Dual parametric sensors for highly sensitive nucleic acid detection

The primary focus of this research work was on the design and development of a molecular scale (nano-scale) capacitive sensing mechanism for the highly sensitive and label-free detection of Nucleic Acid hybridization. These novel capacitive sensors with nano-scale electrode spacing offer solutions to many problems suffered by the conventional signal transduction mechanisms, thereby immensely improving the sensitivity of the biomolecular detection processes. Reducing the separation between the capacitive electrodes to the same scale as the Debye length of the sample solution, results in the overlapping of the electrical double layers of the two electrodes, thereby confining them to occupy a major fraction of the dielectric volume. This decreases the potential drop across the electrodes and thus dielectric measurements at low frequencies are made possible. The dielectric properties during hybridization reaction were measured using 10- mer nucleotide sequences. A 30-40% change in relative permittivity (capacitance) was observed due to DNA hybridization at 10Hz, which is much more sensitive than the previously reposted detection measurements (2-8% signal change). In parallel to the above work, a second label-free sensing mechanism based on field effect capacitive sensors with Metal-Oxide-Semiconductor (MOS) structure has been developed and its ability to provide real-time monitoring of oligonucleotide immobilization and hybridization events are studied. The immobilization of probe oligomers on the sensor surface and their hybridization with the target oligomers of complimentary sequences has produced significant shifts (140mV and 73mV respectively) in the Capacitance-Voltage characteristics measured across the device. In an attempt to utilize the individual merits of the nano-scale electrochemical capacitive sensor and the field effect MOS capacitive structure, a novel dual parametric sensing architecture comprising of both these transducing elements on a single sensor is designed. The detection scheme based on the combined analysis of the two parameters- Dielectric property and intrinsic molecular charge- of Nucleic acid molecules has found to reveal complimentary information of significance about the analyte-probe interactions. As a separate experiment the applications and promises of a novel technique of enhancing the speed and selectivity of the molecular detection processes by the application of an external electric field of precisely controlled intensity was studied. Experiments were conducted with 10-mer sequences and proved the feasibility of this technique in inducing in providing a faster and selective immobilization and hybridization reactions. The research work in this direction has been in collaboration with the Rational Affinity Devices, LLC, a New Jersey based corporation. The above mentioned biosensing mechanisms and detection techniques have the advantage of simplifying the readout and increasing the speed and ease of nucleic acid assays, which is especially desirable for characterizing infectious agents, scoring sequence polymorphism and genotypes, and measuring mRNA or miRNA levels during expression profiling. Once fully optimized and well assembled they have great potential to be developed in to a commercial full-scale biosensor capable of providing high-value diagnostic testing at the point of patient care places

Review on carbon-derived, solid-state, micro and nano sensors for electrochemical sensing applications

