Master of Science / Department of Chemistry / Jun Li / This study is focused on exploring the mechanisms of DNA dynamics at carbon electrode surfaces under a strong electric field for the development of novel DNA hybridization sensors. Oligonucleotides with FAM6 attached at the distal end are covalently tethered on the carbon electrode surface. The fluorescence emission from the FAM6 is strongly quenched in close proximity to the electrode surface. The modulation to the fluorescence intensity is correlated with the reversible reorientation of the negatively charged DNA molecules under the electric field within the electric double layer. The orientation dynamics are apparently determined by the interplay of the electropotential, salt concentration, and stiffness of the DNA molecules. We have observed that dsDNAs switch with fast dynamics (in < 0.05 second) followed by relaxation at a slower rate (in > 0.1 second) when the electric field is altered by stepping the electropotential to a more positive or negative value. The DNA reorientation exhibits strong dependence on the PBS buffer concentration and electric double layer thickness. A preliminary calculation based on dipole-surface energy transfer theory indicates that the critical distance between FAM6 and glassy carbon surface is 10.95 nm. In connection with the fluorescence study, the effect of DNA hybridization on electrochemical impedance spectroscopy (EIS) has also been investigated by two methods in an attempt to develop a fast electronic detection method. First, EIS at high AC amplitude (141 mV rms) with DNA-modified glassy carbon electrodes before and after target DNA hybridization have shown notable change at high frequencies, likely related to the DNA reorientation processes. Second, reversible EIS detection of DNA hybridization has been demonstrated with patterned regular carbon nanofiber arrays at normal AC amplitude (10 mV rms). The combination of these two methods will be explored in future studies. The effects of the electric field on surface-tethered molecular beacons (MBs) have also been studied with fluorescence spectroscopy. An increase in fluorescence at negative bias is observed accompanying the opening of the MB stem, which leads to larger separation between fluorophore and quencher. At positive bias, the rehybridization of the MB stem leads to a decrease in fluorescence intensity.

Quinones have been the subject of much interest due to their various biological activities, mainly as antitumor and as trypanocidal agents. Quinones are cytotoxic by two main mechanisms: the generation of ROS resulting in oxidative stress and alkylation of cellular nucleophiles, such as DNA and some enzymes such as topoisomerases. Their activity depends on bioreduction, similarly to what happens to nitroaromatic compounds. They also catalyze electron transfer reactions in biological processes and, after reduction generate radical anions (semiquinone radical anion and nitro), which depending on stability, can furnish their free electrons to acceptor molecules. In the present study, compounds with mixed functionalities derived from nor-β-lapachone, including a nitroaniline group were electrochemically studied in protic (acetate buffer) and aprotic (DMF+TBABF4, DMSO+TBAP and Acetonitrile+TBABF4) media, using glassy carbon and mercury as working electrodes. The compounds showed a complex redox behavior and the mechanism was elucidated using electron spin resonance. The electroreduced products of nor-β-lapachone and of the nitroquinones reacted with oxygen, indicative of the generation of reactive oxygen species, reactivity in the order of 2 > nor-β-lapachone > 3 > 1. We investigated their interaction with DNA, which was shown to be positive for nitroquinones and negative for the precursor nor-β-lapachone, in agreement with biological assays which had also shown that the nitroquinones cause DNA damage. The stability of the nitrosemiquinones, their half-life times were measured using mercury electrode, and the reaction rates for the electrochemical process-following-up-isproportionation reaction were measured. From these studies, a lower stability for the meta-substituted nitrophenylaniline (k2 = 5.188 x 103 L mol-1 s-1 and t1/2 = 0.06 s) was