DNA nanotechnology for cell research :  from bioanalysis to biomedicine / 
edited by Zhou Nie. 
 - 1 online resource :  illustrations (some color) 
 - 
<br/><br/>Includes bibliographical references and index. 
<br/><br/>Table of Contents<br/>Preface xv<br/><br/>Part I DNA Nanotechnology for Cellular Recognition (Cell SELEX, Cell Surface Engineering) 1<br/><br/>1 Developing DNA Aptamer Toolbox for Cell Research 3<br/>Liang Yue, Shan Wang, and Weihong Tan<br/><br/>1.1 Cells and Their Complexity 3<br/><br/>1.2 Features and Advantages of DNA Aptamers 4<br/><br/>1.3 On-demand Synthesis and Screening of DNA Aptamers 5<br/><br/>1.4 Toward a Toolbox of DNA Aptamers for Cellular Applications 9<br/><br/>1.4.1 Chemical Modifications via Solid-Supported Synthesis Strategy 10<br/><br/>1.4.2 Chemical Modifications Through Covalent Conjugation 13<br/><br/>1.4.3 Self-assembly Systems Based on Chemically Modified DNA Aptamers 15<br/><br/>1.4.4 DNA Aptamers Engineered with Nanotechnology 19<br/><br/>1.5 Summary and Outlook 21<br/><br/>Acknowledgments 22<br/><br/>References 22<br/><br/>2 Bacterial Detection with Functional Nucleic Acids: Escherichia coli as a Case Study 31<br/>Yash Patel and Yingfu li<br/><br/>2.1 General Introduction to Bacteria 31<br/><br/>2.2 E. coli 32<br/><br/>2.3 Conventional Methods for General E. coli Detection 33<br/><br/>2.3.1 Sorbitol MacConkey Agar 34<br/><br/>2.3.2 Pcr 34<br/><br/>2.4 Biosensors for E. coli Detection 35<br/><br/>2.4.1 Protein Biosensors for E. coli Detection 35<br/><br/>2.4.2 Functional Nucleic Acid-Based Sensors for E. coli Detection 36<br/><br/>2.5 Conclusion 41<br/><br/>References 42<br/><br/>3 From Ligand-Binding Aptamers to Molecular Switches 47<br/>Sanshu Li, Xiaojun Zhang, Tao Luo, Xuejiao Liu, Tingting Zhai, and Hongzhou Gu<br/><br/>3.1 Aptamers Can Be Generated by SELEX 47<br/><br/>3.2 Various Subtypes of SELEX Have Been Invented 48<br/><br/>3.3 Riboswitches Are Natural RNA Aptamers Carrying Expression Platforms 49<br/><br/>3.4 Riboswitches Use Various Mechanisms to Regulate Gene Expression 52<br/><br/>3.5 Riboswitches Are Potential Drug Targets 55<br/><br/>3.6 Fusing Aptamer with Expression Platform to Construct Artificial RNA Switches 55<br/><br/>3.7 Conclusions 57<br/><br/>Acknowledgments 57<br/><br/>References 57<br/><br/>4 DNA Nanotechnology-Based Microfluidics for Liquid Biopsy 63<br/>Qi Niu, Shanqing Huang, Chaoyong Yang, and Lingling Wu<br/><br/>4.1 Introduction 63<br/><br/>4.2 DNA Nanotechnology-Based Microfluidics for Isolation of Circulating Targets 65<br/><br/>4.2.1 Aptamer-Modified Micro/Nano-Substrate Microfluidic Chip 65<br/><br/>4.2.2 DNA Framework-Supported Affinity Substrate Microfluidic Chip 73<br/><br/>4.3 DNA Nanotechnology-Based Microfluidics for Release and Detection of Circulating Targets 77<br/><br/>4.3.1 Efficient Release 77<br/><br/>4.3.2 Analysis and Destruction of CTCs 81<br/><br/>4.3.3 Sensitive Detection of EVs 85<br/><br/>4.4 DNA-Assisted Microfluidics for Single-Cell/Vesicle Analysis 88<br/><br/>4.4.1 Single-Cell Analysis by Sequencing 89<br/><br/>4.4.2 Single-Cell Analysis by Spectroscopy 93<br/><br/>4.4.3 Single-Vesicle Analysis 95<br/><br/>4.5 Summary and Outlook 97<br/><br/>References 98<br/><br/>5 Spatiotemporal-Controlled Cell