Effective design principles for leakless strand displacement systems

Artificially designed molecular systems with programmable behaviors have become a valuable tool in chemistry, biology, material science, and medicine. Although information processing in biological regulatory pathways is remarkably robust to error, it remains a challenge to design molecular systems that are similarly robust. With functionality determined entirely by secondary structure of DNA, strand displacement has emerged as a uniquely versatile building block for cell-free biochemical networks. Here, we experimentally investigate a design principle to reduce undesired triggering in the absence of input (leak), a side reaction that critically reduces sensitivity and disrupts the behavior of strand displacement cascades. Inspired by error correction methods exploiting redundancy in electrical engineering, we ensure a higher-energy penalty to leak via logical redundancy. Our design strategy is, in principle, capable of reducing leak to arbitrarily low levels, and we experimentally test two levels of leak reduction for a core “translator” component that converts a signal of one sequence into that of another. We show that the leak was not measurable in the high-redundancy scheme, even for concentrations that are up to 100 times larger than typical. Beyond a single translator, we constructed a fast and low-leak translator cascade of nine strand displacement steps and a logic OR gate circuit consisting of 10 translators, showing that our design principle can be used to effectively reduce leak in more complex chemical systems

Compartmentalization of DNA-Based Molecular Computing Elements Using Lipid Bilayers

This dissertation will present a progression from the detection of double-stranded DNA using a combination of toehold-mediated strand displacement and DNAzyme reactions in dilute saline solutions, to the generation of separate compartments to allow standardization of DNA computing elements, by protecting from complementary strands. In well-mixed solutions complementary regions cause spurious interactions. Importantly, these compartments also provide protection from nucleases. Along the way we will also explore the use of silica microsphere supported lipid bilayers to run compartmentalized DNA reactions on a fluid surface and the design of a molecule capable of DNA-based transmembrane signal transduction

DNA multi-bit non-volatile memory and bit-shifting operations using addressable electrode arrays and electric field-induced hybridization.

DNA has been employed to either store digital information or to perform parallel molecular computing. Relatively unexplored is the ability to combine DNA-based memory and logical operations in a single platform. Here, we show a DNA tri-level cell non-volatile memory system capable of parallel random-access writing of memory and bit shifting operations. A microchip with an array of individually addressable electrodes was employed to enable random access of the memory cells using electric fields. Three segments on a DNA template molecule were used to encode three data bits. Rapid writing of data bits was enabled by electric field-induced hybridization of fluorescently labeled complementary probes and the data bits were read by fluorescence imaging. We demonstrated the rapid parallel writing and reading of 8 (23) combinations of 3-bit memory data and bit shifting operations by electric field-induced strand displacement. Our system may find potential applications in DNA-based memory and computations

Aptamer-based sequence verification platform for rapid multiplexed detection of viral RNA targets

Diagnostic detection of viruses is a cornerstone method for the management of emerging epidemics and pandemics. However, current limitations in commercially available and gold standard diagnostic detection platforms like cost, time to signal readout, and sensitivity, expose gaps in viral surveillance. To address these limitations, we have developed a novel Point-of-Care aligned method for the rapid isothermal amplification of viral RNA targets using RT-LAMP, and amplicon sequence verification using an aptamer-based colorimetric signal readout. With this method established, we then developed multiplexing detection platforms that target globally impactful mosquito-borne viral diseases and pathogens, including Dengue virus and Malaria, as well as the viruses that they are often misdiagnosed with, like Zika and Chikungunya viruses. With these platforms, we demonstrate both a quantitative and qualitative distinguishment of up to four mosquito borne pathogenic RNA targets at once in a single multiplexed detection platform

Innovative Bioanalytical Tools & Methods for Combinatorial Non-Coding RNA Analysis

