8-Oxo-Dg in DNA Design, 237–238 Sensing

Index

A 8-Aza-7-deazapurine-2-amine Adap triphosphate (dAdapTP), 240, 241 20-deoxyribonucleoside Adenosine-diazaphenoxazine analog (Adap) (8-aza-7-deaza-2AP, 2), 30 8-Oxo-dG in DNA design, 237–238 sensing, 239–240 B single nucleotide primer extension, Base-discriminating fluorescent (BDF) 240–243 nucleosides, 39 synthesis, 238 Base-modified purine nucleoside triphosphate thermal stabilization effects, 239 biarylboronates, 48 Adenosine in RNA, 232–233 dABIF and dABOX,49 2AP analogs dNTPs, 48 AT monomer, 31 N-heteroatom, 49 isomorphic fluorescent nucleosides, photophysical data, 49 29, 30 polymerase synthesis, 48–51 melting temperatures (Tm), 30 Suzuki–Miyaura/Sonogoshira nucleic acids, 29 cross-coupling reactions, 48 oligonucleotides, 29 Benner’s base pairs, 256–258 photophysical properties, 30 Benzo-fused nucleosides (xDNA), 36–38 ribozymes, 30 20,40-Bridged nucleic acids thermal stability, 30 C–C glycosidic bonds, 213 triazole-adenine derivatives, 31 C30-endo conformation, 211 8vdA, 31 CG base pair, 214, 215 Watson–Crick base pair, 29 cysteine protonation, 212 Watson–Crick hydrogen bonding, 31 cytosine nucleobase, 212 Aromatic π-stack assembly homopurinic regions, 213 applications, 111–112 methyl analog, 213 DNA-templated chromophore methyleneoxymethylene/ethyleneoxy assembly, 113 bridge, 213 oligo-DNA, 112 N-type and S-type conformation, 213 structure, 112, 113 TA base pair thymine base, 112 4-carbonyl group, 215, 216 Artificially Expanded Genetic Information hydroxyl groups, 216 Systems (AEGIS), 257 steric repulsion, 216 Artificial nucleic acids, 149–150 UV-melting, 213

C Conjugated 6-membered heterocycles, 18–19 Cell-SELEX method, 257 CT. See Charge transfer (CT) CG base pair Cyanine–indole–quinolinium (CyIQ), 89 heteroaromatics, 215 90, 92 hydrogen bond, 214, 215 Cyanine-styryl dyes N,N-disubstituted cytosines, 214 CyIP/TR-CN pair, 91, 95 2-pyridone nucleobase, 214 CyIQ, 92 UV-melting, 214 DNA traffic lights, 90 Charge transfer (CT) double-stranded DNA, 94, 95 aniline nitrogen, 13 dye–dye and dye–nucleic acid chromophores, 13 interactions, 96 cyanine nucleoside analogue, 12 excitation/emission wavelength, 95 deoxyuridine phosphoramidites, 12 fluorophores, 91 in DNA, 110–111 melting temperatures, 91 ESIPT, 13 methoxylation, 93 fluorescence quenching, 12 nucleic acid probes, 90 1,8-naphthalimide, 13 phosphoramidites, 90 naphthalene units, 12 photodegradation process, 92, 95 ODN, 12 singlet oxygen, 91, 92 oligonucleotides, 12, 13 structures, 93 polarity sensitive emission, 12 triazole linkage, 90 Scorpion and HyBeacons probes, 12 3-Cyanovinylcarbazole-modified artificial solid-phase synthesis, 12 nucleic acid, 148–149 Sonogashira and Algar–Flyn–Oyamada Cytidine, 230–232 coupling reactions, 13 uracil-based nucleoside derivatives, 12 uridine π-system, 12 D Conjugated 5-membered heterocycles DANP, 202 absorption and emission spectra, 14 DEER. See Double electron–electron advantages, 15 resonance (DEER) benzothiazoline derivative 35a–l, 17 20-Deoxycytidine, 69 biochemical and medicinal chemistry 20-Deoxynucleoside 50-O-triphosphates applications, 15 (dNTPs) chromophore–chromophore quenching, 15 cross-coupling reactions π-conjugated system, 16 catalytic system, 126 deoxyuridines, 17 drawback, 127 dimethoxy derivative 35i, 17 Heck reaction, 131–132 fluorescence, 14 methodology, 126 furano/thiophene moiety, 16 Sonogashira coupling, 127–129 groove’s micropolarity, 14 Suzuki–Miyaura coupling, 129–131 hybridization, 14 50-O-triphosphorylation, 124–126 isomorphic nucleosides, 14 20-Deoxy-8-oxoguanosine, 234–243 molecular rotor character, 14 DNA aptamer generation ODN, 15 AccuPrime Pfx polymerase, 258 oligonucleotides, 15 anti-VEGF165, 262, 263 rolling-cycle amplification, 16 applications, 258 selenophene, 16 doped selection, 260, 262 synthetic pathways and photophysical Ds base, 258 properties, 16 Ds–Px pairs, 259 T7 RNA polymerase, 15 in vitro selection conditions, 260 thiophene analogue, 15 Ion Torrent deep sequencing, 260 triphosphates, 15 Kd values, 262 uridine derivative, 15 PCR amplification, 258 Index 271

