Zhou Nie is Professor at the College of Chemistry and Chemical Engineering, Hunan University, China. His research is focused on the development of new nucleic acid nanotechnology-based toolkits for detection and regulation of key factors in crucial biological events, such as cellular signal transduction and transcription regulation. He was awarded by the National Science Fund for Distinguished Young Scholars in 2017, the WuXi AppTec Life Chemistry Research Award in 2022, and the Chinese Chemical Society Young Chemist Award in 2015.

• Preface xvPart I DNA Nanotechnology for Cellular Recognition (Cell SELEX, Cell Surface Engineering) 11 Developing DNA Aptamer Toolbox for Cell Research 3Liang Yue, Shan Wang, and Weihong Tan1.1 Cells and Their Complexity 31.2 Features and Advantages of DNA Aptamers 41.3 On-demand Synthesis and Screening of DNA Aptamers 51.4 Toward a Toolbox of DNA Aptamers for Cellular Applications 91.4.1 Chemical Modifications via Solid-Supported Synthesis Strategy 101.4.2 Chemical Modifications Through Covalent Conjugation 131.4.3 Self-assembly Systems Based on Chemically Modified DNA Aptamers 151.4.4 DNA Aptamers Engineered with Nanotechnology 191.5 Summary and Outlook 21Acknowledgments 22References 222 Bacterial Detection with Functional Nucleic Acids: Escherichia coli as a Case Study 31Yash Patel and Yingfu li2.1 General Introduction to Bacteria 312.2 E. coli 322.3 Conventional Methods for General E. coli Detection 332.3.1 Sorbitol MacConkey Agar 342.3.2 Pcr 342.4 Biosensors for E. coli Detection 352.4.1 Protein Biosensors for E. coli Detection 352.4.2 Functional Nucleic Acid-Based Sensors for E. coli Detection 362.5 Conclusion 41References 423 From Ligand-Binding Aptamers to Molecular Switches 47Sanshu Li, Xiaojun Zhang, Tao Luo, Xuejiao Liu, Tingting Zhai, and Hongzhou Gu3.1 Aptamers Can Be Generated by SELEX 473.2 Various Subtypes of SELEX Have Been Invented 483.3 Riboswitches Are Natural RNA Aptamers Carrying Expression Platforms 493.4 Riboswitches Use Various Mechanisms to Regulate Gene Expression 523.5 Riboswitches Are Potential Drug Targets 553.6 Fusing Aptamer with Expression Platform to Construct Artificial RNA Switches 553.7 Conclusions 57Acknowledgments 57References 574 DNA Nanotechnology-Based Microfluidics for Liquid Biopsy 63Qi Niu, Shanqing Huang, Chaoyong Yang, and Lingling Wu4.1 Introduction 634.2 DNA Nanotechnology-Based Microfluidics for Isolation of Circulating Targets 654.2.1 Aptamer-Modified Micro/Nano-Substrate Microfluidic Chip 654.2.2 DNA Framework-Supported Affinity Substrate Microfluidic Chip 734.3 DNA Nanotechnology-Based Microfluidics for Release and Detection of Circulating Targets 774.3.1 Efficient Release 774.3.2 Analysis and Destruction of CTCs 814.3.3 Sensitive Detection of EVs 854.4 DNA-Assisted Microfluidics for Single-Cell/Vesicle Analysis 884.4.1 Single-Cell Analysis by Sequencing 894.4.2 Single-Cell Analysis by Spectroscopy 934.4.3 Single-Vesicle Analysis 954.5 Summary and Outlook 97References 985 Spatiotemporal-Controlled Cell Membrane Engineering Using DNA Nanotechnology 105Wenxue Xie, Cong Ren, Minjie Lin, and Hang Xing5.1 Background 1055.2 DNA Modifications on the External Cell Membrane Surface 1075.2.1 Strategies to Incorporate DNA onto External Cell Membrane Surface 1075.2.2 Applications of External Membrane-modified DNA 1145.3 DNA Modifications on the Internal Cell Membrane Surface 1205.3.1 Transmembrane Modification of DNA 1215.3.2 Inner Leaflet Modification Approaches 1245.3.3 Liposome Fusion-Based Transport (LiFT) Approach 1295.4 Perspectives 