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Page references beginning with an ‘E’ indicate that the entry is in Chapter 15 (the electronic online Appendix) but not in the print book.

  • abacavir, ABC, 103, 158

  • acceptor stem

    • tRNA structure, 249, 250, 606

  • acetal-based approaches (RNA synthesis), 295, 297

    • acetal levulinyl ester, ALE, 295

    • PivOM, 295

    • triisopropylsilyloxymethyl, TOM, 295

  • acetylaminofluorene, AAF, 433, 472

  • acetylation, 182, 395, 534, 558, 627

  • aciclovir, 97, 161

  • actinomycin, 440

  • acute lymphoblastic leukaemia, 383, 443

  • acute myeloid leukaemia, AML, 498

  • acrylonitrile

    • from cyanoethyl deprotection, 292

  • acyclic nucleotide analogues, 161

  • acyclonucleosides

    • synthesis, 103

  • acyloxonium ion, 98

  • adaptor molecule, 13

  • adefovir dipivoxil, 165

  • N6-adenine methyltransferase, 459

  • adenine, A, Ade

    • nucleosides & nucleotides, 22

    • structure, 4

  • adenosine deaminase, 241

  • adenosine deaminase acting on RNA, ADAR, 241, 370, 581, 583, 627

  • adenoviral vectors, 385–386

  • adenoviruses, 385

  • A-DNA, 12

    • secondary structure, 33, 37–38

  • ADP, adenosine 5′-diphosphate, 151, 607

  • adriamycin, 440, 485

  • adsorbent, E29

  • affinity distributions, 594

  • aflatoxin B1, 438

  • agarose, 405, 505, 627, E27

  • AIDS, 158

  • alkaline phosphatase, 310, 313

  • allele, 269, 627, 630, 631

  • allogeneic cell therapy, 383, 627

  • allosteric control, 489, 498, 562, 619, 627

  • alternative splicing

    • mRNA biosynthesis, 229, 627

    • therapeutic applications, 617–619

  • Altman, Richard, 3

  • Altman, Sidney

    • catalytic RNA, 13

  • Alzheimer’s disease

    • 8-oxoguanine DNA glycosylase, 8-oxoG, 465, 471

  • aminoacyl tRNA

    • protein biosynthesis, 249–250, 605–606

  • aminoglycosides, 500, 504, 505

  • aminoimidazole carboxamide ribonucleotide, AICAR, 107

  • 2-aminopurine nucleosides, 298

    • synthesis, 113

  • AMP, adenosine 5′-monophosphate

    • biosynthesis, 148

    • structure, 23

  • amplification, 408, 628

    • on-chip, 330–332

    • PCR, 336–337, 340–342

    • separation and, 404–405

  • analytical ultracentrifugation, AUC, E30, E32

    • sedimentation equilibrium, E31–32

    • sedimentation velocity, E31

  • anhydronucleosides, 115

  • anion-exchange, AEX, chromatography, E29–30

  • anneal, 82–84, 238–239, 315–319, 628

  • anthracycline

    • antibiotic drugs, 485–486

    • intercalators, 485

    • structure, 485

  • anthramycin, 440

  • antibiotics

    • aziridine, 440

    • C-1027, 444

    • enediyne, 442–444

      • Bergman cyclization, 444

      • calicheamicin γ1I, 443, 444

      • neocarzinostatin, 443

    • generating superoxide, 445

  • antibody, 217, 338, 410, 443, 628

  • anticancer agent, 154–155

    • brain tumour & temozolomide, 439, 464, 466

    • first generation, 439–440

    • mitomycin C, 440

    • Mylotarg, 443

    • second generation, 440

    • sequence-specific DNA binding, 442

  • anticancer chemotherapy, 155, 160, 440, 513

  • anticancer drugs, 483

    • covalent reactions with nucleic acids, 439–445

  • anticodon loop

    • tRNA structure, 242

  • antigen, 217, 386, 389–390, 398, 619, 628

  • antigene therapy

    • TFO, triplex-forming oligonucleotide, 511

  • antimetabolites, 155

  • antiparasitic drugs, 483, 490

  • antiperiplanar, ap, 31–32

  • antisense

    • DNA, 77, 78, 628

    • oligonucleotide, ASO, 12, 100, 568–569, 614

      • delivery, 370

      • mechanism of action, 355, 362–370

      • recruit RNase H, 363–365

    • principle, 362–363

    • RNA, 370

    • targeting, 239

  • antiviral agents, 154, 161

    • emtricitabine, 158, 426

    • naturally occurring, 165–166

    • ribavirin, 160

  • antiviral chemotherapy, 157–166

    • aciclovir, 97, 161

    • adefovir dipivoxil prodrug, 165

    • agents in clinical use, 162

    • combination therapy, 159

    • drug design, 166

    • famiciclovir, 162

    • ganciclovir, 161

    • penciclovir, 161

    • prodrug valaciclovir, 161

    • tenofir disoproxil prodrug, 165

  • antiviral vaccines, 155

  • Ap3A, 137, 139

  • Ap4A

    • P1,P4-diadenosyl tetraphosphate, 137, 139

  • Ap4G

    • P1-adenosyl-P4-guanosyl tetraphosphate, 139

  • apolipoprotein B mRNA editing enzymes, catalytic polypeptide-like, APOBECs, 241, 370, 628

