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(A) 25 Adenosine 88 Adeno

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(A) 25 Adenosine 88 Adeno 371 Index a aminoacyl-transfer RNA (tRNA) 88, A1B11 SIRT2-selective inhibitors 233, 90, 102 235 ARSs 90, 91 A2B57 SIRT2-selective inhibitors 233, aminoacyl-pdCpA dinucleotide with 235 91, 93 acridine 8 post-aminoacylation modification adenine (A) 25 93 adenosine 88 preparing noncanonical 91 adenosine triphosphate (ATP) 8, 35, aminoacyl-tRNA synthetases (ARSs) 117 90–91, 96, 354 affinity-guided DMAP (AGD) 4-[(2-aminoethyl)carbomoyl]benzyl catalyst-mediated selective thioester (ABT) 95 chemical protein labeling 309 2-amino-4-pentenoic acid 98 affinity-guided DMAP AMPA receptors (4-dimethylaminopyridine) chemical labeling and fluorescent chemistry 309 visualization 303 affinity ligand-tethered DMAP catalyst FRAP analysis 304 309 anti-arrhythmic 43 [1-13C]alanine-NH2 282 antibody-drug conjugates (ADCs) 253 α-amino acid-based HP 13C chemical anti-cancer 43 probes 293 anticodon sequence 88 α-hydroxyl acids 95, 101 anti-malarial agents 43 amacrine/horizontal interneurons 78 antisense oligonucleotides (ASO) amino acids 258–260 incorporation of noncanonical aquaporin 183 101–103 4-armed star-shaped copolymers 209 misacylation of non-proteinogenic ASO conjugated with tocopherol 94–96 (Toc-ASO) 261–262 misincorporation 87 Aspidosperma alkaloids 45, 48, 49, 51, ribosomal translation 103, 104 64 aminoacylation assembly lines class I ARSs 90 artificial 68 ribozyme 94, 95 biogenetically inspired synthesis tRNA 90–91, 93, 95 58–68 aminoacyl dinucleotide 92 biomimetic 43, 52 Molecular Technology: Life Innovation, Volume 2, First Edition. Edited by Hisashi Yamamoto and Takashi Kato. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2018 by Wiley-VCH Verlag GmbH & Co. KGaA. 372 Index assembly lines (contd.) budding 183 biosynthetic 45, 48, 58 bulk degradation 204 development of 45 bump and hole technology 313 Macmillan’s collective total synthesis 45–52 c nature of 62 [1-13C]α-amino acid 292, 293 synthesis of indole alkaloids 52–57 [1-13C]ascorbate 283–284 atomic force microscope (AFM) 29 13 C-benzylformic acid, for H2O2 detection 284 b [1-13C]bicarbonate,forpHsensing benzodiazepines 306 283 benzoxadiazole 124 [1-13C]dehydroascorbate 284 β-amino acids 87, 95, 335 [13C,D3]-p-anisidine 284–285 β-Cyclodextrin (β-CD) 190 cell-based yeast display method 347 bicycle-phage display approach 352 cell-cycle regulation 75 biodegradable poly(ether urethane) cell-free emulsion based encapsulation 213 method 347 biodegradable thermoplastics 207 cell-free ribosome display method 347 biogenetically inspired synthesis cell membranes 58–68 components of 118 biomimetic cyclization 49 negatively-charged 119 bioorthogonal reaction-based cell-penetrating peptides (CPP) 10 glycosylation 136 cell-surface AMPA receptors, diffusion 1,4-bis(4-phenylethynyl)benzene (BPEB) dynamics 302 units 186, 187 cellular uptake block catiomers efficiency 8, 10, 15 for gene delivery system 1–18 pDNA packaging 2–6 process 17 rod-shape/toroid-shape 17–18 rod-length limitation for 14 systemic gene therapy 14–16 CEST 126 13 blood cells 8 C-ethylenediaminetetraacetic acid blood circulation (EDTA) 285–286 13 of biological compounds 8 