DNA-Mediated Charge Transport Devices for Protein Detection

Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the π-stack. Electrochemical sensors based on DNA CT have previously been used for single-nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.

First, improvements to the control over DNA monolayer formation are reported through the incorporation of copper-free click chemistry into DNA monolayer assembly. As opposed to conventional film formation involving the self-assembly of thiolated DNA, copper-free click chemistry enables DNA to be tethered to a pre-formed mixed alkylthiol monolayer. The total amount of DNA in the final film is directly related to the amount of azide in the underlying alkylthiol monolayer. DNA monolayers formed with this technique are significantly more homogeneous and lower density, with a larger amount of individual helices exposed to the analyte solution. With these improved monolayers, significantly more sensitive detection of the transcription factor TATA binding protein (TBP) is achieved.

Using low-density DNA monolayers, two-electrode DNA arrays were designed and fabricated to enable the placement of multiple DNA sequences onto a single underlying electrode. To pattern DNA onto the primary electrode surface of these arrays, a copper precatalyst for click chemistry was electrochemically activated at the secondary electrode. The location of the secondary electrode relative to the primary electrode enabled the patterning of up to four sequences of DNA onto a single electrode surface. As opposed to conventional electrochemical readout from the primary, DNA-modified electrode, a secondary microelectrode, coupled with electrocatalytic signal amplification, enables more sensitive detection with spatial resolution on the DNA array electrode surface. Using this two-electrode platform, arrays have been formed that facilitate differentiation between well-matched and mismatched sequences, detection of transcription factors, and sequence-selective DNA hybridization, all with the incorporation of internal controls.

For effective clinical detection, the two working electrode platform was multiplexed to contain two complementary arrays, each with fifteen electrodes. This platform, coupled with low density DNA monolayers and electrocatalysis with readout from a secondary electrode, enabled even more sensitive detection from especially small volumes (4 μL per well). This multiplexed platform has enabled the simultaneous detection of two transcription factors, TBP and CopG, with surface dissociation constants comparable to their solution dissociation constants.

With the sensitivity and selectivity obtained from the multiplexed, two working electrode array, an electrochemical signal-on assay for activity of the human methyltransferase DNMT1 was incorporated. DNMT1 is the most abundant human methyltransferase, and its aberrant methylation has been linked to the development of cancer. However, current methods to monitor methyltransferase activity are either ineffective with crude samples or are impractical to develop for clinical applications due to a reliance on radioactivity. Electrochemical detection of methyltransferase activity, in contrast, circumvents these issues. The signal-on detection assay translates methylation events into electrochemical signals via a methylation-specific restriction enzyme. Using the two working electrode platform combined with this assay, DNMT1 activity from tumor and healthy adjacent tissue lysate were evaluated. Our electrochemical measurements revealed significant differences in methyltransferase activity between tumor tissue and healthy adjacent tissue.

As differential activity was observed between colorectal tumor tissue and healthy adjacent tissue, ten tumor sets were subsequently analyzed for DNMT1 activity both electrochemically and by tritium incorporation. These results were compared to expression levels of DNMT1, measured by qPCR, and total DNMT1 protein content, measured by Western blot. The only trend detected was that hyperactivity was observed in the tumor samples as compared to the healthy adjacent tissue when measured electrochemically. These advances in DNA CT-based platforms have propelled this class of sensors from the purely academic realm into the realm of clinically relevant detection.

Towards in situ Single Cell Systems Biology

Systems-level studies of biological systems rely on observations taken at a resolution lower than the essential unit of biology, the cell. Recent technical advances in DNA sequencing have enabled measurements of the transcriptomes in single cells excised from their environment, but it remains a daunting technical problem to reconstruct in situ gene expression patterns from sequencing data. In this thesis I develop methods for the routine, quantitative in situ measurement of gene expression using fluorescence microscopy.

The number of molecular species that can be measured simultaneously by fluorescence microscopy is limited by the pallet of spectrally distinct fluorophores. Thus, fluorescence microscopy is traditionally limited to the simultaneous measurement of only five labeled biomolecules at a time. The two methods described in this thesis, super-resolution barcoding and temporal barcoding, represent strategies for overcoming this limitation to monitor expression of many genes in a single cell. Super-resolution barcoding employs optical super-resolution microscopy (SRM) and combinatorial labeling via-smFISH (single molecule fluorescence in situ hybridization) to uniquely label individual mRNA species with distinct barcodes resolvable at nanometer resolution. This method dramatically increases the optical space in a cell, allowing a large numbers of barcodes to be visualized simultaneously. As a proof of principle this technology was used to study the S. cerevisiae calcium stress response. The second method, sequential barcoding, reads out a temporal barcode through multiple rounds of oligonucleotide hybridization to the same mRNA. The multiplexing capacity of sequential barcoding increases exponentially with the number of rounds of hybridization, allowing over a hundred genes to be profiled in only a few rounds of hybridization.

