Chiral a -hydroxy ketones are important structural units in many natural products, biologically active compounds and the hydroxyl group has frequently been used as a reagent directing group, such as for the selective elaboration of aldol products. In this work, enzymatic synthesis of both enantiomers of the a -hydroxy ketones (2-hydroxy indanone, 2-hydroxy tetralone) using Aspergillus niger by selective &amp / #945 / -oxidation of ketones (1-indanone, 1-tetralone) was studied. The &amp / #945 / -oxidation of ketones was carried out by using whole cells of Aspergillus niger in different growth media. A. niger whole cell catalyzed reactions afforded (S)-configurated 2- hydroxy-1-tetralone with %87 e.e. in DMSO at pH 5.0. In addition to this,while (S)-configurated 2-hydroxy-1-indanone with %33 e.e. in pH 8.0 (in DMSO) was synthesized, (R)-configurated-2-hyroxy-1-indanone with %32 e.e. in pH 7.0 ( in DMSO) was synthesized.

Rhizopus oryzae is a filamentous fungus, which can produce high amounts of L(+)-lactic acid and produces ethanol as the main by-product. In an effort to understand the pyruvate branch point of this organism, fermentations under different inoculum and glucose concentrations were carried out. At low inoculum size (1x103 spores ml-1), high amount of lactate (78 g l-1) was produced, whereas high ethanol concentration (37 g l-1) was obtained at high inoculum sizes (1x106 spores ml-1). Decreasing working volume increased lactate production significantly at high inoculum sizes (1x105 and 1x106 spores ml-1), but did not influenced the physiology at low inoculum sizes (1x103 and 1x104 spores ml-1). In shake flask cultures, at low initial glucose concentrations biomass yield was high and lactate and ethanol yields were low. Higher lactate and ethanol and lower biomass yields were obtained by increasing the initial glucose concentrations. In alginate immobilized, semi-continuous cultures with cell retention, glucose level in the medium was kept at low values. Like in shake flask cultures, as the glucose concentration decreased lactate and ethanol yields decreased and biomass yields increased. Increasing the glucose concentration by a pulse of glucose caused increases in branch point enzyme activities, as well as in concentrations of the metabolites. In fed batch cultures higher biomass yield (0.25 g DCW g glucose-1) could be obtained. Lactate dehydrogenase was influenced by the inoculum size and glucose concentration more than pyruvate decarboxylase and alcohol dehydrogenase. It showed higher activity at lactate producing fermentations. Unlike lactate dehydrogenase, pyruvate decarboxylase and alcohol dehydrogenase showed high activity even at low glucose concentrations.

In this study, the aim was identification and classification of the enzyme having phenol oxidase activity produced by a thermophilic fungus, Scytalidium thermophilum. For this purpose, enzyme production, purification, biochemical characterization and structural analysis by X-ray crystallography studies have been performed. At the beginning of the research, this enzyme was considered as a phenol oxidase and analyzed accordingly. However, during purification, amino acid sequencing and structural studies, the enzyme was shown to be a catalase, with an additional catechol oxidase activity. This novel bifunctional catalase-catechol oxidase (CCO) was purified 10 fold with 45 % yield by anion exchange and gel filtration chromatographies. CCO was determined as a tetrameric protein having total and subunit molecular weights of 320 and 80 kDa, respectively. Isoelectric point of CCO was verified as 5.0. CCO catalase and catechol oxidase activities were characterized in terms of their kinetic behavior at different pH and temperatures. Depending on the substrate specificity and inhibitor studies of CCO, the phenol oxidase activity was determined as catechol oxidase but not tyrosinase or laccase. The best crystallization condition for CCO was determined and X-ray diffraction data was collected at the Daresbury Synchrotron Radiation Source (United Kingdom) at 2.7 &Aring / resolution. The preliminary structure was solved by molecular replacement method using Penicilium vitale catalase structure. CCO was verified to have a tetrameric structure with two homodimers and a metal center in each polypeptide chain.

In this study, the effects of oxygen transfer conditions on the synthesis of the enzyme benzaldehyde lyase as intracellular in recombinant E. coli BL21 (DE3) pLysS was investigated sistematically and a comprehensive model was developed to determine benzaldehyde lyase activity. For this purpose, the research program was carried out in mainly two parts. In the first part of study, the effects of oxygen transfer together with the mass transfer coefficient (KLa), enhancement factor E (=KLa/KLao), volumetric oxygen transfer rate, volumetric and specific oxygen uptake rates, mass transfer and biochemical reaction resistances / moreover, the variation in product and by-product distribution, specific substrate uptake rates, yield and maintenance coefficient were investigated in the pilot scale batch bioreactor at QO/VR = 0.5 vvm and agitation rates of N= 250, 500, 625, and 750 min-1, and dissolved oxygen levels DO= 20%, 40% conditions, while medium components were CGlucose= 8.0 kg m-3, C(NH4)2HPO4= 5.0 kg m-3 and salt solution at controlled pHc=7.2. The highest cell concentration and benzaldehyde lyase activity were obtained at DO=40% condition as 3.0 kg m-3 and A=1095 Ucm-3, respectively. v Then a mathematical model was proposed to estimate benzaldehyde lyase activity as function of time, agitation rate, cell concentration, dissolved oxygen concentration, and by-product concentration with reasonable accuracy.

