Multiaddressable Photochromic Architectures: From Molecules to Materials

Multiaddressable architectures comprising light‐responsive photochromic molecules and different stimuli‐responsive components are appealing platforms for intelligent materials because of not only the potential diversity of components and corresponding properties, but also the functions resulting from their synergistic interactions. A variety of multiaddressable photochromic architectures are being designed to meet the demands of applications in different areas ranging from molecular machines to smart materials. This review highlights exciting recent advances in the field of multiaddressable systems that employ photoswitching molecules, specifically with regard to photo‐/chemical‐addressable, photo‐/pH‐addressable, photo‐/thermal‐addressable, photo‐/redox‐addressable, and multi‐photoaddressable architectures. Design concepts, crosstalk between different components, and photoswitch integration in these multiaddressable systems are discussed

지질 이중층 상 플라즈모닉 나노입자 기반 나노바이오 검지 및 컴퓨팅

학위논문 (박사)-- 서울대학교 대학원 : 자연과학대학 화학부, 2019. 2. 남좌민.Supported lipid bilayer is a two-dimensional lipid bilayer self-assembled on a hydrophilic substrate with two-dimensional fluidity. By introducing plasmonic nanoparticles with strong scattering signals into the supported lipid bilayer, it is possible to observe and track thousands of nanoparticles and their interactions at a single-nanoparticle level in real time. In this thesis, I expand the nanoparticle-lipid bilayer platform by engineering plasmonic nanoparticles to construct a complex nanoparticle network system and develop multiplexed bio-detection and bio-computing strategies. Chapter 1 describes a supported lipid bilayer platform incorporating plasmonic nanoparticles. Section 1 introduces the optical properties and biosensing application of plasmonic nanoparticles, and Section 2 introduces tethering technique, characteristics, and advantages for introducing nanoparticles into supported lipid bilayer platforms. In Chapter 2, I introduce a system that can distinguish nine types of nanoparticle assembly reactions occurring simultaneously by introducing optically encoded plasmonic nanoparticles that scatter red, blue, and green light into supported lipid bilayers. I performed multiplexed detection of nine types of microRNAs, which are important gene regulators and cancer cell biomarker. In Chapter 3, I develop a bio-computing platform that recognizes molecular inputs, performs logic circuits, and generates nanoparticle assembly/disassembly output signals. Complex logic circuits are designed and implemented by combining two strategies: (i) interfacial design that constructs a logic circuit through DNA functionalization of the interface of nanoparticles, and (ii) a network design that connects assembly/disassembly reactions. In Chapter 4, I develop a bio-computing calculator capable of performing arithmetic logic operations. I use the nanoparticle-lipid bilayer platform as the hardware that stores, processes, and outputs information, and constructs software that contains logic circuit functions through DNA solution. An information storage nanoparticle stores solution-phase molecular input signals on the surface of nanoparticles. The bio-computing lipid nanotablet recognizes an arithmetic logic circuit programmed with DNA information and generates outputs a result of a kinetic difference between nanoparticle assembly reaction according to the storage state of the input signal.