DNA Conjugates and Sensors

Contents......Page 8
1.1. Introduction......Page 14
1.2. LNA – a Primer......Page 15
1.3.1. Introduction......Page 16
1.3.2. N20-Functionalised 20-amino-LNA......Page 17
1.3.3. N20-Functionalised 20-amino-a-L-LNA......Page 21
1.3.4 C5-Functionalised LNA......Page 23
1.3.5 LNA with Fluorescent Nucleobase Surrogates......Page 27
1.4.1 Formation of Pyrene Arrays......Page 28
1.4.2 Hybridisation Probes......Page 32
1.4.3 Base Discriminating Fluorescent Probes......Page 34
1.4.4 Excimer-based Probes......Page 36
1.5 Summary and Perspective......Page 40
References......Page 42
2.1 Introduction......Page 47
2.1.1 Single Molecule Detection Techniques......Page 48
2.2.1 Selection of Fluorophores......Page 51
2.2.2 Dye Photophysics......Page 56
2.2.3 Labelling Strategies......Page 60
2.3.2 Elucidating DNA Structure and Function......Page 63
2.4 Conclusions......Page 79
References......Page 81
3.1 Introduction......Page 88
3.2.1 Duplex Formation and the Antisense Strategy......Page 89
3.2.2 Triplex Formation and the Antigene Strategy......Page 90
3.3 Small Molecule–Oligonucleotide Conjugation......Page 91
3.4.1 Stabilisation by Edge Binders......Page 92
3.4.2 Stabilisation by Intercalators......Page 93
3.4.3 Stabilisation by Groove Binders......Page 97
3.5 Cross-linking Oligonucleotides to Nucleic Acid Targets......Page 101
3.5.1 Photoactive Cross-linkers......Page 102
3.5.2 Alkylating and Alkylating-like Cross-linkers......Page 104
3.6.1 Metal Complexes......Page 106
3.6.2 Topoisomerase Inhibitors......Page 107
References......Page 108
4.1 Introduction......Page 116
4.2.1 Examples of Naturally Occurring SmallMolecule–RNA Conjugates......Page 117
4.2.2 Synthetic Small Molecule–RNA Conjugates......Page 120
4.2.3 Other Synthetic Small Molecule–RNAConjugates......Page 127
4.3 Concluding Remarks......Page 129
References......Page 130
5.1 Introduction to Click Chemistry......Page 132
5.2 The CuAAC Reaction for Oligonucleotide Labelling......Page 133
5.3 Reverse Click Labelling of Oligonucleotides by the CuAAC Reaction......Page 137
5.4 DNA Labelling in vivo......Page 139
5.5 Other Click Reactions for Oligonucleotide Labelling......Page 141
5.6 Click Chemistry for Oligonucleotide Strand Ligation......Page 142
5.7 Click Chemistry in Nanotechnology......Page 143
5.8 Synthesis of Cyclic DNA......Page 145
5.9 The SPAAC Reaction on DNA......Page 147
References......Page 149
6.1 Introduction......Page 153
6.2 Alternative Chemistries Improve Oligonucleotide Stability, Bioavailability and Distribution......Page 155
6.2.1 Nucleotide Modification......Page 156
6.2.2 End Modification......Page 158
6.3 Oligonucleotide Conjugates as Novel Targeted Therapies......Page 162
6.3.1 Aptamer Smart Drugs......Page 163
6.3.2 Oligonucleotide Hybrids and Chimeras......Page 164
6.3.3 Aptamers Delivering Toxic Cargo......Page 165
6.3.4 Aptamer-targeted Delivery Vehicles......Page 167
6.4 Oligonucleotide Conjugates as Imaging Reagents......Page 168
6.6 Toxicology......Page 169
References......Page 170
7.1 Introduction......Page 179
7.2.1 Structural Features of Triplexes......Page 180
7.2.2 Molecular Devices Based on Triplexes......Page 182
7.3.1 Structural Features of i-Motifs......Page 184
7.3.2 Molecular Devices Based on i-Motifs......Page 187
7.4.1 Structural Characteristics of Poly rA and Poly dA Oligomers......Page 191
7.4.2 Molecular Devices Based on A-Motifs......Page 194
7.5 Outlook......Page 195
References......Page 196
8.1.1 Discovery of DNAzymes through in vitro Selection......Page 203
8.1.2 RNA-Cleaving DNAzymes......Page 204
8.1.3 Other Reactions Catalysed by DNAzymes......Page 206
8.2.1 DNAzyme–Fluorophore Conjugates......Page 207
8.2.2 Fluorescent Sensors using Existing DNAzymes......Page 208
8.2.4 Fluorescence-generating Aptazymes: Linking Target Recognition to Catalytic Activity......Page 211
8.2.5 Using DNAzymes to Amplify Fluorescent Signals......Page 214
8.3.1 Gold Nanoparticle-based Sensors......Page 215
8.3.2 Electrochemical-based Sensors......Page 216
8.4 Conclusions and Future Prospects......Page 219
References......Page 220
9.1.1 Aptamers......Page 224
9.1.2 Aptamers as Biosensors......Page 226
9.2.1 Introduction to Electrochemical Transduction......Page 227
9.2.2 Electrochemical Aptasensors......Page 230
9.3 Conclusions and Future Prospects......Page 247
References......Page 248
10.1 Introduction......Page 255
10.2 Linear Probes......Page 257
10.3 Binary (Split) Probes......Page 260
10.4 Molecular Beacons......Page 263
References......Page 267
11.1 Introduction......Page 271
11.1.1 SERS......Page 272
11.1.2 SERRS......Page 273
11.1.4 Nanoparticles......Page 274
11.2.1 Colloid-based Detection Techniques......Page 278
11.2.2 Bulk Substrate-based Detection Techniques......Page 284
11.3 Conclusion......Page 287
References......Page 288
12.1 Introduction......Page 291
12.2.1 Combination of Oligonucleotide Additives and Ce(IV)/EDTA for Site-Selective Scission of Single-Stranded DNA......Page 293
12.2.2 Promotion of Site-Selective Scission by Conjugating Oligonucleotide with a Multiphosphonate Ligand......Page 295
12.2.3 Scission of Human Telomeric Overhang DNA......Page 298
12.2.4 Use of Peptide Nucleic Acid (PNA) toPrepare Artificial Enzymes for Site-Selective Scission of Double-Stranded DNA......Page 302
12.3 Preparation of an Artificial DNA Cutter from Ce(III) as a Precursor of Catalytically Active Ce(IV)......Page 303
12.4 Conclusion......Page 304
References......Page 305
Subject Index......Page 309