The utility of sequential barcoding was further demonstrated by adapting this method to study gene expression in mammalian tissues. Mammalian tissues suffer both from a large amount of auto-fluorescence and light scattering, making detection of smFISH probes on mRNA difficult. An amplified single molecule detection technology, smHCR (single molecule hairpin chain reaction), was developed to allow for the quantification of mRNA in tissue. This technology is demonstrated in combination with light sheet microscopy and background reducing tissue clearing technology, enabling whole-organ sequential barcoding to monitor in situ gene expression directly in intact mammalian tissue.

The methods presented in this thesis, specifically sequential barcoding and smHCR, enable multiplexed transcriptional observations in any tissue of interest. These technologies will serve as a general platform for future transcriptomic studies of complex tissues.

Problemas direto e inverso de processos de separação em leito móvel simulado mediante mecanismos cinéticos de adsorção

Diversas aplicações industriais relevantes envolvem os processos de adsorção, citando como exemplos a purificação de produtos, separação de substâncias, controle de poluição e umidade entre outros. O interesse crescente pelos processos de purificação de biomoléculas deve-se principalmente ao desenvolvimento da biotecnologia e à demanda das indústrias farmacêutica e química por produtos com alto grau de pureza. O leito móvel simulado (LMS) é um processo cromatográfico contínuo que tem sido aplicado para simular o movimento do leito de adsorvente, de forma contracorrente ao movimento do líquido, através da troca periódica das posições das correntes de entrada e saída, sendo operado de forma contínua, sem prejuízo da pureza das correntes de saída. Esta consiste no extrato, rico no componente mais fortemente adsorvido, e no rafinado, rico no componente mais fracamente adsorvido, sendo o processo particularmente adequado a separações binárias. O objetivo desta tese é estudar e avaliar diferentes abordagens utilizando métodos estocásticos de otimização para o problema inverso dos fenômenos envolvidos no processo de separação em LMS. Foram utilizados modelos discretos com diferentes abordagens de transferência de massa, com a vantagem da utilização de um grande número de pratos teóricos em uma coluna de comprimento moderado, neste processo a separação cresce à medida que os solutos fluem através do leito, isto é, ao maior número de vezes que as moléculas interagem entre a fase móvel e a fase estacionária alcançando assim o equilíbrio. A modelagem e a simulação verificadas nestas abordagens permitiram a avaliação e a identificação das principais características de uma unidade de separação do LMS. A aplicação em estudo refere-se à simulação de processos de separação do Baclofen e da Cetamina. Estes compostos foram escolhidos por estarem bem caracterizados na literatura, estando disponíveis em estudos de cinética e de equilíbrio de adsorção nos resultados experimentais. De posse de resultados experimentais avaliou-se o comportamento do problema direto e inverso de uma unidade de separação LMS visando comparar os resultados obtidos com os experimentais, sempre se baseando em critérios de eficiência de separação entre as fases móvel e estacionária. Os métodos estudados foram o GA (Genetic Algorithm) e o PCA (Particle Collision Algorithm) e também foi feita uma hibridização entre o GA e o PCA. Como resultado desta tese analisouse e comparou-se os métodos de otimização em diferentes aspectos relacionados com o mecanismo cinético de transferência de massa por adsorção e dessorção entre as fases sólidas do adsorvente.