evidenced. Upon spectroelectrochemical reduction studies of the nitroquinones, the generation of radicalar intermediates (semiquinone radical anion and nitro radical anion) was observed, with differences between o- and m-derived compounds and the p-substituted one. To increase the solubility of the nitroquinones, in order to allow in vivo studies, the formation of inclusion complexes with β-cyclodextrin were evaluated. Positive results were obtained, leading to a viable formulation alternative for further biological studies with the compounds. / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Quinonas despertam muito interesse devido às suas diversas atividades biológicas, principalmente como agentes antitumoral e tripanossomicida. A citotoxicidade de quinonas decorre de dois mecanismos principais: geração de EROs resultando no estresse oxidativo e alquilação de nucleófilos celulares, como o DNA e algumas enzimas, como as topoisomerases. Sua atividade depende de biorredução, similarmente ao que acontece com compostos nitroaromáticos. Eles também catalisam reações de transferência de elétrons biológicas e, após a redução geram ânions radicais (ânions radicais semiquinona e nitro), que dependendo da estabilidade, podem transferir seus elétrons livres a moléculas aceptoras. Neste trabalho, compostos de funcionalidade mista derivados da nor-β-lapachona, com um grupo nitroanilina, foram estudados eletroquimicamente nos meios prótico (tampão acetato) e aprótico (DMF + TBABF4, DMSO + TBAP e acetonitrila + TBABF4), utilizando carbono vítreo e mercúrio como eletrodos de trabalho. Os compostos apresentaram um comportamento redox complexo e o mecanismo elucidado por espectroeletroquímica. Os produtos da eletro-redução da nor-β-lapachona e nitroquinonas reagiram com oxigênio, indicativo da geração de EROs, na ordem de reatividade 2 > nor-β-lapachona > 3 > 1. Foi investigada a interação com DNA, que se mostrou positiva para as nitroquinonas e negativa para o precursor nor-β-lapachona, concordantes com ensaios biológicos que também evidenciou que as nitroquinonas causam dano ao DNA. A estabilidade do nitrosemiquinona, tempos de meia-vida e as taxas reacionais referentes à reação química de desproporcionamento acoplada ao processo eletroquímico para cada derivado foram determinadas usando eletrodo de mercúrio. A partir desses estudos, foi evidenciada a menor estabilidade para o nitrofenilamina meta-substituída (k2 = 15,188 x 103 L mol-1 s-1 and t1/2 = 0,06 s). Nos estudos por espectroeletroquímica das nitroquinonas, observou-se a geração de intermediários radicalares (ânions radicais semiquinona e nitro), com diferenças entre os nitroderivados o- e m-, assim como para o p- derivado. Com objetivo de aumentar a solubilidade das nitroquinonas, para posteriores estudos in vivo, foi avaliada a formação de complexos de inclusão com β-ciclodextrina. Foram obtidos resultados positivos, refletindo em alternativa viável para formulações posteriores com estes compostos e ensaios biológicos.

Philosophiae Doctor - PhD / Electroanalytical and optical properties of nanoscale materials are very important for biosensing applications as well as for understanding the unique one-dimensional carrier transport mechanism. One-dimensional semiconductor nanomaterials such as semiconductor quantum dots are extremely attractive for designing high-density protein arrays. Because of their high surfaceto-volume ratio, electro-catalytic activity as well as good biocompatibility and novel electron transport properties make them highly attractive materials for ultra-sensitive detection of biological macromolecules via bio-electronic or bio-optic devices. A genosensor or gene based biosensor is an analytical device that employs immobilized deoxyribonucleic acid (DNA) probes as the recognition element and measures specific binding processes such as the formation of deoxyribonucleic acid-deoxyribonucleic acid (DNA-DNA), deoxyribonucleic acid- ribonucleic acid (DNA-RNA) hybrids, or the interactions between proteins or ligand molecules with DNA at the sensor surface.In this thesis, I present four binary and two ternary-electrochemically and optically modulated selenide and telluride quantum dots, all synthesised at room temperature