  • apoptosis

    • by DNA damage, 463, 612, 628

    • drug induced, 155

  • aptamer, 354, 404, 406, 628

    • aptamer drug, Macugen, 418

    • chemical modifications, 407–408

    • clinical trials, 415

    • diagnostics and imaging applications, 410–411

    • limit RNases, 407

    • as research tools, 409–410

    • targeted delivery, 413–414

    • therapeutic potential, 415, 418

    • therapeutics, 411–413

  • Aquifex aeolicus, 581, 583, 603

  • arabinonucleosides

    • synthesis, 115

    • ara-cytidine, 97

  • archae, 186, 198, 533–535, 559, 628

  • argonaute, AGO, protein, 264, 371, 372, 588

  • aristeromycin

    • structure, synthesis, 105

  • A-RNA

    • duplex, 67

    • secondary structure, 67–68

  • A′-RNA, 67

  • aromatic interactions, 547

  • aromatic nitro compounds, 436

  • association, 488

  • AstraZeneca, 386, 390

  • A•T base-pair

    • structure, 8

  • atomic force microscope, AFM, E24

  • atomic form factor f, E16

  • ATP, adenosine 5′-triphosphate

    • chemical synthesis, 90, 606

    • oxygen isotope enriched, 146

    • structure, 23

  • ATPase, 206, 231, 251, 620, 628

  • autoimmune syndrome, 141

  • autologous cell therapy, 383, 628

  • autonomous replication sequence, ARS, 201

  • Avery, Oswald

    • bacterial transformation, 2

  • 1-azabenzimidazole, 496

  • 2′-azido-2′-deoxyuridine, 115

  • 3′-azido-2′,3′-dideoxyuridine, 115

  • aziridine antibiotics, 440

  • AZT

    • 3′-azido-2′,3′-dideoxythymidine, 158

    • synthesis, 97, 117

  • bacteria

    • gene expression, 196–198

    • restriction enzymes, 308

    • structure, 186, 629

    • transcription, 561

  • bacteriophage, 186, 629

    • bacteriophage phi29, 273

    • packaging motor, 273–274

  • Baker’s 1,2-trans-rule, 98

  • Baran, Phil, 289

  • base, 629

    • base-ratio, 7

    • base-tautomer, 8

    • misincorporation, 342

    • prevent water donating H-bond, 125

  • base methylation, 35

  • base-pair

    • A+•C pair, 71

    • alternative in RNA, 71

    • bowing, 41

    • clashing, 34

    • G•A pair, 72

    • G•U ‘wobble’ pair, 71

    • Hoogsteen, 26–27, 72

    • mismatch, 46

    • non-Watson–Crick pairs, 574, 579, 580

    • opening, E41

    • separation, 486

    • twist and roll, 41

    • Watson–Crick, 8, 511

    • ‘wobble’ pair, 26–27, 46, 460

  • base-pairing, 629

    • complementary, 8

    • quadruple interaction, 72

    • self-pairing, 8

    • triple interaction, 72

  • base-pair mismatch, 46–48, 395–396

    • insertion–deletion, 47–48, 631

    • repair, 395, 470

    • transition, 46

    • transversion, 46, 646

  • base-resolution mapping, 340

  • bases

    • electrostatic interactions, 42

    • keto–enol forms, 7–8

  • mutagenic, 8-oxoguanine, 465

  • base-stacking, 27, 40, 532

    • coaxial stacking, 73

    • interstrand, 68

    • intrastrand, 68

    • π–π interactions, 40, 42, 576

    • stability matrix, 81

  • base-triples

    • Hoogsteen, 26–27

    • reversed Hoogsteen, 26–27

  • Bay Region architecture, 436

  • B-DNA, 12, 33, 38–39, 44

    • circular dichroism, E5

  • Beer’s law, E5

  • bent DNA, 45, 49–52, 539

  • benzimidazole, 504

  • benzo[a]pyrene, 436

  • benzofuranone, 510

  • benzyl zipper motifs, 408

  • berenil, 490

  • β-globin gene, 173, 174

  • β-site amyloid precursor protein cleaving enzyme-1-antisense, BACE1-AS, 270

  • bifunctional alkylating agent

    • mustard gas, 428

  • binding free energy, 577

  • binding landscapes, 594

  • binding stoichiometry, 486

  • bioinformatics, 188–192, 351, 629

  • biopolymers, 404

  • bisacridine, 518

  • bisintercalation, 486–488

  • bisulfite, 425, 431

  • bisulfite sequencing, BS-Seq, 340, 425

  • bleomycin, 440, 442

  • blotting, 84–85, 629

  • boronophosphate diester, 135

  • BRACO-19, 515

  • Bragg’s Law, E18

  • branaplam, 619

  • branch point, 230

  • Brenner, Sidney

    • triplet code, 9

  • 5-bromo-dU, 298

  • budding yeast, 176, 188, 201, 564, 629

  • BVDU

    • (E) -5-(2-bromovinyl)-2′-deoxyuridine, 160

  • B–Z junction

    • B–Z transition, 54, 57

    • circular dichroism, E5

    • energetics, 85–86

  • cadeguomycin

    • synthesis, 112

  • calicheamicin, 444

  • Calladine’s rules, 44–45

  • calorimetry, E37–39

    • differential scanning, DSC

      • DNA phase transitions, 60, E37, E39

    • isothermal titration, ITC

      • DNA–ligand binding, E37–39

  • Cambridge Crystallographic Data Centre, CCDC, E19

  • Cambridge Structural Database, CSD, E19

  • cAMP

    • adenosine 3′,5′-cyclic phosphate, 23, 139

  • cancer, 17

    • bladder & aromatic amines, 433, 435

    • colon & aflatoxins, 433, 438, 487

    • scrotal & benzo[a]pyrene, 436

    • skin cancer and photolesions, 446, 452

    • testicular & cisplatin, 429

  • Candida albicans (yeast), 242, 504

  • CanSino, 386

  • cap-binding complex, CBC, 235

  • capecitabine, 118

  • cap structure, 313, 629

  • carbazole dications, 502

  • carbocyclic nucleosides

    • synthesis, 104

  • carbonyl di-imidazole

    • condensing reagent, 142

  • carbovir, 105

  • 5-carboxycytosine, 340

  • carboxyl terminal domain, CTD, 226

  • carcinogen

    • N-aryl carcinogen, 433

    • chrysene, 437

    • dimethylnitrosamine, 436

    • heterocyclic amines, HCAs, 435

    • metabolic activation

      • covalent reaction with nucleic acids, 432–437, 629

    • 4-nitroquinoline N-oxide, 436

    • polycyclic aromatic hydrocarbons, PAHs, 435, 436–437

    • proximate & ultimate, 433

  • Caruthers, Marvin, v-vii, 134, 287

  • carzinophilin A, 440

  • catabolite activator protein, CAP, 558

  • catalytic-linked assays, 615

  • cationic polymers, 373

  • cationic porphyrins, 488, 514

  • c-di-AMP

    • bis-(3′-5′)-cyclic diadenylic acid, 141

  • cDNA, complementary DNA, 193, 241, 306–307, 336, 629

  • Caenorhabditis elegans

    • small RNAs in, 370

  • Cech, Thomas 13

  • centrifugation, E30–32

    • analytical ultracentrifugation, AUC, E30, E32

    • equilibrium density gradient centrifugation, E30

  • 2′,3′-cGAMP, 141

  • 3′,3′-cGAMP, 141

  • C•G base-pair, 8, 43, 533

  • cGMP, 139

  • chain-sense paradox, 40

  • chain termination

  • Chargaff, Erwin; Chargaff’s Rules, 7, 8

  • Charpentier, Emanuelle, 17, 391

  • childhood acute lymphoblastic leukaemia, 155

  • chimera, 10

  • chimeric antigen receptor, CAR, T-cell therapy, 383, 409, 410

  • chlorofluorocarbons, CFCs, 452

  • chloroplast, 186

  • chloroquine, 501, 502

  • chlorosugar, 98

  • chromatin, 629

    • DNA-modification mapping, 193–194

    • loops, 179

    • packing, 179, 556, 569

    • structure, 87, 179, 272, E22

    • structure & gene expression, 192–193

  • chromatin immunoprecipitation sequencing, ChIP-Seq, 193, 194, 337–338, 629

  • chromatography, E29

  • chromosome, 3, 87–88, 171, 177–184, 629

    • acentric, 212, 627

    • artificial – bacterial (BACs), 315

    • centromere, 177–179, 184, 190, 629

    • conformation capture, 194

    • dicentric, 212, 631

    • ends, 210–211

    • eukaryotic, 178–179

    • homologous, 214, 634

    • metaphase, 87, 178, 179, 637

    • segregation, 88, 171, 177–178, 186–187

    • structure, 178, E22, E23

      • linear, 178–179

    • territories, 179

  • chronic lymphocytic leukaemia, CLL, 156, 412

  • cidofovir, 162

  • circular consensus sequence, CCS, 334

  • circular dichroism, CD, 28, E5

  • circular DNA

    • supercoiling, 55–58, 315

  • circularization, 250

  • circular RNA, cirRNA, 231, 272–273, 621

  • cisplatin, 430

  • clamp loader, 206, 630

  • class switching, 219, 630

  • clofarabine, 156

  • cloning, 17, 48, 83, 314–315, 630

  • closed complex, 225

  • closed promoter complex, 225–226

  • CMG complex, 201, 203

  • c-MYC promoter, 513

  • C-nucleosides

    • synthesis, 101

  • coding sequence, CDS, 235

  • coding strand, 226

  • codon, 630

    • optimality, 254, 620

    • reassignment, 243

    • start, 190, 235, 242, 370, 388, 645

    • stop, 190, 242, 253–254, 645

    • synonym, 190, 388, 645

    • usage, 190, 255, 620, 630

  • codon–anticodon interaction, 72, 249, 460

  • coenzyme A, CoA

    • structure, synthesis, 137, 138

  • cohesin, 89

  • combination therapy, 159

  • combinatorial chemistry, 404

  • compartmentalization, 550–551

  • competing endogenous RNAs, ceRNAs, 270

  • complementarity, 531

  • condensin, 88

  • conformational ensemble, E39, E40–41

  • conjugation, 304, 370, 374–375, 630

  • consensus sequence, 230, 512, 584, 595, 630

  • contig, 188, 189, 630

  • controlled pore glass (CPG), 289

  • cooperativity

    • in DNA ligand binding, 489

    • DNA–protein binding, 526

      • the chelate effect, 547

      • DNA allostery, 547

    • indirect, 597

  • copper-catalysed azide-alkyne cycloaddition, CuAAC, 194

  • coronavirus see COVID-19

  • correlation spectroscopy, COSY, 28, E8

  • co-transcriptionally, 262

  • co-transcriptional RNA processing, 226

  • counter-ion binding, 545

    • condensation, 481

    • entropically favourable release, 481

  • coupling reaction, 281

  • covalent modifications, 527–528

  • COVID-19, 105, 166

    • mRNA sequence, 353

    • pandemic, 16, 158, 313, 385, 389, E21

    • vaccines, 386, 387, 389

  • CpG-rich island, 183, 630

  • crenarchae, 533

  • Crick, Francis

    • DNA structure, 7, E21

  • CRISPR: clustered, regularly interspersed, short palindromic repeats, 391–398, 568, 630

