Title Page -- Copyright Page -- Contents -- List of Contributors -- Preface -- Part I (Non-) Covalently Modified DNA with Novel Functions -- 1.1 DNA-Based Construction of Molecular Photonic Devices -- 1.1.1 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 -- 1.1.4.1 Intercalation -- 1.1.4.2 Minor-groove binding -- 1.1.5 Towards the construction of photonic devices -- 1.1.6 Outlook -- 1.1.6.1 Optoelectronic circuits -- 1.1.6.2 Diagnostic platforms -- 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 -- 1.2.2.1 Molecular diagnostics -- 1.2.2.2 Therapeutics -- 1.2.2.3 Optoelectronics -- 1.2.3 Targeting duplex DNA -- 1.2.3.1 Examples of π-conjugated compounds interacting with double-stranded DNA - minor groove binders -- 1.2.3.2 Examples of π-conjugated DNA binders interacting with double-stranded DNA - intercalators -- 1.2.4 Examples of π-conjugated compounds interacting with hybrid duplexes and higher order nucleic acid structures -- 1.2.4.1 Examples of π-conjugated compounds interacting with DNARNA and DNAPNA hybrid duplexes -- 1.2.4.2 Examples of π-conjugated compounds interacting with 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.

1.4.1 Introduction -- 1.4.2 Metal-mediated base pairs with natural nucleobases -- 1.4.2.1 Pyrimidines -- 1.4.2.2 Purines -- 1.4.3 Metal-mediated base pairs with artificial nucleobases -- 1.4.3.1 Individual metal-mediated base pairs -- 1.4.3.2 Stacks of metal-mediated base pairs -- 1.4.3.3 Doubly metalated base pairs -- 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 DNA junction structures -- 1.5.6 Summary and outlook -- References -- Part II DNA Wires and Electron Transport Through DNA -- 2.1 Gating Electrical Transport Through DNA -- 2.1.1 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 -- 2.2.3.1 STM break junction -- 2.2.3.2 Conductive AFM -- 2.2.4 Lithographically defined junctions -- 2.2.4.1 Mechanically controllable break junctions -- 2.2.4.2 Direct contacts -- 2.2.4.3 Carbon nanotube contacts -- 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 -- 2.3.2.1 Redox probes for ground state DNA-mediated charge transport detection -- 2.3.2.2 Different platforms for DNA electrochemistry -- 2.3.2.3 Detection of single base mutations and DNA lesions -- 2.3.3 Detection of DNA-binding proteins -- 2.3.3.1 Detection of transcriptional regulators.

2.3.3.2 Methyltransferase and methylation detection -- 2.3.3.3 Photolyase activity and detection -- 2.3.3.4 ATP-dependent XPD activity on surfaces -- 2.3.4 DNA CT within the cell -- 2.3.4.1 DNA CT can occur within biologically relevant environments -- 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 -- 2.4.3.1 G-quadruplex DNA -- 2.4.3.2 i-motif DNA -- 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 -- 3.3.2.1 Interaction with single-stranded DNA -- 3.3.2.2 Double helix conformations B- and Z-DNA -- 3.3.2.3 G-quadruplex.

3.3.3 Porphyrins covalently linked to DNA -- 3.3.3.1 Porphyrins attached to 5'- and 3'-termini of DNA with phosphates and amides -- 3.3.3.1.1 5'-Phosphate linkage -- 3.3.3.1.2 Detection of the B- to Z-transition -- 3.3.3.1.3 3'-Amide linkage -- 3.3.3.1.4 5'-Amide linkage -- 3.3.3.2 Capping effect -- 3.3.3.3 Porphyrin C-nucleoside replacement of natural nucleobases -- 3.3.3.4 Porphyrins embedded in the backbone of DNA -- 3.3.3.5 Diastereochemically pure anionic porphyrin-DNA dimers -- 3.3.3.6 Incorporation of rigid and flexible linked porphyrins to DNA nucleobases -- 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 -- 3.4.3.1 Genetically encoded reporters -- 3.4.3.2 Hybridization-responsive oligonucleotide probes -- 3.4.3.3 Fluorogenic templated reactions -- 3.4.3.3.1 Nucleophilic substitution reactions -- 3.4.3.3.2 Staudinger reduction -- 3.4.3.4 Photochemical reactions -- 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 -- 3.5.5.1 Colorimetric detection -- 3.5.5.2 Luminescence-fluorescence detection -- 3.5.5.3 Electrochemical detection -- 3.5.6 Quadruplex-DNA mimics -- 3.5.6.1 Intermolecular SQ: G-monomers -- 3.5.6.2 Intermolecular interconnected SQ: G-dimers -- 3.5.6.3 Intramolecular SQ (or iSQ): G-tetramers -- 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 -- 4.1.3.1 Reactions on intracellular RNA -- 4.1.3.2 Reactions on large biogenic DNA and RNA templates in vitro -- 4.1.3.3 Drug screening -- 4.1.3.4 Materials science -- 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 -- 4.2.2.1 Solid-phase (or pre-synthetic) approach -- 4.2.2.1.1 Lipid conjugation at the 3'-terminal -- 4.2.2.1.2 Lipid conjugation at 5'-terminal -- 4.2.2.1.3 Lipid conjugation at internal position (intra-chain) -- 4.2.2.2 Solution-phase (or post-synthetic) approach -- 4.2.3 Biomedical applications -- 4.2.3.1 LONs as efficient delivery vehicles in gene therapy -- 4.2.3.2 Other biomedical applications of LONs -- 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 -- 4.4.2.1 Metallic sensors -- 4.4.2.2 Small molecule sensors -- 4.4.2.3 Protein sensors -- 4.4.2.4 Nucleic acid sensors -- 4.4.2.4.1 DNA sensors -- 4.4.2.4.2 MiRNAs sensors -- 4.4.2.5 Cells -- 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.