DNA in Supramolecular Chemistry and Nanotechnology

EUGEN STULZ, School of Chemistry, University of Southampton, UK

GUIDO H. CLEVER, Department for Inorganic Chemistry, Georg-August University, Germany

List of Contributors xv

Preface xix

Part I (Non-) Covalently Modified DNA with Novel Functions 1

1.1 DNA-Based Construction of Molecular Photonic Devices 3

1.1.1 Introduction 3

1.1.2 Using DNA as a template to construct discrete optoelectronic nanostructures 5

1.1.3 Assembly of photonic arrays based on the molecular recognition of single-stranded DNA templates 7

1.1.4 Assembly of photonic arrays based on the molecular recognition of double-stranded DNA templates 10

1.1.5 Towards the construction of photonic devices 13

1.1.6 Outlook 13

References 15

1.2 π-Conjugated DNA Binders: Optoelectronics, Molecular Diagnostics and Therapeutics 22

1.2.1 π-Conjugated compounds 22

1.2.2 DNA binders for different applications 23

1.2.3 Targeting duplex DNA 27

1.2.4 Examples of π-conjugated compounds interacting with hybrid duplexes and higher order nucleic acid structures 32

1.2.5 Conclusions 33

References 34

1.3 Metal Ion- and Perylene Diimide-Mediated DNA Architectures 38

1.3.1 Introduction 38

1.3.2 Metal ion complexes as DNA modifications: hydroquinoline and terpyridine 39

1.3.3 Perylene diimide-based DNA architectures 42

1.3.4 Conclusions 49

References 49

1.4 DNA with Metal-Mediated Base Pairs 52

1.4.1 Introduction 52

1.4.2 Metal-mediated base pairs with natural nucleobases 53

1.4.3 Metal-mediated base pairs with artificial nucleobases 54

1.4.4 Outlook 61

References 61

1.5 Metal-Aided Construction of Unusual DNA Structural Motifs 65

1.5.1 Introduction 65

1.5.2 DNA duplexes containing metal-mediated base pairs 66

1.5.3 Metal-aided formation of triple-stranded structures 69

1.5.4 Metal-aided formation of four-stranded structures 71

1.5.5 Metal-aided formation of DNA junction structures 73

1.5.6 Summary and outlook 75

References 75

Part II DNA Wires and Electron Transport Through DNA 79

2.1 Gating Electrical Transport Through DNA 81

2.1.1 Introduction 81

2.1.2 DNA structure 82

2.1.3 Direct electrical measurements of DNA 82

2.1.4 Gate modulation of current flow in DNA 84

2.1.5 DNA transistors 86

2.1.6 Summary and outlook 92

References 92

2.2 Electrical Conductance of DNA Oligomers — A Review of Experimental Results 94

2.2.1 Introduction 94

2.2.2 DNA structures 95

2.2.3 Scanning probe microscopy 95

2.2.4 Lithographically defined junctions 98

2.2.5 Conclusions 101

References 102

2.3 DNA Sensors Using DNA Charge Transport Chemistry 105

2.3.1 Introduction 105

2.3.2 DNA-functionalized electrochemical sensors 107

2.3.3 Detection of DNA-binding proteins 111

2.3.4 DNA CT within the cell 115

2.3.5 Conclusions 117

Acknowledgements 117

References 117

2.4 Charge Transfer in Non-B DNA with a Tetraplex Structure 121

2.4.1 Introduction 121

2.4.2 CT in dsDNA (B-DNA) 122

2.4.3 CT in non-B DNA with a tetraplex structure 123

2.4.4 Conclusions 132

Acknowledgments 132

References 132

Part III Oligonucleotides in Sensing and Diagnostic Applications 137

3.1 Development of Electrochemical Sensors for DNA Analysis 139

3.1.1 Introduction 139

3.1.2 Genosensors based on direct electrocactivity of nucleic bases 140

3.1.3 Genosensors based on electrochemical mediators 141

3.1.4 Genosensors based on free diffusional redox markers 142

3.1.5 Genosensors incorporating DNA probes modified with redox active molecules – ‘signal-off’ and ‘signal-on’ working modes 145

3.1.6 Genosensors for simultaneous detection of two different DNA targets 151

3.1.7 Conclusions 154

Acknowledgements 154

References 154

3.2 Oligonucleotide Based Artificial Ribonucleases (OBANs) 158

3.2.1 Introduction 158

3.2.2 Early development of OBANs 159

3.2.3 Metal ion based artificial nucleases 159

3.2.4 Non-metal ion based systems 161

3.2.5 Creating bulges in the RNA substrate 162

3.2.6 PNAzymes and creation of artificial RNA restriction enzymes 164

3.2.7 Conclusions 167

References 168

3.3 Exploring Nucleic Acid Conformations by Employment of Porphyrin Non-covalent and Covalent Probes and Chiroptical Analysis 172