This thesis reports design, fabrication, and implementation of two different micro electrophoresis system architectures for DNA analyses. The first architecture is traditional single channel layout with several design alternatives for size-based separation of DNA fragments. The second one is novel double channel architecture specialized for rapid mutation detection using heteroduplex analysis (HDA) method with an application of a newly designed injection technique. Besides achieving high resolution separations within the length of 1 mm with single channel arrangement, HDA was successfully applied for 590 base pair (bp) long PCR sample with 3 bp mutations in a separation length of 50 &micro / m in less than 3 minutes with double channel structure. Microchannels were formed using parylene-C due to its conformal deposition, no surface treatment requirement, transparency, biocompatibility, low background fluorescence, etc. Using the advantage of parylene in fabrication, the microchannels were fabricated with an only three-mask process. New double channel architecture is obtained by dividing the 200 &micro / m-wide separation channel into two parts by a 20 &micro / m-thick wall between them. For sample injection, various techniques, such as traditional cross, double-T, and double-L were investigated and optimized for single channel architecture assisting with pullback injection method. For double channel architecture, a novel, u-turn injection technique was applied. Precise control of sample amount by adjusting the injection time was accomplished by this new technique. Using high resolution cross-linked polyacrylamide gel as sieving material, separations were achieved in a very short length and time. Electrophoresis was performed in both channels of the double channel microchips simultaneously under the same conditions. This gives the chance of having a control channel in microchip format, which is very critical for the accuracy and reliability of the results in genetic analyses.

The objective of the study presented here was to develop either enzymatic or whole cell mediated green procedures for the syntheses of a-hydroxy ketones. Production of optically active synthons is crucial for the preparation of fine chemicals. Enzymes and whole-cell biocatalysts have proven to be excellent vehicles with their chiral nature for the biotransformations. Under the light of this discussion, firstly benzaldehyde lyase [BAL, (EC 4.1.2.38)] was used in novel C-C bond formation reactions to obtain interesting and biologically important precursors / 2-Hydroxy-1-arylethan-1-ones and functionalized aliphatic acyloin derivatives. All the compounds were obtained with high yields and in the case of aliphatic acyloin derivatives with high enantiomeric excesses (ee&rsquo / s). Another strategy was to use whole cell biocatalysis. A.flavus 200120 was found to be a promising biocatalyst with the ability to catalyze a broad range of reactions / reduction, hydrolysis and deracemization, while another fungus / A. oryzae 5048 was utilized in bioreduction reactions of benzil and its derivatives. Each reaction was investigated, optimized and thus enhanced via medium design. Products were obtained with high yields and ee&rsquo / s. To sum up, in this study novel efficient green procedures were developed to synthesize various ahydroxy ketones with high yield and stereoselectivity. These newly established methods present promising alternatives to classical chemical methodologies.

In this study various microbial and enzymatic methods developed for enantioselective acyloin synthesis for preparation of some pharmaceutically important intermediates. By performing Aspergillus flavus (MAM 200120) mediated biotransformation, enantioselective bio-oxidation of meso-hydrobenzoin was achieved with a high ee value (76%). Racemic form of hydrobenzoin was also employed for the same bio-oxidation process and this bioconversion was resulted in accumulation of meso form (&gt / 90% yield) confirming the suggested mechanism of oxidation-reduction sequence of hydrobenzoin. Wieland-Miescher ketone (3,4,8,8a-tetrahydro-8a-methylnaphthalene-1,6(2H,7H)-dione) is an important starting material for bioactive compounds like steroids and terpenoids. Many synthetic approaches include enantioselective reduction of this compound. In this study Aspergillus niger (MAM 200909) mediated reduction of Wieland-Miescher ketone was achieved with a high yield (80%), de (79%) and ee (94%) value and these results were found much more superior than previously reported studies. Carboligating enzymes benzaldehyde lyase (BAL) (EC 4.1.2.38) and benzoiyl formate decarboxilase (BFD) (E.C. 4.1.1.7) are used for biocatalytic acyloin synthesis. These enzymes are immobilized to surface modified superparamagnetic silica coated nanoparticles by using metal ion affinity technique. With this system recombinant histidine tagged BAL and BFD purified and immobilized to magnetic particles by one-pot purification-immobilization procedure. SDS page analysis showed that our surface modified magnetic particles were eligible for specific binding of histidine tagged proteins. Conventional BAL and BFD catalyzed benzoin condenzation reactions and some representative acyloin reactions were performed with this system with a high enantioselectivity (99-92%) and yield. Results obtained with magnetic particle-enzyme system were also found comparable with that of free enzyme catalyzed reactions.