SELEX method, 258, 260, 261 Electron spin resonance (ESR), 160 SPR and gel-mobility shift assays, 260 Emissive 5-substituted uridine analogues sublibraries, 259 isomorphic nucleosides, 14–21 DNA-assisted multichromophore assembly photophysical properties and applications advantages, 101 conjugated fluorophores, 12–13 aromatic π-stack assembly, 111–113 labeling of ODN, 10–11 chemical and biochemical methods, 102 non-conjugated fluorophores, 10 CT, 110, 111 synthesis fluorescent DNA-perylene complex alkyl-lithium synthesis, 4, 5 108, 109 anomeric ambiguity, 2 nucleic acids, 101 C-5 modifications, 2 pyrene π-stack array, 102–105 compounds, 4 DNA polymerases, 133, 134 cross-coupling methods, 2 Double electron–electron resonance (DEER), Cu(I)-catalyzed cyclization, 4 161 α-5-cyanovinyldeoxyuridine synthetic Double-stranded DNA (dsDNA) pathway, 2, 3 azobenzene unit, 197 20-deoxyuridine, 4 20,40-Bridged nucleic acids (see fused benzalkoxy uridine surrogate, 4, 5 20,40-Bridged nucleic acids) fused pyrrolo-20-deoxycytidine bulge nucleotide, 200 analogues, 4, 5 cytosine bulge and application, 200–204 glycosylation reactions, 2 DNAP, 200 halide precursors, 2, 3 electron spin, 195 nucleosides, 4 ethidium bromide, 192 organostannanes, 2 fluorescent DNA, 197 palladium-based reactions, 2, 3 homopurinic regions, 211 palladium coupling, 2, 4 hybridization, 192 pyrimidine rings, 4 hydrogen-bonds, 190, 210 quinazolines, 4 isomorphic, 211 5-substituted-6-aza-uridine synthesis ligand-inducible nanostructure 4, 5 formation, 194 Vorbru¨ggen condensation conditions MBL, 191 2, 4 NCD, 191 Enzymatic synthesis, DNA NCD-TEMPO, 195 applications, 137–138 nucleic acids, 190 competitive incorporation, nucleotides, oligonucleotides, 189 136–137 PCR, 201, 202, 204 incorporation, 132–133 photoswitchable molecular glue, 198 ONs, methods, 134–136 polyU and polyA, 209 polymerases, 133–134 ssDNAs, 193 EPR. See Electron paramagnetic resonance supramolecular switch, 199 (EPR) telomere, 190 ESR. See Electron spin resonance (ESR) triplex nucleic acids, 210 triplex stability, 211 Excited state intramolecular proton transfer Dual fluorescent purine nucleosides (ESIPT), 13 C7-substituted 8-aza-7-deazaadenosine Exciton-controlled hybridization-sensitive derivatives, 54–56 fluorescent oligonucleotide (ECHO) C3-substituted 3-deazaadenosine probes derivatives, 56–57 backbones modification locked nucleic acid, 74–75 20-O-methyl RNA, 74 E conventional phosphoramidite method, 68 Electron paramagnetic resonance (EPR) cross-validation tests, 70 161, 163 20-deoxycytidine, 69 272 Index