    • CRISPR-based activators and repressors, 395

    • guides, 397–398

    • nucleases, 394–395

    • mediated genome editing, E22

  • CRISPR-associated, Cas, proteins, 391, 629

    • Cas9, 17, 309, 391, 629

      • dead Cas9, dCas9, 395

  • crosslinking, 298, 338, 440, 590, 630

  • crosslinking and immunoprecipitation, CLIP, 590, 592

  • cryogenic electron tomography, cryo-ET, E22

  • cryptic unstable transcripts, CUTs, 176

  • crystallography, 17, 26, 35, 52, 62, 76–77, 90-91, 528, E16

  • curved DNA, 48–49, 557

  • C-value paradox, 185

  • cyanoethylation, 431

  • 2-cyanoethyl phosphates

    • in synthesis, 137, 287

    • deprotection, 292

  • cyclic ADP ribose, 139

  • cyclic dinucleotide, CDN, 140

  • cyclonucleosides

    • synthesis, 115, 117

  • cyclophosphamide, 434

    • anti-cancer agent, 156

  • cyclopurines, 451

  • cytarabine, 156

  • cytidine, Cyd

    • nucleosides & nucleotides, 4, 25–28

  • cytidine deamination, 425

  • cytidine triphosphate, CTP, 151

  • cytomegalovirus, 157, 162

  • cytoplasm, 173, 631

  • cytosine, C, Cyt, structure, 4, 22

    • methylation, 409

  • daunomycin, 440, 485, 486

  • DB213

    • HIV drug, 508

  • DB2277

    • azabenzimidazole compound, 497

  • deamination, 154

  • 7-deaza-dG, 297

  • 7-deazapurine, 112

  • Debye–Hückel interactions, 481

  • density functional theory, DFT, E42

  • deoxyadenosine, 22

  • deoxyadenosine analogues

    • cladribine, 156

    • fludarabine, 156

  • deoxycytidine, dC, 22

  • 3′-deoxy-3′,4′-didehydronucleotides, 166

  • 2-deoxy-d-ribose

    • structure, 4, 22

  • 2′-deoxyformycin A

    • MutY inhibition, 465

  • 2′-deoxygenation, 103

  • 2′-deoxy-5-methylcytidine, 5mC, 22

  • 3′-deoxynucleotide, dNP, 23

  • deoxyribonuclease, DNase, 87, 125, 184, 487, 631

  • deoxyribonucleotide biosynthesis

    • ribonucleotide reductase, 151

  • 2′-deoxyribonucleotides, 22

  • deoxythymidine, dT, dThd, 22

  • de-repression, 369

  • Dervan, Peter,

    • footprinting, 424

    • Dervan pairing rules, 424, 495

  • desolvation, 547

  • deoxyguanosine, dG, 22, 428

  • diamidines, 490

  • 2,6-diaminopurines, 113

  • dianophore, 352, 353, 631

  • 2′,3′-didehydro-2′,3′-dideoxynucleosides

    • synthesis, 117

  • 2′,3′-dideoxycytidine, ddC, 158

  • 2′,3′-dideoxy-5-fluoro-3′-thiacytidine, FTC, 158

  • 2′,3′-dideoxynucleosides

    • synthesis, 117

    • triphosphates, ddNTPs, 326

    • dideoxy DNA sequencing, 109

  • 2′,3′-dideoxyinosine, ddI

    • antiviral agent, 158, 159

  • diffusion coefficient, D, E33

  • digital droplet technique, 405

  • 5,6-dihydropyrimidine nucleosides

    • synthesis, 423

  • dihydrouridine

    • synthesis, 432

    • tRNA structure, 424

  • 5,6-dihydrouridine, 424

  • 4,4′-dimethoxytrityl, DMT

    • protecting group, 283

  • 1,2-dimethylhdrazine, 433

  • dimethyl sulfate, DMS

    • DNA alkylation, 428–429

  • diphenylpyrimidine, 502

  • diploid, 185

  • dipolar couplings, E8

  • directed evolution, 384

  • direct electron detectors, E21

  • Direct Methods (crystallography), E19

  • direct RNA sequencing, dRNA-Seq, 336

  • dispersity

    • monodisperse vs. polydisperse, E34

  • dissociation, 488

  • ditercalinium, 487

  • divergent transcripts, 272

  • DNA, 21–91

    • alpha-helix, 501

    • aptamers, 354, 628

    • bendability, 49–52

    • bent, 45

    • bifurcated, 493

    • biological importance of, 2

    • blunt ends, 308

    • breathing, 488

    • bypass replication, 449

    • catalytic, 132–133

    • catenated, 59, 629

    • chips, 293

    • circular, 55–57, E27

    • copying, 198–211

    • crescent shape, 492

    • cross-links, 431, 449

    • curved, 48–49

    • demethylation, 459

    • donor, 395, 631

    • double helix, 8, 21

    • double strand cleavage, 444

    • double-stranded, 479

    • duplex stability, 526

    • elongation, 203–210

    • fingerprinting, 192, 325, 344–345, 631

    • flexibility, 486

    • flipped out, 437, 456, 458

    • footprinting, 424, 429, 633

    • gyre, 558, 634

    • helix

      • melting curve, 60

    • helix–coil transition

      • circular dichroism, 28

    • helix distortion by BPDE-adduct, 437

    • hybridization, 82–86

    • inserts, 315

    • intercalation, 85, 486, 489

    • intergenic, 178, 271

    • intrastrand linking, 430

    • isomorphous geometry, 26

    • knotted, 59

    • length, 484

    • linking number, E27

    • melting curve, 80–81

    • methylation, 266

    • methylation & gene expression, 183

    • nanotechnology, 91

    • nicked, 310, 442, 637

    • origami, 90

    • palindromic sequence, 61, 226, 391

    • primary structure, 32

    • rapid motions, 86

    • recombinant, 314

    • repetitious, 177

    • replication, 183, 198–211

    • replication initiation, 198–199

    • reversible chain terminators, 161, 311, 330, 332

    • satellite, 177, 178, 643

    • secondary structure, 33, 37

    • sedimentation coefficient, 484

    • self-assembly, 90–91

    • semi-conservative replication, 198, 644

    • sequence determination, 6, 10, 325, 327–328

    • sequence-specific recognition, 492

    • sequencing, 10, 188–192

    • shape, 492

    • single molecule

      • single molecule force spectroscopy, E26

    • standard structure, 32

    • sticky ends, 305, 308, 645

    • supercoiling, 37, 57–59, E27

    • superhelical, 51, 55–56, 88

    • topology, 55, 566

    • transcription, 171–172, 646

    • triple-stranded, 59–61

    • triplex, 511

    • vector, 314, 315

    • writhing, 49

    • zig-zag structure, 40

  • DNA adenine methylase, 320

  • DNA alkylation

    • biological consequences, 455–458

    • chloroacetaldehyde etheno-derivatives, 428

    • ‘hard’ alkylating agents, (SN1 agents),

      • primary carcinogens, 428, 456, 457

    • phosphate triester, 456–457

    • ‘soft’ alkylating agents,

      • (SN2 agents), 428, 456

  • DNA annealing, 82

  • DNA binding proteins

    • cooperative features, 526

    • single-stranded DNA, 540–541

  • DNA-binding by protein loops

    • Rel & Stat proteins, 540

  • DNA duplex manipulation, 563–567

  • DNA gyrase, 567

  • DNA helicases, 563–564

    • relationship to F1 ATPase, 566

  • DNA photodimer repair

    • photolyase, 463

  • DNA-protein binding

    • kinetic aspects, 549–550

  • DNA pumps

    • bacterial infection, 565–566

    • plasmid transfer in conjugation, 566

  • DNA recognition specificity

    • direct readout, 543

    • indirect readout, 543, 546

  • DNA target selectivity

    • sliding, hopping, inter-segmental transfer, 550

  • DNA topoisomerase I

    • single strand break, 566

  • DNA topoisomerase II

    • double strand break, 566

  • DNA breathing, 85

  • DNA cation binding, 527, 545

  • DNA cellular content

    • by species, 7, 16

  • DNA cleavage, 392, 394–396

  • DNA conformation, 32–40, 45

    • average rise (Dz), 37

    • conformational adaptability, 546–547

    • conformational flexibility, 550

    • helix axis, 37

    • helix parameters, 33

    • helix rotation (Ω), 37

    • sequence-dependent conformational effects, 527

    • tilt angle (τ), 37

  • DNA cross-link

    • interstrand cross-links, ICLs, 449

    • intrastrand , 430

  • DNA cross-linking

    • by azinomycin B, 440

  • DNA damage, 192

    • chlorofluorocarbons, CFCs, 452

    • clustered damage, 455

    • double-strand break, DSB, 214, 455, 468, 631

    • ozone barrier, 446, 452–453

  • DNA enzymes

    • topoisomerase I, 57–58, 566

    • topoisomerase II, 58, 125, 566–567

  • DNA Fluorocode, E4

  • DNA footprinting, 424, 429, 633

  • DNA glycosylase, 464–465, E43

  • DNA glycohydrolase, 465

    • inhibition by nucleoside analogues, 464

    • mechanisms, 465–468

  • DNA G-quadruplex, 511–518

  • DNA helix

    • average parameters, 33

    • energy of bending, 546

    • energy of twisting, 546

    • sequence-dependent modulation, 41–44

  • DNA hydration, 38, 480

  • DNA intercalation, 480, 483–489

    • bisintercalators, 486, 517

    • classical intercalation model, 483

    • ethidium, propidium, proflavine, 483

    • free energy of binding, 550

    • neighbour exclusion principle, 486

    • non-classical threading, 488–489

    • planar aromatic ring system, 480

    • polycyclic aromatic hydrocarbons, 436–437

    • structure of intercalators, 483, 485

    • thermodynamic parameters, 482

  • DNA intrinsic viscosity, 484

  • DNA ligase

    • gene manipulation, 305, 310, 468

  • DNA methylation, 183, 266

    • enzymatic, 458

    • fully-methylated, 183

    • hemi-methylated, 183, 634

    • phosphate triesters, 135

    • in vivo, 455

  • DNA methyl transferases, DNMTs, 458

  • DNA microarray analysis, 590, 591, 593

  • DNA microarrays

    • analysis, 293–294, 325, 345–346

  • DNA mutation see mutation

  • DNA nuclease η, 130

  • DNA packaging, 178–179, 182

    • in archaea and bacteria, 186

    • eukaryotic, 178

  • DNA photodimer

    • intrastrand, 447

    • photoreversion, 447–448

  • DNA photoproducts, 448

    • psoralen, 449–450

  • DNA-Points Accumulation for Imaging in Nanoscale Topography, DNA-PAINT, 347, E24

