targeted therapy that circumvents these issues is the use of small molecules that stabilize DNA secondary structures called G-quadruplexes. G-quadruplexes are present in the promoter region of many potential oncogenes and have regulatory roles in their transcription. This study analyzes the therapeutic potential of the compound GQC-05 in AML. This compound was shown in vitro to bind and stabilize the regulatory G-quadruplex in the MYC oncogene, which is commonly misregulated in AML. Through qPCR and western blot analysis, a GQC-05 mediated downregulation of MYC mRNA and protein was observed in AML cell lines with high MYC expression. In addition, GQC-05 is able to reduce cell viability through induction of apoptosis in sensitive AML cell lines. Concurrent treatment of AML cell lines with GQC-05 and the MYC inhibitor (+)JQ1 showed an antagonistic effect, indicating potential competition in the silencing of MYC. However, GQC-05 is not able to reduce MYC expression significantly enough to induce apoptosis in less sensitive AML cell lines. This resistance may be due to the cells’ lack of dependence on other potential GQC-05 targets that may help upregulate MYC or stabilize its protein product. Three such genes identified by RNA-seq analysis of GQC-05 treated cells are NOTCH1, PIM1, and RHOU. These results indicate that the use of small molecules to target the MYC promoter G-quadruplex is a viable potential therapy for AML. They also support a novel mechanism for targeting other potentially key genetic drivers in AML and lay the groundwork for advances in treatment of other cancers driven by G-quadruplex regulated oncogenes. / Dissertation/Thesis / Masters Thesis Molecular and Cellular Biology 2017

abstract: The bonding and electrostatic properties of gold containing molecules are highly influenced by relativistic effects. To understand this facet on bonding, a series of simple diatomic AuX (X=F, Cl, O and S) molecules, where upon bond formation the Au atom donates or accepts electrons, was investigated and discussed in this thesis. First, the optical field-free, Stark, and Zeeman spectroscopic studies have been performed on AuF and AuCl. The simple polar bonds between Au and typical halogens (i.e. F and Cl) can be well characterized by the electronic structure studies and the permanent electric dipole moments, el. The spectroscopic parameters have been precisely determined for the [17.7]1, [17.8]0+ and X1+ states of AuF, and the [17.07]1, [17.20]0+ and X1+ states of AuCl. The el have been determined for ground and excited states of AuF and AuCl. The results from the hyperfine analysis and Stark measurement support the assignments that the [17.7]1 and [17.8]0+ states of AuF are the components of a 3 state. Similarly, the analysis demonstrated the [19.07]1 and [19.20]0+ states are the components of the 3 state of AuCl. Second, my study focused on AuO and AuS because the bonding between gold and sulfur/oxygen is a key component to numerous established and emerging technologies that have applications as far ranging as medical imaging, catalysis, electronics, and material science. The high-resolution spectra were record and analyzed to obtain the geometric and electronic structural data for the ground and excited states. The electric dipole moment, el, and the magnetic dipole moment, m, has been the precisely measured by applying external static electric and magnetic fields. el andm are used to give insight into the unusual complex bonding in these molecules. In addition to direct studies on the gold-containing molecules, other studies of related molecules are included here as well. These works contain the pure rotation measurement of PtC, the hyperfine and Stark spectroscopic studies of PtF, and the Stark and Zeeman spectroscopic studies of MgH and MgD. Finally, a perspective discussion and conclusion will summarize the results of AuF, AuCl, AuO, and AuS from this work (bond lengths, dipole moment, etc.). The highly quantitative information derived from this work is the foundation of a chemical description of matter and essential for kinetic energy manipulation via Stark and Zeeman interactions. This data set also establishes a synergism with computation chemists who are developing new methodologies for treating relativistic effects and electron correlation. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2017