Membrane Engineering Using DNA Nanotechnology 105<br/>Wenxue Xie, Cong Ren, Minjie Lin, and Hang Xing<br/><br/>5.1 Background 105<br/><br/>5.2 DNA Modifications on the External Cell Membrane Surface 107<br/><br/>5.2.1 Strategies to Incorporate DNA onto External Cell Membrane Surface 107<br/><br/>5.2.2 Applications of External Membrane-modified DNA 114<br/><br/>5.3 DNA Modifications on the Internal Cell Membrane Surface 120<br/><br/>5.3.1 Transmembrane Modification of DNA 121<br/><br/>5.3.2 Inner Leaflet Modification Approaches 124<br/><br/>5.3.3 Liposome Fusion-Based Transport (LiFT) Approach 129<br/><br/>5.4 Perspectives 130<br/><br/>Acknowledgments 132<br/><br/>References 132<br/><br/>Part II Dna Nanotechnology for Cell Imaging and Intracellular Sensing 141<br/><br/>6 Metal-Dependent DNAzymes for Cell Surface Engineering and Intracellular Bioimaging 143<br/>Ruo-Can Qian, Yuting Wu, Zhenglin Yang, Weijie Guo, Ze-Rui Zhou, andYiLu<br/><br/>6.1 Cellular Surface Engineering and Intracellular Bioimaging Show Great Potential in Biological and Medical Research 143<br/><br/>6.2 Metal-Specific DNAzymes: A Suitable Choice for Artificial Manipulation of Living Cells 144<br/><br/>6.3 Cell Surface Engineering by Programmable DNAzymes 145<br/><br/>6.3.1 Cell Surface Engineering Using DNAzyme-Based Control Switches 145<br/><br/>6.3.2 Dynamic Inter- and Intra-Cellular Regulation Using Engineered DNAzyme Molecular Machines 147<br/><br/>6.3.3 Cell Surface Imaging of Extracellular Signaling Molecule Using DNAzyme Sensors 149<br/><br/>6.4 Intracellular Imaging of Metal Ions with DNAzyme-Based Biosensors 150<br/><br/>6.4.1 DNAzyme-Based Catalytic Beacon for Intracellular Imaging 150<br/><br/>6.4.2 Caged DNAzymes for Temporally Controlled Imaging 154<br/><br/>6.4.3 DNAzyme-Based Sensing with Signal Amplification 159<br/><br/>6.4.4 Genetically Encoded Sensors for Metal Sensing in Living Cells 159<br/><br/>6.5 Conclusion 161<br/><br/>Acknowledgments 161<br/><br/>References 161<br/><br/>7 DNA Nanomotors for Bioimaging in Living Cells 169<br/>Hanyong Peng, Aijiao Yuan, Hang Xiao, Zi Ye, Lejun Liao, Shulin Zhao, and X. Chris Le<br/><br/>References 184<br/><br/>8 Illuminating RNA in Live Cells with Inorganic Nanoparticles-Based DNA Sensor Technology 189<br/>Fangzhi Yu, Xiangfei li, Xiulin Yi, and Lele li<br/><br/>8.1 RNA Detection and Imaging 189<br/><br/>8.2 RNA Imaging Based on Direct Hybridization 190<br/><br/>8.3 RNA Imaging Based on Strand Displacement Reactions 192<br/><br/>8.4 Signal-amplified RNA Imaging 194<br/><br/>8.4.1 HCR-Based DNA Nanosensors for Amplified RNA Imaging 194<br/><br/>8.4.2 CHA-Based DNA Nanosensors for Amplified RNA Imaging 196<br/><br/>8.4.3 Amplified RNA Imaging Based on DNA Nanomachines 198<br/><br/>8.5 Spatiotemporally Controlled RNA Imaging in Live Cells 203<br/><br/>8.6 Conclusion 206<br/><br/>Acknowledgment 207<br/><br/>References 207<br/><br/>9 Building DNA Computing System for Smart Biosensing and Clinical Diagnosis 211<br/>Jiao Yang and Da Han<br/><br/>9.1 DNA Computing 211<br/><br/>9.1.1 DNA Logic Gates Based on Functional DNA Motifs 212<br/><br/>9.1.2 DNA Logic Gates Based on DNA Cascading Reactions 215<br/><br/>9.2 DNA-Based Computing Devices for Biosensing 217<br/><br/>9.2.1 In Vitro