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