DNA in supramolecular chemistry and nanotechnology / edited by Eugen Stulz, Guido H. Clever. -- Chichester, West Sussex : John Wiley & Sons, Inc., c2015. – (58.174252/D629s)

Contents

List of Contributors

Preface

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

1.1  DNA-Based Construction of Molecular Photonic Devices

l.1.1  Introduction

1.1.2  Using DNA as a template to construct discrete optoelectronic nanostructures

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

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

1.1.5  Towards the construction of photonic devices

1.1.6  Outlook

References

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

1.2.1  π-Conjugated compounds

1.2.2  DNA binders for different applications

1.2.3  Targeting duplex DNA

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

1.2.5  Conclusions

References

1.3  Metal Ion- and Perylene Diimide-Mediated DNA Architectures

1.3.1  Introduction

1.3.2  Metal ion complexes as DNA modifications: hydroquinoline and terpyridine

1.3.3  Perylene diimide-based DNA architectures

1.3.4  Conclusions

References

1.4  DNA with Metal-Mediated Base Pairs

1.1.1  Introduction

1.4.2  Metal-mediated base pairs with natural nucleobases

1.4.3  Metal-mediated base pairs with artificial nucleobases

1.4.4  Outlook

References

1.5  Metal-Aided Construction of Unusual DNA Structural Motifs

1.5.1  Introduction

1.5.2  DNA duplexes containing metal-mediated base pairs

1.5.3  Metal-aided formation of triple-stranded structures

1.5.4  Metal-aided formation of four-stranded structures

1.5.5  Metal-aided formation of DNAjunction structures

1.5.6  Summary and outlook

References

Part II  DNA Wires and Electron Transport Through DNA

2.1  Gating Electrical Transport Through DNA

2.l.1  Introduction

2.1.2  DNA structure

2.1.3  Direct electrical measurements of DNA

2.1.4  Gate modulation of current flow in DNA

2.1.5  DNA transistors

2.1.6  Summary and outlook

References

2.2  Electrical Conductance of DNA Oligomers -- A Review of Experimental Results

2.2.1  Introduction

2.2.2  DNA structures

2.2.3  Scanning probe microscopy

2.2.4  Lithographically defined junctions

2.2.5  Conclusions

References

2.3  DNA Sensors Using DNA Charge Transport Chemistry

2.3.1  Introduction

2.3.2  DNA-functionalized electrochemical sensors

2.3.3  Detection of DNA-binding proteins

2.3.4  DNA CT within the cell

2.3.5  Conclusions

Acknowledgements

References

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

2.4.1  Introduction

2.4.2  CT in dsDNA (B-DNA)

2.4.3  CT in non-B DNA with a tetraplex structure

2.4.4  Conclusions

Acknowledgments

References

Part III  Oligonucleotides in Sensing and Diagnostic Applications

3.1  Development of Electrochemical Sensors for DNA Analysis

3.1.1  Introduction

3.1.2  Genosensors based on direct electrocactivity of nucleic bases

3.1.3  Genosensors based on electrochemical mediators

3.1.4  Genosensors based on free diffusional redox markers

3.1.5  Genosensors incorporating DNA probes modified with redox active molecules - 'signal-off' and 'signal-on' working modes