Being at the center of most metabolic pathways and also one of the best known pathways, the glycolytic pathway has been of interest to modeling studies. This study is composed of our attempts to model ethanolic fermentation by yeast through kinetic equations of glycolytic steps and its branches. Model was based totally on experimentally measured kinetics of enzymes and transport steps, either obtained in this study or from the literature. Effect of ethanol on enzyme activities was tested in the range of ethanol 0 to 20% (v/v) in assay mixture. All enzymes were inhibited by ethanol to some degree and these inhibitions started at different ethanol concentrations, the least affected being the pyruvate kinase and the most inhibited ones being glycerol-3-phosphate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, phosphogluco kinase, and alcohol dehydrogenase (forward). Effect of temperature on the activities of enzymes was tested within 10-30 &deg / C with five degrees of increments. Activation energies of enzymes were calculated using the Arrhenius equation. Activation energies of upper part of the glycolysis and the glycerol branch (glycerol-3-phosphate dehydrogenase) were relatively higher than that of lower part enzymes as well as the ethanol branch (alcohol dehydrogenase). Results obtained from these in vitro studies were incorporated into the model as mathematical relations. Model output thus obtained was compared with results of experiments conducted at several temperatures and initial ethanol concentrations. Model could estimate general trend in ethanolic fermentation that fermentation is inhibited by increasing concentrations of ethanol. Decrease in glycerol yields at lower temperatures was also estimated by the model. However, model did not fit exactly to experimental results, especially at low temperature and high ethanol concentrations. This could be attributed to stress responses of cells under these conditions, which are not considered in the model.

Sol-gel processing routes for encapsulation of double stranded DNA in solid porous silica hosts have been established. The encapsulation was carried out in two steps: hydrolysis of a silica-forming alkoxide-based sol was followed by condensation/gelation to a solid form upon addition of a buffer solution containing DNA molecules. The effects of gelation chemistry and DNA amount on chemical and microstructural properties of resultant silica matrices and on DNA encapsulation efficiency were investigated. The analytical characterization was performed by UV-vis spectroscopy, 29Si nuclear magnetic resonance spectroscopy and by nitrogen adsorption studies. It was demonstrated that DNA incorporation had a pH-dependent catalytic effect on gelation kinetics and promoted silica network completion. In addition, the scale of porosity and the average pore size of the resultant silica increased with gelation pH and also with DNA-buffer solution in the starting sol-gel formulation. The chemistry-derived pore size variation controls the DNA encapsulation efficiency in the silica matrices and the DNA holding capacity strongly depends on the scale of the porosity attained. The selective adsorption of ethidium bromide- a DNA-intercalative reagent molecule- on DNA-silica gels confirmed that the DNA molecules remained entrapped within the silica host in their native state without any deterioration. Besides pure silica, amine-functionalized hybrid silica hosts were also formed by sol-gel. The hybrid gels were found not to be suitable for DNA encapsulation, as these matrices dissolve in aqueous environment due to incomplete silica network formation. The DNA-doped silica hosts may provide promising matrices for development of biosensors, bioreactors and bioassay platforms.

The aim of this study was to investigate the viability of patterning by immobilization, photocatalytic removal, and re-immobilization steps of the enzyme on photocatalytically active thin films for biosensor fabrication purposes. For this aim, TiO2-SiO2-Au sol-gel colloids were synthesized and deposited on glass substrates as thin films by dip coating. Cysteamine linker was assembled on gold nanoparticles to functionalize thin films with amine groups for immobilization of model enzyme invertase. Effect of immobilization temperature, enzyme concentration of the immobilization solution and immobilization period on invertase immobilization were investigated. The immobilized invertase activity was found independent from the immobilization temperature in the range tested (4oC-room temperature). The optimum enzyme concentration and period for immobilization was determined as 10&micro / g/ml and 12 hours respectively. The resulting invertase immobilized thin films showed high storage stability retaining more that 50% of their initial activity after 9 weeks of storage. Photocatalytic enzyme removal and re-immobilization studies were carried out by irradiating the invertase immobilized thin films with blacklight. Upon 30 minutes of irradiation, immobilized invertase was completely and irreversibly inactivated. Initial immobilized invertase activity (before the irradiation) was attained when invertase was re-immobilized on thin films that were irradiated for 5 hours. Thus it was inferred that with sufficient exposure, enzymes can be completely removed from the surfaces which makes the re-immobilization possible. The possibility of enzyme removal with photocatalytic activity and re-immobilization can pave the way to new patterning techniques to produce multi-enzyme electrode arrays.