Avaliação da indução de lesões no DNA por lasers terapêuticos de baixa potência

Na medicina regenerativa há uma crescente utilização de lasers de baixa intensidade em protocolos terapêuticos para tratamento de doenças em tecidos moles e no tecido ósseo. Lasers emitem feixes de luz com características específicas, nas quais o comprimento de onda, a frequência, potência e modo de missão são propriedades determinantes para as respostas fotofísica, fotoquímica e fotobiológica. Entretanto, sugere-se que lasers de baixa potência induzem a produção de radicais livres, que podem reagir com biomoléculas importantes, como o DNA. Essas reações podem causar lesões e induzir mecanismos de reparo do DNA para preservar a integridade do código genético e homeostase celular. Portanto, o objetivo deste trabalho foi avaliar lesões no DNA de células do sangue periférico de ratos Wistar e a expressão dos genes ERCC1 e ERCC2 em tecidos biológicos expostos a lasers de baixa intensidade em comprimentos de onda, fluências, potências e modos de emissão utilizados em protocolos terapêuticos. Para tal, amostras de sangue periférico foram expostas ao laser vermelho (660 nm) e infravermelho (808 nm) em diferentes fluências, potências e modos de emissão, e a indução de lesões no DNA foi avaliada através do ensaio cometa. Em outros experimentos, lesões no DNA foram analisadas através do ensaio cometa modificado, utilizando as enzimas de reparo: formamidopirimidina DNA glicosilase (FPG) e endonuclease III. Pele e músculo de ratos Wistar foram expostos aos lasers e amostras desses tecidos foram retiradas para extração de RNA, síntese de cDNA e avaliação da expressão dos genes por PCR quantitativo em tempo real. Os dados obtidos neste estudo sugeriram que a exposição aos lasers induz lesões no DNA dependendo da fluência, potência e modo de emissão, e que essas lesões são alvos da FPG e endonuclease III. A expressão relativa do RNAm de ERCC1 e de ERCC2 foi alterada nos tecidos expostos dependendo do comprimento de onda e fluência utilizada. Os resultados obtidos neste estudo sugerem que danos oxidativos no DNA poderiam ser considerados para segurança do paciente e eficácia terapêutica, bem como alterações na expressão dos genes de reparo do DNA participariam dos efeitos de bioestimulação que justificam as aplicações terapêutica de lasers de baixa potência.

Stepwise loss of motilin and its specific receptor genes in rodents

Specific interactions among biomolecules drive virtually all cellular functions and underlie phenotypic complexity and diversity. Biomolecules are not isolated particles, but are elements of integrated interaction networks, and play their roles through specific interactions. Simultaneous emergence or loss of multiple interacting partners is unlikely. If one of the interacting partners is lost, then what are the evolutionary consequences for the retained partner? Taking advantages of the availability of the large number of mammalian genome sequences and knowledge of phylogenetic relationships of the species, we examined the evolutionary fate of the motilin (MLN) hormone gene, after the pseudogenization of its specific receptor, MLN receptor (MLNR), on the rodent lineage. We speculate that the MLNR gene became a pseudogene before the divergence of the squirrel and other rodents about 75 mya. The evolutionary consequences for the MLN gene were diverse. While an intact open reading frame for the MLN gene, which appears functional, was preserved in the kangaroo rat, the MLN gene became inactivated independently on the lineages leading to the guinea pig and the common ancestor of the mouse and rat. Gain and loss of specific interactions among biomolecules through the birth and death of genes for biomolecules point to a general evolutionary dynamic: gene birth and death are widespread phenomena in genome evolution, at the genetic level; thus, once mutations arise, a stepwise process of elaboration and optimization ensues, which gradually integrates and orders mutations into a coherent pattern.

Immobilization of cell-binding peptides on poly-ε-caprolactone film surface to biomimic the peripheral nervous system.

Cell-material interactions are crucial for cell adhesion and proliferation on biomaterial surfaces. Immobilization of biomolecules leads to the formation of biomimetic substrates, improving cell response. We introduced RGD (Arg-Gly-Asp) sequences on poly-ε-caprolactone (PCL) film surfaces using thiol chemistry to enhance Schwann cell (SC) response. XPS elemental analysis indicated an estimate of 2-3% peptide functionalization on the PCL surface, comparable with carbodiimide chemistry. Contact angle was not remarkably reduced; hence, cell response was only affected by chemical cues on the film surface. Adhesion and proliferation of Schwann cells were enhanced after PCL modification. Particularly, RGD immobilization increased cell attachment up to 40% after 6 h of culture. It was demonstrated that SC morphology changed from round to very elongated shape when surface modification was carried out, with an increase in the length of cellular processes up to 50% after 5 days of culture. Finally RGD immobilization triggered the formation of focal adhesion related to higher cell spreading. In summary, this study provides a method for immobilization of biomolecules on PCL films to be used in peripheral nerve repair, as demonstrated by the enhanced response of Schwann cells.

