Enzymatic Polymerization of High Molecular Weight DNA

The use of DNA as a polymeric building material transcends its function in biology and is exciting in bionanotechnology for applications ranging from biosensing, to diagnostics, and to targeted drug delivery. These applications are enabled by DNA’s unique structural and chemical properties, embodied as a directional polyanion that exhibits molecular recognition capabilities. Hence, the efficient and precise synthesis of high molecular weight DNA materials has become key to advance DNA bionanotechnology. Current synthesis methods largely rely on either solid phase chemical synthesis or template-dependent polymerase amplification. The inherent step-by-step fashion of solid phase synthesis limits the length of the resulting DNA to typically less than 150 nucleotides. In contrast, polymerase based enzymatic synthesis methods (e.g., polymerase chain reaction) are not limited by product length, but require a DNA template to guide the synthesis. Furthermore, advanced DNA bionanotechnology requires tailorable structural and self-assembly properties. Current synthesis methods, however, often involve multiple conjugating reactions and extensive purification steps.

The research described in this dissertation aims to develop a facile method to synthesize high molecular weight, single stranded DNA (or polynucleotide) with versatile functionalities. We exploit the ability of a template-independent DNA polymerase−terminal deoxynucleotidyl transferase (TdT) to catalyze the polymerization of 2’-deoxyribonucleoside 5’-triphosphates (dNTP, monomer) from the 3’-hydroxyl group of an oligodeoxyribonucleotide (initiator). We termed this enzymatic synthesis method: TdT catalyzed enzymatic polymerization, or TcEP.

Specifically, this dissertation is structured to address three specific research aims. With the objective to generate high molecular weight polynucleotides, Specific Aim 1 studies the reaction kinetics of TcEP by investigating the polymerization of 2’-deoxythymidine 5’-triphosphates (monomer) from the 3’-hydroxyl group of oligodeoxyribothymidine (initiator) using in situ 1H NMR and fluorescent gel electrophoresis. We found that TcEP kinetics follows the “living” chain-growth polycondensation mechanism, and like in “living” polymerizations, the molecular weight of the final product is determined by the starting molar ratio of monomer to initiator. The distribution of the molecular weight is crucially influenced by the molar ratio of initiator to TdT. We developed a reaction kinetics model that allows us to quantitatively describe the reaction and predict the molecular weight of the reaction products.

Specific Aim 2 further explores TcEP’s ability to transcend homo-polynucleotide synthesis by varying the choices of initiators and monomers. We investigated the effects of initiator length and sequence on TcEP, and found that the minimum length of an effective initiator should be 10 nucleotides and that the formation of secondary structures close to the 3’-hydroxyl group can impede the polymerization reaction. We also demonstrated TcEP’s capacity to incorporate a wide range of unnatural dNTPs into the growing chain, such as, hydrophobic fluorescent dNTP and fluoro modified dNTP. By harnessing the encoded nucleotide sequence of an initiator and the chemical diversity of monomers, TcEP enables us to introduce molecular recognition capabilities and chemical functionalities on the 5’-terminus and 3’-terminus, respectively.

Building on TcEP’s synthesis capacities, in Specific Aim 3 we invented a two-step strategy to synthesize diblock amphiphilic polynucleotides, in which the first, hydrophilic block serves as a macro-initiator for the growth of the second block, comprised of natural and/or unnatural nucleotides. By tuning the hydrophilic length, we synthesized the amphiphilic diblock polynucleotides that can self-assemble into micellar structures ranging from star-like to crew-cut morphologies. The observed self-assembly behaviors agree with predictions from dissipative particle dynamics simulations as well as scaling law for polyelectrolyte block copolymers.

In summary, we developed an enzymatic synthesis method (i.e., TcEP) that enables the facile synthesis of high molecular weight polynucleotides with low polydispersity. Although we can control the nucleotide sequence only to a limited extent, TcEP offers a method to integrate an oligodeoxyribonucleotide with specific sequence at the 5’-terminus and to incorporate functional groups along the growing chains simultaneously. Additionally, we used TcEP to synthesize amphiphilic polynucleotides that display self-assemble ability. We anticipate that our facile synthesis method will not only advance molecular biology, but also invigorate materials science and bionanotechnology.