C-ethyleneglycol tetraacetic acid 286 capability 14 C–H activation reaction 224–228 capacity 2, 9, 14 chondroitin sulfate (HS) 8 13 in longevity 8 C hyperpolarized molecular probes molecular weight on 115 aminopeptidase N detection time 115 282–283 blood flow 73 [1-13C]ascorbate 283–284 blood vessel 13C-benzylformic acid 284 endothelial cells 114 [1-13C]bicarbonate 283 formation 73 [1-13C]dehydroascorbate 284 BNA/LNA chemistry 260 [13C,D]EDTA 285–286 13 Borromean rings 28 [ C,D3]-p-anisidine 284–285 bow-tie-shape dendrimers 115, 116 [1-13C]pyruvate 277–278 brain-derived neurotrophic factor chemical environment analysis 283 (BDNF) 80 enzymatic activity analysis 277 Index 373 γ-glutamyl transpeptidase 278–281 dissolution dynamic nuclear glycolysis and tricarboxylic acid cycle polarization process 274 analysis 278 1,2-distearoyl-sn-glycero- scaffold structure 292 3-phosphocholine (DSPC) 191 circular dichroism (CD) spectra 188 disuccinimidyl glutarate crosslinker click chemistry approach 352 HDAC3-selective inhibitor disulfide bond 10 identification 221–224 DMAP-antibody conjugates 312 HDAC8-selective inhibitor DMAP-tethered lectins 310 identification 224 DMF 6 SIRT2-selective inhibitors 232–234 DNA-based molecular technologies coordination chemistry-based fluorescence blinking control chemogenetic approach 171–177 312–320 genetic alphabet expansion copper-catalyzed cycloaddition 136 168–171 Coulomb repulsion 118, 120, 122 DNA computing 36 cyanomethyl ester (CME) 94 DNA condensation 1, 5, 18 cyclic peptides 329 DNA duplex 35 cyclization, of peptides 349 DNA forceps 33 cyclosporin 336, 337 DNA intercalators 8 cysteine conjugation 133–136 DNA nanorobot 33 cytidine 88 DNA nanotechnology 25, 26, 36 cytosine (C) 26 DNA origami box-shaped 3D 31 d design 31 d-α-amino acids 95 molecular machines made 33 d-amino acid 87, 101, 335 molecular peg board 32–33 degradation behavior of hydrogels 203 pinching devices 33–35 degree of polymerization (DP) 1, 4 2D nanostructures 31 degree of protonation 11 DNA packaging 1 deoxyribonucleic acids (DNA) 25, 339 DNA pliers 33, 35 characteristic of 26 DNA/RNA heteroduplex design principles 35 oligonucleotide (HDO) DNA-PAINT 36 concept 262–264 immobile DNA junctions 26–28 conjugated with tocopherol molecular architecture 25–36 (Toc-HDO) 264–268 molecule structure of 25–26 DNA sequence 105 nanostructures 25 DNA strands 26, 28 tiles and their assemblies 28–29 chemical synthesis of 339 topologically 28 DNA zipping mechanism 34 unzipping mechanism 35 double-stranded DNA 3 2′-deoxyribose ring 25 doxorubicin 120, 121 De-SPIO 118 DREADD technology 313 D-glucosamine 119 drug delivery system (DDS) 113 Diels–Alder cycloaddition 45 drug discovery platforms 104–105 diethylenetriamine (DET) 11 druggable proteins 330–332 374 Index Ds–Px pair 169 fluorescent imaging plate reader d-tyrosine 91 (FLIPRTM) 304 dynamic light scattering (DLS) 2 fluorescent labeling, of GABAA receptor 306 e fluorescent nanogel thermometer (FNT) eight-armed PEG 209 124 elastic pressure 204 fluorescent polymeric thermometer emitting fluorescent dye 36 (FPT) 124, 125 endosomal escape 15 fluorescent ZnII chemosensors 314 endosome escape 11–12 2-fluorodeoxy-d-glucose (2FDG) 117 endothelial cells formylmethionine (fMet) 89 growth 72 four-base codon method 