지지형 지질 이중층은 친수성 기판 위에 조립된 2차원의 지질 이중층으로 2차원 상의 유동성을 가진다. 지지형 지질 이중층에 강한 산란 신호를 지니는 플라즈모닉 나노입자를 도입하면 수천 개의 나노입자와 그 상호작용을 단일 나노입자 수준으로 실시간 관찰이 가능하다. 본 학위논문에서는 나노입자-지질 이중층 플랫폼에서의 나노입자 종류 및 개질 방법을 확장하여 복잡한 나노입자 네트워크 시스템을 구성하고, 바이오 검지, 바이오 컴퓨팅 응용을 개발한다. 1장에서는 플라즈모닉 나노입자가 도입된 지지형 지질 이중층 플랫폼을 설명한다. 1절에서 플라즈모닉 나노입자의 광학적 특성과 산란신호를 이용한 바이오센싱 응용 연구를 소개하고 2절에서는 지지형 지질 이중층 플랫폼에 나노입자의 도입 방법, 특징, 장점, 분석방법 등을 소개한다. 2장에서는 빨강, 초록, 파랑 빛을 산란하는 플라즈모닉 나노입자를 합성하고, 지지형 지질 이중층에 도입하여 동시에 일어나는 9종류의 나노입자 결합 반응을 각각 구분할 수 있는 플랫폼을 개발한다. 이를 이용하여 세포 내 중요한 단백질 번역 조절물질이자 암 바이오마커인 마이크로RNA를 동시 다중 검지한다. 3장에서는 지지형 지질 이중층 상에 도입된 나노입자를 다종의 DNA로 기능화하여 특정 DNA 분자 입력 신호 인식, 논리회로 수행, 나노입자 결합/분리 출력 신호 생성하는 바이오 컴퓨팅 플랫폼을 개발한다. 나노입자의 계면을 DNA로 디자인하여 논리 회로를 구성하는 인터페이스 프로그래밍과 나노입자의 결합/분리 반응을 연결하여 네트워크를 디자인하여 논리 회로를 집적하는 네트워크 프로그래밍을 조합하여 복잡한 논리 회로를 설계하고 수행한다. 4장에서는 지지형 지질 이중층에 도입된 나노입자 표면에 용액 상 분자 입력신호를 저장하는 정보 저장 장치를 개발하고 모든 종류의 산술논리연산을 수행할 수 있는 생분자 계산기을 개발한다. 나노입자-지질 이중층 플랫폼을 정보저장, 수행, 출력하는 매체인 하드웨어로 이용하고, DNA 분자 조합 용액을 산술논리회로 기능을 담고있는 소프트웨어로 구성한다. 바이오 컴퓨팅 칩은 DNA 정보로 프로그래밍된 산술논리회로를 인식하여 입력신호의 저장 상태에 따라 나노입자 결합 반응에 반응속도에 차이를 일으키고 결과를 출력한다.Chapter 1. Introduction: Plasmonic Nanoparticle-Tethered Supported Lipid Bilayer Platform 1 1.1. Plasmonic Nanoparticles and Their Bio-Applications 2 1.1.1. Introduction 4 1.1.2. Fundamentals of Plasmonic Nanoparticles 8 1.1.3. Plasmonic Nanoparticle Engineering for Biological Application 11 1.1.4. Plasmonic Nanoparticles for Rayleigh Scattering-Based Biosensing 16 1.1.5. References 21 1. 2. Supported Lipid Bilayer as a Dynamic Platform 24 1.2.1. Introduction 26 1.2.2. Basic Setups and Strategies 29 1.2.3. Nanoparticle-Tethering Techniques 33 1.2.4. Real-Time Imaging and Tracking of Single Nanoparticles on SLB 39 1.2.5. Observation of Interactions between Single Nanoparticles 44 1.2.6. References 50 Chapter 2. Multiplexed Biomolecular Detection Strategy 53 2.1. Introduction 55 2.2. Experimental Section 60 2.3. Results and Discussion 66 2.4. Conclusion 77 2.5. Supporting Information 79 2.6. References 83 Chapter 3. Nano-Bio Computing on Lipid Bilayer 84 3.1. Introduction 85 3.2. Experimental Section 88 3.3. Results and Discussion 98 3.4. Conclusion 120 3.5. Supporting Information 124 3.6. References 161 Chapter 4. Development of Nanoparticle Architecture for Biomolecular Arithmetic Logic Operation 163 4.1. Introduction 165 4.2. Experimental Section 167 4.3. Results and Discussion 171 4.4. Conclusion 177 4.5. References 179 Abstract in Korean 180Docto

DNA-Powered Stimuli-Responsive Single-Walled Carbon Nanotube Junctions

Reconfigurable stimuli-responsive molecular materials play an important role in the fabrication of nanoscale systems and devices. Here, we report a bottom-up strategy for the reversible assembly of single-walled carbon nanotube linear junctions in solution. The assembly/disassembly of the nanotubes can be controlled via the intrinsic responsiveness to different stimuli of sequence-specific deoxyribonucleic acid linkers forming the junctions

Fabrication and microfluidic analysis of graphene-based molecular communication receiver for Internet of Nano Things (IoNT).