130Acknowledgments 132References 132Part II Dna Nanotechnology for Cell Imaging and Intracellular Sensing 1416 Metal-Dependent DNAzymes for Cell Surface Engineering and Intracellular Bioimaging 143Ruo-Can Qian, Yuting Wu, Zhenglin Yang, Weijie Guo, Ze-Rui Zhou, andYiLu6.1 Cellular Surface Engineering and Intracellular Bioimaging Show Great Potential in Biological and Medical Research 1436.2 Metal-Specific DNAzymes: A Suitable Choice for Artificial Manipulation of Living Cells 1446.3 Cell Surface Engineering by Programmable DNAzymes 1456.3.1 Cell Surface Engineering Using DNAzyme-Based Control Switches 1456.3.2 Dynamic Inter- and Intra-Cellular Regulation Using Engineered DNAzyme Molecular Machines 1476.3.3 Cell Surface Imaging of Extracellular Signaling Molecule Using DNAzyme Sensors 1496.4 Intracellular Imaging of Metal Ions with DNAzyme-Based Biosensors 1506.4.1 DNAzyme-Based Catalytic Beacon for Intracellular Imaging 1506.4.2 Caged DNAzymes for Temporally Controlled Imaging 1546.4.3 DNAzyme-Based Sensing with Signal Amplification 1596.4.4 Genetically Encoded Sensors for Metal Sensing in Living Cells 1596.5 Conclusion 161Acknowledgments 161References 1617 DNA Nanomotors for Bioimaging in Living Cells 169Hanyong Peng, Aijiao Yuan, Hang Xiao, Zi Ye, Lejun Liao, Shulin Zhao, and X. Chris LeReferences 1848 Illuminating RNA in Live Cells with Inorganic Nanoparticles-Based DNA Sensor Technology 189Fangzhi Yu, Xiangfei li, Xiulin Yi, and Lele li8.1 RNA Detection and Imaging 1898.2 RNA Imaging Based on Direct Hybridization 1908.3 RNA Imaging Based on Strand Displacement Reactions 1928.4 Signal-amplified RNA Imaging 1948.4.1 HCR-Based DNA Nanosensors for Amplified RNA Imaging 1948.4.2 CHA-Based DNA Nanosensors for Amplified RNA Imaging 1968.4.3 Amplified RNA Imaging Based on DNA Nanomachines 1988.5 Spatiotemporally Controlled RNA Imaging in Live Cells 2038.6 Conclusion 206Acknowledgment 207References 2079 Building DNA Computing System for Smart Biosensing and Clinical Diagnosis 211Jiao Yang and Da Han9.1 DNA Computing 2119.1.1 DNA Logic Gates Based on Functional DNA Motifs 2129.1.2 DNA Logic Gates Based on DNA Cascading Reactions 2159.2 DNA-Based Computing Devices for Biosensing 2179.2.1 In Vitro Biosensing 2179.2.2 Cellular Biosensing 2209.3 DNA Computing for Clinical Diagnosis 2239.4 Conclusion 226References 22610 Intelligent Sense-on-Demand DNA Circuits for Amplified Bioimaging in Living Cells 233Yuqiu He, Zeyue Wang, Yuqian Jiang, and Fuan Wang10.1 DNA Circuit: The Promising Technique for Bioimaging 23310.2 Nonenzymatic DNA Circuits 23410.2.1 Hybridization Chain Reaction (HCR) 23410.2.2 Catalytic Hairpin Assembly (CHA) 23510.2.3 Entropy-Driven DNA Catalytic Reaction (EDR) 23610.2.4 DNAzyme-Powered Catalytic Reaction (DZR) 23610.3 Intelligent Integrated DNA Circuits for Amplified Bioimaging 23710.3.1 Hybridization-Dependent Cascade DNA Circuits 23710.3.2 DNAzyme-Assisted Tandem DNA Circuits 23910.3.3 Autocatalysis-Driven Feedback DNA Circuits 24110.4 Stimuli-Responsive DNA Circuits for Reliable Bioimaging 24310.4.1 Photo-Responsive DNA Circuits for Amplified Bioimaging 24310.4.2 Enzyme-Activated DNA Circuits for Amplified Bioimaging 24510.4.3 RNA-Stimulated DNA Circuits for Amplified Bioimaging 24610.4.4 Other Strategies for Regulating DNA Circuits 24910.5 Conclusion and Perspectives 251Acknowledgments 252References 25211 DNA Nanoscaffolds for Biomacromolecules Organization and Bioimaging Applications 259Yuanfang Chen, Jiayi Li, and Yuhe R. Yang11.1 Introduction 25911.2 Assembly of DNA-Scaffolded Biomacromolecules 