Exciton-controlled hybridization-sensitive pyrene carbonyl compounds, 40 fluorescent oligonucleotide (ECHO) pyrene-1-carboxaldehyde, 39 probes (cont.) PyU and PyC, 40 DNA strand, 68, 69 quencher-free molecular beacons, 42–43 D514 nucleotide, 68, 69 spectra of 7-deazapurine and dyes modification 8-aza-7-deazapurine desmethyl TO, 72–74 oligonucleotide, 44, 45 fluorescent colors, 72 strong emission, 41 emission spectra, 69 Forced intercalation (FIT), 67 exciton coupling theory, 67 Forster€ resonance energy transfer (FRET) FISH, 70 64, 160 interdye excitonic interaction, 69 FRET. See Forster€ resonance energy live cell RNA imaging, 71 transfer (FRET) nascent duplex structure, 68 nucleobases modification G caging technologies, 76, 77 GMPS. See Guanosine inosine and N-ethylcytidine, 75–76 monophosphorothioate (GMPS) Py quenching mechanism, 69 Guanosine ( G), 44–48 thermodynamic parameters, 70 Guanosine monophosphorothioate TO-tethered nucleic acids, 67 (GMPS), 176 Exciton coupling theory, 67 H Hairpin primer PCR, 203 F Heck reaction, 131, 132 FISH. See Fluorescent in situ HeLa cells, 242 hybridization (FISH) Hirao’s base pairs FIT. See Forced intercalation (FIT) development process, 254 Fluorescence emissions, 200 Ds–Pa, 253 Fluorescent DNA-perylene complex Ds–Px, 253, 255 hydrophobic pocket, 108–109 Dss base, 255 quenching, 109 first generation, 253 nanomolar concentration, 109, 110 functional groups, 253 Fluorescent in situ hybridization (FISH), 70 hydrophilic and hydrophobic base Fluorescent purine nucleosides analogues, 254 2AP, 28 hydrophobic unnatural base pairs, 254–255 aromatic/heteroaromatic chromophores, 28 Kool’s group, 253 aromatic ring system, 28 large and small base analogue, 253 biopolymers, 28 replication and transcription, 255 fluorescent molecules, 28 unnatural base pairs, 254 functions, 28 ligand binding, 28 ODNs, 28 I oligonucleotides, 29 In-stem molecular beacon (ISMB), 67 Fluorophore-tethered purine nucleosides ISMB. See In-stem molecular beacon (ISMB) BDF nucleosides, 39 Isomorphic emissive uridine analogues DNA microenvironment, 39 conjugated 6-membered heterocycles, fluorescence intensities, 39 18–19 fluorogenic dyes, 43, 44 isomorphic nucleosides, 14 local environments, 39 5-substituted-6-azauridine, 19–21 nonpolar solvents, 39 Isomorphic emissive uridine analogues. See nucleobase and pyrene residue, 43, 45 Conjugated 5-membered PyA and PyG, 44–48 heterocycles 8PyA and AcA, 41 Isomorphic fluorescent purine nucleosides Index 273

2AP (see 2AP analogs) NEAR. See Nicking enzyme amplification thieno analogs, ribo and deoxyribo reaction (NEAR) nucleosides Nicking enzyme amplification reaction 2AP, 31 (NEAR), 135 B–Z transition, 33 NMR. See Nuclear magnetic resonance (NMR) thdG, 33 Non-conjugated fluorophores, 8–10 fluorescence intensity, 33 Nuclear magnetic resonance (NMR), 160, 161, thG, 33 191, 192 thGTP, 33 Nucleic acids high quantum yield, 32 ECHO probes, 67–77 long-wavelength UV-absorption fluorophores, 160 maxima, 31 interrogating spins, 161 thermal stability, 32 nitroxide radicals, 162 Zαβ protein, 33 nitroxide spin labels, 162 Isomorphic nucleosides photo-cross-linking reaction (see conjugation Photo-cross-linking reaction) 5-membered heterocycles, 14–18 riboswitches, 160 6-membered heterocycles, 18–19 SDSL (see Site-directed spin labeling emissive 5-substituted-6-azauridine, 19–21 (SDSL)) Isosteric and non-isosteric base substitutions single nucleotide recognition, 221–243 2AP, 85 TO and TR, 63–67 API, 85 wavelength-shifting fluorescent probes, DAP, 85 83–96 20-desoxyribofuranose, 85 Nucleotides, dNTPs, 136 DNA architecture, 84 ethidium, 85 excimer formation, 86 O fluorescent and solvatochromic ODNs. See Oligodeoxynucleotides (ODNs) properties, 85 Oligodeoxynucleotides (ODNs), 10–11 fluorophores, 84 147, 222 hydrogen bonding pattern, 85 OxoG-clamp, 234–235 protic solvents, 86 8-Oxoguanine, 243 π-systems, 85 thymidine (DNA)/uridine (RNA), 85 UV/vis absorption, 85 Isothermal titration calorimetry (ITC), 212 P ITC. See Isothermal titration calorimetry (ITC) PCR. See Polymerase chain reaction (PCR) PELDOR. See Pulsed electron–electron double resonance (PELDOR) L PEX. See Primer extension (PEX) Live cell RNA imaging, 71 Photo-cross-linking reaction C5–C6 carbons, 145, 146 3-cyanovinylcarbazole-modified artificial M nucleic acids, 148–149 Methoxybenzodeazaadenosine (MDA), 38 cyclobutane ring, 145, 146 Methoxybenzodeazainosine (MDI), 38 gene expression Mismatch-binding ligands (MBLs), 190 photodynamic antisense, 151 Molecular beacons, 64 target mRNA, 150 nanotechnology AB-staggered tiles, 153 N DNA nanocrystal and DNA Naphthyridine derivatives (NCD), 191, 198 origami, 152 274 Index