Biosensing 217<br/><br/>9.2.2 Cellular Biosensing 220<br/><br/>9.3 DNA Computing for Clinical Diagnosis 223<br/><br/>9.4 Conclusion 226<br/><br/>References 226<br/><br/>10 Intelligent Sense-on-Demand DNA Circuits for Amplified Bioimaging in Living Cells 233<br/>Yuqiu He, Zeyue Wang, Yuqian Jiang, and Fuan Wang<br/><br/>10.1 DNA Circuit: The Promising Technique for Bioimaging 233<br/><br/>10.2 Nonenzymatic DNA Circuits 234<br/><br/>10.2.1 Hybridization Chain Reaction (HCR) 234<br/><br/>10.2.2 Catalytic Hairpin Assembly (CHA) 235<br/><br/>10.2.3 Entropy-Driven DNA Catalytic Reaction (EDR) 236<br/><br/>10.2.4 DNAzyme-Powered Catalytic Reaction (DZR) 236<br/><br/>10.3 Intelligent Integrated DNA Circuits for Amplified Bioimaging 237<br/><br/>10.3.1 Hybridization-Dependent Cascade DNA Circuits 237<br/><br/>10.3.2 DNAzyme-Assisted Tandem DNA Circuits 239<br/><br/>10.3.3 Autocatalysis-Driven Feedback DNA Circuits 241<br/><br/>10.4 Stimuli-Responsive DNA Circuits for Reliable Bioimaging 243<br/><br/>10.4.1 Photo-Responsive DNA Circuits for Amplified Bioimaging 243<br/><br/>10.4.2 Enzyme-Activated DNA Circuits for Amplified Bioimaging 245<br/><br/>10.4.3 RNA-Stimulated DNA Circuits for Amplified Bioimaging 246<br/><br/>10.4.4 Other Strategies for Regulating DNA Circuits 249<br/><br/>10.5 Conclusion and Perspectives 251<br/><br/>Acknowledgments 252<br/><br/>References 252<br/><br/>11 DNA Nanoscaffolds for Biomacromolecules Organization and Bioimaging Applications 259<br/>Yuanfang Chen, Jiayi Li, and Yuhe R. Yang<br/><br/>11.1 Introduction 259<br/><br/>11.2 Assembly of DNA-Scaffolded Biomacromolecules 259<br/><br/>11.3 Application of DNA Nanoscaffold for Regulation of Enzyme Cascade Reaction 261<br/><br/>11.3.1 Distance Control of Enzyme Cascade 261<br/><br/>11.3.2 Enzyme Compartmentalization 263<br/><br/>11.3.3 Directed Substrate Channeling with Swinging Arms 264<br/><br/>11.3.4 Scaffolded Enzyme Cascade in Living Cells 265<br/><br/>11.4 DNA Nanostructures Empowered Bioimaging Technologies 267<br/><br/>11.4.1 DNA Nanostructures Scaffolded Fluorophore Expansion 267<br/><br/>11.4.2 DNA-PAINT-Based Super-Resolution Fluorescence Imaging 269<br/><br/>11.4.3 DNA Nanostructures-Assisted Cryogenic Electron Microscopy Characterization 269<br/><br/>11.5 Summary and Outlook 270<br/><br/>References 271<br/><br/>Part III Dna Nanotechnology for Regulation of Cellular Functions 279<br/><br/>12 Adopting Nucleic Acid Nanotechnology for Genetic Regulation In Vivo 281<br/>Friedrich C. Simmel<br/><br/>12.1 Introduction 281<br/><br/>12.2 Toehold-Mediated Strand Displacement: Switching Nucleic Acids with Nucleic Acids 282<br/><br/>12.3 Toehold Riboregulators and Related Systems 283<br/><br/>12.3.1 Riboswitches 283<br/><br/>12.3.2 Translational Switching with Toehold Switches 284<br/><br/>12.3.3 Toehold Switching in Eukaryotes 285<br/><br/>12.3.4 Transcriptional Switching 286<br/><br/>12.3.5 Applications as Sensors 286<br/><br/>12.3.6 Applications in Biocomputing 287<br/><br/>12.4 Applying Nucleic Acid Nanotechnology to CRISPR and RNA Interference 288<br/><br/>12.4.1 CRISPR Techniques 288<br/><br/>12.4.2 Switchable Guide RNAs 289<br/><br/>12.4.3 Implementing More Complex Programs in Mammalian Cells 291<br/><br/>12.4.4 Combining CRISPR