98, 100 survival of 73 fucose-glycoconjugates 138 VEGFRs 73 functional peptides enhanced permeable retention (EPR) cell-based yeast display 347 effect 114, 117, 118, 123, 124, cell-free emulsion based 129 encapsulation methods 347 enzymatic activity, 13C molecular probes cell-free ribosome display 347 277 DNA sequencing techniques 346 enzymatic glycosylation 136–137 intracellular peptide selection 340–341 epidermal growth factor receptor mRNA-display method 345–347 (EGFR) 9 natural peptide synthesis 339–340 epigenetics 219–221 phage display method 341–345 ethylene diamine (EDA) 11 ribosomal synthesis 337–339 extracellular matrix (ECM) 74, 78, 118, 119 g GABAA receptors 306, 307 f galactose-modified proteins 137 flavin adenine dinucleotide (FAD) 239 gamma-aminobutyric acid (GABA) flexizymes 355–356 306 Flory–Rehner model 204 γ-amino acids 95 fluorescence 139, 147, 152 γ-glutamyl-[1-13C]glycine fluorescence-activated cell sorting (γ-Glu-[1-13C]Gly) 278–279, (FACS) device 33 281 fluorescence blinking γ-glutamyl transpeptidase (GGT) blinking kinetics 172 analysis 278–281 isomerization blinking 176 GB-GC-SPIO 118 redox blinking 175 GC-SPIO 117, 119 single molecule detection 171 gene delivery triplet blinking 174 impact for 6 fluorescence correlation spectroscopy nuclease attack 6 (FCS) 172 polyplex micelles 6–14 fluorescence recovery after gene silencing photobleaching (FRAP) method after ASO or Toc-HDO injection 302 265 fluorescent biosensors 305 Toc-ASO 262 Index 375 gene therapy 14–16 h genetic alphabet expansion HDAC3-selective inhibitors 221–224 high-affinity DNA aptamer HDAC6-insensitive inhibitors generation 169 224–228 nucleotide modifications 168 HDAC8-selective inhibitors 224 unnatural base-pair 168 HDO Conjugated with Tocopherol genetic code (Toc-HDO) decoding 88–90 adverse effect 266–268 expansion 352 on ApoB mRNA levels 265 flexizymes 355–356 construction 264 in vitro chemical ligation approach design 264 353 mechanism 268 limitation 354 potency 264–266 messenger RNA (mRNA) Heck cyclization 49 88, 90 Henderson–Hasselbalch equation non-standard base method 101 283 RaPID system 356–361 heparan sulfate (HS) 8 reprogramming 97–98 hexaethylene glycol chains 127 glomerular cells 115, 116 hexammine cobalt 17 glycan molecule technology 132 histone bioorthogonal reaction-based acetylation and methylation 219, glycosylation 136 220 cysteine conjugation 133–136 chemical modification 220 enzymatic glycosylation histone deacetylase (HDAC) inhibitors 136–137 221 in vivo organ selective Au-catalyzed HDAC3-selective inhibitors reactivity 153 221–224 on live cells 148–150 HDAC6-insensitive inhibitors lysine conjugation 133 224–228 as metal carriers 151 HDAC6-selective inhibitors 228, glycans 132 229 natural 155 HDAC8-selective inhibitors 224, protein-conjugation 133 225 glycol chitosan (GC) 117 SIRT1-selective inhibitors 228–232 glycolide 207 SIRT2-selective inhibitors 232–234 glycolysis 117 histone lysine demethylase (KDM) glycoprotein labeling, with inhibitors DMAP-tethered lectin 311 KDM4C inhibitors 235–237 glycosaminoglycans (GAGs) 8–10 KDM5A inhibitor identification gold nanoparticles 32 237–238 gold nanorods 32 KDM7B inhibitor identification G-quadruplex formation 35 238–239
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