In vitro antioxidant and immunomodulatory activity of transglutaminase-treated sodium caseinate hydrolysates

Sodium caseinate (NaCN) was incubated prior to and after hydrolysis with a microbial transglutaminase (TGase) and hydrolysed with Prolyve 1000. The resultant hydrolysates were tested for their immunomodulatory and antioxidant activity. TGase-treated hydrolysates significantly reduced (p < 0.05) the production of IL-6 at 0.5 and 1 mg mL−1 and the non-TGase treated hydrolysate reduced the production of IL-6 at 1 mg mL−1 in concanavalin (ConA) stimulated Jurkat T cells. None of the samples had an effect on IL-2. The hydrolysates showed higher oxygen radical absorbance capacity assay and ferric reducing antioxidant power activity than unhydrolysed NaCN, but no significant (p > 0.05) differences were found between the TGase-treated and non-TGase-treated samples. In the presence of hydrogen peroxide, the non-TGase-treated sample exhibited the highest DNA protective effect in U937 cells. These findings suggest that NaCN derived hydrolysates with and without treatment with TGase may exert specific antioxidant, genoprotective and anti-inflammatory effects.

C-MEMS Based Micro Enzymatic Biofuel Cells

Miniaturized, self-sufficient bioelectronics powered by unconventional micropower may lead to a new generation of implantable, wireless, minimally invasive medical devices, such as pacemakers, defibrillators, drug-delivering pumps, sensor transmitters, and neurostimulators. Studies have shown that micro-enzymatic biofuel cells (EBFCs) are among the most intuitive candidates for in vivo micropower. In the fisrt part of this thesis, the prototype design of an EBFC chip, having 3D intedigitated microelectrode arrays was proposed to obtain an optimum design of 3D microelectrode arrays for carbon microelectromechanical systems (C-MEMS) based EBFCs. A detailed modeling solving partial differential equations (PDEs) by finite element techniques has been developed on the effect of 1) dimensions of microelectrodes, 2) spatial arrangement of 3D microelectrode arrays, 3) geometry of microelectrode on the EBFC performance based on COMSOL Multiphysics. In the second part of this thesis, in order to investigate the performance of an EBFC, behavior of an EBFC chip performance inside an artery has been studied. COMSOL Multiphysics software has also been applied to analyze mass transport for different orientations of an EBFC chip inside a blood artery. Two orientations: horizontal position (HP) and vertical position (VP) have been analyzed. The third part of this thesis has been focused on experimental work towards high performance EBFC. This work has integrated graphene/enzyme onto three-dimensional (3D) micropillar arrays in order to obtain efficient enzyme immobilization, enhanced enzyme loading and facilitate direct electron transfer. The developed 3D graphene/enzyme network based EBFC generated a maximum power density of 136.3 μWcm-2 at 0.59 V, which is almost 7 times of the maximum power density of the bare 3D carbon micropillar arrays based EBFC. To further improve the EBFC performance, reduced graphene oxide (rGO)/carbon nanotubes (CNTs) has been integrated onto 3D mciropillar arrays to further increase EBFC performance in the fourth part of this thesisThe developed rGO/CNTs based EBFC generated twice the maximum power density of rGO based EBFC. Through a comparison of experimental and theoretical results, the cell performance efficiency is noted to be 67%.

Prétraitement d'un isolat de protéines de lin par haute pression hydrostatique : impacts sur la structure protéique, l'hydrolyse enzymatique et les capacités antioxydantes des hydrolysats finaux