  • DNA polymerase, 204–205

    • erroneous activity, 470

    • nucleotide polymerization, 280, 304

    • proofreading, 305, 317, 560

    • polymerase I, 305, 560

  • DNA promoter, 173, 225, 641

  • DNA protein recognition motifs, 533–542

  • DNA quadruplex, 541–542

  • DNA recombination, 175, 216–219, 642

  • DNA renaturation, 81, 642

  • DNA repair, 212–219, 462–473

    • accurate repair, 394

    • adaptive Ada response, 464

    • base-mismatch repair, MMR, 470

    • cross-link repair, 468

    • cut and patch-type reaction, 468

    • direct reversal of damage, DRD, 464, 471

    • double strand scission, 443

    • endonucleases

      • APE1, 553

    • error-prone, 472

    • excision repair, 115, 451, 468

    • homology-directed repair, 395, 634

    • human DNA glycosylases, 464–465, 554–555

    • insertions or deletions, indels, 394, 635

    • mechanisms, 213

    • phosphate triesters, 464

    • photodimer repair, 468, 469, 471, 473

    • post-replication repair, 470

    • preferential repair, 471

    • recombination repair, 212, 642

    • replication bypass, 449

    • SOS repair, 472

    • transcription-coupled repair, TCR, 468–469, 470–471

    • translesion synthesis, 472–473

  • DNA–RNA hybrid, 363, 581

    • NMR, 45

  • DNA structure

    • anisomorphic, 50

    • A-tract, 41, 53, 491

    • bases pointing outwards, 7

    • cruciforms, 50, 51, 631

    • Dickerson dodecamer, 12, 38, 39, 41, 46, 50

      • anthramycin complex, 442

    • G-tract, 53

    • hairpin loops, 50

    • helical geometry, 523–527

    • helical rise, 41

    • helical twist, 21, 41

    • i-motif, 63, 511, 635

    • linear polynucleotide, 5

    • non-canonical, 61–65

    • palindromes, 50, 308, 526, 639

    • sequence-dependence, 41

    • slipped structures, 50

    • twofold symmetry, 7–8, 10

    • unusual, 48

  • DNA synthesis

    • whole-gene, 17

  • DNA translocation, 564

  • domains, 171, 560, 569, 631

  • Donohue, Jerry

    • keto–enol forms, 8

  • double stranded RNA binding domain, dsRBD, 579, 581

  • Doudna, Jennifer, 17, 391

  • d-ribose

    • structure, 22

  • Drosophila melanogaster, 174, 188, 236, 265, 535, 633

  • drug binding, E41

  • drug discovery, E19

  • Duchenne muscular dystrophy, DMD, 365

  • dumb-bell former 4 (Dbf4)-dependent kinase, DDK, 201

  • duplex destabilization, 564

  • dUPTases, 130

  • dyad centre of symmetry, 552

  • dynemicin, 444

  • dynemicin A, 444

  • Eckstein, Fritz

    • phosphorothioates, 299

  • efavirenz, 159

  • electophoresis, E27–28

  • electron density, E21

    • map, E18

  • electron diffraction, ED, E20

  • electron microscopy tomography, EMT, 87

  • electrophiles

    • hard and soft, 427, 456

  • electrophoresis

    • agarose gel electrophoresis, 633, E27

    • capillary electrophoresis, E28

    • polyacrylamide gel electrophoresis, PAGE, 292–293, 633, E27

    • pulsed field electrophoresis, E28

  • electrophoretic mobility shift assays, EMSA, E28

  • electrostatic interactions, 532, 547

  • electrostatic potential, 68

    • 3D map, E21

  • elongation

    • prokaryotic transcription, 225, 226

  • emtricitabine, 158, 426

  • emulsion, 405

  • Encyclopaedia of DNA Elements, ENCODE, project, 193–194, 622

  • endonucleases, 255, 632

  • endosymbionts, 186, 632

  • enediyne antibiotics, 442–444

  • energy minimization

    • global minimum & local minimum, E40

  • energy surface, E40

  • enhancer RNAs, eRNAs, 272, 632

  • Enterobacter aerogenes, 108

  • enzymatic domains, 574

  • enzyme-linked assays, 615

  • enzymes

    • DNA

      • BamHI restriction endonuclease, binding to DNA, 544

      • 3′-exonucleases, 208, 305, 319

      • gyrase, 58, 90, 567

      • helicase, 198, 563–564, 634

      • human DNA glycosylases, 459, 464–467

      • integrase, 158

      • ligase, 305, 310, 468

      • methyl transferases, Mtases, 210, 458

      • polymerase, 204–205, 304–305, 560

      • polymerase I, 305, 560

      • polynucleotide kinase, 309, 315

      • ten–eleven translocation, TET, dioxygenase, 458

      • thermostable DNA polymerase, 305

      • topoisomerase, 57–58, 155, 207, 646

      • topoisomerase I, 57–58

      • topoisomerase II, 58

    • DNA repair

      • AP endonuclease, 464, 466

      • bacterial Ada protein, 464

      • human MUTYH, 465

      • O6-alkylguanine

        • DNA alkyltransferase, 113, 555

      • O6-methylguanine

        • DNA methyltransferase, 463

      • 8-oxoguanine DNA glycosylase, 465

      • photolyase, 463, 555

      • uracil DNA glycohydrolase, UDG, 464, E43

    • metabolic

      • acetate transferase, 433

      • cytochrome CYP1A1, 436

      • cytochrome P-450 oxidase, 433

      • epoxide hydrolase, 436

      • sulfotransferase, 433

    • nucleoside

      • adenosine deaminase, 241

      • thymidine kinase, 160

    • nucleotide

      • 8-oxoGTP hydrolase, 472

      • thymidylate synthase, 151, 157, 426

    • RNA

      • Dicer, RNA endoribonuclease, 265, 371, 372, 506, 603, 631

      • Drosha, RNA endoribonuclease, 265, 506, 631

      • eukaryotic RNA polymerases, 225

      • helicase, 607

      • poly-A polymerase, 228, 388

      • reverse transcriptase, 158, 304, 306–307, 336

      • ribonuclease, RNase, 599, 643

      • RNA exonuclease, 255

      • RNA polymerase, 195–196, 225–227, 304, 307, 561

      • RNA polymerase I, 225

      • RNA polymerase II, 225, 267, 567

      • RNA polymerase III, 225

      • RNA polymerase – viral, 161

      • RNA primase, 205, 560

      • RNase III, 235, 581, 601–603

      • RNase III domain, RIIID, 601

      • RNase A, 125, 131, 599, 600

      • RNase H, 127, 363–365, 569, 643

      • RNase P, 131, 235, 643

      • RNase T1, 600

      • telomerase, 210

      • terminal transferase, 304, 307

    • RNA debranching, 231

    • tRNA

      • aminoacyl tRNA synthetases, 605–606

  • epigenetics, 431, 527, 632

    • regulation, 269

  • episome, 383, 632

  • epoxidation

    • natural products, 438

  • erasing

    • DNA demethylation, 458–460

  • Escherichia coli, 9, 89

  • esperamicin, 444

  • esperamicin A1, 444

  • ethidium, 483, 484

  • ethidium bromide

    • DNA intercalation, 484, 485, E27

  • eubacteria, 559–560

  • euchromatin, 182, 184, 632

  • eukaryotes, 171, 533, 567, 632

  • excision repair

    • base-mismatch repair, MMR, 470, 632

    • BER, base excision, enzymes and mechanisms, 451, 464–465, 629