3.3.1 Introduction 172

3.3.2 Non-covalent interaction of porphyrin–DNA complexes 174

3.3.3 Porphyrins covalently linked to DNA 187

3.3.4 Conclusions 203

References 203

3.4 Chemical Reactions Controlled by Nucleic Acids and their Applications for Detection of Nucleic Acids in Live Cells 209

3.4.1 Introduction 209

3.4.2 Intracellular nucleic acid targets 211

3.4.3 Methods for monitoring ribonucleic acids in live cells 211

3.4.4 Perspectives 225

References 226

3.5 The Biotechnological Applications of G-Quartets 229

3.5.1 Introduction 229

3.5.2 Nucleobases and H-bonds 229

3.5.3 Duplex-DNA mimics 231

3.5.4 Guanine and G-quartets 232

3.5.5 G-Quartets and G-quadruplexes 232

3.5.6 Quadruplex-DNA mimics 236

3.5.7 Conclusions 244

References 244

Part IV Conjugation of DNA with Biomolecules and Nanoparticles 247

4.1 Nucleic Acid Controlled Reactions on Large Nucleic Acid Templates 249

4.1.1 Introduction 249

4.1.2 Nucleic acid controlled chemical reactions 250

4.1.3 Applications 257

4.1.4 Conclusions 268

References 270

4.2 Lipid Oligonucleotide Bioconjugates: Applications in Medicinal Chemistry 276

4.2.1 Introduction 276

4.2.2 Chemical approach to the synthesis of lipid–oligonucleotide conjugates 277

4.2.3 Biomedical applications 286

4.2.4 Conclusions 288

Acknowledgements 289

References 289

4.3 Amphiphilic Peptidyl–RNA 294

4.3.1 Introduction 294

4.3.2 Three souls alas! are dwelling in my breast [2] 295

4.3.3 Why RNA? Why peptides? 296

4.3.4 Hydrolysis-resistant amphiphilic 3ʹ-peptidyl–RNA 297

4.3.5 Synthetic strategy 299

4.3.6 Pros’n cons 300

4.3.7 Alternative methods and strategies 302

4.3.8 Molecular properties 302

4.3.9 Supramolecular properties 302

4.3.10 Conclusions and perspectives 304

Acknowledgements 306

References 306

4.4 Oligonucleotide-Stabilized Silver Nanoclusters 308

4.4.1 Introduction 308

4.4.2 Sensors 311

4.4.3 DNA computing (logic gates) 321

4.4.4 Assorted examples 322

4.4.5 Conclusions 323

References 323

Part V Alternative DNA Structures, Switches and Nanomachines 329

5.1 Structure and Stabilization of CGC+ Triplex DNA 331

5.1.1 Introduction 331

5.1.2 Classification of DNA triplets 332

5.1.3 Structure of triplexes 332

5.1.4 Triplex stabilizing factors 334

5.1.5 Formation of stable CGC+ triplex DNA 337

5.1.6 Summary 346

References 346

5.2 Synthetic Molecules as Guides for DNA Nanostructure Formation 353

5.2.1 Introduction 353

5.2.2 Covalent insertion of synthetic molecules into DNA 353

5.2.3 Non-covalently guided DNA assembly 364

5.2.4 Conclusions 369

References 369

5.3 DNA-Based Nanostructuring with Branched Oligonucleotide Hybrids 375

5.3.1 Introduction 375

5.3.2 Branched oligonucleotides 377

5.3.3 Hybrids with rigid cores 378

5.3.4 Second-generation hybrids with a rigid core 382

5.3.5 Solution-phase syntheses: Synthetic challenges 385

5.3.6 Hybrid materials 389

5.3.7 Outlook 392

5.3.8 Conclusions 394

Acknowledgements 394

References 394

5.4 DNA-Controlled Assembly of Soft Nanoparticles 397

5.4.1 Introduction 397

5.4.2 Sequence design 399

5.4.3 Lipid membrane anchors 400

5.4.4 DNA-controlled assembly studied by UV spectroscopy 402

5.4.5 Assembly on solid support 406

5.4.6 Assembly of giant unilamellar liposomes (GUVs) 408

5.4.7 Conclusions 409

Acknowledgements 409

References 409

5.5 Metal Ions in Ribozymes and Riboswitches 412

5.5.1 Introduction 412

5.5.2 Coordination chemistry of RNA 413

5.5.3 Ribozymes 415

5.5.4 Riboswitches 420

5.5.5 Summary 425

Acknowledgement 426

References 426

5.6 DNA Switches and Machines 434

5.6.1 Introduction 434

5.6.2 Ion-stimulated and photonic/electrical-triggered DNA switches 438

5.6.3 Switchable DNA machines 447

5.6.4 Applications of DNA switches and machines 459

5.6.5 Conclusions and perspectives 466

References 467

5.7 DNA-Based Asymmetric Catalysis 474

5.7.1 Introduction 474

5.7.2 Concept of DNA-based asymmetric catalysis 474

5.7.3 Design approaches in DNA-based asymmetric catalysis 475

5.7.4 Covalent anchoring 476

5.7.5 Supramolecular anchoring 478

5.7.6 Conclusions and perspectives 488

References 489

Index 491