with Origami 292<br/><br/>12.4.5 MicroRNAs and RNA Interference 292<br/><br/>12.5 Delivery of Nucleic Acid Devices, In Vivo Production, and Challenges for In Vivo Operation 293<br/><br/>12.5.1 Delivery 293<br/><br/>12.5.2 In Vivo Production 293<br/><br/>12.5.3 Challenges 294<br/><br/>12.6 Conclusion and Outlook 294<br/><br/>Acknowledgments 295<br/><br/>References 295<br/><br/>13 Cell Membrane Functionalization via Nucleic Acid Tools for Visualization and Regulation of Cellular Receptors 303<br/>Shan Chen, Jingying Li, and Huanghao Yang<br/><br/>13.1 Nucleic Acid-Based Functionalization Strategies: From Receptor Information to DNA Probes 303<br/><br/>13.2 Uncovering Molecular Information of Cellular Receptors 307<br/><br/>13.3 Governing Cellular Receptors-Mediated Signal Transduction 313<br/><br/>13.4 Conclusion 318<br/><br/>Acknowledgments 318<br/><br/>References 318<br/><br/>14 Harnessing DNA Nanotechnology for Nongenetic Manipulation and Functionalization of Cell Surface Receptor 325<br/>Hexin Nan, Hong-Hui Wang, and Zhou Nie<br/><br/>14.1 Introduction 325<br/><br/>14.2 Principle of DNA-enabled Molecular Engineering for Receptor Regulation 329<br/><br/>14.2.1 Recognition Module for Receptor Manipulation 330<br/><br/>14.2.2 Spatial Scaffold Module for Receptor Organization 330<br/><br/>14.2.3 Dynamic Assembly Module for Kinetic Control of Receptor 331<br/><br/>14.3 DNA Nanodevices for Programming Receptor Function 332<br/><br/>14.3.1 Bivalent Aptamer Mimicking Natural Ligand to Induce Receptor Dimerization 332<br/><br/>14.3.2 DNA Nanodevices to Customize Receptor Responsiveness 333<br/><br/>14.3.3 Light-Responsive DNA Nanodevices for Spatiotemporal Receptor Regulation 335<br/><br/>14.3.4 DNA Nanodevices for Visualization of Receptor Activation 337<br/><br/>14.4 Elaborate and Intelligent DNA Nanodevices Reprogramming Receptor Function 339<br/><br/>14.4.1 Mechanical Control Over Receptor-Mediated Cellular Behavior 339<br/><br/>14.4.2 Precise Cell Targeting for Selective Receptor Modulation 341<br/><br/>14.4.3 Spatial Organization of Nanoscale Receptor Distribution 344<br/><br/>14.5 Conclusions and Perspectives 347<br/><br/>Acknowledgments 348<br/><br/>References 348<br/><br/>15 DNA-Based Cell Surface Engineering for Programming Multiple Cell–Cell Interactions 355<br/>Mingshu Xiao, Yueyang Sun, Li Li, and Hao Pei<br/><br/>15.1 DNA Nanotechnology: The Tool of Choice for Programming Cell–Cell Interactions 355<br/><br/>15.2 Modifying Cell Surface with DNA 356<br/><br/>15.3 Programming Cell–Cell Interactions by DNA Nanotechnology 359<br/><br/>15.3.1 Ligand–Receptor Binding-Based Cell–Cell Interactions 359<br/><br/>15.3.2 DNA Hybridization-Based Cell–Cell Interactions 362<br/><br/>15.3.3 DNA Circuit-Regulated Cell–Cell Interactions 364<br/><br/>15.4 Conclusion 366<br/><br/>Acknowledgments 367<br/><br/>References 367<br/><br/>16 Designer DNA Nanostructures and Their Cellular Uptake Behaviors 375<br/>Jing Ye, Donglei Yang, Chenzhi Shi, Fei Zhou, and Pengfei Wang<br/><br/>16.1 Introduction 375<br/><br/>16.2 DNA Nanotechnology 376<br/><br/>16.2.1 The Beginning of DNA Nanotechnology 376<br/><br/>16.2.2 DNA Origami 377<br/><br/>16.2.3 Single-Stranded DNA Tiles 378<br/><br/>16.2.4 Dynamic DNA Structures 379<br/><br/>16.3 