Note: DNA Conjugates and Sensors -- Contents -- Chapter 1 Fluorophore-functionalised Locked Nucleic Acids (LNAs) -- 1.1 Introduction -- 1.2 LNA - a Primer -- 1.3 Fluorophore-functionalised LNA - an Overview -- 1.3.1 Introduction -- 1.3.2 N2'-Functionalised 2'-amino-LNA -- 1.3.3 N2'-Functionalised 2'-amino-α-L-LNA -- 1.3.4 C5-Functionalised LNA -- 1.3.5 LNA with Fluorescent Nucleobase Surrogates -- 1.4 Applications of Fluorophore-functionalised LNA -- 1.4.1 Formation of Pyrene Arrays -- 1.4.2 Hybridisation Probes -- 1.4.3 Base Discriminating Fluorescent Probes -- 1.4.4 Excimer-based Probes -- 1.5 Summary and Perspective -- References -- Chapter 2 Fluorophore Conjugates for Single Molecule Work -- 2.1 Introduction -- 2.1.1 Single Molecule Detection Techniques -- 2.2 Labelling DNA for Single Molecule Detection -- 2.2.1 Selection of Fluorophores -- 2.2.2 Dye Photophysics -- 2.2.3 Labelling Strategies -- 2.3 Applications -- 2.3.1 DNA Sequence Analysis -- 2.3.2 Elucidating DNA Structure and Function -- 2.4 Conclusions -- Acknowledgements -- Con ict of Interest Statement -- References -- Chapter 3 Small Molecule-Oligonucleotide Conjugates -- 3.1 Introduction -- 3.2 The Recognition of Nucleic Acids by Synthetic Oligonucleotides -- 3.2.1 Duplex Formation and the Antisense Strategy -- 3.2.2 Triplex Formation and the Antigene Strategy -- 3.3 Small Molecule-Oligonucleotide Conjugation -- 3.4 Improving the Hybridisation Properties of Oligonucleotides -- 3.4.1 Stabilisation by Edge Binders -- 3.4.2 Stabilisation by Intercalators -- 3.4.3 Stabilisation by Groove Binders -- 3.5 Cross-linking Oligonucleotides to Nucleic Acid Targets -- 3.5.1 Photoactive Cross-linkers -- 3.5.2 Alkylating and Alkylating-like Cross-linkers -- 3.6 Oligonucleotide-directed Cleavage of Nucleic Acid Targets -- 3.6.1 Metal Complexes -- 3.6.2 Topoisomerase Inhibitors. , 3.7 Summary and Future Directions -- References -- Chapter 4 Small Molecule-RNA Conjugates -- 4.1 Introduction -- 4.2 Small Molecule-RNA Conjugates -- 4.2.1 Examples of Naturally Occurring Small Molecule-RNA Conjugates -- 4.2.2 Synthetic Small Molecule-RNA Conjugates -- 4.2.3 Other Synthetic Small Molecule-RNA Conjugates -- 4.3 Concluding Remarks -- References -- Chapter 5 Click Chemistry - a Versatile Method for Nucleic Acid Labelling, Cyclisation and Ligation -- 5.1 Introduction to Click Chemistry -- 5.2 The CuAAC Reaction for Oligonucleotide Labelling -- 5.3 Reverse Click Labelling of Oligonucleotides by the CuAAC Reaction -- 5.4 DNA Labelling in vivo -- 5.5 Other Click Reactions for Oligonucleotide Labelling -- 5.6 Click Chemistry for Oligonucleotide Strand Ligation -- 5.7 Click Chemistry in Nanotechnology -- 5.8 Synthesis of Cyclic DNA -- 5.9 The SPAAC Reaction on DNA -- 5.10 Conclusion -- Acknowledgements -- References -- Chapter 6 Therapeutic Applications of Nucleic Acid Aptamer Conjugates -- 6.1 Introduction -- 6.2 Alternative Chemistries Improve Oligonucleotide Stability, Bioavailability and Distribution -- 6.2.1 Nucleotide Modi cation -- 6.2.2 End Modi cation -- 6.3 Oligonucleotide Conjugates as Novel Targeted Therapies -- 6.3.1 Aptamer Smart Drugs -- 6.3.2 Oligonucleotide Hybrids and Chimeras -- 6.3.3 Aptamers Delivering Toxic Cargo -- 6.3.4 