Bio-inspired molecular communications (MC), where molecules are used to transfer information, is the most promising technique to realise the Internet of Nano Things (IoNT), thanks to its inherent biocompatibility, energy-efficiency, and reliability in physiologically-relevant environments. Despite a substantial body of theoretical work concerning MC, the lack of practical micro/nanoscale MC devices and MC testbeds has led researchers to make overly simplifying assumptions about the implications of the channel conditions and the physical architectures of the practical transceivers in developing theoretical models and devising communication methods for MC. On the other hand, MC imposes unique challenges resulting from the highly complex, nonlinear, time-varying channel properties that cannot be always tackled by conventional information and communication tools and technologies (ICT). As a result, the reliability of the existing MC methods, which are mostly adopted from electromagnetic communications and not validated with practical testbeds, is highly questionable. As the first step to remove this discrepancy, in this study, we report on the fabrication of a nanoscale MC receiver based on graphene field-effect transistor biosensors. We perform its ICT characterisation in a custom-designed microfluidic MC system with the information encoded into the concentration of single-stranded DNA molecules. This experimental platform is the first practical implementation of a micro/nanoscale MC system with nanoscale MC receivers, and can serve as a testbed for developing realistic MC methods and IoNT applications.Tis work was supported in part by the ERC (Project MINERVA, ERC-2013-CoG #616922) and by the AXA Research Fund (AXA Chair for Internet of Everything at Koc University)

Single Walled Carbon Nanotubes Assembly: Nanohybrids toward Photodetection and Junction Engineering.

PhD ThesesBy synergistically combining the individual properties of more than one nanoscale component, novel features of hybrid structure assemblies represent a key motivation for making future functional nanomaterials. In this thesis, the successful construction of a multiplexed photo-responsive chip from DNA-wrapped single walled carbon nanotubes (DNA-CNTs) and DNA-CNT templated inorganic-organic hybrid structures is first demonstrated. The effective assembly of the hybrids was characterized by atomic force microscopy (AFM) and the corresponding device performance as well as the key mechanisms behind were investigated. Then a facile approach for the fabrication of end-to-end SWCNT junctions exploiting oligonucleotides as molecular linkers is presented. The assembled junctions show clear stimuli-responsive features stemming from the designed sequences of oligonucleotides; this grants the SWCNTs the ability to self-assemble and disassemble under specific conditions in aqueous solutions. The junction formation was confirmed by Atomic Force Microscopy (AFM) and time-dependent fluorescence analysis. Moreover, an efficient strategy to sort DNA-wrapped SWCNTs (DNA-CNTs) by length via a gel electrophoresis technique was developed (confirmed by AFM). In addition to the application of oligonucleotides, the use of diazonium salts not only as a molecular linker but also the major reactive agent for CNT junction formation was also explored. In conclusion, by integrating DNA-CNTs with other active components, we have achieved the assembly for organic-inorganic nanohybrids of multiplexed photo-sensing capabilities and the assembly of reconfigurable SWCNT junctions with stimuli-responsive features. Moreover, the facile and efficient strategies developed in our work can contribute to the controlled assembly of CNT based functional nanohybrids

Nano/Bio-Receiver Architectures and Detection Methods for Molecular Communications