Photo-cross-linking reaction (cont.) guanine, 227 thymine base, 154 homopurine, 227 nucleic acids analysis, 152 kinetic parameters, 225 psoralen magnesium monoperoxyphthalate, 228 natural DNA, 146 nucleic acids, 222 psoralen-modified artificial nucleic ODN3 and duplex, 226 acids, 147 oligonucleotides, 222, 229 Polymerase chain reaction (PCR), 135 oxidants, 222 Polymerase synthesis 8-Oxo-dG, 239 applications, 123, 137, 138 8-oxoG-clamp, 235, 236 competitive incorporation, 136 sigmoidal curves, 228 dNTPs (see 2-0Deoxynucleoside van der Waals contact, 226 50-O-Triphosphates (dNTPs)) vinyl ketone, 230 enzymatic synthesis, 132–138 Single nucleotide incorporation (SNI), 136 Primer extension (PEX), 134, 241 Single-stranded DNAs (ssDNAs), 193 Psoralen, 146 Site-directed spin labeling (SDSL) Psoralen-modified artificial nucleic acids, 147 base labeling Pulsed electron–electron double resonance C–C bond formation, 165 (PELDOR), 161 C5-halogenated nucleobases, 165 Pyrene π-stack array C5, pyrimidines, 167, 169 DNA nucleosides/nucleotides, 166 chemical/biochemical method, 106 phosphoramidite method, 168 covalent modification, 106 purine modifications, 170 molecular arrays, 106 purine nucleobases, 165 nucleosides, 106, 107 purine nucleotides, 171 organic semiconductor devices, 106 pyrimidine modifications, 169, 170 perylenedimide dimer, 107, 108 pyrimidines and purines, 165–167 photophysical properties, 107 rigid labels, 171, 172 transient absorption spectra, 107, 108 biopolymers, 160, 163 RNA CD, 160 biomolecules, 102 cellular functions, 159 CD spectra, 104 chemical/enzymatic synthesis, 163 characterization, 105 CW, 161 consecutive incorporation, 103 DNA and RNA, 159 fluorescence spectra, 102–104 exocyclic amino groups, 165 Pyrene-tethered 7-deazaadenosine (PyA), fluorophores, 160 44–48 interrogating spins, 161 nitroxide radicals, 162 nitroxide spin labels, 162 R noncovalent RDC. See Residual dipolar coupling (RDC) base-pairing nucleotide, 178 Residual dipolar coupling (RDC), 160 intercalators, 176 Romesberg’s base pairs, 255–256 phosphoramidite and post-synthetic methods, 178 oligonucleotide, 163 S phosphate SDSL. See Site-directed spin labeling (SDSL) helices, 174 Single nucleotide recognition internucleotide linkage, 175 biological application, 229 oligonucleotide synthesis, 175 cross-linking agent, 223 phosphodiesters, 176 20-deoxy-4-vinylpyrimidine nucleoside, riboswitches, 160 223, 224 sugar FRET strategy, 240 DNA and RNA nucleotides, 172 Index 275