Les graines de lin sont des oléagineux largement cultivés au Canada. Cependant, les résidus générés suite au processus d’extraction de l’huile contiennent une importante quantité de protéines et peuvent être valorisées dans l’alimentation humaine en raison, principalement, de certaines fractions peptidiques possédant des propriétés bioactives. Dans le cadre de ce travail, l’influence des hautes pressions hydrostatiques (HPH) sur un isolat de protéines de lin a été étudiée concernant les modifications de la structure protéique, l’hydrolyse enzymatique ainsi que l’activité antioxydante des hydrolysats. Ainsi, des solutions protéiques de lin (1% m/v) ont été soumises à un traitement de HPH à 600 MPa pendant 5 et 20 minutes, à 20°C et comparés à des échantillons non-pressurisés. Deux traitements subséquents d’hydrolyse ont été effectués suite au traitement ou non de pressurisation : une première hydrolyse trypsique suivie d’une deuxième par la pronase. Dans un premier temps, la caractérisation de l’isolat protéique de lin pressurisé et non pressurisé a été réalisée par spectrofluorimétrie et par une analyse de la taille des particules afin d’étudier l’effet de la pressurisation sur les HPH la matrice protéique végétale. Par la suite, les hydrolysats protéiques ont été caractérisés par HPLC-MS et leur capacité antioxydante a été déterminée par ORAC. Les résultats ont démontré que le niveau de pressurisation et la durée du traitement ont un impact sur la structure protéique en induisant la dissociation des protéines, et la formation d’agrégats. Ceux-ci seraient occasionnés par la décompression ou créés durant l’entreposage des isolats. Suite à l’hydrolyse enzymatique des solutions protéiques pressurisées ou non par la trypsine seule et par la trypsine-pronase, les analyses chromatographiques ont révélé que la concentration de certains peptides a été modifiée lorsque la trypsine seule était utilisée après un traitement à HPH. Enfin, les HPH ont amélioré la capacité antioxydante des hydrolysats obtenus lors de l’hydrolyse trypsine-pronase comparativement au contrôle non-pressurisé.

Desorption isotherms and thermodynamics properties of anchovy in natura and enzymatic modified paste

The thermodynamic properties of anchovy fillets and enzymatic modified pastes in two hydrolysis degrees (3% HD and 14% HD), at 50, 60 and 70 C were evaluated. The GAB model was used to calculate the values of the monolayer moisture content and the thermodynamic properties of the samples. The enzymatic modification led to the increases of the superficial area and differential enthalpies, and decrease of the differential entropies in relation the samples in natura. The enthalpy–entropy compensation showed that the process was controlled by the enthalpy, it was only spontaneous for the samples in natura. Pore size decreased with enzymatic modification, and all samples were in the limit of region between micropores and mesopores (<2 nm) for moisture content of 15%, and mesopores (from 2 to 50 nm) to moisture content above 15%.

Obtenção de um hidrogel proveniente de proteínas da corvina (micropogonias furnieri) e solubilização das proteínas fibrosas residuais

Com o aumento na captura de pescado e da poluição do meio ambiente, esta-se à margem de exceder a estimativa do limite da sustentabilidade, e obviamente isto faz com se utilize os recursos marítimos com mais inteligência e precaução. Aplicando tecnologia enzimática ou química é possível recuperar as proteínas do processamento do pescado, produzindo hidrolisados e isolados protéicos. Uma grande quantidade de proteínas insolúveis está disponível em escamas, peles e ossos, subprodutos do processamento do pescado, que podem ser solubilizadas através de fungos e bactérias. Utilizando isolados protéicos é possível obter biopolímeros, estes têm chamado a atenção nos últimos anos, pois são biodegradáveis, não-tóxicos e geralmente biocompatíveis. Os hidrogéis protéicos são polímeros que podem absorver uma quantidade de água a partir de 10 até centenas de vezes o seu peso seco. O objetivo deste trabalho foi desenvolver um hidrogel protéico, com propriedades superabsorventes, a partir das proteínas solúveis e insolúveis da corvina (Micropogonias furnieri). Para a produção dos hidrolisados a partir das proteínas solúveis foi utilizado processo enzimático (Alcalase e Flavourzyme) e químico (solubilização ácida e alcalina). Nos processos de solubilização das proteínas insolúveis foram utilizados microrganismos (bactérias e fungos). Tanto as bactérias como os fungos avaliados apresentaram capacidade de solubilizar as proteínas insolúveis presentes nos resíduos (escamas, ossos, cartilagens e outros). A bactéria que atingiu a maior atividade proteolítica foi a Bacillus velesensis (47,56 U mL-1) e o fungo foi o Penicillium sp. (E20) (31,20 U mL-1). Para a produção dos hidrogéis, foram utilizados isolados protéicos provenientes de solubilização ácida ou alcalina, produzidos a partir de resíduos da industrialização de pescado, modificados quimicamente com dianidrido etilenodiamino tetraacético (EDTAD) e adicionados de agente de ligação cruzada (glutaraldeído). Algumas proteínas modificadas ainda foram submetidas a tratamento com etanol. Foram realizadas análise estrutural das proteínas modificadas e estudo da capacidade de retenção de água dos hidrogéis assim obtidos. Os hidrogéis produzidos apresentaram alta capacidade de retenção de água. A máxima absorção de água foi alcançada pelo hidrogel ácido sem o tratamento com etanol foi de 103,25 gágua/ggel seco, enquanto que a mesma amostra tratada com etanol alcançou 216,05 gágua/ggel seco. Os hidrogéis produzidos podem ser utilizados em diversas indústrias, tais como, farmacêutica, alimentícia, médica, agroindústria, entre outras, que necessitem de hidrogéis com alta capacidade de retenção de água.