3.1.6  Genosensors for simultaneous detection of two different DNA targets

3.1.7  Conclusions

Acknowledgements

References

3.2  Oligonucleotide Based Artificial Ribonucleases (OBANs)

3.2.1  Introduction

3.2.2  Early development of OBANs

3.2.3  Metal ion based artificial nucleases

3.2.4  Non-metal ion based systems

3.2.5  Creating bulges in the RNA substrate

3.2.6  PNAzymes and creation of artificial RNA restriction enzymes

3.2.7  Conclusions

References

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

3.3.1  Introduction

3.3.2  Non-covalent interaction of porphyrin-DNA complexes

3.3.3  Porphyrins covalently linked to DNA

3.3.4  Conclusions

References

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

3.4.1  Introduction

3.4.2  Intracellular nucleic acid targets

3.4.3  Methods for monitoring ribonucleic acids in live cells

3.4.4  Perspectives

References

3.5  The Biotechnological Applications of G-Quartets

3.5.1  Introduction

3.5.2  Nucleobases and H-bonds

3.5.3  Duplex-DNA mimics

3.5.4  Guanine and G-quartets

3.5.5  G-Quartets and G-quadruplexes

3.5.6  Quadruplex-DNA mimics

3.5.7  Conclusions

References

Part IV  Conjugation of DNA with Biomolecules and Nanoparticles

4.1  Nucleic Acid Controlled Reactions on Large Nucleic Acid Templates

4.1.1  Introduction

4.1.2  Nucleic acid controlled chemical reactions

4.1.3  Applications

4.1.4  Conclusions

References

4.2  Lipid Oligonucleotide Bioconjugates: Applications in Medicinal Chemistry

4.2.1  Introduction

4.2.2  Chemical approach to the synthesis of lipid-oligonucleotide conjugates

4.2.3  Biomedical applications

4.2.4  Conclusions

Acknowledgements

References

4.3  Amphiphilic Peptidyl-RNA

4.3.1  Introduction

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

4.3.3  Why RNA? Why peptides?

4.3.4  Hydrolysis-resistant amphiphilic 3'-peptidyl-RNA

4.3.5  Synthetic strategy

4.3.6  Pros'n cons

4.3.7  Alternative methods and strategies

4.3.8  Molecular properties

4.3.9  Supramolecular properties

4.3.10 Conclusions and perspectives

Acknowledgements

References

4.4  Oligonucleotide-Stabilized Silver Nanoclusters

4.4.1  Introduction

4.4.2  Sensors

4.4.3  DNA computing (logic gates)

4.4.4  Assorted examples

4.4.5  Conclusions

References

Part V  Alternative DNA Structures, Switches and Nanomachines

5.1  Structure and Stabilization of CGC+ Triplex DNA

5.1.1  Introduction

5.1.2  Classification of DNA triplets

5.1.3  Structure of triplexes

5.1.4  Triplex stabilizing factors

5.1.5  Formation of stable CGC+ triplex DNA

5.1.6  Summary

References

5.2  Synthetic Molecules as Guides for DNA Nanostructure Formation

5.2.1  Introduction

5.2.2  Covalent insertion of synthetic molecules into DNA

5.2.3  Non-covalently guided DNA assembly

5.2.4  Conclusions

References

5.3  DNA-Based Nanostructuring with Branched Oligonucleotide Hybrids

5.3.1  Introduction

5.3.2  Branched oligonucleotides

5.3.3  Hybrids with rigid cores

5.3.4  Second-generation hybrids with a rigid core

5.3.5  Solution-phase syntheses: Synthetic challenges

5.3.6  Hybrid materials

5.3.7  Outlook

5.3.8  Conclusions

Acknowledgements

References

5.4  DNA-Controlled Assembly of Soft Nanoparticles

5.4.1  Introduction

5.4.2  Sequence design

5.4.3  Lipid membrane anchors

5.4.4  DNA-controlled assembly studied by UV spectroscopy

5.4.5  Assembly on solid support

5.4.6  Assembly of giant unilamellar liposomes (GUVs)

5.4.7  Conclusions

Acknowledgements

References

5.5  Metal Ions in Ribozymes and Riboswitches

5.5.1  Introduction

5.5.2  Coordination chemistry of RNA

5.5.3  Ribozymes

5.5.4  Riboswitches

5.5.5  Summary

Acknowledgement

References

5.6  DNA Switches and Machines

5.6.1  Introduction

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

5.6.3  Switchable DNA machines

5.6.4  Applications of DNA switches and machines

5.6.5  Conclusions and perspectives

References

5.7  DNA-Based Asymmetric Catalysis

5.7.1  Introduction

5.7.2  Concept of DNA-based asymmetric catalysis

5.7.3  Design approaches in DNA-based asymmetric catalysis

5.7.4  Covalent anchoring

5.7.5  Supramolecular anchoring

5.7.6  Conclusions and perspectives

References

Index