The aim of this review is to summarize the most relevant contributions in the development of electrochemical sensors based on carbon materials in the recent years. There have been increasing numbers of reports on the first application of carbon derived materials for the preparation of an electrochemical sensor. These include carbon nanotubes, diamond like carbon films and diamond film-based sensors demonstrating that the particular structure of these carbon material and their unique properties make them a very attractive material for the design of electrochemical biosensors and gas sensors. Carbon nanotubes (CNT) have become one of the most extensively studied nanostructures because of their unique properties. CNT can enhance the electrochemical reactivity of important biomolecules and can promote the electron-transfer reactions of proteins (including those where the redox center is embedded deep within the glycoprotein shell). In addition to enhanced electrochemical reactivity, CNT-modified electrodes have been shown useful to be coated with biomolecules (e.g., nucleic acids) and to alleviate surface fouling effects (such as those involved in the NADH oxidation process). The remarkable sensitivity of CNT conductivity with the surface adsorbates permits the use of CNT as highly sensitive nanoscale sensors. These properties make CNT extremely attractive for a wide range of electrochemical sensors ranging from amperometric enzyme electrodes to DNA hybridization biosensors. Recently, a CNT sensor based fast diagnosis method using non-treated blood assay has been developed for specific detection of hepatitis B virus (HBV) (human liver diseases, such as chronic hepatitis, cirrhosis, and hepatocellular carcinoma caused by hepatitis B virus). The linear detection limits for HBV plasma is in the range 0.5–3.0 μL−1 and for anti- HBVs 0.035–0.242 mg/mL in a 0.1 M NH4H2PO4 electrolyte solution. These detection limits enables early detection of HBV infection in suspected serum samples. Therefore, non-treated blood serum can be directly applied for real-time sensitive detection in medical diagnosis as well as in direct in vivo monitoring. Synthetic diamond has been recognized as an extremely attractive material for both (bio-) chemical sensing and as an interface to biological systems. Synthetic diamond have outstanding electrochemical properties, superior chemical inertness and biocompatibility. Recent advances in the synthesis of highly conducting nanocrystalline-diamond thin films and nano wires have lead to an entirely new class of electrochemical biosensors and bio-inorganic interfaces. In addition, it also combines with development of new chemical approaches to covalently attach biomolecules on the diamond surface also contributed to the advancement of diamond-based biosensors. The feasibility of a capacitive field-effect EDIS (electrolyte-diamond-insulatorsemiconductor) platform for multi-parameter sensing is demonstrated with an O-terminated nanocrystalline-diamond (NCD) film as transducer material for the detection of pH and penicillin concentration. This has also been extended for the label-free electrical monitoring of adsorption and binding of charged macromolecules. One more recent study demonstrated a novel bio-sensing platform, which is introduced by combination of a) geometrically controlled DNA bonding using vertically aligned diamond nano-wires and b) the superior electrochemical sensing properties of diamond as transducer material. Diamond nanowires can be a new approach towards next generation electrochemical gene sensor platforms. This review highlights the advantages of these carbon materials to promote different electron transfer reactions specially those related to biomolecules. Different strategies have been applied for constructing carbon material-based electrochemical sensors, their analytical performance and future prospects are discussed

Biosensors for Rapid Detection of Avian Influenza

The scope of this chapter was to review the advancements made in the area of biosensors for rapid detection of avian influenza viruses (AIVs). It is intended to provide general background about biosensor technology and to discuss important aspects for developing biosensors, such as selection of the suitable biological recognition elements (anti-AIV bioreceptors) as well as their immobilization strategies. A major concern of this chapter is also to critically review the biosensors’ working principles and their applications in AIV detection. A table containing the types of biosensor, bioreceptors, target AIVs, methods, etc. is given in this chapter. A number of papers for the different types of biosensors give hints on the current trends in the field of biosensor research for its application on AIV detection. By discussing recent research and future trends based on many excellent publications and reviews, it is hoped to give the readers a comprehensive view on this fast-growing field

Mechanical resonating devices and their applications in biomolecular studies

To introduce the reader in the subjects of the thesis, Chapter 1 provides an overview on the different aspects of the mechanical sensors. After a brief introduction to NEMS/MEMS, the different approaches of mechanical sensing are provided and the main actuation and detection schemes are described. The chapter ends with an introduction to microfabrication. Chapter 2 deals with experimental details. In first paragraph the advantages of using a pillar instead of common horizontal cantilever are illustrated. Then, the fabrication procedures and the experimental setup for resonance frequencies measurement are described. The concluding paragraph illustrates the technique, known as dip and dry, I used for coupling mechanical detection with biological problems. In Chapter 3, DNA kinetics of adsorption and hybridization efficiency, measured by means of pillar approach, are reported. Chapter 4 gives an overview of the preliminary results of two novel applications of pillar approach. They are the development of a protein chip technology based on pillars and the second is the combination of pillars and nanografting, an AFM based nanolithography. Chapter 5 starts with an introduction about the twin cantilever approach and of the mechanically induced functionalization. Fabrication procedure is described in the second paragraph. Then the chemical functionalizations are described and proved. Cleaved surface analyses and the spectroscopic studies of the mechanically induced functionalization are reported. In Appendix A there is an overview of the physical models that are used in this thesis

Design, Simulation And Analysis Of Piezoresistive Microcantilever For Biosensing Applications