Plasma biochemical responses of the omnivorous crucian carp (Carassius auratus) to crude cyanobacterial extracts

Healthy crucian carp (Carassius auratus) were treated by intraperitoneal (i.p.) injection of crude cyanobacterial extracts at two doses, 50 and 200 mu g MC-LR equiv kg(-1) BW. High mortality (100%) was observed within 60 h post injection in the high-dose group. In the treated fish, activities of four plasma enzymes, alanine aminotransferase (ALT), alkaline phosphatase (ALP), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH), all showed substantial increases, with both dose and time-dependent effects. These increases of enzyme activity indicate severe impairment occurred in the liver of crucian carp over time. Plasma concentrations of energy-related biomolecules including glucose (GLU), cholesterol (CHO), triglyceride (TG), and total protein (TP) showed marked changes in the high-dose group, possibly a nutritional imbalance correlated with the liver injury caused by intraperitoneal exposure to crude cyanobacterial extracts.

Laser irradiation cell photothermal therapy assisted by gold nanoparticles

The strong absorption of gold nanoparticles in the visible spectral range allows the localized generation of heat in a volume of only a few tens of nanometer. The efficient conversion of strongly absorbed light by plasmonic gold nanoparticles to heat energy and their easy bioconjugation suggest that the gold nanoparticles can be used as selective photothermal agents in molecular cell targeting. The selective destruction of alkaline phosphatase, the permeabilization of the cell membrane and the selective killing of cells by laser irradiating gold nanoparticles were demonstrated. The potential of using this selective technique in molecularly targeted photothermal therapy and transfection is discussed.

色谱法分离稀土元素和生物小分子的研究

本论文利用高效离心分配色谱仪进行了稀土元素抗、忆、斓的分离研究和菱角壳中黄酮类化合物的分离研究；探讨了氨基酸在双水相体系中的分配行为；利用气相色谱一质谱法测定了野生菱角壳中的多糖类化合物的组成；利用高效制备色谱法对野生菱角壳中的黄酮类和生物碱类化合物分别进行了制备分离的研究。1．首次采用新型梭酸类萃取剂CA-12（仲辛基苯氧基乙酸）的庚烷溶液作为固定相，以氯乙酸一氢氧化钠混合溶液为流动相，利用高效离心分配色谱（HPCPC）分离伉、铭、斓，考察了流动相酸度、流速及HPCPC转速对分离效率的影响，通过梯度PH洗脱，实现了杭、忆、悯的基线分离，并对CA-12萃取金属离子的机理进行了探讨，同时利用HPCPC，对黄酮类化合物进行了分离研究，优选出溶剂系统（正己烷一乙酸乙醋一甲醇一水）的最佳配比，实现了混合物的分离。2．首次对四种氨基酸在聚乙二醇（PEG）一磷酸盐双水相体系中的分配行为进行了研究。考察了PEG分子量、磷酸盐溶液的pH值对相图的影响，测定了两相的组成、密度和折射率等参数，并对缓冲溶液的pH值、盐离子的存在和氨基酸的支链结构对氨基酸在双水相中分配比的影响进行了探讨。3．用乙醇分级沉淀法，首次从野生菱角壳中提取出多糖化合物。通过Molisch试验、红外光谱、核磁共振波谱分析确定了多糖的存在，用气相色谱一质谱法，确定了菱角壳多糖化合物的单糖组成。首次从野生菱角壳中提取出黄酮类化合物和生物碱类化合物，利用高效制备液相色谱（HPLC），通过考察流动相的组成配比、流速、检测波长等分离条件对分离效果的影响，优选出最佳色谱分离条件和制备条件，分离制备出四个黄酮化合物和三个生物碱化合物单组分，经化学法、红外光谱、质谱法和核磁共振法等初步确定了黄酮类化合物和生物碱类化合物的基本结构单元。

带电粒子辅照生物分子改性的研究

本文是从超低能（110KeV）、低能（1-20MeV/u）重离子注入生物材料引起突变效应及其机理研究中产生的新生长点，从辐射化学角度通过对脱氧核糖核酸（DNA）、蛋白质以及组成DNA和蛋白质的基本单元的辐照损伤的调研，从物理角度对带电粒子（包括质子和重离子）高低传能线密度（LET）辐射与X射线、γ射线等低LET辐射加以比较，提出了采用带电粒子注入生物分子改性研究的新思路；并在此基础上，开展了一些实验工作。 在用质子束注入的甘氨酸水溶液的辐照产物的分析实验中，用气相色谱和质谱（GC-MS）联用技术的分析，得到了不同于X射线、γ-射线辐照甘氨酸水溶液的辐照产物——甘氨酰甘氨酸（甘甘二肽），并根据有关文献提出了产生这种产物的可能机理。从而从辐射化学方面为带电粒子对生物分子的辐照损伤反应提供了进一步的认识，也为从辐射生物学角度解释带电粒子对蛋白质这样大分子的作用机制提供了新的依据。