    • global genomic nucleotide excision repair, GGNER, 468

    • long patch repair, LP, 466

    • NER, nucleotide excision, enzymes and mechanisms, 451–452, 468–470

    • short patch repair, SP, 466

  • exon, 173, 229, 336, 632

    • inclusion, 367

    • skipping, 365, 367, 632

  • exon junction complex, EJC, 236

  • exonucleases, 255, 632

  • exosome, 228, 255

  • experimental noise, 193, 632

  • extinction coefficient, 27, E36

  • FapydAdo, 4,6-diamino-5-formamidopyrimidine deoxyriboside, 455

  • FapydGuo, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, 455

  • Felgner, Philip, 386

  • fialuridine, 159

  • fibres, 12

    • 30 nanometer, 179

    • spindle, 179, 645

  • fidelity, 320

  • fingerprinting

    • in biotechnology, 192, 325, 344–345

  • Fire, Andrew, 16, 370

  • flap endonuclease, 207, 633

  • flavin adenine dinucleotide, FAD, 137, 138, 460

  • Flemming, Walther

    • chromatin, 3

  • fluorescence, E3–4

  • fluorescence detection method, 506

  • fluorescence in situ hybridization, FISH, 346–347, E23

  • fluorescence intensity, 615

  • fluorescence microscopy, E22

  • fluorescence polarization, FP, 615

  • fluorescence resonance energy transfer, FRET, 303, 614, 633

  • fluorophores, 331

  • 2′-fluoro-2′-deoxysugars, 355–356

  • 5-fluorouracil

    • anticancer drug, 426, 434

    • structure, 109, 157

    • thymidylate synthase inhibitor, 426

  • 5-fluorouridine, 118

  • footprinting, 424, 429, 633

  • forensic genetics, 192, 325, 344, 633

  • formaldehyde, 427

  • form factor, E33

  • 5-formylcytosine, 5fC, 340, 459

  • Förster resonance energy transfer, 615, E3, E24

  • Fourier transform, E7, E18

  • Fourier transform infrared absorption, FTIR, E6

  • four-stranded DNA structure, 61–64, 513

  • fragile X mental retardation 1, FMR1, gene, 614

  • fragile X syndrome, FXS, 509, 614

  • Franklin, Rosalind

    • DNA structure, 7

  • Friedreich ataxia, 509

  • fruit fly see Drosophila melanogaster

  • furamidine, 490

  • furanose ring

    • nucleoside structure, 22

  • GalNAc

    • use as targeting ligand, 374

  • gel electrophoresis, 633

    • agarose, 633, E27

    • polyacrylamide, PAGE, 292–293, 633, E27

    • pulsed field electrophoresis, E28

  • gel-filtration chromatography, E30

  • gene, 9, 171, 633

    • assembly, 293, 318–319

    • manipulation, 10

    • non-coding, 176–177

    • protein-coding, 171–175, 641

    • selfish, 177

    • single copy, 185

    • tandemly arrayed, 174

  • gene cloning, 314

  • gene duplication, 175, 192, 216

  • gene editing, 17, 319

    • CRISPR technology, 391–398

    • machinery, 390

    • reverse transcriptase based, 396–397

  • gene expression, 633

    • control, 338–340

    • permissive, 184, 639

  • gene families, 174–175, 633

  • gene mutagenesis, 319–321

  • gene sequence

    • overlapping frame, 252

    • small RNA, 263

  • gene structure, 173–174

    • complex, 174

    • eukaryotic, 173

  • gene synthesis, 11, 17, 315–318

  • gene therapy, 16, 382–386, 633

    • AAV, 385

    • nonviral, 386

  • genetic code, 9, 242–244, 633

  • genetic fingerprint, 192, 633

  • genetic map, 15

  • genetic recombination, 177, 217, 633

  • genome, 171, 260, 633

    • assembly, 190, 344

    • conformation mapping, 194

    • expression mapping, 193

    • function analysis, 192–193

    • instability, 197

    • non-transcribed functional genetic elements, 177

    • reference, 190, 642

    • repetitive sequences, 177

    • sequence analysis, 188

    • sequence content, 185

    • size by species, 185

    • structure, 184–188

      • compartments, 185

    • structure in 3D, 185–186

    • viral, 507

  • genomic island, 197, 633

  • germline, 211, 634

  • Gibbs free energy, 531, E37

  • Gibson assembly

    • isothermal, 318–319

  • glycosylation

    • nucleobase anion, 101

  • glycosylic bond, 98, 103, 107, 634

  • glycosylic bond cleavage

    • DNA repair, 464–467

  • GMP, guanosine 5′-monophosphate

    • biosynthesis, 148

  • GNRA tetraloop, 74

  • Golden Gate assembly, 309

  • gout, 153

  • gRNA

    • guide RNA, 241

  • G-tetrad

    • G-quartet, 62, 72, 634

  • GTPase-activating protein, GAP, 129

  • GTP hydrolases, 128

  • guanine, G, Gua

    • base-structure, 4, 22

  • guide RNAs, 239

  • Gulland, Masson, 5

  • H19

    • lncRNA, 269

  • hairpin loops, 50, 68, 69

  • hairpins

    • DNA, 50, 634

    • kissing hairpin complex, 73

    • polyamide ligands, 495

    • ribozyme, 132, 133

    • RNA, 68–69

  • hairy-cell leukaemia, HCL, 156

  • halogenation reactions, 108–109, 426

  • haploid, 185, 634

  • Hayflick limit, 211

  • H-DNA, 59, 61

  • heavy atom, E18

  • Heck reaction, 109, 112

  • helix

    • A-form, 37, 574, 575

    • α-helix 2, 587

    • B-form, 38

    • helix–coil transitions, 28, 79

    • Z-form, 39

  • helix lengthening

    • intercalation, 444, 483, 484

  • helix unwinding

    • duplex lengthening, 484

  • helper cells, 382

  • Hepatitis C virus, HCV, 159, 251

  • herpes simplex keratinitis, 97

  • herpesvirus, HSV, 159

  • heterochromatin, 182, 558, 634

    • constitutive, 184, 630

    • facultative, 184, 632

  • heterogeneity, E21

  • heteronuclear single quantum correlation, 2D HSQC, E10

  • hexamer d(CGTACG)2, 485

  • hexaploid, 185

  • Hi-C molecular technique, 180

  • higher-order DNA structure, 86, 511

  • highest occupied molecular orbital, HOMO, 125, 427

  • high fidelity, HiFi, reads, 334

  • highly active antiretroviral therapy, HAART, 158–159

  • high-throughput fluorescence assay, 509

  • high-throughput sequencing, HITS, 176, 189, 330–332, 590, 634

  • high-throughput sequencing kinetics, HITS-Kin, 593

  • high-throughput sequencing-RNA-affinity profiling, HITS-RAP, 593

  • histogram plots, 594

  • histone, 179, 558, 634

    • acetylation, 182

  • histone H3 lysine 9, H3-K9, 266

  • HITS-CLIP, 590–592, 622

  • Hoechst 33258

    • DNA binding, 490–493

  • Holley, Robert

    • tRNA structure, 9

  • Holliday junction, 52, 214, 517, 634

    • stacked conformers, 518

    • X-shaped structures, 518

  • holoenzyme, 225, 634

  • homodimer, 544

  • homologous recombination, HR, 214, 468, 517, 634

  • homologous sequences, 584

  • homologues, 174, 634

  • Hoogsteen duplex, 64–65

  • horizontal gene transfer, 192, 634

  • HOX antisense intergenic RNA, HOTAIR, 269

  • human genome, 15

  • human genome project, 15