Tez (Yüksek Lisans) -- İstanbul Teknik Üniversitesi, Fen Bilimleri Enstitüsü, 2016Thesis (M.Sc.) -- İstanbul Technical University, Institute of Science and Technology, 2016Son on yılda, çeşitli araştırma çalışmaları, Biyolojik Mikroelektromekanik Sistem (Bio-MEMS) biyosensörlerinin Deoksiribonükleik Asit (DNA), proteinler, Bakteri ve Antijenler gibi biyomolekülleri belirleme yeteneğini ortaya koydu. Ancak, numunelerde tespit edilmesi gereken analitlerin düşük konsantrasyonundan dolayı, sensörün çıktısına ufak bir sinyal neden olur. Buna cevap olarak, numunedeki birkaç analitin bulgulanmasına yanıt olarak yüksek çıktı sinyali verebilen optimize edilmiş bir biyosensör için bir ihtiyaç ortaya çıkmıştır; Nihai hedef tek bir biyomoleküle yapışmayı ölçülebilir bir miktara dönüştürmektir. Bu amaçla, basit, ucuz, oldukça hassas ve daha önemlisi analitlerin optik etiketlenmesine ihtiyaç duymadığı için (Etiketsiz), MEMS mikrokantilever tabanlı biyosensörler umut verici bir algılama çözümü olarak ortaya çıkmıştır. Farklı mikrokandilever ileten teknikler arasında, piezoresistif tabanlı mikrokantilever biyosensörler, ucuz, yüksek hassasiyetli, minyatür olan, sıvı ortamlarda iyi çalışan ve entegre okuma sistemi olan cazip bir çözüm gibi gözükmektedir. Literatürde piezoresistif mikrokolantların hassasiyetini arttırmaya odaklanan birçok yayın olmasına rağmen, sırf birkaç tasarım ve işlem parametresini optimize etmeyi düşündükleri için sonuçta elde edilen hassaslık arttırmaları pratik uygulamalar için yetersiz kalıyordu. Literatürde yapılan çalışmanın analizinden sonra, Piezoresistif mikrokandilöre dayalı sensörlerin hassasiyetini arttırmak için optimize edilebilen / kullanılabilen parametreler / yaklaşımlar: kantilever boyutları, kantilever Malzemesi, kantilever şekli, Piezoresistör malzemesi, Piezoresistör Doping seviyesi, Piezoresistör Boyutları, Piezoresistörün konumu, Stres konsantrasyon Bölgesinin (SCR) şekli ve konumu. Bu çalışmada, tüm tasarım ve işlem parametrelerinin duyarlılık üzerindeki etkisini analizi yapıldıktan sonra, kademeli optimizasyon yaklaşımı geliştirilmiş. Bu yaklaşımında neredeyse tüm parametreleri , her adımda biri olmak üzere, değiştirerek öbtimsyon yapılmış ve öyleyse hassasiyet maksimum düzeyde olmasını sağlamıştır. Bu çalışma boyunca, sensör performansını simüle etmek için ticari bir Sonlu Elemanlar Analizi (FEA) aracı olan COMSOL Multiphysics 5.0 kullanıldı. Her bir optimizasyon adımında, aynı uygulanan kuvvet için piezoresistor bölgelerindeki gerilimi en üst düzeye çıkaracak ve yoğunlaştıracak şekilde parametrenin optimize edilmesi hedefi daha yüksek duyarlılık elde etmektir. Toplamda, son optimize edilmiş sensörü elde etmek için neredeyse 46 farklı simülasyon yapıldı. Biyolijik uygulamalarında kullanılan etkileşimli kuvvetler onlarca ila yüzlerce pN arasında olduğu için, bu sensörde kullanılacak 25 ila 250 pN aralığı seçilmiştir. Optimizasyon işlemindeki tüm simülasyonlar sırasında 250 pN'lik bir toplam xxvi dağıtılmış kuvvet, analitlerin sensöre bağlanmasını temsil eden Altın katmanın üzerine uygulanır. Başlangıç olarak sırasıyla uzunluk, genişlik ve kalınlık için boyutları (200μm × 120μm × 1.5μm) olan dikdörtgen bir tek kristal Silicon Microcantilever kullanılmıştır. Konsolun üst kısmında, analitlerin tutturulması için 100μm × 100μm × 0.2μm Gold katmanı kullanılırken, piezo rezistanslı algılama için 20μm × 5μm × 0.5μ dikdörtgen polisilik piezoresistor kullanılır. Burada kullanılan piezoresistor, 1 x 1016 cm-3 'lük bir p-tipi dopant yoğunluğuna, 400 nm'lik bir kalınlığa ve 1V'lık uyarılma voltajına sahiptir. Dikdörtgen bir konsoldan başlamak üzere piezoresistor malzemesi ve doping seviyesi iki aşamada optimize edilmiştir. Piezistoristor malzemesi değiştiğinde (tek kristal silikon ve Poly-silikon), tek kristal silikon durumunda ΔR / R duyarlılığının daha yüksek olduğu bulundu. Fakat bu sensör tasarımı için, hassasiyet kristal yönüne bağlı olmayan, sensör imalatı daha kolay, daha ucuz ve ITUnano laboratuarında gerçekleştirilebildiğinden, piezoresistor malzemesi olarak polisilikon seçilmiştir. Sonra, doping düzeyini 1 x 1015 cm-3 ile 1 x 1020 cm-3 aralığında değiştirerek ve ΔR / R hassasiyetini hesaplayarak, aşağıdaki simülasyonlar boyunca kullanılacak doping seviyesi belirlendi. 