Abstract ¡@¡@Biosensor chip has a lot of advantages, such as label-free, ultra-sensitive, highly selective, fast and real-time detection. Fabricating biosensor chip has great benefits for gene-detection, protein-detection, medical diagnosis and development of new medicine. This research will integrate the biomedical, chemistry, and physics, and also combined with biochemical technology and semiconductor technology to produce biosensor chip. ¡@¡@We use microelectronic semiconductor process technology to fabricate silicon nanowire field effect transistors (SiNW-FET). The source-drain current versus the voltage curve (Isd-Vsd) shows that the contact pad and the silicon nanowire form ohmic contact. And then we use chemical surface modification technologies to modified biotin on SiNW-FET to detect streptavidin. ¡@¡@In addition, we also grow AlGaN/GaN film by MBE, and fabricate nitride¡Vbased high electron mobility transistor (HEMT) by microelectronic semiconductor process technology. In this study, we apply HEMT in biosensor for pancreatic cancer marker CA19-9 antigen. And we modify pancreatic cancer marker CA19-9 antibody on the biosensor chip surface to detect pancreatic cancer marker CA19-9 antigen molecule. ¡@¡@Most of biomolecules are with weak charges, which can form chemical gating effect and change the conductance of p-type SiNW. And according to the streptavidin microfluidic measurement of biotin-modified SiNW-FET, the detection limit of streptavidin was 10-9 M. And the detection limit of pancreatic cancer marker CA19-9 antigen for N-HEMT biosensor was 150 U/mL.

Utilizing self-assembled monolayer nanotechnology, micro-electro-mechanical systems (MEMS) and IC technologies, a novel flexural plate-wave (FPW) biosensor is developed in this dissertation for detecting the immunoglobulin-E (IgE) concentration of human serum. The acoustic waves of the proposed FPW devices are launched by the 25-pair inter-digital transducer (IDT) input electrodes and propagated through the 4.82 £gm-thick Si/SiO2/Si3N4/Cr/Au/ZnO floating thin-plate. Since the thickness of such floating thin-plate is much smaller than the designed wavelength of FPW device (80 £gm), most of the propagating wave energy will not be dissipated into outside of thin-plate and the mass sensitivity is very high. To further reduce the insertion loss of the proposed FPW devices, two 3 £gm-thick Al reflection grating electrodes (RGE) are designed beside the input and output IDTs. To implement a FPW-based IgE biosensor, a Cr/Au electrode layer has to be deposited on the backside of the floating thin-plate to serve as a substrate for further coating the cystamine SAM/glutaraldehyde/IgE antibody layers. Once the IgE antigens of human serum are bound to the IgE antibody layer, the small change in the mass of floating thin-plate will result in a shift of center frequency of the testing FPW-based biosensor. Compared to the reference FPW biosensors, the shift of center frequency generated by the testing FPW biosensor under different IgE antigen concentration can be detected by commercial network analyzer or the frequency-shift readout system developed by our collaboration laboratory (VLSI Design Lab. of NSYSU). Compared to commercial enzyme linked immunosorbent assay (ELISA) analyzer (sample volume >25 £gl/well, testing time >60 min, dimension>40 cm ¡Ñ30 cm¡Ñ10 cm), the implemented FPW-based IgE biosensor presents a smaller sample volume (<5 £gl), faster response (<10 min) and smaller size (<9 mm¡Ñ6 mm¡Ñ0.5 mm). In addition, a very low insertion loss (-9.2 dB), a very high mass sensitivity (-6.08¡Ñ109 cm2 g-1) and a very high sensing linearity (99.46 %) of the proposed IgE biosensor can be demonstrated at 6.6 MHz center frequency. This study successfully developed a novel FPW-based allergy biosensor by MEMS technology, which has great potential to be further applied into point-of-care testing (POCT) microsystem.

Phenolic compounds are the chemicals which are used by many different industries and as a result of this spread to the environment. These compounds can be absorbed easily through the human and animal skin and through the mucosal membrane, mix in to the blood circulation and thus create a toxic effect on several tissue and organs including, liver, lung and kidneys. For this reason, determination of phenolic compounds emitted to environment is a very important issue. In fact, there are standard methods for the determination of these compounds like HPLC, Spectrophotometric and calorimetric methods however, these are time consuming methods and requires to be expertise. On the other hand, there are also different types of biosensors developed for the phenolic compound detection. In this study, a new, disposable, cheap and convenient tyrosinase biosensor was developed for the phenolic compound detection. By means of absorption method, the enzyme tyrosinase and the chromophore MBTH were immobilized on the support material and as a model substrate L- dopa was used. As a result of optimization studies 1mg/ml tyrosinase concentration and 1.5mM MBTH concentration were determined for using in biosensor construction. Detection limit of l-dopa, model substrate, found as 0,064 mM and for other phenolic compounds, 4-chlorophenol, catechol, m-cresol and p-cresol, detection limit was obtained 0.032 mM, 0.032 mM, 0.128 mM, 0.128 mM, respectively. In addition, we found that the biosensor response was not affected by pH changes ranging from 3 to 11. The stability of biosensor which is one of the important parameter for commercialization was not change through 70 days at room temperature and 4&deg / C when compared to at the beginning response.