25911.3 Application of DNA Nanoscaffold for Regulation of Enzyme Cascade Reaction 26111.3.1 Distance Control of Enzyme Cascade 26111.3.2 Enzyme Compartmentalization 26311.3.3 Directed Substrate Channeling with Swinging Arms 26411.3.4 Scaffolded Enzyme Cascade in Living Cells 26511.4 DNA Nanostructures Empowered Bioimaging Technologies 26711.4.1 DNA Nanostructures Scaffolded Fluorophore Expansion 26711.4.2 DNA-PAINT-Based Super-Resolution Fluorescence Imaging 26911.4.3 DNA Nanostructures-Assisted Cryogenic Electron Microscopy Characterization 26911.5 Summary and Outlook 270References 271Part III Dna Nanotechnology for Regulation of Cellular Functions 27912 Adopting Nucleic Acid Nanotechnology for Genetic Regulation In Vivo 281Friedrich C. Simmel12.1 Introduction 28112.2 Toehold-Mediated Strand Displacement: Switching Nucleic Acids with Nucleic Acids 28212.3 Toehold Riboregulators and Related Systems 28312.3.1 Riboswitches 28312.3.2 Translational Switching with Toehold Switches 28412.3.3 Toehold Switching in Eukaryotes 28512.3.4 Transcriptional Switching 28612.3.5 Applications as Sensors 28612.3.6 Applications in Biocomputing 28712.4 Applying Nucleic Acid Nanotechnology to CRISPR and RNA Interference 28812.4.1 CRISPR Techniques 28812.4.2 Switchable Guide RNAs 28912.4.3 Implementing More Complex Programs in Mammalian Cells 29112.4.4 Combining CRISPR with Origami 29212.4.5 MicroRNAs and RNA Interference 29212.5 Delivery of Nucleic Acid Devices, In Vivo Production, and Challenges for In Vivo Operation 29312.5.1 Delivery 29312.5.2 In Vivo Production 29312.5.3 Challenges 29412.6 Conclusion and Outlook 294Acknowledgments 295References 29513 Cell Membrane Functionalization via Nucleic Acid Tools for Visualization and Regulation of Cellular Receptors 303Shan Chen, Jingying Li, and Huanghao Yang13.1 Nucleic Acid-Based Functionalization Strategies: From Receptor Information to DNA Probes 30313.2 Uncovering Molecular Information of Cellular Receptors 30713.3 Governing Cellular Receptors-Mediated Signal Transduction 31313.4 Conclusion 318Acknowledgments 318References 31814 Harnessing DNA Nanotechnology for Nongenetic Manipulation and Functionalization of Cell Surface Receptor 325Hexin Nan, Hong-Hui Wang, and Zhou Nie14.1 Introduction 32514.2 Principle of DNA-enabled Molecular Engineering for Receptor Regulation 32914.2.1 Recognition Module for Receptor Manipulation 33014.2.2 Spatial Scaffold Module for Receptor Organization 33014.2.3 Dynamic Assembly Module for Kinetic Control of Receptor 33114.3 DNA Nanodevices for Programming Receptor Function 33214.3.1 Bivalent Aptamer Mimicking Natural Ligand to Induce Receptor Dimerization 33214.3.2 DNA Nanodevices to Customize Receptor Responsiveness 33314.3.3 Light-Responsive DNA Nanodevices for Spatiotemporal Receptor Regulation 33514.3.4 DNA Nanodevices for Visualization of Receptor Activation 33714.4 Elaborate and Intelligent DNA Nanodevices Reprogramming Receptor Function 33914.4.1 Mechanical Control Over Receptor-Mediated Cellular Behavior 33914.4.2 Precise Cell Targeting for Selective Receptor Modulation 34114.4.3 Spatial Organization of Nanoscale Receptor Distribution 34414.5 Conclusions and Perspectives 347Acknowledgments 348References 34815 DNA-Based Cell Surface Engineering for Programming Multiple Cell–Cell Interactions 355Mingshu Xiao, Yueyang Sun, Li Li, and Hao Pei15.1 DNA Nanotechnology: The Tool of Choice for Programming Cell–Cell Interactions 35515.2 Modifying Cell Surface with DNA 35615.3 Programming Cell–Cell Interactions by DNA Nanotechnology 35915.3.1 Ligand–Receptor