1 × 1018 cm -3 doping seviyesinin, termal gürültü etkisini azaltacak kadar yüksek olduğu, aynı zamanda duyarlılığın da o kadar fazla etkilemediği görülmektedir. Böylece, bu doping seviyesi tüm sonrakı simülasyonlar boyunca seçildi ve kullanıldı. Daha sonra konsol malzemesi, aynı uygulanan kuvvet için maksimum gerilme ve sapma sağlayan malzeme bulmak için çeşitlendirilir. Beklendiği gibi, farklı konsol malzemeler, farklı maksimum sapma ve gerilme değerleri verdi. Elde edilen bulgulara göre, Silikon Dioksit (SiO2) düşük genç modül değerleri nedeniyle diğer malzemelere kıyasla en yüksek azami sapma ve gerilme değerlerine sahip olduğu bulundu.Tekli kristal silikon (başlangıç konsol malzemesi) durumunda olduğu gibi SiO2'nin neredeyse 2.5 kat daha yüksek sapma ve 1.7 kat daha yüksek hassaslık ile sonuçlandı ve böylece bu biyosensörün konsol malzemesi olarak SiO2 seçildi ve aşağıdaki optimizasyon adımlarda kullanıldı. Daha sonra, çeşitli konsol şekilleri (Dikdörtgen, Pi-şekli, T-şekli, Trapezoid, Kademeli-Trapezoid ve Üçgen) tanıtıldı ve her şekil için boyutlar, işlem ve cihaz sınırlamaları göz önünde bulundurularak değiştirildi. Bütün bu simülasyonların sonuçları, maksimum hassaslığı veren optimize şekli bulmak için karşılaştırıldı. Dikdörtgen şekil mikrokantilever optimizasyon adımı sırasında konsol kalınlığının konsol uzunluğu ve genişliğindeki değişimle karşılaştırıldığında sensör hassasiyeti üzerinde en yüksek etkiye sahip olduğu bulunmuştur. Konsol kalınlığı 3μm ve 1.5μm arasında değiştiğinde, konsol kalınlığı azaldığında duyarlılık arttığı bulundu. 1.5μm kalınlıktaki konsolun kullanılması, 3μm kalınlıktaki konsoldan 4 kat daha fazla yüksek hassasiyet göstermiştir. Böylece, 1.5μm son optimize konsol kalınlığı olarak seçildi. Konsol uzunluğu 150μm ila 350μm arasında değiştirildiğinde, konsol uzunluğu arttıkça hassasiyet artmaktadır. Elde edilen sonuçlara göre, 350μm uzunluğunda konsolun 150μm uzunluğundaki konsoldan yaklaşık 3.5 kat daha yüksek bir xxvii hassaslık verdiğini görüyoruz. Böylece, 350μm son optimize konsol uzunluğu olarak seçildi. Konsol genişliği 120μm ve 250μm arasında değiştirildiğinde, konsol genişliği arttıkça hassasiyet azalmaktadır. Elde edilen sonuçlara göre, 120μm genişlikli konsolun 250μm genişliğinde konsoldan 2.4 kat daha yüksek bir hassaslık verdiğini görüyoruz. Böylece, 120μm son optimize konsol genişliği olarak seçildi. Buna ek olarak, farklı dikdörtgen mikrokantilever boyutları optimize edildikten sonra (uzunluk, genişlik ve kalınlık), duyarlılık 18.3x kat arttı. Ayrıca, dikdörtgen konsol yapısına (T şekli) iki yan delik eklenmesi, duyarlılığı 1,6 oranında arttırmıştır. Farklı trapezoid biçimli konsollardan elde edilen sonuçlardan, sıkıştırılmış konsol kenarı ile serbest kenar arasındaki 1:4 oranındaki yapının en yüksek maksimum von Mises stresini ve en yüksek duyarlılığı verdiğini görülebilir. Bunların 1:1'lik durumundan (optimize edilmiş dikdörtgen konsol) neredeyse 2.5 kat daha fazla hassasiyet vardır. Böylece, bu tasarım optimize edilmiş yamuk şeklinde konsol tasarımı olarak seçildi. Farklı basamaklı trapezoid şekilli konsollardan elde edilen sonuçlara göre, sıkıştırılmış konsol kenarı ile serbest kenara arasındaki oran 1: 4 olan yapıda, en yüksek maksimum von Mises gerilmesi ve en yüksek duyarlılık görülürken, bunun neredeyse 2.5 kat arttığı görülmektedir 1: 1'den daha büyüktür (optimize edilmiş dikdörtgen konsol). Böylece, bu tasarım optimize edilmiş basamaklı trapez şeklinde konsol tasarımı olarak seçildi. Aynı uygulanan kuvvet için, trapez şeklinde mikrokancilever tasarımı, başlangıç sensöründen 46 