Internet of Nano Things (IoNT) is an emerging technology, which aims at extending the connectivity into nanoscale and biological environments with collaborative networks of artificial nanomachines and biological entities integrated into the Internet. To enable the IoNT and its groundbreaking applications, such as real-time intrabody health monitoring, it is imperative to devise nanoscale communication techniques with low-complexity transceiver architectures. Bio-inspired molecular communications (MC), which uses molecules to transfer information, is the most promising technique to realise IoNT due to its inherent biocompatibility and reliability in physiologically-relevant environments. Despite the substantial body of work concerning MC, the implications of an interface between MC channel and practical MC transceiver architectures are largely neglected, leading to a major gap between theory and practice. As the first step to remove this discrepancy, in this thesis, I develop a realistic analytical ICT model for microfluidic MC with surface-based receivers as a convection-diffusion-reaction system. In the second part, I focus on biological MC receivers, which can be implemented in living cells using synthetic biology tools. In this direction, I theoretically develop low-complexity and reliable MC detection methods exploiting the various statistics of the stochastic ligand-receptor interactions at the membrane of biological MC receivers. The estimation and detection theoretical analysis of these detection methods demonstrate that even single type of receptors can provide sufficient statistics to overcome the receptor saturation problem, cope with the interference of non-cognate molecules, and simultaneously sense the concentration of multiple types of ligands. I also propose synthetic receptor designs for the transduction of decision statistics into a representation by concentration of intracellular molecules, and design chemical reaction networks performing decoding with intracellular reactions. Finally, I fabricate a micro/nanoscale MC receiver based on graphene field-effect transistor biosensors and perform its ICT characterisation in a custom-designed microfluidic MC system with the information encoded into the concentration of DNAs. This experimental platform is the first practical demonstration of micro/nanoscale MC, and can serve as a testbed for developing realistic MC methods

Design and Functional Assembly of Synthetic Biological Parts and Devices

Programming living cells with synthetic gene circuits to perform desired tasks has been a major theme in the emerging field of synthetic biology. However, gene circuit engineering currently lacks the same predictability and reliability as seen in other mature engineering disciplines. This thesis focuses on the design and engineering of novel modular and orthogonal biological devices, and the predictable functional assembly of modular biological elements (BioParts) into customisable larger biological devices. The thesis introduces the design methodology for engineering modular and orthogonal biological devices. A set of modular biological devices with digital logic functions, including the AND, NOT and combinatorial NAND gates, were constructed and quantitatively characterised. In particular, a novel genetic AND gate was engineered in Escherichia coli by redesigning the natural HrpR/HrpS heteroregulation motif in the hrp system of Pseudomonas syringae. The AND gate is orthogonal to E. coli chassis, and employs the alternative σ54-dependent gene transcription to achieve tight transcriptional control. Results obtained show that context has a large impact on part and device behaviour, established through the systematic characterisation of a series of biological parts and devices in various biophysical and genetic contexts. A new, effective strategy is presented for the assembly of BioParts into functional customised systems using engineered ‘incontext’ characterised modules aided by modelling, which can significantly increase the predictability of circuit construction by characterising the component parts and modules in the same biophysical and genetic contexts as anticipated in their final systems. Finally, the thesis presents the design and construction of an application-oriented integrated system – the cell density-dependent microbe-based biosensor. The in vivo biosensor was programmed to be able to integrate its own cell density signal through an engineered cell-cell communication module and a second environmental signal through an environment-responsive promoter in the logic AND manner, with GFP as the output readout

Utilisation de la spectroscopie d'impédance électrochimique pour étudier les biocapteurs électrochimiques à base d'aptamère

