DNA in Supramolecular Chemistry and Nanotechnology (eBook, PDF)

Redaktion: Stulz, Eugen; Clever, Guido H.

• Format: PDF

Produktbeschreibung

This book covers the emerging topic of DNA nanotechnology and DNA supramolecular chemistry in its broader sense. By taking DNA out of its biological role, this biomolecule has become a very versatile building block in materials chemistry, supramolecular chemistry and bio-nanotechnology. Many novel structures have been realized in the past decade, which are now being used to create molecular machines, drug delivery systems, diagnosis platforms or potential electronic devices. The book combines many aspects of DNA nanotechnology, including formation of functional structures based on covalent and non-covalent systems, DNA origami, DNA based switches, DNA machines, and alternative structures and templates. This broad coverage is very appealing since it combines both the synthesis of modified DNA as well as designer concepts to successfully plan and make DNA nanostructures. Contributing authors have provided first a general introduction for the non-specialist reader, followed by a more in-depth analysis and presentation of their topic. In this way the book is attractive and useful for both the non-specialist who would like to have an overview of the topic, as well as the specialist reader who requires more information and inspiration to foster their own research.

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Produktdetails

• Verlag: John Wiley & Sons
• Seitenzahl: 528
• Erscheinungstermin: 14. Juli 2015
• Englisch
• ISBN-13: 9781118696941
• Artikelnr.: 43419587

Autorenporträt

EUGEN STULZ School of Chemistry, University of Southampton, UK GUIDO H. CLEVER Department for Inorganic Chemistry, Georg-August University, Germany

Inhaltsangabe

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 pi-Conjugated DNA Binders:
Optoelectronics, Molecular Diagnostics and Therapeutics 22 1.2.1
pi-Conjugated compounds 22 1.2.2 DNA binders for different applications 23
1.2.3 Targeting duplex DNA 27 1.2.4 Examples of pi-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 3¹-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