kat daha fazla daha yüksek hassasiyet vermiştir Hassasiyet), Kademeli-Trapezoid şekli en fazla azami sapma göstermiştir. Ardından, daha fazla duyarlılık geliştirme arayışında olan farklı konum ve yönlerde optimize trapezoid yapıda Stres Yoğunlaştırma Bölgesi (SCR) tanıtıldı. Simülasyonlardan, kelepçelenmiş konsol kenarından 15μm uzakta bulunan optimize edilmiş trapezoid yapıya 30μ × 10μm SCR dikdörtgen bir delik açılmasının, diğer konumlara kıyasla en iyi hassasiyet değerini veren neredeyse 1.6x kat daha fazla hassasiyet artışı sağladığı bulundu. Nihai sensör duyarlılığı, uygulanan kuvvete karşı dirençteki normalize edilmiş değişim açısından -1.5×10-8 Ω/Ω ⁄pN 'ye eşittir. Bu, her bir 1pN (10-10 g) için biyomoleküllerin bu biyosensöre tutunması için, piezoresistor direnci 1.5×10-8 Ω kadar azalacaktır. Başlangıç sensörüne kıyasla, son sensör tasarımı 73.5x kat daha iyi ΔR / R duyarlılığı sağlamış ve daha önce literatürde bildirilen diğer sensör tasarımlarına göre daha duyarlıdır. Bu sensörün üretim sırası hazırlanmış ancak ITUnano laboratuvarında bulunan bazı cihazlarda teknik problemler nedeniyle sensör üretilmemiştir. Gelecekteki bir çalışma olarak, önerilen imalat dizisi sensörü imal etmek ve sonuçları simülasyon sonuçları ile karşılaştırmak için kullanılacaktır. Simülasyon sonuçlarına göre, konsol kalınlığı ve piezoresistor kalınlığı sensör hassasiyetini kolayca etkiler. Bu tasarımda silisyum dioksit konsol ve polisilikon piezoresistor için en düşük kalınlık sınırı olarak 1.5μm ve 0.5μm ayarlandı. Aynı tasarım için bu malzemelerin daha ince katmanlarının kullanılması duyarlılığın daha da artmasına neden olacaktır.In the past decade, several research works demonstrated the ability of Biological Microelectromechanical System (Bio-MEMS) biosensors to detect of biomolecules such as Deoxyribonucleic Acid (DNA), proteins, Bacteria and Antigens. But due to the low concentration of the analytes that need to be detected in the samples,a minuscule signal results in the output of the sensor. In response to this, a need arisen for an optimized biosensor capable of giving high output signal in response the detection of few analytes in the sample; the ultimate goal is being able to convert the attachment of a single biomolecule into a measurable quantity. For this purpose, MEMS microcantilevers based biosensors have emerged as a promising sensing solution because it is simple, cheap, highly sensitive and more importantly does not need analytes optical labeling (Label-free). Among the different microcantilever transducing techniques, piezoresistive based microcantilever biosensors seem to be a more attractive solution being cheap, high sensitive, miniature, works well in liquid environments and having integrated readout system. Even though there are many publications in literature that concentrated on increasing the piezoresistive microcantilevers sensitivity, they only considered in optimizing few design and process parameters thus the resultant sensitivity enhancements are not good enough for practical applications. After the analyzation of the work found in literature, it was found that the parameters/approaches that be can be optimized/used to enhance the sensitivity of Piezoresistive microcantilever-based sensors are: Cantilever dimensions, Cantilever Material, Cantilever Shape, Piezoresistor's material, Piezoresistor's doping level, Piezoresistor's Dimensions, Piezoresistor's position, Stress concentration Region's (SCR) shape and position. In this study, after a systematic analyzation of the effect of each design and process parameters on the sensitivity, a step-wise optimization approach was developed in which almost all these parameters were variated one at each step while fixing the others to get the maximum possible sensitivity at the end. Throughout this work, COMSOL Multiphysics 5.0, a commercial Finite Element Analysis (FEA) tool, was used to simulate the sensor