Submitted by Hugo de Oliveira Batael (hugobatelll@gmail.com) on 2018-04-11T17:47:35Z No. of bitstreams: 1 dissertação.pdf: 1370283 bytes, checksum: 904b4b44fde0f31ac327ecf977a567d0 (MD5) / Approved for entry into archive by Elza Mitiko Sato null (elzasato@ibilce.unesp.br) on 2018-04-11T18:15:11Z (GMT) No. of bitstreams: 1 batael_ho_me_sjrp.pdf: 1370283 bytes, checksum: 904b4b44fde0f31ac327ecf977a567d0 (MD5) / Made available in DSpace on 2018-04-11T18:15:11Z (GMT). No. of bitstreams: 1 batael_ho_me_sjrp.pdf: 1370283 bytes, checksum: 904b4b44fde0f31ac327ecf977a567d0 (MD5) Previous issue date: 2018-03-21 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Nesse trabalho o estado fundamental para a molécula de H2 é calculado usando o método variacional. A abordagem proposta aqui usa a função de onda molecular do tipo Valence Bond (VB), escrita como sendo a soma do termo de valência com o termo iônico, sendo ao último dado um peso diferente em relação ao primeiro. A molécula é confinada em uma caixa elipsoidal impenetrável. Como uma primeira aproximação esse tipo de geometria pode ser usada para simular moléculas dentro de cavidades proteicas. Os orbitais atômicos são construídos através de sugestões inspiradas no método de fatorização da equação de Schrödinger. A polarizabilidade, momento de quadrupolo e os autovalores de energia para a parte vibracional também são calculados. O objetivo desse trabalho é propor uma função de onda simples, em comparação com as encontradas na literatura, para a molécula de hidrogênio confinada. Os resultados numéricos estão de acordo com os encontrados na literatura e levam à discussão de quanto o termo iônico é relevante para o sistema estudado. / The ground state energies for the confined H2 molecules are computed by using the variational method. The approach proposed here uses the wave function molecular of the type Valence Bond (VB), written as the sum of the covalent term with ionic term, for last term is given a weight different in relation the first term. The molecules are confined in impenetrable prolate spheroidal boxes. In first approach this system can be used for simulate molecules in protein cavities. The atomic orbitals are built from previous suggestion inspired from the factorization of Schrödinger equation. The aim of this work is to propose a new simple and efficient wave function to be used for confined hydrogen molecule. The polarizability, quadrupole moment and vibrational states are also calculated. The results obtained are in agreement with other results presents in the literature and they lead to discussion about of relevance of ionic term in the wave function.

Proteomic studies at the single molecular level could provide better understanding of the protein’s behaviour and the effects of its interactions with other biomolecules. This could have an impact on drug development methods, disease diagnosis, and targeted therapy. Aperture assisted optical trapping is a proven technique for isolating single proteins in solution without the use of tethers or labels, and without denaturing them. Thus enabling studies of protein-protein interactions, protein-small molecule interactions, and protein-DNA interactions. In this work, double nanohole (DNH) optical tweezers were used to analyze the protein composition of heterogeneous mixtures. The trapped proteins were grouped by molecular mass based on two metrics: standard deviation of the trapping laser intensity fluctuations, and the time constant of the autocorrelation function of these fluctuations. The quantitative analysis is demonstrated first for two separate standard-size proteins, then for a mixed solution of both. Finally, the approach is applied to real unprocessed egg white solution. The results correspond well with the known protein composition of egg white found in the literature. The DNH optical tweezers’ ability to distinguish proteins in unpurified heterogeneous mixtures, can progress this technique to the next level, allowing for single biomolecular studies of unprocessed physiological solutions like blood, urine, or saliva. / Graduate

Orientador: Antonio Soares de Castro / Banca: Denis Dalmazi / Banca: Manuel Bastos Malheiro de Oliveira / Resumo: O foco deste trabalho é o espectro de inversão da molécula de amônia, resultado do fenômeno do tunelamento quântico. Para isso, usamos um modelo simpli…cado, uni- dimensional, suscetível a uma análise teórica rigorosa usando a mecânica quântica não- relativística. Dentre as diversas funções hamiltonianas já estudadas para este modelo, …zemos uma rápida apreciação dos trabalhos de Cohen, Dennison-Uhlenbeck, Manning, Merzbacher e Rosen-Morse. Para um estudo mais profundo, usamos o potencial do poço duplo …nito que, posteriormente, descobrimos já fora analisado por Peacock-López. Re- …zemos a análise deste potencial usando um caminho diferente do realizado por aquele autor. Analisamos os casos limites para este potencial e notamos que realmente, nesses regimes, ele tende para um poço …nito único ou dois poços …nitos separados. Então, de- senvolvemos um software grá…co centrado no pacote MINUIT, desenvolvido pelo CERN, para analisar e ajustar os parâmetros aos dados experimentais da amônia e, ao …nal, comparamos os resultados obtidos com aqueles encontrados na literatura. No ajuste dos parâmetros à amônia, houve uma melhoria acentuada quando passamos de uma fórmula mais simples da massa reduzida para outra mais so…sticada. No caso especí…co do po- tencial de Peacock-López, a comparação revela que os nossos resultados, de uma maneira geral, são mais precisos. Nossa análise se soma àquelas que contêm uma discussão quan- titativa do potencial de poço duplo. Como parte integrante deste trabalho, uma versão unidimensional simétrica do potencial de Morse foi exatamente resolvida em termos de funções de Kummer e um par de equações transcendentes para as autoenergias. A tentativa de ajustar este resultado à molécula de amônia, porém, mostrou que os padrões de poço duplo deste potencial... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract:The focus of this work is the inversion spectrum of the ammonia molecule, a result of the phenomenon of quantum tunneling. For this, we use a simpli…ed, one-dimensional model, amenable to a rigorous theoretical analysis using the non-relativistic quantum me- chanics. Among the various Hamiltonian functions previously studied for this model, we made a quick appraisal of the work of Cohen, Dennison-Uhlenbeck, Manning, Merzbacher and Rosen-Morse. For a deeper study, we used the …nite double-well potential which, as we later discovered, had been considered by Peacock-López. We redid the analysis of this potential using a di¤erent path made by that author. We analyze the limiting cases for this potential and actually noticed that in these schemes, it tends to one …nite well or two separate …nite wells. So, we developed a graphical software centered on the MINUIT pack- age, developed by CERN, to analyze and adjust the parameters to the experimental data of ammonia and at the end, we compared the results with those found in the literature. In setting the parameters of ammonia, there was a marked improvement when we move from a simpler formula for the reduced mass to a more sophisticated one. In the speci…c case of the potential of Peacock-López, the comparison shows that our results, in general, are more accurate and precise. Our analysis adds to those that contain a quantitative discussion of the double-well potential. As part of this work, a symmetric one-dimensional version of the Morse potential is exactly solved in terms of the Kummer functions and a pair of transcendental equations for the eigenenergies. Attempting to adjust this result to the ammonia molecule, however, showed that the double-well patterns of this potential well are irreconcilable with the energy spectrum of ammonia: Close pairs separated by long intervals / Mestre