Abstract : One of the significant challenges in the healthcare industry is medication errors, which can lead to severe consequences for patients, including adverse drug reactions and even death. Recently, to tackle this issue, personalized medicine solutions are emerging as potential alternatives to improve the efficiency with which drug dosing is achieved. Specifically, these approaches involve tailoring medical treatment to the specific needs of a patient based on their genetics, environments and lifestyles. To achieve true personalized medicine requires the development of analytical methods capable of providing real-time monitoring of molecules. To date, however, current analytical approaches, at best, only provide a single snapshot of one’s health and require venous draws that are sent to external laboratories where trained personnel perform analyses on cumbersome instrumentation. Biosensors, in contrast, can provide continuous and accurate measurements of various biomarkers and can allow for early detections providing information for early intervention. Additionally, biosensors can be used to monitor the efficacy of treatments and adjust medication dosages in real time, which can lead to better therapeutic outcomes. The development of personalized medicine and real-time monitoring sensing platforms has the potential to revolutionize the healthcare industry, providing better patient outcomes and improving the overall efficiency and quality of the healthcare system. Electrochemical aptamer-based (E-AB) sensors have emerged as candidates to develop personalized medicine tools. Being comprised of a redox-reporter-modified short nucleic acid sequence (i.e., aptamer) immobilized on an electrode surface affords real-time and continuous measurements of diverse molecular species, such as proteins, nucleic acids, and small molecules directly in undiluted complex matrices. The flexibility with which aptamers can be swapped in this sensing platform makes them an optimal platform for designing personalized medicine tools for diverse clinical applications. The widespread implementation of E-AB sensors has been hampered by their restricted aptamer affinity (μM−mM range), which falls short of covering the entire range of clinically relevant concentrations at which molecules need to be assessed. In the first part of this memoir, we investigated two electrochemical interrogation techniques, namely, square-wave voltammetry and electrochemical impedance spectroscopy, in measuring the dissociation constants of E-AB sensors. The results revealed that although square-wave voltammetry has been the most used interrogation technique, it systematically yields aptamers’ dissociation constants higher than ones measured for the same aptamer with other techniques and thus in certain cases leaves E-AB sensors unable to measure the concentration of molecules in the target clinical range. We found that electrochemical impedance spectroscopy, in contrast, proved to be a superior technique due to its ability to deconvolute interfacial resistive and capacitive contributions to the measured current and quantify electrochemical processes occurring on several time scales with higher resolution. When comparing dissociation constants measured via electrochemical impedance spectroscopy with the gold standard method in aptamer characterization isothermal titration calorimetry we found that these were either within experimental errors or only 2−3-fold apart. Therefore, our study proposes that electrochemical impedance spectroscopy is a more reliable and accurate electrochemical technique compared to square-wave voltammetry for interrogating E-AB sensors. In the second part of this memoir, we discovered a new signal transduction mechanism for E-AB sensors which involves the widely used redox reporter methylene blue, which competes with ligand binding. The results demonstrated that methylene blue folds the aptamer we tested and dislodges ligands from its binding pocket. Consequently, the electrochemical properties of methylene blue change, leading to a measurable signal. Given the prevalence of methylene blue in E-AB sensors, this finding challenges the widely accepted conventional "conformational change" mechanism of E-AB sensors and suggests an alternative signal transduction scheme. Our study provides important insights into the underlying physicochemical properties at E-AB sensors’ surface and their fundamentals.L’occurrence d'erreurs médicamenteuses pouvant entraîner des conséquences graves pour les patients (réactions indésirables aux médicaments, décès, etc.) demeure un enjeu de taille pour les soins de santé. Récemment, pour faire face à ce problème, la médecine personnalisée a émergé comme une alternative efficace afin d’améliorer l'efficacité des