Hidrolisados protéicos de anchoita (engraulis anchoita): obtenção, atividade antioxidante e aplicação em embutido emulsionado

Uma alternativa para pescados subaproveitados e subprodutos da industrialização de pescado é o desenvolvimento de processos para recuperação e/ou alteração das proteínas musculares de pescados. O objetivo deste trabalho foi a obtenção de hidrolisados protéicos de carne mecanicamente separada (CMS) de anchoita (Engraulis anchoita) e a avaliação da sua atividade antioxidante, aplicando-os bem embutido preparado com o surimi de anchoita. Foram produzidos diferentes hidrolisados com as enzimas microbianas Alcalase, Flavourzyme e Protamex, fixando a concentração de substrato e de enzima e os parâmetros pH e temperatura foram variados. Os hidrolisados foram efetivos contra a inibição da peroxidação lipídica (43,8±0,2%) e no poder redutor, onde o hidrolisado com a enzima Flavourzyme em 1 hora de reação mostrou-se mais efetivo. No seqüestro de radicais livres, como o DPPH, o hidrolisado com a enzima Flavourzyme, obtido em tempo de hidrólise de 5 horas, alcançou valores acima de 45,0% em concentração de 5 mg/mL. Na produção de surimi foram testadas lavagens da CMS de anchoita com soluções de bicarbonato de sódio 0,5%, ácido fosfórico 0,05% e cloreto de sódio 0,3%. O maior rendimento (90,5%) e uma coloração mais clara (W= 50,24±1,81) foram encontrados no surimi obtido por lavagens com bicarbonato de sódio e cloreto de sódio (BS), em comparação ao surimi que se utilizou água, ácido fosfórico e cloreto de sódio (AF) ou com soluções de cloreto de sódio, ácido fosfórico e bicarbonato de sódio (AB). Na força de gel o surimi AF (1154,25 ± 4,37 g.mm) obteve maior valor, sendo utilizado para a produção de salsichas. Foram analisadas diferentes concentrações de surimi (70, 75 e 80%) em salsichas, que foram submetidas às análises de cor e textura. Não houve influência da concentração de surimi nas características tecnológicas da salsicha, exceto nos valores de luminosidade. A salsicha com 75% de surimi de anchoita foi caracterizada pela composição proximal, valor energético total (VET) e conteúdo de sódio. A salsicha com surimi e comercial apresentou composição semelhante. O produto com surimi apresentou menor VET (193,7Kcal/100g) e conteúdo de sódio (520 mg/100g) que a salsicha comercial. Nas condições de estudo, no embutido emulsionado, não foi verificada ação antioxidante de hidrolisados, porém houve efeito sobre a CMS de anchoita.