Pathways of Cell Endocytosis 381<br/><br/>16.3.1 Clathrin-Mediated Endocytosis 381<br/><br/>16.3.2 Clathrin-Independent Endocytosis 382<br/><br/>16.3.3 Phagocytosis 384<br/><br/>16.3.4 Macropinocytosis 384<br/><br/>16.3.5 Caveolin-Mediated Endocytosis 385<br/><br/>16.4 Analysis of DNA Nanostructures’ Cellular Uptake Behaviors 386<br/><br/>16.4.1 Effect of Size and Shape on Cellular Uptake 386<br/><br/>16.4.2 Effect of Surface Modifications on Cellular Uptake 389<br/><br/>16.4.3 Effect of Other Aspects on Cellular Uptake 392<br/><br/>References 395<br/><br/>Part IV Dna Nanotechnology for Cell-targeted Medical Applications 401<br/><br/>17 Toward Production of Nucleic Acid Nanostructures in Life Cells and Their Biomedical Applications 403<br/>Mengxi Zheng, Victoria E. Paluzzi, Cuizheng Zhang, and Chengde Mao<br/><br/>17.1 DNA Nanostructures 403<br/><br/>17.1.1 Strategies of DNA Nanostructures Construction 403<br/><br/>17.1.2 Production of ssDNA Nanostructures in Living Cells 404<br/><br/>17.2 RNA Nanostructures 406<br/><br/>17.2.1 Strategies of RNA Nanostructures Construction 406<br/><br/>17.2.2 Production of ssRNA Nanostructures in Living Cells 407<br/><br/>17.3 Applications 409<br/><br/>17.4 Conclusion 412<br/><br/>References 412<br/><br/>18 Engineering Nucleic Acid Structures for Programmable Intracellular Biocomputation 415<br/>Na Wu, Pengyan Hao, Chunhai Fan, and Yongxi Zhao<br/><br/>References 432<br/><br/>19 DNA Supramolecular Hydrogels for Biomedical Applications 437<br/>Ziwei Shi, Yuanchen Dong, and Dongsheng Liu<br/><br/>19.1 Introduction 437<br/><br/>19.2 Classification and Preparation of DNA Supramolecular Hydrogels 438<br/><br/>19.2.1 Pure DNA Supramolecular Hydrogels 438<br/><br/>19.2.2 Hybrid Supramolecular DNA Hydrogels 440<br/><br/>19.3 Biomedical Application of DNA Supramolecular Hydrogels 443<br/><br/>19.3.1 DNA Supramolecular Hydrogels for Bio-sensing 443<br/><br/>19.3.2 DNA Supramolecular Hydrogels for Drug Delivery 446<br/><br/>19.3.3 DNA Supramolecular Hydrogels for Immunotherapy 449<br/><br/>19.3.4 DNA Supramolecular Hydrogels for 3D Cell Culture 451<br/><br/>19.3.5 DNA Supramolecular Hydrogels for Tissue Engineering 454<br/><br/>19.4 Conclusions and Perspectives 458<br/><br/>References 459<br/><br/>20 Rolling Circle Amplification-Based DNA Nanotechnology for Cell Research 467<br/>Nachuan Song, Yiwen Chu, Xun You, and Dayong Yang<br/><br/>20.1 Introduction 467<br/><br/>20.2 Principle and Synthetic Methods of RCA 468<br/><br/>20.2.1 Principle 468<br/><br/>20.2.2 DNA Hydrogel 469<br/><br/>20.2.3 DNA Nanoparticles 469<br/><br/>20.3 RCA-Based DNA Nanotechnology for Cell Separation 469<br/><br/>20.4 RCA-Based DNA Nanotechnology for Nucleic Acid Drug Delivery 475<br/><br/>20.5 Conclusion 484<br/><br/>Acknowledgment 485<br/><br/>References 485<br/><br/>21 Precise Integration of Therapeutics in DNA-Based Nanomaterials for Cancer Treatments 489<br/>Yimeng Li, Lijuan Zhu, and Chuan Zhang<br/><br/>21.1 DNA-Based Nanomaterials in Biomedicine 490<br/><br/>21.1.1 Properties of DNA-Based Nanomaterials 491<br/><br/>21.1.2 Architectures of DNA-Based Nanomaterials 492<br/><br/>21.1.3 Interactions Between DNA-Based Drug Delivery Systems (DDSs) and Cells 495<br/><br/>21.2 Strategies on Constructing DNA-Based DDSs 498<br/><br/>21.2.1 DNA-Based DDSs Engineered Through Non-covalent Interactions 499<br/><br/>21.2.2 DNA-Based DDSs Engineered Through Covalent Interactions 502<br/><br/>21.3 Precise Integration of Therapeutics into DNA-Based DDSs to Achieve Synergistic Cancer Treatment 507<br/><br/>21.3.1 Chemogenes 507<br/><br/>21.3.2 Chemogene-Based DNA Nanomaterials 508<br/><br/>References 511<br/><br/>Index 515 