hammerhead ribozyme, 173 halogenated nucleosides and minor groove, 172 nucleotides, 129 oligonucleotide termini, 172 isolation, 131 phosphodiester linkage, 174 Systematic Evolution of Ligands by sodium borohydride, 174 EXponential enrichment (SELEX), sodium cyanoborohydride, 174 250, 258 trityl radicals, 174 Size-expanded fluorescent purine nucleosides MDA and MDI, 38 T 1,N6-Ethenoadenosine (εA) TFO. See Triplex-forming ODN (TFO) chloroacetaldehyde, 34 TFOs. See Triplex-forming oligonucleotides π-conjugation, 34 (TFOs) etheno nucleosides, 34 Thiazole orange (TO) oligonucleotides, 34 asymmetric cyanines, 65 solid-phase phosphoramidite fluorescence intensity, 64, 65 chemistry, 34 FRET, 64 temperature-dependent fluorescent functional nucleotides, 64 measurements, 36 heterocyclic systems, 65 xDNA, 36–38 hybridization, 63 SNI. See Single nucleotide incorporation (SNI) live cell imaging, 64 Solvatochromicity molecular beacons, 64 C7-substituted 8-aza-7-deazapurine nucleic acids, 63 nucleosides, 53–54 organic dyes, 64 C8-substituted deoxypurine nucleosides, photochemical mechanisms, 64 51–53 tosylate, 65 Solvatochromism, 16, 18 TOTO, 65 Sonogashira coupling, 127–129 and TR (see Thiazole red (TR) and TO) SPR. See Surface plasmon resonance (SPR) Thiazole red (TR) and TO 5-Substituted-6-Azauridine, 19–21 bathochromic fluorescence shift, 87 5-Substituted uridines CHO cells, 87 anomeric ambiguity, 2 click-type chemistry, 89 C-5 modifications, 2 confocal microscopy, 87 compounds, 4 cyanine dyes, 87 cross-coupling methods, 2 CyIQ dye, 89 Cu(I)-catalyzed cyclization, 4 DNA hairpins, 89 20-deoxyuridine, 4 double helical architecture, 87, 88 glycosylation reactions, 2 emission intensity, 87 halide precursors, 2, 3 energy transfer efficiencies, 88, 89 nucleosides, 4 excimer formation, 86 organostannanes, 2 excitonic interactions, 89 palladium-based reactions, 2 fluorescence wavelength shift, 87 pyrimidine rings, 4 Huisgen–Sharpless–Meldal quinazolines, 4 cycloaddition, 89 Vorbru¨ggen condensation conditions, 2 melting temperature (Tm), 88 Surface plasmon resonance (SPR), 260 perylene diimides and pyrene, 87 Suzuki–Miyaura coupling thermal dehybridization, 87 aldehyde moiety, 131 wavelength shift, 86 arylation reaction, 129, 130 TO. See Thiazole orange (TO) aryl boronic acid, 129 TO-tethered nucleic acids, 66–67 conditions, 131 Transfer reaction, 232 guanine moiety, 130–131 Triplex-forming ODNs (TFOs), 147, 209 276 Index

U heterocycle, 21 Unnatural base pair isomorphicity, 2 amplification process, 250 nucleobases, 1 aptamers, 250 ODN, 10–11 bacterial strain bearing plasmids, 263 pyrimidine and purine heterocycles, 1 chemical and physical diversities, 251 synthetic pathways, 2 chemical structures, 252 DNA/RNA, 250 genetic alphabet expansion systems, 251 hydrophilicity, 250 V hydrophobic groups, 251 8-Vinyl-20-deoxyadenosine (8vdA, 4), 31 iG–iC pair, 252 Kd values, 250 nucleotide modifications, 250 PCR amplification technique, 250 W polymerase reactions, 252 Wavelength-shifting fluorescent probes research groups and applications, 253 cellular components, 84 SOMAmer, 251 double helical architecture, 96 vitro selection/SELEX, 250 fluorophores, 84 Uridine analogues high resolution techniques, 84 biological systems, 1 isosteric and non-isosterics, 84–86 chemical modifications, 2 molecular imaging, 84 chromophores, 6, 21 nucleic acids, 84 fluorophores, 2 parameters, 84 conjugated, 12–13 PCR amplification, 84 non-conjugated, 6, 10 photostable cyanine-styryl dyes, 90–96 fluorescent nucleosides, 21 proteins, 84 fluorescent spectroscopy, 1 TO and TR, 86–90