performance. At each optimization step, the goal was to optimize the parameter in such a way that it maximizes and concentrates the stress in piezoresistors region for the same applied force thus get the higher sensitivity. In total, almost 46 different simulations were done to get the final optimized sensor. Starting with a rectangular cantilever, the piezoresistor material and doping level were optimized in two steps. When the piezoresistor material was varied (single crystal silicon and Poly-silicon), it was found that the ΔR⁄R sensitivity is higher in the case of single crystal silicon. xxiv But for this sensor design, polysilicon has been chosen as the piezoresistor material because it’s sensitivity does not depend on the crystal orientation, the sensor fabrication is easier, cheaper and can be realized in ITUnano laboratory. Next, by changing the doping level in the range between 1×1015 cm−3 to 1×1020 cm−3 and calculating the ∆R/R sensitivity, the doping level that will be used throughout the following simulations was determined. It was found that, 1×1018 cm−3 doping level is high enough to reduce the thermal noise effect, at the same time it does not be affected the sensitivity that much. Thus this doping level was chosen and used throughout the following simulations. Afterward, the cantilever material is varied to find the material that gives maximum stress and deflection for the same applied force. It was found that SiO2 resulted into almost 2.5x higher deflection and 1.7x higher sensitivity when compared to single crystal silicon (the starting cantilever material) case thus SiO2 has been selected as the cantilever material for this biosensor and it is used in the following optimization steps. Next, various cantilever shapes (Rectangular, Pi-shape, T-shape, Trapezoid, SteppedTrapezoid, and Triangular) were introduced, and for each shape, the dimensions were varied bearing in mind the process and device limits. The results from all these simulations were compared to find the optimized shape which gives the maximum sensitivity. During the rectangular shape microcantilever optimization step, it was found that the cantilever thickness has the highest effect on the sensor sensitivity when compared to the change in cantilever length and width. In addition to that, after the different rectangular microcantilever dimensions were optimized (length, width and thickness), the sensitivity increased 18.3x folds. Also, adding two side holes to the rectangular cantilever structure (T-shape) increased the sensitivity by 1.6 factor. Overall, for the same applied force, the trapezoid-shaped microcantilever design gave higher sensitivity (more than 46x times greater than the starting sensor sensitivity) whereas the stepped-trapezoid shaped gave the highest maximum deflection. Afterward, Stress Concentration Region (SCR) was introduced in the optimized trapezoid structure in different locations and orientations seeking for further sensitivity enhancement. From the simulations, it was found that adding a 30µ×10µm SCR rectangular hole to the optimized trapezoid structure 15µm away from the clamped cantilever edge, resulted in almost 1.6x times sensitivity enhancement which gave the best sensitivity value compared to the other positions. Regarding the normalized change in resistance to the applied force the final sensor’s sensitivity equals to -1.5×10-8 Ω/Ω ⁄pN; this means that for each 1pN (10-10 g) biomolecules attach to this biosensor; the piezoresistor resistivity will decrease by 1.5×10-8 Ω. When compared to the starting sensor, the final sensor design gave 73.5x times better ΔR⁄R sensitivity and it is more sensitive than the other sensor designs previously reported in the literature. The fabrication sequence for this sensor was prepared, but due to technical problems in some of the devices found in ITUnano laboratory, the sensor has not been fabricated.Yüksek LisansM.Sc