abstract: The F1Fo ATP synthase is required for energy conversion in almost all living organisms. The F1 complex is a molecular motor that uses ATP hydrolysis to drive rotation of the γ–subunit. It has not been previously possible to resolve the speed and position of the γ–subunit of the F1–ATPase as it rotates during a power stroke. The single molecule experiments presented here measured light scattered from 45X91 nm gold nanorods attached to the γ–subunit that provide an unprecedented 5 μs resolution of rotational position as a function of time. The product of velocity and drag, which were both measured directly, resulted in an average torque of 63±8 pN nm for the Escherichia coli F1-ATPase that was determined to be independent of the load. The rotational velocity had an initial (I) acceleration phase 15° from the end of the catalytic dwell, a slow (S) acceleration phase during ATP binding/ADP release (15°–60°), and a fast (F) acceleration phase (60°–90°) containing an interim deceleration (ID) phase (75°–82°). High ADP concentrations decreased the velocity of the S phase proportional to 'ADP-release' dwells, and the F phase proportional to the free energy derived from the [ADP][Pi]/[ATP] chemical equilibrium. The decreased affinity for ITP increased ITP-binding dwells by 10%, but decreased velocity by 40% during the S phase. This is the first direct evidence that nucleotide binding contributes to F1–ATPase torque. Mutations that affect specific phases of rotation were identified, some in regions of F1 previously considered not to contribute to rotation. Mutations βD372V and γK9I increased the F phase velocity, and γK9I increased the depth of the ID phase. The conversion between S and F phases was specifically affected by γQ269L. While βT273D, βD305E, and αR283Q decreased the velocity of all phases, decreases in velocity due to βD302T, γR268L and γT82A were confined to the I and S phases. The correlations between the structural locations of these mutations and the phases of rotation they affect provide new insight into the molecular basis for F1–ATPase γ-subunit rotation. / Dissertation/Thesis / Ph.D. Molecular and Cellular Biology 2012

abstract: Surface plasmon resonance (SPR) has emerged as a popular technique for elucidating subtle signals from biological events in a label-free, high throughput environment. The efficacy of conventional SPR sensors, whose signals are mass-sensitive, diminishes rapidly with the size of the observed target molecules. The following work advances the current SPR sensor paradigm for the purpose of small molecule detection. The detection limits of two orthogonal components of SPR measurement are targeted: speed and sensitivity. In the context of this report, speed refers to the dynamic range of measured kinetic rate constants, while sensitivity refers to the target molecule mass limitation of conventional SPR measurement. A simple device for high-speed microfluidic delivery of liquid samples to a sensor surface is presented to address the temporal limitations of conventional SPR measurement. The time scale of buffer/sample switching is on the order of milliseconds, thereby minimizing the opportunity for sample plug dispersion. The high rates of mass transport to and from the central microfluidic sensing region allow for SPR-based kinetic analysis of binding events with dissociation rate constants (kd) up to 130 s-1. The required sample volume is only 1 μL, allowing for minimal sample consumption during high-speed kinetic binding measurement. Charge-based detection of small molecules is demonstrated by plasmonic-based electrochemical impedance microscopy (P-EIM). The dependence of surface plasmon resonance (SPR) on surface charge density is used to detect small molecules (60-120 Da) printed on a dextran-modified sensor surface. The SPR response to an applied ac potential is a function of the surface charge density. This optical signal is comprised of a dc and an ac component, and is measured with high spatial resolution. The amplitude and phase of local surface impedance is provided by the ac component. The phase signal of the small molecules is a function of their charge status, which is manipulated by the pH of a solution. This technique is used to detect and distinguish small molecules based on their charge status, thereby circumventing the mass limitation (~100 Da) of conventional SPR measurement. / Dissertation/Thesis / Ph.D. Electrical Engineering 2013