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.

The aim of this study was to immobilize the redox enzyme laccase over TiO2-SiO2-Au thin film coated ITO glass substrates in order to prepare electrochemically active surfaces for biosensor applications. Colloidal TiO2-SiO2-Au solution was synthesized by sol-gel route and thin film was deposited onto the substrates by dipcoating method. The cysteamine was utilized as a linker for immobilization of enzyme covalently through gold active sites. Preliminary studies were conducted by using invertase as model enzyme and Pyrex glasses as substrates. The effect of immobilization parameters such as immobilization temperature, concentration of enzyme deposition solution, immobilization time for laccase were examined. Leakage studies were conducted and storage stability of immobilized laccase was determined. Highest laccase activity was achieved when immobilization was performed with 50 &micro / g/ml solution at 4&deg / C for 2 hours. Laccase activity decreased after 4 hours of impregnation in enzyme solution. Laccase leakage was observed in the first usage of substrates and 55% activity decrease was determined in the subsequent use which might be attributed to the presence of uncovalently adsorbed enzyme on the fresh samples. In air and in buffer storage stabilities were also tested. It was found that the activity of samples almost vanished after 6 days regardless of storage conditions. Both enzymes had more activity on ITO substrate.

Electrochemical biosensors are cost effective, fast and portable devices, which can determine the existence and amounts of chemicals in a specific medium. These devices have many potential applications in many fields such as determination of diseases, process and product control, environmental monitoring, and drug research. To realize these potentials of the devices, many studies are being carried out to increase their sensitivity, selectivity and long term stabilities. Surface modification studies with various types of particles (metal nano particles, carbon nano tubes etc.) can be count among these studies. Although zeolites and zeo-type materials are investigated for many years, they still hold interest on them due to their capabilities. By means of their chemical resistances, large surface areas, tailorable surface properties, and porous structures they can be applied in many applicational fields. In some recent studies, these properties are intended to be used in the field of biosensors. The purpose of the current study was to investigate the effect of zeolite nanoparticles on electrochemical biosensor performances. Firstly, several different procedures were investigated in order to find the best and optimum methodology to attach previously synthesized zeolites on Si wafer substrates for the first time. For this purpose, the ultrasonication, spin coating and direct attachment methods were used and their efficiencies were compared. Perfectly oriented, fully covering, zeolite monolayers are produced by direct attachment method. Successively produced zeolite thin films were then patterned with the help of Electron Beam Lithography technique to show the compatibility of coating methods to the CMOS technology. Combination of Direct Attachment and EBL techniques resulted well controlled zeolite monolayer patterns. Then zeolite modified electrochemical biosensors were tested for their performances. With these experiments it was intended to improve the selectivity, sensitivity and storage stabilities of standard electrochemical biosensors. Experiments, conducted with different types of zeolites, showed that zeolites have various effects on the performances of electrochemical biosensors. Amperometric biosensor response magnitudes have been doubled with the addition of Silicalites. Faster conductometric electrode responses were achieved with enzyme immobilization on zeolite film technique. Also it is seen that Beta type zeolites modified through different ion exchange procedures, resulted different responses in IS-FET measurements.

DNA arrays have become a major bioanalytical method as they enable high-throughput screening and they can be manufactured on different surfaces depending on the nature of diagnostic purpose. However, current technologies to produce and detect arrays of DNA probes are expensive due to the requirement of specialized instrumentation. In this study we have established an array platform in sandwich hybridization format for the detection of label-free nucleic acid targets. Unlike direct hybridization, which is the main microarray hybridization principle, sandwich assay enables unlabeled target detection, lowering the cost and assay time. To this end, sequence specific signal development was achieved by a sandwich complex which is composed of a surface immobilized capture DNA probe (Probe1) and a fluorescein-tagged signal DNA probe (Probe 2), which are partially complementary to the sequence to be analyzed (target oligonucleotide). As the solid support of the array platform both 3-aminopropyl-3-methoxysilane (APTMS) activated and commercially purchased poly-L lysine coated glass slides were used and due to the less background noise property the latter one was preferred. Similarly, for the immobilization of the capture Probe (P1) onto the solid support two different methods were tried / heat immobilization and immobilization via a heterobifunctional cross-linker (HBCL). In regard to the experiments, it is observed that using a cross-linker instead of heat immobilization reduces the ratio of false negative control results in a significant manner. Following the solid support and immobilization method choice comparative optimization studies which include cross-linker type, probe concentration, sensitivity of the platform and hybridization conditions (sequence, temperature and duration) were conducted. Optimum hybridization signal was obtained with a 32.5