in aqueous media. Cationic gallium (Ga3+) synthesized in form of hydrated gallium perchlorate salt[Ga(ClO4)3.6H2O] from the reaction of hot perchloric acid and gallium metal was used to tailor the optical and electrochemical properties of the selenide and telluride quantum dots. The synthesized cationic gallium also allowed successful synthesis of novel water soluble and biocompatible capped gallium selenide nanocrystals and gallium telluride quantum dots. Cyclic voltammetric studies inferred that presence of gallium in a ZnSe-3MPA quantum dot lattice improved its conductivity and significantly increased the electron transfer rate in ZnTe-3MPA.Utraviolet-visible (UV-vis) studies showed that incorporation of gallium into a ZnSe-3MPA lattice resulted in a blue shift in the absorption edge of ZnSe-3MPA from 350 nm to 325 nm accompanied by decrease in particle size. An amphiphilic bifunctional molecule, 3-Mercaptopropionic acid (3-MPA) was used as a capping agent for all quantum dots. It was found that 3-MPA fully solubilised the quantum dots, made them stable, biocompatible, non agglomerated and improved their electron transfer kinetics when immobilized on gold electrodes.Retention of the capping agent on the quantum dot surface was confirmed by Fourier transform infrared spectroscopy (FTIR) which gave scissor type bending vibrations of C-H groups in the region 1365 cm-1 to 1475 cm-1, stretching vibrations of C=O at 1640 cm-1, symmetric and asymmetric vibrations of the C-H in the region 2850 cm-1 to 3000 cm-1 as well as stretching vibrations of –O-H group at 3435 cm-1. The particle size and level of non-agglomeration of the quantum dots was studied by high resolution transmission electron microscopy (HRTEM). The optical properties of the quantum dots were studied using UV-vis and fluorescence spectroscopic techniques.Quantum dot/nanocrystal modified gold electrodes were prepared by immersing thoroughly cleaned electrodes in the quantum dot/nanocrystal solution, in dark conditions for specific periods of time. The electrochemical properties of the modified electrodes were characterized by cyclic voltammetry (CV), square wave voltammetry (SWV), electrochemical impedance and spectroscopy (EIS). Six sensing platforms were then prepared using quantum dot/nanocrystal, one of which was used for detection of dopamine while the rest were used for detection of a DNA sequence related to 5-enolpyruvylshikimate-3-phosphate synthase, a common vector gene in glyphosate resistant transgenic plants.The first sensing platform, consisting of ZnSe-3MPA modified gold electrode (Au|ZnSe-3MPA) gave rise to a novel method of detecting dopamine in presence of excess uric acid and ascorbic acid. Using a potential window of 0 to 400 mV, the ZnSe-3MPA masked the potential for oxidation of uric and ascorbic acids, allowing detection of dopamine with a detection limit of 2.43 x 10-10 M (for SWV) and 5.65 x 10-10 M (for steady state amperometry), all in presence of excess uric acid (>6500 higher) and ascorbic acid (>16,000 times higher). The detection limit obtained in this sensor was much lower than the concentration of dopamine in human blood(1.31 x 10-9 M), a property that makes this sensor a potential device for detection of levels of dopamine in human blood.The other sensing platforms were prepared by bioconjugation of amine-terminated 20 base oligonucleotide probe DNA (NH2-5′-CCC ACC GGT CCT TCA TGT TC-3′) onto quantum dot modified electrodes with the aid of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS). The prepared DNA electrodes were electrostatically hybridized with different sequences which included 5′-GAA CAT GAA GGA CCG GTG GG-3′ (complementary target), 5′-CATAGTTGCAGCTGCCACTG-3′ (non complementary target) and 5′-GATCATGAAGCACCGGAGGG-3′ (3-base mismatched target).The hybridization events were monitored using differential pulse voltammetry (DPV) and SWV by monitoring the guanine oxidation signal or using EIS by monitoring changes in the charge transfer resistance. The quantum dot genosensors were characterized by low detection limits (in the nanomolar range), long linear range (40 - 150 nM) and were able to discriminate among complementary, non-complementary and 3-base mismatched target sequences.