Recently researchers have discovered that groups of small non-coding RNAs (ncRNAs) play regulatory roles in gene expression and participate in various biological processes. For example, pathogenesis of many diseases, cell cycle regulation, and signaling pathways. Intracellular and live cell imaging of small ncRNA groups will reveal their relative expression levels and provide unparalleled detail on spatial and temporal heterogeneities within a single cell. The ability to measure heterogeneities will help define cell types and cell states for differentiating cell populations. Having analytical tools that reveal heterogeneities among cell populations will provide unique insights on the physiological changes and processes (e.g. aging and apoptosis) of each cell and how the cells work together to maintain homeostasis or drive disease progression. To profile small ncRNAs expression, one popular analytical tool is known as programmable molecular logic sensors. Relying on nucleic acids, a natural building block8, molecular logic sensors are constructed for computing what groups of small ncRNAs are in a cell. As a model system to design innovative molecular logic sensors around, I picked microRNAs. MicroRNAs (miRs) are small non-coding single-stranded RNAs that are approximately 22 nucleotides in length.9 The roles of miRs are to regulate gene expression, mainly post-transcriptionally, during messenger-RNA translation. Current nucleic-acid-based in situ sensors that are capable of revealing a cells miR pattern suffer from 1) low multiplexing ability (up to two miR inputs per sensor), 2) poor selectivity, and 3) false signals due to sensor degradation by nucleases. Therefore, I conducted research to design, characterize, optimize, and apply two different designs of logic sensors to overcome some of the bottlenecks facing current in situ sensors. My research in the field of molecular logic centered around contributing innovative designs and establishing design principles for constructing nanodevices. The term “AND” means the sensor’s signal only turns ON when all miR inputs are present. My first logic sensor design, published in Nanoscale, is called a nano-assembly logic gate (NALG). My contribution to the molecular logic field is a unique multi-hairpin motif designed. The purpose the multi-hairpin motif was to improve input number (multiplexing ability), selectivity, and robustness to false signal generation. Furthermore, the motif’s design will serve as the base building block for a modular design for scaling up the multiplexing ability. NALG was designed for three miRs: miR27a, miR96, and miR182. The signal transduction mechanism of NALG was based on Frster Resonance Energy Transfer (FRET) enhancement. The results showed that NALG had: (1) low nanomolar (nM) limits of detection (LOD), (2) selectivity against off-analyte cocktails (sequence similariaty ranged from 13% to 27%), (3) no false-positive signal from nuclease degradation, and (4) the ability to respond to three miRs in a matrix mimicking the cellular environment (i.e. crude MCF-7 cell lysate). However, NALG needed refinement to improve its ability to differentiate input numbers because it showed signal response in the presence of two out of three miRs. In order to reduce NALG’s signal response from two miRs, I studied how to fine-tune the multi-hairpin motif to better resist biochemical and biophysical interactions with two miRs. The manuscript for this work is currently under review at Analytical Chemistry. Three new motif types were developed based on the original motif. The motif designs were assessed based on the following design metrics: (1) the location of the inputs’ complementary sequence, (2) the predicted number of Hydrogen-bonds formed in the motif, (3) the predicted change in thermodynamic values of the motif after the addition of the inputs, and (4) the predicted molarity percentage of motif forming complex with different numbers of inputs (two versus three). We measured the fluorescence response from these motifs in the presence of inputs and discovered gaps between the predicted and experimental results. Our findings provide a noteworthy improvement to the design process of molecular logic sensors for measurement science. To overcome the limitations in the first logic sensor (NALG) design and applying what I learned about the design process, I came up with an innovative design that I call: autowalk AND logic operator (AALO). AALO was designed for a three-miR combination: miR27a, miR24, and miR210. Different from current nucleic-acid-based sensors that recognize analyte miRs through a single toehold-mediated strand displacement reaction (TMSDR), AALO relies on a cascading (five-step) TMSDRs. The cascading TMSDRs mechanism exposes one toehold per step to initiate successive TMSDRs. The toehold (~3-6 nucleotides sequence) in the gate strand initiates binding with an incoming strand and subsequently displaces a pre-bound strand from the gate. Such a recognition mechanism requires the presence of all miR inputs to complete the cascading process and achieve signal change. AALO’s lower signal change in the presence of two miRs (19% from AALO compared to 53% from NALG) means that AALO’s recognition mechasim was able lower the false response from incomplete miR combinations. The five-step TMSDRs were thus able to improve the logic sensors’ differentiating-input-number ability. Compared to NALG, AALO showed increased selectivity against off-analyte miRs with sequence similiarity ranging from 41% to 95%. We have prelimitary data that shows AALO was transfected into the cell line HEK 293T through nucleofection

Assessing the potential of surface-immobilized molecular logic machines for integration with solid state technology