<br/><br/> "DNA Nanotechnology for Cell Research  Comprehensive coverage of DNA nanotechnology with a focus on its biomedical applications in disease diagnosis, gene therapy, and drug delivery Bringing together multidisciplinary aspects of chemical, material, and biological engineering, DNA Nanotechnology for Cell Research: From Bioanalysis to Biomedicine presents an overview of DNA nanotechnology with emphasis on a variety of different applications in cell research and engineering, covering a unique collection of DNA nanotechnology for fundamental research and engineering of living cells, mostly in cellulo and in vivo, for the first time. Broad coverage of this book ranges from pioneering concepts of DNA nanotechnology to cutting-edge reports regarding the use of DNA nanotechnology for fundamental cell science and related biomedical engineering applications in sensing, bioimaging, cell manipulation, gene therapy, and drug delivery. The text is divided into four parts. Part I surveys the progress of functional DNA nanotechnology tools for cellular recognition. Part II illustrates the use of DNA-based biochemical sensors to monitor and image intracellular molecules and processes. Part III examines the use of DNA to regulate biological functions of individual cells. Part IV elucidates the use of DNA nanotechnology for cell-targeted medical applications. Sample topics covered in DNA Nanotechnology for Cell Research include: Selections and applications of functional nucleic acid toolkits, including DNA/RNA aptamers, DNAzymes, and riboswitches, for cellular recognition, metabolite detection, and liquid biopsy. Developing intelligent DNA nanodevices implemented in living cells for amplified cell imaging, smart intracellular sensing, and in cellulo programmable biocomputing. Harnessing dynamic DNA nanotechnology for non-genetic cell membrane engineering, receptor signaling reprogramming, and cellular behavior regulation. Construction of biocompatible nucleic acid nanostructures as precisely controlled vehicles for drug delivery, immunotherapy, and tissue engineering. Providing an up-to-date tutorial style overview along with a highly valuable in-depth perspective, DNA Nanotechnology for Cell Research is an essential resource for the entire DNA-based nanotechnology community, including analytical chemists, biochemists, materials scientists, and bioengineers."-- 
<br/><br/><br/>About the Author<br/>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. 
<br/><br/><label>ISBN: </label>9783527840793 3527840796 9783527840809 352784080X 9783527840816 3527840818 
<br/><br/><label>Subjects--Topical Terms: </label><br/>DNA nanotechnology.
<br/><br/><label>Index Terms--Genre/Form: </label><br/>Electronic books.
<br/><br/><label>LC Class. No.: </label>QP624 
<br/><br/><label>Dewey Class. No.: </label>572.8/6