Binding-Based Cell–Cell Interactions 35915.3.2 DNA Hybridization-Based Cell–Cell Interactions 36215.3.3 DNA Circuit-Regulated Cell–Cell Interactions 36415.4 Conclusion 366Acknowledgments 367References 36716 Designer DNA Nanostructures and Their Cellular Uptake Behaviors 375Jing Ye, Donglei Yang, Chenzhi Shi, Fei Zhou, and Pengfei Wang16.1 Introduction 37516.2 DNA Nanotechnology 37616.2.1 The Beginning of DNA Nanotechnology 37616.2.2 DNA Origami 37716.2.3 Single-Stranded DNA Tiles 37816.2.4 Dynamic DNA Structures 37916.3 Pathways of Cell Endocytosis 38116.3.1 Clathrin-Mediated Endocytosis 38116.3.2 Clathrin-Independent Endocytosis 38216.3.3 Phagocytosis 38416.3.4 Macropinocytosis 38416.3.5 Caveolin-Mediated Endocytosis 38516.4 Analysis of DNA Nanostructures’ Cellular Uptake Behaviors 38616.4.1 Effect of Size and Shape on Cellular Uptake 38616.4.2 Effect of Surface Modifications on Cellular Uptake 38916.4.3 Effect of Other Aspects on Cellular Uptake 392References 395Part IV Dna Nanotechnology for Cell-targeted Medical Applications 40117 Toward Production of Nucleic Acid Nanostructures in Life Cells and Their Biomedical Applications 403Mengxi Zheng, Victoria E. Paluzzi, Cuizheng Zhang, and Chengde Mao17.1 DNA Nanostructures 40317.1.1 Strategies of DNA Nanostructures Construction 40317.1.2 Production of ssDNA Nanostructures in Living Cells 40417.2 RNA Nanostructures 40617.2.1 Strategies of RNA Nanostructures Construction 40617.2.2 Production of ssRNA Nanostructures in Living Cells 40717.3 Applications 40917.4 Conclusion 412References 41218 Engineering Nucleic Acid Structures for Programmable Intracellular Biocomputation 415Na Wu, Pengyan Hao, Chunhai Fan, and Yongxi ZhaoReferences 43219 DNA Supramolecular Hydrogels for Biomedical Applications 437Ziwei Shi, Yuanchen Dong, and Dongsheng Liu19.1 Introduction 43719.2 Classification and Preparation of DNA Supramolecular Hydrogels 43819.2.1 Pure DNA Supramolecular Hydrogels 43819.2.2 Hybrid Supramolecular DNA Hydrogels 44019.3 Biomedical Application of DNA Supramolecular Hydrogels 44319.3.1 DNA Supramolecular Hydrogels for Bio-sensing 44319.3.2 DNA Supramolecular Hydrogels for Drug Delivery 44619.3.3 DNA Supramolecular Hydrogels for Immunotherapy 44919.3.4 DNA Supramolecular Hydrogels for 3D Cell Culture 45119.3.5 DNA Supramolecular Hydrogels for Tissue Engineering 45419.4 Conclusions and Perspectives 458References 45920 Rolling Circle Amplification-Based DNA Nanotechnology for Cell Research 467Nachuan Song, Yiwen Chu, Xun You, and Dayong Yang20.1 Introduction 46720.2 Principle and Synthetic Methods of RCA 46820.2.1 Principle 46820.2.2 DNA Hydrogel 46920.2.3 DNA Nanoparticles 46920.3 RCA-Based DNA Nanotechnology for Cell Separation 46920.4 RCA-Based DNA Nanotechnology for Nucleic Acid Drug Delivery 47520.5 Conclusion 484Acknowledgment 485References 48521 Precise Integration of Therapeutics in DNA-Based Nanomaterials for Cancer Treatments 489Yimeng Li, Lijuan Zhu, and Chuan Zhang21.1 DNA-Based Nanomaterials in Biomedicine 49021.1.1 Properties of DNA-Based Nanomaterials 49121.1.2 Architectures of DNA-Based Nanomaterials 49221.1.3 Interactions Between DNA-Based Drug Delivery Systems (DDSs) and Cells 49521.2 Strategies on Constructing DNA-Based DDSs 49821.2.1 DNA-Based DDSs Engineered Through Non-covalent Interactions 49921.2.2 DNA-Based DDSs Engineered Through Covalent Interactions 50221.3 Precise Integration of Therapeutics into DNA-Based DDSs to Achieve Synergistic Cancer Treatment 50721.3.1 Chemogenes 50721.3.2 Chemogene-Based DNA Nanomaterials 508References 511Index 515