prescriptions de médicaments. Cette approche consiste à adapter les traitements aux besoins spécifiques d'un patient en fonction de sa génétique, de son environnement et de son mode de vie. Toutefois, pour parvenir à une véritable médecine personnalisée, il est nécessaire de développer des méthodes analytiques capables de fournir un suivi en temps réel des molécules. À ce jour, les approches analytiques actuelles ne permettent au mieux qu'une seule mesure instantanée de l'état de santé et nécessitent des prélèvements veineux envoyés à des laboratoires externes où des professionnels qualifiés effectuent des analyses à l'aide d'instruments encombrants. En revanche, les biocapteurs peuvent fournir des mesures continues et précises de divers biomarqueurs et fournir des informations pour une intervention précoce. De plus, les biocapteurs peuvent être utilisés pour surveiller l'efficacité des traitements et ajuster les doses de médicaments en temps réel, ce qui peut conduire à de meilleurs résultats thérapeutiques. Le développement de la médecine personnalisée et de plateformes de surveillance en temps réel a le potentiel de révolutionner les soins de santé en améliorant la qualité et la qualité de résultats pour les patients. Les biocapteurs électrochimiques à base d'aptamères (E-AB) ont émergé comme des candidats pour le développement d'outils de médecine personnalisée. Composés d'une courte séquence d'acide nucléique spécifique à une cible moléculaire (un aptamère) modifiée par un rapporteur rédox immobilisé sur une surface d'électrode, ces capteurs permettent des mesures en temps réel et continues de diverses espèces moléculaires telles que des protéines, des acides nucléiques et des petites molécules directement dans des matrices complexes non diluées. La flexibilité avec laquelle les aptamères peuvent être échangés dans cette plateforme de détection en fait une plateforme optimale pour la conception d'outils de médecine personnalisée pour diverses applications cliniques. Toutefois, la mise en oeuvre des capteurs E-AB dans diverses applications a été entravée par la faible affinité des aptamères (dans la plage μM−mM), qui ne couvre pas l'ensemble de la plage de concentrations cliniquement pertinente sur laquelle les molécules doivent être quantifiées. Dans la première partie de cette étude, nous avons examiné deux techniques d'interrogation électrochimiques, à savoir la voltampérométrie à onde carrée et la spectroscopie d'impédance électrochimique, pour mesurer les constantes de dissociation des capteurs E-AB. Les résultats ont révélé que, bien que la voltampérométrie à onde carrée soit la technique d'interrogation la plus couramment utilisée, elle produit des constantes de dissociation des aptamères plus élevées que celles mesurées pour le même aptamère avec d'autres techniques, ce qui, dans certains cas, empêche les capteurs E-AB de mesurer la concentration des molécules dans la plage clinique cible. Nous avons constaté que la spectroscopie d'impédance électrochimique, en revanche, s'est révélée être une technique supérieure en raison de sa capacité à déconvoluer les contributions résistives et capacitives interfaciales au courant mesuré et à quantifier les processus électrochimiques se produisant à différentes échelles de temps avec une résolution plus élevée. Lors de la comparaison des constantes de dissociation mesurées par spectroscopie d'impédance électrochimique avec la méthode de référence en caractérisation d'aptamères, le titrage calorimétrique isotherme, nous avons constaté que ces constantes étaient soit dans les limites des erreurs expérimentales, ou différenciées par un facteur de 2 à 3. Par conséquent, notre étude propose que la spectroscopie d'impédance électrochimique soit une technique électrochimique plus fiable et précise par rapport à la voltampérométrie à onde carrée pour l'interrogation des capteurs E-AB. Dans la deuxième partie de cette étude, nous avons découvert un nouveau mécanisme de traduction du signal pour les capteurs E-AB, impliquant le rapporteur rédox largement utilisé, le bleu de méthylène, qui entre en compétition avec la liaison du ligand. Les résultats ont démontré que le bleu de méthylène replie l'aptamère que nous avons testé et déloge les ligands de sa poche de liaison. Par conséquent, les propriétés électrochimiques du bleu de méthylène changent, ce qui entraîne un signal mesurable. Étant donné la prévalence du bleu de méthylène dans les capteurs E-AB, cette découverte remet en question le mécanisme conventionnel largement accepté du "changement conformationnel" des capteurs E-AB et suggère un schéma alternatif de traduction du signal. Notre étude apporte des éclaircissements importants sur les propriétés physico-chimiques sous-jacentes à la surface des capteurs E-AB et leurs fondements