  • human immunodeficiency virus, HIV, 97, 158, 382–383, 507

  • humidity, 480, E15

    • high, 33

    • low, 33

  • Huntington’s disease, 509

  • hybridization

    • base composition, 83

    • detection of DNA sequences, 344

    • detection of NA sequences, 82–86, 344–347, 635

    • parameters affecting, 83–84

  • hydration

    • DNA, 38, 480–481

  • hydrodynamic radius, Rh, E32

  • hydrogen bond, 528

    • acceptors, 25, 119, 528

    • bidentate, 528

    • donors, 25, 528

    • network, 123, 125

    • π−hydrogen bonds, 529

  • hydrogen bonding, 525–530, 547

    • lexitropsin in DNA minor groove, 496

    • protein-DNA sequence-specificity, 543

    • structural aspects, 8, 25–27, 539

    • water molecules in DNA grooves, 526, 531

  • hydrolysis, 233

  • N4-hydroxy-2′-deoxycytidine, 112

  • 8-hydroxyguanine (see 8-oxoguanosine), 465

  • hydroxylamine, 424

  • N1-hydroxymethyladenine, 1hmA, 461

  • N6-hydroxymethyladenine, 461

  • 5-hydroxymethylcytosine, 5hmC, 340, 459

  • 5-hydroxymethyl-2′-deoxycytidine, 5hmdC, 111, 431

  • 5-hydroxymethyl-2′-deoxyuridine, 5hmU, 453

  • hyperchromic effect, E3

  • hyperthermophiles, 237

  • hypochromicity, 28, 79, 635, E2, E36

  • idoxuridine

    • antiviral agent, 160

  • Illumina sequencing, 188, 189, 330, 332

  • imidazole riboside, 107–108

  • iminium sugar analogues, 466

  • immune modulation, 380–381

    • as therapeutic approach, 381–382

  • immune responses, 381–382

  • immunoprecipitation, 338, 635

  • informational drugs, 352–354

  • Inforna, 505–507

  • infrared, IR, spectroscopy, E5–6

    • Fourier transform

      • nucleic acid crystals, E6

  • inosine 5′-monophosphate, IMP

    • biosynthesis, 148

  • insulin, 10

  • intasome, 90, 635

  • integrase

    • RNA viruses, 158

  • integration, 234

  • intercalation, 480, 483–489, 635, E41

    • DNA conformational changes, 486

    • ethidium

      • dependence on DNA intercalation, 486

    • helix lengthening, 444, 483, 484

    • therapeutic applications, 483, 617–623

  • interdomain linkers, 597

  • interference RNA, RNAi see RNA interference

  • interferon, 66

  • internal ribosome entry sites, IRES, 251

  • International Agency for Research on Cancer, IARC, 433

  • internucleotide linkage, 299

  • interphase, 179, 635

  • intrinsically disordered regions, IDRs, 551

  • intron

    • gene structure, 172, 262, 336, 635

    • group I, 232

    • group II, 232–234, 509, 510

    • group II reverse-splice, 233, 234

    • lariat, 230

    • self-splicing, 231–232

  • inversions, 216

  • 5-iodo-2′-deoxycytidine, 111

  • 5-iodo-2′-deoxyuridine

    • antiviral nucleoside, 160

    • synthesis, 97, 109

  • 5-iodo-dU, 298

  • 6-iodouridine 5′-phosphate, 109

  • ion-exchange HPLC, E29–30

  • Ion Torrent sequencing, 189

  • isochores, 178, 635

  • isoforms, 174, 635

  • J-couplings, E8–9

  • Jefferies, Alan

    • DNA fingerprinting, 344

  • Johnson & Johnson, 386

  • Karikó, Katalin, 387

  • Khorana, Har Gobind

    • gene synthesis, 10

    • trinucleotide synthesis, 9

    • oligonucleotide synthesis, 284–285

  • kinase, 309–310, 635

    • acetate kinase, 121

    • adenylate kinase, 143

    • cyclin-dependent kinase (CDK), 199-202

    • guanylate kinase, 161

    • myotonic dystrophy kinase (DMPK), 369

    • nucleoside diphosphate kinase, 151-152, 161, 164

    • pyruvate kinase, 158

    • T4 polynucleotide kinase, 309, 315

    • TFIIH kinase, 563

    • thymidine kinase, 137, 157-158

    • thymidylate kinase, 152, 160

    • tyrosine kinase, 213

    • tyrosine kinase receptor (VEGF), 415

    • uridine kinase, 150

    • UMP kinase, 151

  • kinetochores, 178, 635

  • Kymriah, CAR T-cell therapy, 383

  • lagging strand

    • DNA strand polarity, 205, 636

  • lamivudine

    • 2′,3′-dideoxy-3′-thiacytidine, 3TC, 99, 101, 158–159

  • leading strand

    • DNA strand polarity, 205, 636

  • lentivirus, 382, 636

  • leukaemia, 152–153, 498–500

  • lexitropsins

    • DNA binding, 495

  • life cycle, 186

  • ligand binding

    • adriamycin, 440

    • anthracycline antibiotics, 485

    • cooperativity, 489

    • daunomycin, 440, 485–486

    • energetics; Gibbs relationship, 531, E37

    • enthalpic & entropic components, 530, 543, 577

    • favourable hydrophobic transfer, 485

    • fluorescence analysis, E3

    • hydrophobic interactions, 576

    • intercalation vs. minor groove, 501–503

    • isothermal titration calorimetry, E38

    • lexitropsins, 495

    • triplex selective ligands, 509

  • ligand interactions

    • cooperativity in, 489

    • 4,6-diamidino-2-phenylindole, DAPI, 490, 492, 502, E22

    • DNA groove binding, 480, 490–492

    • DNA intercalation, 480

    • dsDNA, 55

    • major groove, 480, 491, 524, 526, 636

    • minor groove, 480, 491, 524, 526

    • outside-edge binding, 480

    • quadruplex DNA, 480

    • salt effects, 33, 79, 83

    • triplex DNA, 511

  • ligase, 207, 310, 636

    • T4 DNA ligase, 305, 310

  • light scattering, E32–34

    • dynamic light scattering, DLS, E32, E33–34

    • static light scattering, SLS, E32–33

  • LIGR-seq, ligation of interacting RNA and high-throughput sequencing, 449

  • linear dichroism, LD

    • transition moment, E5

  • linker, 303, 636

  • Liu, David

    • base editing, prime editing, 395-396

  • lipid nanoparticles, LNPs, 373, 636

  • liquid crystal, E10

  • lncRNA, long non-coding RNA, 176, 268–272, 621, 636

  • locked nucleic acids, LNA, 100, 356, 407, 636

  • locus control region, 175

  • lowest unoccupied molecular orbital, LUMO, 125, 427

  • magnetic anisotropy, E10

  • magnetic field, E6

  • major groove

    • agents, 500–501

      • TATA-binding protein, TBP, 539

    • β-sheet binding

      • integration host factor, IHF, 90, 538

      • met repressor, 538, 539

    • electrostatic potential, 53

    • protein binding

      • α-helix orientation, 537–538

    • structure, 26, 37, 42

    • Temozolomide alkylation in, 439

    • tRNA acceptor stem

      • class II synthetase binding, 606

    • width, 37, 41, 54

  • manipulative proteins

    • DNA helicases, 563–564

    • DNA pumps, 565–566

    • topoisomerases, 566–567

  • Markiewicz reagent

    • synthetic use, 103

  • mass spectrometry, MS, 636, E11, E32

    • electrospray ionization, ESI

      • ribosome analysis, E14–15

    • electrospray ionization mass spectrometry, ESMS

      • large oligonucleotide analysis, E11, E13–15