[Ru(bpy)(3)](2+)-doped silica nanoparticles within layer-by-layer biomolecular coatings and their application as a biocompatible electrochemiluminescent tag material

[Ru(bpy)(3)](2+)-doped silica (RuSi) nanoparticles were synthesized by using a water/oil microemulsion method. Stable electrochemiluminescence (ECL) was obtained when the RuSi nanoparticles were immobilized on a glassy carbon electrode by using tripropylamine (TPA) as a coreactant. Furthermore, the ECL of the RuSi nanoparticles with layer-by-layer biomolecular coatings was investigated. Squential self-assembly of the polyelectrolytes and biomolecules on the RuSi nanoparticles gave nanocomposite suspensions, the ECL of which decreased on increasing the number of bilayers.

Glucose biosensor based on gold nanoparticle-catalyzed luminol electrochemiluminescence on a three-dimensional sol-gel network

An electrochemiluminescent glucose biosensor was proposed based on gold nanoparticle-catalyzed luminol electrochemiluminescence (ECL). Gold nanoparticles were self-assembled onto silica sol-gel network, and then glucose oxidase was adsorbed on the surface of gold nanoparticles. The surface assembly process and the electrochemistry and ECL behaviors of the biosensor were investigated. The assembled gold nanoparticles could efficiently electrocatalyze luminol ECL ECL intensity of the biosensor depended on scan rate, luminol concentration, and size of gold nanoparticles.

Single-walled carbon nanotubes binding to human telomeric i-motif DNA under molecular-crowding conditions: More water molecules released

The natural occurrence of the human telomeric G-quadruplex or i-motif in vivo has not been demonstrated and the biological effects of the induction of these structures need to be clarified. Intracellular environments are highly crowded with various biomolecules and in vitro studies under molecular-crowding conditions will provide important information on how biomolecules behave in cells. Here we report that cell-mimic crowding can increase i-motif stability at acid pH and cause dehydration.

Biomolecule-nanoparticle hybrids for electrochemical biosensors

Inorganic nanoparticles (NPs) with attractive electronic, optical, magnetic, thermal and catalytic properties have attracted great interest due to their important applications in physics, chemistry, biology, medicine, materials science and interdisciplinary fields. Biomolecule-NP hybrid systems, which combine recognition and catalytic properties of biomolecules with electronic, optical, magnetic and catalytic properties of NPs, are particularly new materials with synergistic properties originating from the components of the hybrid composites. The biomolecule-NP hybrid system has excellent prospects for interfacing biological recognition events with electronic signal transduction so as to design a new generation of bioelectronic devices with high sensitivity.

Surface plasmon resonance and electrochemistry for detection of small molecules using catalyzed deposition of metal ions on gold substrate

Small molecules are difficult to detect by conventional surface plasmon resonance (SPR) spectroscopy due to the fact that the changes in the refractive index resulted from the binding process of small biomolecules are quite small. Here, we report a simple and effective method to detect small biomolecule using SPR spectroscopy and electrochemistry by catalyzed deposition of metal ions on SPR gold film. As an example, the ascorbic acid-mediated deposition of Ag on gold film was monitored by in situ SPR spectrum. The deposition of Ag atom on gold film resulted in an obvious decrease of depth in SPR angular scan curves of reflectance intensity and minimum reflectivity angle. The depth change of the SPR reflectance intensity and minimum reflectivity angle curves mainly relied on the amount of Ag atom deposited on gold film that can be controlled by the concentration of ascorbic acid. By monitoring the deposition of Ag atom on gold film, ascorbic acid was detected in the concentration range of 2 x 10(-5) M to 1 x 10(-3) M. After each of detections, the SPR sensor surface was completely regenerated by a potential step that stripped off the Ag atom. Furthermore, the regeneration process of the sensor surface provides the feasibility for detecting the concentration of ascorbic acid by electrochemical method.