Over the last decade, immobilization of proteins onto inorganic materials is becoming more crucial to extend a deep understanding of interaction between proteins and nanoparticles. With understanding of the real interaction lying under the protein-nanoparticle relations, it is possible to organize the conformation and orientation of surface and framework species of nanoparticles to generate ideal surfaces for potential biotechnological applications. Due to their unique properties such as large clean surface, tunable surface properties, adjustable surface charge, and dispersibility in aqueous solutions, zeolite and zeo-type materials are one of the remarkable classes of inorganic materials that are widely studied in the literature. These properties make zeolites promising alternative candidates for the immobilization of enzymes and incorporation into biosensing devices. In the current study, a new approach was developed for direct determination of urea, glucose, and butyrylcholine where zeolites were incorporated to the electrode surfaces of a conductometric biosensor and Ion Sensitive Field Effect Transistors were used to immobilize the enzymes. Biosensor responses, operational stabilities, and storage stabilities of the new approach were compared with results obtained from the standard membrane methods for the same measurements. For this purpose, different surface modification technique, which are simply named as Zeolite Modified Transducers (ZMTs) were compared with Standard Membrane Transducers (SMTs). During the conductometric measurements ZMT electrodes were used, which allowed the direct evaluation of the effect of zeolite morphology on the biosensor responses for the first time. It was seen that silicalite added electrodes lead to increased performances with respect to SMTs. As a result, the zeolite modified urea and glucose biosensors were successfully applied for detecting urea and glucose, which can offer improved possibilities to design biosensors. The results obtained show that zeolites could be used as alternatives for enzyme immobilization in conductometric biosensors development. Furthermore, the sensitivities of urease and butyrylcholinesterase biosensors, prepared by the incorporation of zeolite Beta crystals with varying acidity on the surface of pH-sensitive

Fast and accurate detection of pathogens such as bacteria, their toxins and viruses at low concentrations is very important. The conventional techniques are time consuming where expensive equipment is required with a consumption of excess amount of blood from patients. Recently, immunosensors are used for the detection of pathogens because they are miniature, sensitive, biocompatible and require low power. According to the Centers for Disease Control and Prevention (CDCP), 76 million people become ill due to food poisoning and 5,000 of them die each year in United States. In addition, SEB causing food poisoning has listed as a bioterrorism agent by CDCP. Thus, accurate and selective detection in short time is very important for SEB detection. Candida albicans (C. albicans) is a yeast-like fungus and causes anxiety, insomnia, constipation, hiatal hernia, panic attacks, denture-induced stomatitis, angular cheilitis, gingivitis and prosthetic implant infections. In addition, it can cause death if the immune system of patient is under failure due to cancer, chemotherapy and AIDS. In this study, a new procedure was developed. A simple and highly selective homogeneous sandwich immunoassay was obtained for ultrasensitive detection of Staphylococcal Enterotoxin B (SEB) using Atomic Force Microscopy (AFM) and Surface Enhanced Raman Scattering (SERS) probe. In the developed procedure, thiolated antibodies were produced and SEB was immobilized on the biosensor surface using these antibodies. In addition, theory of SEB adsorption on a gold surface was studied and the reaction rate constant between SEB and its toxin was calculated. Moreover, C. albicans was detected using the developed procedure by a microscope. Thus, it is proved that, the developed procedure can be used for detection of different pathogens. Furthermore, nonspecific interaction between SEB antibody and BSA was determined in this study. Also, the developed procedure and a procedure found from literature were compared. In the procedure used in the literature (second procedure), self-assembled monolayer (SAM) was formed and antibodies were immobilized on SAM. After formation of sandwich structure, the roughness of gold surface and the minimum concentration of SEB detected were determined by AFM and SERS, respectively.