    • matrix-assisted laser desorption/ionization mass spectrometry, MALDI-MS

      • small oligonucleotide mass determination, E11–13

  • maturase protein

    • group II intron product, 234

  • mediator complex, 226

  • meiosis, 216, 636

  • meiotic recombination, 212, 216–217, 637

  • Mello, Craig, 16, 370

  • melting curve, 80–81, E3

  • melting temperature, Tm

    • deconvolution of complex curve, 637, E3, E36

    • DNA denaturation, 77, 79, 81, 90, 631

  • 6-mercaptopurine

    • anticancer agent, 155

  • Meselson, Matthew

    • restriction enzymes, 9

  • mesitylenesulfonyl nitrotriazole, MSNT, 134

  • mesitylenesulfonyl tetrazole, MST, 134

  • mesoscopic modelling, E41

  • messenger ribonucleoprotein particles, mRNPs, 235

  • metal ions, 52–54

  • metaphosphate

    • hypothetical phosphorylation species, 122

  • metastasis associated lung adenocarcinoma transcript 1, MALAT1, 271

  • 3-methyladenine, 3mA, 464

  • N6-methyladenine, 6mA, 459

  • N6-methyladenosine, 6mA, 460

    • 6mA demethylase, 460

  • N-methylbenzimidazole, 496

  • 5-methylcytosine, 5mC, 22, 340, 457

  • methylenebisphosphonate, 141

  • 7-methylguanosine cap structure, 7mG cap, 227, 228

  • methyl methanesulfonate, MMS, 428, 456

  • N-methyl-N-nitrosourea, MNU, 428

  • 2′-O-methylnucleosides

    • structure, 117

  • methylphosphonate, 359

  • microarrays

    • detection of DNA sequences, 293–294, 325, 345–346, 505, 637

  • microcrystal electron diffraction, micro-ED, E20

  • micrographs, E20

  • microhomology-mediated end joining, MMEJ, 214, 637

  • microRNAs, miRNAs, 262–266, 637

    • let-7 miRNA, 612–613

    • miRNA sponges, 272

    • RNA interference & processing, 603–605

    • therapeutics, 265–266, 372, 506

  • microsatellites, 613

  • microscopy, E20–26

    • atomic force microscopy

      • contact, tapping, non-contact modes, E24–26

    • electron microscopy

      • cryogenic EM, cryo EM, 17–18, 528, 603, E20–22

      • scanning EM, E20

      • transmission EM, E20

    • scanning probe microscopy, SPM

      • scanning tunnelling microscope, STM, E24

  • Miescher, Friedrich

    • nuclein, 2–3

  • Miller indices, E16

  • minichromosome maintenance, MCM, complex, 200

  • minor groove

    • cation binding, 527

    • α-helix binding expansion, 538

    • ligand binding features, 480

    • mitomycin binding, 440

    • nucleosomal DNA alignment, 546

    • rRNA packing, 76

    • structure, 26, 37, 42, 637

    • tRNA acceptor stem

      • class I synthetase binding, 606

    • water network, 498

    • width, 37, 41, 54, 78

  • minor groove agents

    • ligand binding, 478–481

  • minor groove binding

    • distamycin A, 493–494

    • electrostatic potential & base composition, 53, 68

    • Hoechst 33258, 490–493

    • inhibition of PU.1 in leukaemia, 498–500

    • isohelical ligands, 493, 494

    • netropsin, 493, 494, 495

    • polyamide dimers, 496

    • pyrrole, furan, imidazole, benzene rings, 491

    • sequence-dependent drugs, 444, 496–498

  • minor groove narrowing

    • tomaymycin, 440, 442

  • mitochondria

    • eukaryotic plastids, 59, 186, 241

  • mitosis, 179, 637, E22

  • mitotic spindle, 178, 637

  • Mitsunobu reaction

    • nucleoside synthesis, 105

  • mobile phase, eluent, E29

  • Moderna, 353, 389–390

  • modified base

    • lysidine, 237

    • O6-methylguanine, 457, 463

    • pseudouridine, 361

    • queuosine, 112

    • reagents for detection, 431

    • RNA, 340–342, 637

  • modified nucleoside

    • 2′-O-methyl groups, 238

    • 5-methylcytidine, 431

  • modified oligonucleotide

    • 2′–5′ linkage, 231

    • 2′-O-methyl ribose, 60

    • backbone modification, 358

    • biotinylation, 432

    • dithioate linkages, 358

    • linkers, 303

    • locked nucleic acids, LNA, 100

    • methylphosphonate linkages, 359

    • peptide nucleic acids, PNA, 302

    • phosphoramidates, 359

    • phosphorothioates, 289

    • SELEX, 406

    • synthesis with modified bases, 297–298

    • terminal modifications, 302

  • modified pyrimidine 2′-deoxyribonucleoside BVDU, 160

    • idoxuridine, 160

    • 5-substituted, 160

  • MODOMICS, 460

  • Mojica, Francisco, 391

  • molecular dynamics, MD

    • simulations, 481, E41, E43

  • molecular evolution, 404

  • molecular imaging, 411

  • molecular mechanics, MM, 123, E40

    • nucleic acid force fields, E39–40, E42

  • molecular modelling, 7, 9, 12, E39–41

    • DNA microcircles, E40–41

    • mesoscopic modelling, E41

    • molecular dynamics

      • DNA flexibility, E41

    • molecular mechanics, E30–40

  • molecular probes, 483

  • molecular weight, E32

  • monoclonal antibodies, mAbs, 411, 637

  • mononucleotides, 5

  • moxifloxacin, 619

  • mRNA, messenger RNA, 9, 13, 242, 637

    • aging, 255

    • capping, 313

    • ‘cap’ structure, 313, 629

    • decapping, 255

    • eukaryotic pre-mRNA, 227–230

    • general mRNA decay pathway, 255

    • processing, 236

    • recoding, 244

    • RNA translation, 172

    • synthetic, 620

    • therapeutics, 313–314, 386, 503

    • viral, 252

  • mRNA therapeutics

    • chemical modification, 386–388

    • nucleobase modifications, 360–362

    • optimization of mRNA sequence and structure, 388–389

  • mRNA vaccines

    • engineering synthetic, 619–621

    • rapid development of, 16, 353, 389–390

  • Mullis, Kary, 305–306

  • multi-wavelength anomalous dispersion, MAD, E16

  • mutagenesis

    • bisulfite deamination, 431

    • bypass mutagenesis, 437

    • formaldehyde, 427

    • hydroxylamine, 112, 424

    • nitrous acid deamination, 426

    • photochemical deamination, 446

    • random, 320–321

    • site-directed, 319, 644

  • mutation

    • DNA damage, 212

    • frameshifting, 507, 633

    • in RBPs, 609–611, 637

    • in splicing factors, 610

  • myelodysplastic syndromes, MDS, 498

  • myotonic dystrophy, DM, 617

  • myotonic dystrophy type 1, DM1, 509

  • napththalene-bisamides, 488

  • nascent strand, 198, 637

  • ncRNA, noncoding RNA, 171, 176, 260, 480, 505, 621, 638

  • near attack conformation, NAC, 468

  • negative-stain EM, E22

  • neocarzinostatin, NCS

    • antibiotic, 443, 444

  • neomycin, 500

  • neplanocin A

    • synthesis, 105

  • netropsin

    • DNA binding, 493, 494, 495

  • neurological disease, 509

  • neuromuscular disease, 610

  • neuro-oncological ventral antigen, NOVA, 591

  • neutron diffraction, E19