Obtenção de biopeptídeos com atividade antioxidante a partir de proteínas de origem animal

Pele, ossos, espinhas, entre outros, separados durante o processamento de produtos cárneos podem ser uma boa fonte de proteína, especialmente de colágeno. Para obtenção de colágeno nativo a partir de ossos é necessário um tratamento prévio de desproteinização e desmineralização. Portanto, o objetivo deste trabalho foi determinar os melhores parâmetros para a desmineralização de ossos de pescado e frango utilizando soluções de HCl e EDTA um complexante de íons metálicos. O melhor efeito da desmineralização foi obtido com solução de HCl 1,0 mol/L. Após 48 h de extração, 99,4 e 95,4% das substâncias minerais foram solubilizadas para os ossos de pescado e para ossos de frango, respectivamente. Paralelamente, a menor perda de colágeno também foi observada nessas condições. O processo realizado empregando soluções de EDTA foi menos eficaz do que com solução de HCl. Após 48 h de extração com EDTA 0,1 mol/L, 37,5 e 32,4% dos compostos minerais foram removidos dos ossos de pescado e dos ossos de frango, respectivamente. Uma maior eficiência foi alcançada com solução de EDTA 0,5 mol/L. O rendimento do processo foi de cerca de 66,6% a partir dos ossos de pescado e 70,6% a partir os ossos de frango. A desmineralização com EDTA não provocou perda de colágeno.

Kinetic study of solid phase demineralization by weak acids in one-step enzymatic bio-refinery of shrimp cuticles

We describe a one-step bio-refinery process for shrimp composites by-products. Its originality lies in a simple rapid (6 h) biotechnological cuticle fragmentation process that recovers all major compounds (chitins, peptides and minerals in particular calcium). The process consists of a controlled exogenous enzymatic proteolysis in a food-grade acidic medium allowing chitin purification (solid phase), and recovery of peptides and minerals (liquid phase). At a pH of between 3.5 and 4, protease activity is effective, and peptides are preserved. Solid phase demineralization kinetics were followed for phosphoric, hydrochloric, acetic, formic and citric acids with pKa ranging from 2.1 to 4.76. Formic acid met the initial aim of (i) 99 % of demineralization yield and (ii) 95 % deproteinization yield at a pH close to 3.5 and a molar ratio of 1.5. The proposed one-step process is proven to be efficient. To formalize the necessary elements for the future optimization of the process, two models to predict shell demineralization kinetics were studied, one based on simplified physical considerations and a second empirical one. The first model did not accurately describe the kinetics for times exceeding 30 minutes, the empirical one performed adequately.

Production of bioplastics from hydrolysates of paper industry by Haloferax mediterranei

The biorefinery concept has attracted much attention over the last decade due to increasing concerns about the use of fossil resources. In this context emerged the use of bioplastics, namely polyhydroxyalkanoates (PHA). PHA are biocompatible and biodegradable plastics that can be obtained from renewable raw materials and can constitute an alternative solution to conventional plastics. In this work, hydrolysed cellulose pulp, coming from Eucalyptus globulus wood cooking, was used as substrate to the PHA-storing bacteria Haloferax mediterranei. The hydrolysed pulp is rich in simple sugars, mainly glucose (81.96 g.L-1) and xylose (20.90 g.L-1). Tests were made in defined medium with glucose and xylose and in hydrolysate supplemented with salts and yeast extract. Different concentrations of glucose were tested, namely 10, 15, 20, 30 and 40 g.L-1. The best accumulation results (27.1 % of PHA) were obtained in hydrolysate medium with 10 g.L-1. Using this concentration, assays were performed in fed-batch and sequencing batch reactor conditions in order to determine the best feeding strategy. The strategy that led to the best results was fed-batch assay with 24.7 % of PHA. An assay without sterile conditions was performed, in which was obtained the same growth than in sterilization test. Finally it was performed an assay in a bioreactor and a fast growth (0.14 h-1) with high glucose and xylose consumption rates (0.368 g.L-1.h-1 and 0.0947 g.L-1.h-1, respectively) were obtained. However 1.50 g.L-1 of PHA, corresponding to 16.1 % (92.52 % of 3HB and 3HV of 7.48 %) of % PHA were observed. The polymer was further characterized by DSC with a glass transition temperature of -6.07 °C, a melting temperature of 156.3 °C and a melting enthalpy of 63.07 J.g-1, values that are in accordance with the literature. This work recognizes for the first time the suitability of the pulp paper hydrolysate as a substrate for PHA production by H. mediterranei.