Zeolites are crystalline aluminosilicates which have highly ordered pore structures and high surface area. Also the tailorable surface properties, high ion-exchange capability, high chemical, thermal, and mechanical strength make these particles an important candidate for various application such as sensors, catalysis, dielectric materials, separation, and membrane technologies. Although zeolites have these unique properties, applications where zeolites are integrated into devices according to their application areas, are limited due to the powder form of the material. The purpose of the current study was to investigate the effect of zeolite nanoparticles on conductometric biosensor performance and cell viability measurements. Firstly, zeolite attachment on silicon surfaces was investigated by attaching silicalite and zeolite A nanoparticles onto the silicon substrates by direct attachment methodology in a closely packed monolayer form with perfect orientation and full coverage without using any chemical linker. Furthermore, the ability to pattern these zeolite crystals on silicon substrates with electron beam lithography and photolithography techniques was investigated. With the combination of electron beam lithography and direct attachment methodology, zeolite patterns were produced with feature sizes as small as a single silicalite nanoparticle thick line, that is approximately 500 nm. This approach has the ability of patterning very small features on silicon substrate, but the drawback is the long patterning time and lack of electron beam stability during long pattern formation process. Accordingly, it is almost impossible to form large patterns with electron beam lithography systems. Afterwards, to have full control on surfaces with differentiated areas on solid substrates, patterns of one type of zeolite crystals was formed on the monolayer of another type of zeolite layer with electron beam lithography for the first time. The same closed packed and highly oriented silicalite patterns were successfully formed on zeolite A monolayers and vice versa. Then photolithography technique was combined with direct attachment methodology to overcome the problem of the lack of total patterned area. With this technique, it was possible to pattern the whole silicon wafer in a couple of seconds, however the feature size of the zeolite patterns was limited with the infrastructures of the mask fabricated for photolithography studies. In this particular study, zeolite lines patterns with a minimum of 5 &micro / m thickness were prepared and the total patterned area was kept constant at 1 cm2. Similar to what was obtained by electron beam lithography study, zeolite A patterns were formed on silicalite monolayers with the minimum feature size of 5 &micro / m and vice versa. In the second part of the study, zeolite films were prepared on the transducers of conductometric biosensors using dip coating technique and named as Zeolite Coated Transducers (ZCT). Electrodes prepared using a mixture of zeolite and enzyme solution and then subjected to casting using glutaraldehyde were called Zeolite Membrane Transducers (ZMT). The operational and storage stabilities were determined to be in an acceptable range using ZCTs for conductometric urea biosensors. It was observed that using electrodes fabricated by the ZCT technique enhanced the biosensor signals up to two times and showed a rapid response after the addition of urea to the medium when it was compared with Standard Membrane Transducers (SMT). This enhancement can be explained by the lack of GA layer on top of the film, which acts as a diffusion barrier and inhibits the activity of the enzyme. On the second part of this conductometric biosensor study, effect of zeolite modification with methyl viologen (MV) and silver nanoparticles (Ag+ and Ag0), as well as the effect of changing Si/Al ratio was investigated with three different zeolite Beta particles which have Si/Al ratios of 40, 50, and 60. There were no significant effect of MV modification on ZMTs and there was no response observed with Ag+ and Ag0 modified zeolites. However, it was observed that conductometric responses increased with increasing Si/Al ratio for ZMTs. This behavior can be due to an increased hydrophobicity and/or the increasing acidic strength with the increasing Si/Al ratio within the zeolite crystals. Also ZCTs showed higher responses with respect to both SMTs and ZMTs. When compared with SMTs and ZMTs, ZCTs had higher reproducibility due to the controlled thickness of zeolite thin film by dip coating, and the controlled amount of enzyme adsorbed on this film. In the third part of the study, effect of zeolites on cell proliferation with MG63 osteoblast cells and NIH3T3 fibroblast cells were investigated. For that purpose, zeolite A, silicalite, and calcined forms of these zeolites were patterned with photolithography technique onto silicon wafers. Three different patterns prepared for this particular study, which has 0.125cm2, 0.08825cm2, and 0.04167cm2 zeolite patterned areas on 1 cm2 samples. In that way, not only the zeolite type and effect of calcination of zeolites, but also the effect of zeolite amount on MG63 osteoblast cells and NIH3T3 fibroblast cells were investigated. Silicalite coated samples were observed to have higher amount of cells than zeolite A coated samples after 24, 48, and 72 hours of incubation. This may be referred to the hydrophilic/hydrophobic properties, surface charge, and/or particle size of zeolites. Also it is observed that higher zeolite amount on samples resulted in an increase in the number of cells attached to the samples. There was also a significant increase in the number of cells upon using calcined silicalite samples. Accordingly, it can be hypothesized that zeolite pores result in an enhancement of protein adsorption and proliferation, even if this only occurs at the pore openings. On the other hand, there was no positive effect of calcining zeolite A. This result was expected since there is no structure directing agent used in synthesis procedure of zeolite A, which again supports the fact that pores might have some role in cell attachment.