Aptamer-targeted Delivery Vehicles -- 6.4 Oligonucleotide Conjugates as Imaging Reagents -- 6.5 Nanoparticles -- 6.6 Toxicology -- 6.7 Perspectives -- References -- Chapter 7 pH Sensitive DNA Devices -- 7.1 Introduction -- 7.2 Triplexes -- 7.2.1 Structural Features of Triplexes -- 7.2.2 Molecular Devices Based on Triplexes -- 7.3 i-Motifs -- 7.3.1 Structural Features of i-Motifs -- 7.3.2 Molecular Devices Based on i-Motifs -- 7.4 P-Helix and A-Motifs. , 7.4.1 Structural Characteristics of Poly rA and Poly dA Oligomers -- 7.4.2 Molecular Devices Based on A-Motifs -- 7.5 Outlook -- References -- Chapter 8 Making Sense of Catalysis: The Potential of DNAzymes as Biosensors -- 8.1 Introduction -- 8.1.1 Discovery of DNAzymes through in vitro Selection -- 8.1.2 RNA-Cleaving DNAzymes -- 8.1.3 Other Reactions Catalysed by DNAzymes -- 8.2 Fluorescent DNAzyme-based Sensors -- 8.2.1 DNAzyme-Fluorophore Conjugates -- 8.2.2 Fluorescent Sensors using Existing DNAzymes -- 8.2.3 Isolation of de novo Fluorescent DNAzyme Sensors through in vitro Selection -- 8.2.4 Fluorescence-generating Aptazymes: Linking Target Recognition to Catalytic Activity -- 8.2.5 Using DNAzymes to Amplify Fluorescent Signals -- 8.3 DNAzyme Sensors with Other Reporting Systems -- 8.3.1 Gold Nanoparticle-based Sensors -- 8.3.2 Electrochemical-based Sensors -- 8.4 Conclusions and Future Prospects -- References -- Chapter 9 Electrochemical Techniques as Powerful Readout Methods for Aptamer-based Biosensors -- 9.1 Introduction to Aptamer-based Sensors (Aptasensors) -- 9.1.1 Aptamers -- 9.1.2 Aptamers as Biosensors -- 9.2 Electrochemical Aptasensors -- 9.2.1 Introduction to Electrochemical Transduction -- 9.2.2 Electrochemical Aptasensors -- 9.3 Conclusions and Future Prospects -- Acknowledgements -- References -- Chapter 10 Oligonucleotide Conjugates for Detection of Speci c Nucleic Acid Sequences -- 10.1 Introduction -- 10.2 Linear Probes -- 10.3 Binary (Split) Probes -- 10.4 Molecular Beacons -- 10.5 Conclusion -- References -- Chapter 11 Nucleic Acid-Nanoparticle Conjugate Sensors for Use with Surface Enhanced Resonance Raman Scattering (SERRS) -- 11.1 Introduction -- 11.1.1 SERS -- 11.1.2 SERRS -- 11.1.3 Suitable SE(R)RS Surfaces -- 11.1.4 Nanoparticles -- 11.2 DNA Detection Methods Based on SE(R)RS -- 11.2.1 Colloid-based Detection Techniques. , 11.2.2 Bulk Substrate-based Detection Techniques -- 11.3 Conclusion -- 11.4 Forward Outlook -- References -- Chapter 12 Covalent and Non-covalent Conjugates of Oligonucleotides as Arti cial Restriction DNA Cutters -- 12.1 Introduction -- 12.2 Ce(IV)/EDTA as Molecular Scissors Showing Remarkable Substrate-Speci city -- 12.2.1 Combination of Oligonucleotide Additives and Ce(IV)/EDTA for Site-Selective Scission of Single-Stranded DNA -- 12.2.2 Promotion of Site-Selective Scission by Conjugating Oligonucleotide with a Multiphosphonate Ligand -- 12.2.3 Scission of Human Telomeric Overhang DNA -- 12.2.4 Use of Peptide Nucleic Acid (PNA) to Prepare Arti cial Enzymes for Site-Selective Scission of Double-Stranded DNA -- 12.3 Preparation of an Arti cial DNA Cutter from Ce(III) as a Precursor of Catalytically Active Ce(IV) -- 12.4 Conclusion -- Acknowledgements -- References -- Subject Index.