Spatial and temporal measurements using polyoxometalate, enzymatic and biofilm layers on a CMOS 0.35 μm 64 X 64-pixel I.S.F.E.T. array sensor

This thesis presents the achievements and scientific work conducted using a previously designed and fabricated 64 x 64-pixel ion camera with the use of a 0.35 μm CMOS technology. We used an array of Ion Sensitive Field Effect Transistors (ISFETs) to monitor and measure chemical and biochemical reactions in real time. The area of our observation was a 4.2 x 4.3 mm silicon chip while the actual ISFET array covered an area of 715.8 x 715.8 μm consisting of 4096 ISFET pixels in total with a 1 μm separation space among them. The ion sensitive layer, the locus where all reactions took place was a silicon nitride layer, the final top layer of the austriamicrosystems 0.35 μm CMOS technology used. Our final measurements presented an average sensitivity of 30 mV/pH. With the addition of extra layers we were able to monitor a 65 mV voltage difference during our experiments with glucose and hexokinase, whereas a difference of 85 mV was detected for a similar glucose reaction mentioned in literature, and a 55 mV voltage difference while performing photosynthesis experiments with a biofilm made from cyanobacteria, whereas a voltage difference of 33.7 mV was detected as presented in literature for a similar cyanobacterial species using voltamemtric methods for detection. To monitor our experiments PXIe-6358 measurement cards were used and measurements were controlled by LabVIEW software. The chip was packaged and encapsulated using a PGA-100 chip carrier and a two-component commercial epoxy. Printed circuit board (PCB) has also been previously designed to provide interface between the chip and the measurement cards.

Enzymatic upgrading of eucalypt paper-grade kraft pulp within dissolving pulp production

Dissolving-grade pulps are commonly used for the production of cellulose derivatives and regenerated cellulose. High cellulose content, low content of non-cellulosic material, high brightness, a uniform molecular weight distribution and high cellulose reactivity are the key features that determine the quality of a dissolving pulp. The first part of this work was an optimization study regarding the application of selected enzymes in different stages of a new purification process recently developed in Novozymes for purifying an eucalypt Kraft pulp into dissolving pulp, as an alternative to the pre-hydrolysis kraft (PHK) process. In addition, a viscosity reduction was achieved by cellulase (endoglucanase) treatment in the beginning of the sequence, while the GH11 and GH10 xylanases contributed to boost the brightness of the final pulp. The second part of the work aimed at exploring different auxiliary enzyme activities together with a key xylanase towards further removal of recalcitrant hemicelluloses from a partially bleached Eucalypt Kraft pulp. The resistant fraction (ca. 6% xylan in pulp) was not hydrolysable by the different combinations of enzymes tested. Production of a dissolving pulp was successful when using a cold caustic extraction (CCE) stage in the end of the sequence O-X-DHCE-X-HCE-D-CCE. The application of enzymes improved process efficiency. The main requirements for the production of a dissolving pulp (suitable for viscose making) were fulfilled: 2,7% residual xylan, 92,4% of brightness, a viscosity within the values of a commercial dissolving pulp and increased reactivity.

Enzymatic hydrolysis and fermentation of ultradispersed wood particles after ultrasonic pretreatment

Background: A study of the correlation between the particle size of lignocellulosic substrates and ultrasound pretreatment on the efficiency of further enzymatic hydrolysis and fermentation to ethanol. Results: Themaximumconcentrations of glucose and, to a lesser extent, di- and trisaccharideswere obtained in a series of experiments with 48-h enzymatic hydrolysis of pine rawmaterials ground at 380–400 rpm for 30min. The highest glucose yield was observed at the end of the hydrolysis with a cellulase dosage of 10 mg of protein (204 ± 21 units CMCase per g of sawdust). The greatest enzymatic hydrolysis efficiency was observed in a sample that combined two-stage grinding at 400 rpm with ultrasonic treatment for 5–10 min at a power of 10 W per kg of sawdust. The glucose yield in this case (35.5 g glucose l−1) increased twofold compared to ground substrate without further preparation. Conclusions: Using a mechanical two-stage grinding of lignocellulosic raw materials with ultrasonication increases the efficiency of subsequent enzymatic hydrolysis and fermentation.