Molecular computation with DNA has great potential for low power, highly parallel information processing in a biological or biochemical context. However, significant challenges remain for the field of DNA computation. New technology is needed to allow multiplexed label-free readout and to enable regulation of molecular state without addition of new DNA strands. These capabilities could be provided by hybrid bioelectronic systems in which biomolecular computing is integrated with conventional electronics through immobilization of DNA machines on the surface of electronic circuitry. Here we present a quantitative experimental analysis of a surface-immobilized OR gate made from DNA and driven by strand displacement. The purpose of our work is to examine the performance of a simple representative surface-immobilized DNA logic machine, to provide valuable information for future work on hybrid bioelectronic systems involving DNA devices. We used a quartz crystal microbalance to examine a DNA monolayer containing approximately 5 × 10^{11} gates cm^{−2}, with an inter-gate separation of approximately 14 nm, and we found that the ensemble of gates took approximately 6 min to switch. The gates could be switched repeatedly, but the switching efficiency was significantly degraded on the second and subsequent cycles when the binding site for the input was near to the surface. Otherwise, the switching efficiency could be 80% or better, and the power dissipated by the ensemble of gates during switching was approximately 0.1 nW cm^{−2}, which is orders of magnitude less than the power dissipated during switching of an equivalent array of transistors. We propose an architecture for hybrid DNA-electronic systems in which information can be stored and processed, either in series or in parallel, by a combination of molecular machines and conventional electronics. In this architecture, information can flow freely and in both directions between the solution-phase and the underlying electronics via surface-immobilized DNA machines that provide the interface between the molecular and electronic domains

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

Synthetic antigen-conjugated DNA systems for antibody detection and characterization

Antibodies are among the most relevant biomolecular targetsfordiagnostic and clinical applications. In this Perspective, we providea critical overview of recent research efforts focused on the developmentand characterization of devices, switches, and reactions based onthe use of synthetic antigen-conjugated DNA strands designed to beresponsive to specific antibodies. These systems can find applicationsin sensing, drug-delivery, and antibody-antigen binding characterization.The examples described here demonstrate how the programmability andchemical versatility of synthetic nucleic acids can be used to createinnovative analytical tools and target-responsive systems with promisingpotentials

DESIGN AND APPLICATIONS OF DNA-BASED DEVICES FOR SELF-ASSEMBLY, MOLECULAR CIRCUITS, AND SOFT MATERIALS

Biologically inspired synthetic materials have led to novel technologies due of their ability to sense, influence, or adapt to their environment. One way to build these materials and devices is to utilize the high sequence specificity and innate biocompatibility of DNA. While once considered as a material useful for only storing genetic information, DNA-based devices are now being realized as molecular tools in fields such as therapeutics, diagnostics, regenerative medicine, and soft robotics. In this dissertation, we investigate the use of DNA to build programmable tools to control self-assembly, implement molecular computation, and direct material change processes. DNA origami nanostructures are useful tools for controlling the spatial patterns of proteins, nanoparticles, and fluorophores because they contain hundreds of independently functionalizable locations that can be engineered with nanoscale precision. However, the addressable surface area is currently limited by the size of single origami structures, and efficient, high-yield self-assembly of multiple origami into higher-order assemblies continues to be a challenge. To investigate the factors important for heterogeneous self-assembly of multiple origami, we experimentally measure the equilibrium distribution of four origami tiles in the monomer, intermediate, and final tetramer states as a function of temperature. We find that the thermodynamics of the self-assembly process is determined by the binding interface between origami. Simulations of the assembly kinetics suggest assembly occurs primarily via hierarchical pathways. Next, we engineer a DNA-based timer circuit that can be used in computational devices for molecular release or material control. The circuit releases target DNA sequences into solution at a programmable time with a tunable, constant rate. Multiple timer circuits can operate simultaneously, each releasing their target sequences at independent rates and times. We further develop the utility of the timer and similar DNA-based circuits as a means to control molecular events in biological environments, such as serum-supplemented cell media, where DNA-degrading nucleases can reduce the functional stability and lifetime of DNA-based devices. By implementing DNA circuit-protective design principles and by adding screening molecules to reduce nuclease activity, the functional lifetime of simple DNA circuits can be significantly increased. We develop a model by fitting parameters for reactions between nucleases and simple DNA circuits. Using the model, we can qualitatively predict the behavior of more complex circuits: multiple circuits in series and circuits containing competitive reactions. Finally, we investigate how DNA-based circuits can be used to trigger the high-degree swelling response of DNA-crosslinked metamorphic hydrogels. By coupling signal amplification to the triggering process, we demonstrate modular control over the timescale and degree of swelling. Further, we show control over the identity of the trigger molecule using molecular translators and computational controllers capable of converting complex chemical inputs into mechanical actuation