Roadmap on semiconductor-cell biointerfaces.

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world

Carbon Nanomaterials and their application to Electrochemical Sensors: A review

Carbon has long been applied as an electrochemical sensing interface owing to its unique electrochemical properties. Moreover, recent advances in material design and synthesis, particularly nanomaterials, has produced robust electrochemical sensing systems that display superior analytical performance. Carbon nanotubes (CNTs) are one of the most extensively studied nanostructures because of their unique properties. In terms of electroanalysis, the ability of CNTs to augment the electrochemical reactivity of important biomolecules and promote electron transfer reactions of proteins is of particular interest. The remarkable sensitivity of CNTs to changes in surface conductivity due to the presence of adsorbates permits their application as highly sensitive nanoscale sensors. CNT-modified electrodes have also demonstrated their utility as anchors for biomolecules such as nucleic acids, and their ability to diminish surface fouling effects. Consequently, CNTs are highly attractive to researchers as a basis for many electrochemical sensors. Similarly, synthetic diamonds electrochemical properties, such as superior chemical inertness and biocompatibility, make it desirable both for (bio) chemical sensing and as the electrochemical interface for biological systems. This is highlighted by the recent development of multiple electrochemical diamond-based biosensors and bio interfaces

Integration of biomolecular logic principles with electronic transducers on a chip

Boolean operations applied in biology and integrated with electronic transducers allow the development of a new class of digital biosensors for the detection of multiple input signals simultaneously and in real-time. With the help of Boolean functions (AND, OR, etc.), an electrical output signal will be directly delivered, representing a ”1” or “0” binary notation, corresponding to a “true” or “false” statement, respectively. Such digital biosensors have the future potential to create medical devices and systems for intelligent or smart diagnostics. The present thesis describes the realization of different enzyme-based biomolecular logic gates combined with electronic transducers for the possible application in medicine or food industry. In a first concept, a so called BioLogicChip is developed combining a “sense-act-treat” function integrated on one chip. The present system exemplarily mimics an “artificial pancreas” designed as a closed-loop drug-release system. A glucose sensor is constructed as enzyme-based AND logic gate, a temperature-depending hydrogel imitates the actuator function switching ON and OFF with its shrinking or swelling property, and an additional insulin sensor is developed to monitor and control the release of the drug (here: insulin) from the actuator. In this study, the results of the individual components such as the amperometric glucose sensor, the temperature-dependent hydrogel and the amperometric insulin sensor are presented, which are necessary to create such BioLogicChip. Moreover, a digital adrenaline biosensor is developed to proof the catheter position during adrenal vein sampling. The sensor consists of an oxygen electrode modified by a bi-enzyme system with the enzymes laccase and pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH) to realize substrate-recycling principle to detect low adrenaline concentrations (in the nanomolar concentration range). The sensor`s behavior at different pH values and at different temperatures is studied. Measurements in Ringer`s solution are performed. In addition, the sensitivity of the biosensor to other catecholamines such as noradrenaline, dopamine and dobutamine is investigated. Furthermore, the adrenaline biosensor is successfully examined in human blood plasma. Finally, “proof-of-principle” experiments have been performed by combining the adrenaline biosensor with Boolean operations to get a rapid qualitative statement of the presence or absence of adrenaline, thus validating the correct position of the catheter in a YES/NO form. This adrenaline biosensor is further miniaturized as a thin-film platinum adrenaline biosensor. Here, the bioelectrocatalytical measurement principle is applied by immobilization of the enzyme PQQ-GDH to detect adrenaline in the nanomolar concentration range, too. The measurement conditions such as pH value, glucose concentration in the analyte solution and temperature are optimized with regard to a high sensitivity and low detection limit. Also, this sensor has been verified towards other catecholamines (noradrenaline, dopamine and dobutamine). The platinum thin-film adrenaline biosensor is successfully applied in blood plasma for the detection of different spiked adrenaline concentrations. Furthermore, the developed adrenalin biosensor is able to detect the concentration difference between adrenal blood and peripheral blood. In contrast to the above-mentioned amperometric biosensor examples for biomolecular gates, also a field-effect-based platform is given attention in this thesis. The field-effect electrolyte-insulator-semiconductor (EIS) sensor consists of a layer structure of Al/p-Si/SiO2/Ta2O5 and is used to create an acetoin biosensor for the first time to control different fermentation processes. The sensor chip is modified by the enzyme acetoin reductase from B. clausii DSM 8716T for the catalytical reaction of (R)-acetoin to (R,R)-butanediol and meso-butanediol, respectively, in the presence of NADH. The linear measurement range, the optimal immobilization strategy (cross-linking by using glutaraldehyde and adsorptive binding) as well as the optimal working pH value and long-term stability are investigated by means of constant-capacitance measurements. Finally, the acetoin sensor was successfully applied in wine probes to detect different spiked acetoin concentrations. The sensor shows opportunities to be further developed as digital acetoin biosensor

Microcantilever-based sensing arrays for evaluation of biomolecular interactions

The controlled immobilization on a surface of biomolecules used as recognition elements is of fundamental importance in order to realize highly specific and sensible biosensors. Microcantilevers (MC) are nanomechanical sensors, which can be used as label free micro-sized mechanical transducers. MC resonant frequency is sensitively modified upon molecules adsorption, demonstrating an impressive mass resolution. A widely used approach for the immobilization of biorecognition elements on silicon substrates consists in the deposition of 3-aminopropyl-triethoxysilane (APTES) followed by the incubation with glutaraldehyde (GA) as a crosslinking agent. However, these derivatization processes produce a variable chemical functionalization because of the spontaneous polymerization of GA in aqueous solutions. With the aim of producing a more reliable chemical functionalization for protein immobilization, the deposition of a thin film of APTES by self-assembly followed by the modification of its amino groups into carboxyl groups by incubating in succinic anhydride (SA) is proposed. Moreover, the activation of these terminal carboxyl groups were performed by using the EDC/s-NHS protocol in order to enhance their reactivity toward primary amine groups present on biomolecules surface. This method was characterized from a physico-chemical point of view by means of compositional and morphological surface analysis. Moreover, data acquired after the application of this functionalization to a MC-based system showed a highly reproducible deposition of APTES/SA when compared to APTES/GA deposition process. APTES/SA derivatized MC arrays were then incubated with biomolecules for the study of its protein binding capability: the quantification of the grafted biomolecules was performed from the gravimetric data and compared with a theoretical surface density calculated through a molecular modeling tool, providing information about the orientation of the proteins tethered to the surface. In order to avoid or reduce non-specific protein interactions, Bovine Serum Albumin and ethanolamine were considered for their blocking capability. Finally, the detection of the envelope glycoprotein domain III of the Dengue virus type 1 based on immune-specific recognition through the DV32.6 antibody was performed, providing a stoichiometry ratio for the DIII-DV1/DV32.6 interaction. Currently, no cure or vaccine are available; thus, a better understanding of the interactions between the viruses and specific antibodies is expected to provide fundamental information for the development of a vaccine