  • next-generation sequencing, NGS, 404, 418

  • nicotinamide adenine dinucleotide, NAD+, NADH

    • bacterial cap, 227-228

    • bacterial ligases, 466-468

    • structure, 137, 139

  • Nirenberg, Marshall

    • molecular biology, 9

  • nitrogen base, 22

  • nitrogen mustard, 428, 439

  • N-nitroso compounds, 436

  • nitrosoguanidine, 436

  • nitrosourea, 436

  • nitrous acid, 426

  • NMR, nuclear magnetic resonance, 25, 528, 638, E6–11

    • nuclear Overhauser effect

      • nOe-walk, E9

    • nucleic acids

      • active nuclei, E6

    • oligonucleotide

      • nuclear Overhauser effect, E8

      • TOCSY & NOESY, E9

  • NMR constraints, E10

  • NMR spectrum, E7–9

    • chemical shift, E7–8

    • downfield & upfield, E7

    • linewidth, E7

  • nogalamycin

    • threading intercalation, 488, 489

  • noncoding strand, 226

  • non-homologous end joining, NHEJ, 214, 394, 468, 638

  • non-nucleoside reverse transcriptase inhibitors, NNRTIs, 158

  • non-ribosomal RNAs, 504–505

  • nonsense mediated decay, NMD, 254, 368, 609

  • Northern blot

    • RNA analysis, 84–85, 638

  • NovaSeq, 332

  • novel proposal, 128

  • nuclear export factors, 236

  • nuclear Overhauser effect (NOE) spectroscopy, NOESY, 28, E8–10

  • nuclear paraspeckle assembly transcript 1, NEAT1, 271

  • nuclear spin, E6

    • nuclear spin systems, E9

  • nucleases, 307, 309, 638

    • CRISPR nucleases, 309, 394

    • restriction endonucleases, 308

    • ribonuclease, RNase, 599, 643

    • RNA exonuclease, 255

    • RNase III, 235, 581, 601–603

    • RNase III domain, RIIID, 601

    • RNase A, 125, 131, 599, 600

    • RNase H, 127, 363–365, 569, 643

    • RNase P, 131, 235, 643

    • RNase T1, 600

    • sequence-specific, 308

    • structure-selective, 555

  • nucleic acid, 2–3

    • alkylation, dimethyl sulfate, 428–429

    • alkylation, methylnitrosourea, 456

    • components, 3–5

    • equal relative proportions, 4

    • exogenous, 379

    • γ-irradiation damage, 453, 455

    • halogenation reactions, 426

    • higher-order structures, 511–518

    • hydration, 39, 68, 480–481

    • hydrolysis, 423

    • ionizing radiation, 453–455

    • oxidation, 424, 462

    • photochemistry, 446–453

    • structural dynamics, 79–86

    • thermodynamic analysis, E36–39

    • water-nucleic acid interactions, 480

    • X-ray damage, 453

  • Nucleic Acid Database, NDB, E16

  • nucleic acids

    • metallation

      • platinum compounds, 429–431

    • polymerization, 304

  • nucleic acid therapeutics, 16

    • chemical modifications, 354–362

    • as informational drugs, 351–354

    • small molecule–DNA interactions, 503–504, 507–510, 515–518

  • nucleobase

    • expanded H-bonding networks, 361–362

    • modifications, 360–362

  • nucleoid

    • chromatin structure, 90, 186, 638

  • nucleolus

    • RNA-packed organelle, 238–239, 260, 516, 551, 638

  • nucleophilic reactions of nucleosides & nucleotides, 424–432

    • carbon electrophiles, 426–429

    • halogenation, 426

    • metallation, 429–431

    • nitrogen electrophiles, 426

    • nitrogen nucleophiles, 424–425

    • sulfur nucleophiles, 425–426

  • nucleoside, 3, 638

    • anomeric effect, 31

    • base halogenation, 108

    • β-anomer, 98

    • bisphosphate, 23

    • chemical synthesis, 97–98

    • C-nucleoside, 101, 104

    • diphosphate, 23

    • enzymatic synthesis, 127

    • fusion synthesis, 98

    • hydrolysis, 423

    • metal salt procedures, 101, 103

    • modified, 97

    • modified sugars – uses, 100

    • NMR, 25

    • oxidation, 424

    • physical properties, 24–27

    • reduction, 423–424

    • rotamers, 31

    • silyl base synthesis, 98–100

    • spectroscopy, 27–28

    • structure, 22

    • sugar anomerization, 98–99

    • syn–anti conformation, 30–31

    • synthesis of modified bases, 108–109, 111–114

    • synthesis of modified sugars, 115, 117–118

    • synthesis using base anions, 101, 103

    • tautomerization, 25

    • transglycosylation synthesis, 107–108

    • triphosphate, 23

    • Vorbrüggen synthesis, 98

  • nucleoside 1,3-dithiotriphosphates, 143

  • nucleoside 5′-phosphoromorpholidates

    • synthesis of nucleotides, 142

  • nucleoside α-boranotriphosphates

    • nucleotide analogues, 142

  • nucleoside analogue

    • therapeutic applications, 154–166

  • nucleoside α-thiotriphosphates

    • synthesis, 142

  • nucleoside diphosphates

    • biosynthesis, 151

  • nucleoside oxidation

    • adenosine N-1 oxide, 424

    • osmium tetroxide, thymine glycol, 424

  • nucleoside reduction

    • Barton reduction, 103

    • catalytic hydrogenation, 423

    • dihydrouridine biosynthesis, 424

  • nucleoside reverse transcriptase inhibitors, NRTIs, 158

  • nucleoside triphosphates

    • biosynthesis, 127–130, 151

    • synthesis, 142

  • nucleosome

    • DNA packaging, 556–559

    • DNA structure in, 546

    • structure, 87, 179, 638

  • nucleotide, 3, 638

    • acyclic, 357

    • analogues, 157, 161, 162, 321

    • biosynthesis, 146–152, 424

    • catabolism

      • purines, 152

      • pyrimidines, 154

    • constrained, 356–357

    • deletion, 217

    • enzymatic polymerization, 304–305

    • flipping DNA glycohydrolase, 465–468

    • fluorescent, chain terminators, 330

    • hydrolysis, 152–154, 423

    • insertion, 217

    • ionization, 24–25

    • L-nucleotide, 411

    • oxidation, 424

    • phosphonate analogues, 162

    • physical properties, 24–27

    • preferred conformation, 31

    • prodrug, ProTides, 161, 162–165

    • shape (conformations), 29

    • spectroscopy, 27–28

    • structure, 21–23

    • virtual bond concept (shape), 31

  • 3′-nucleotide, Np, 23

  • 5′-nucleotide, pN, 23

  • nucleotide biosynthesis

    • feedback inhibition, 149

  • nucleus, 177, 638

  • O4-methylthymidine, 4mT, 112

  • O6-methylguanine-DNA methyltransferase, MGMT, 463

  • O6-sulfonate esters, 113

  • Okazaki fragments, 205, 207, 209, 638

  • oligodeoxyribonucleotide, 12, 39

    • antisense, 78

    • chemical synthesis, 280–294

    • enzymatic synthesis, 311

    • NMR

      • TOCSY and NOESY, E9

    • synthesis

      • 2′-protection, 281

      • 5′-hydroxyl protection, 280, 283–284

      • attachment to support, 289–290

      • chain assembly, 290–292

      • deprotection, 292

      • H-phosphonate route, 135

      • HPLC, 293

      • nucleobase protection, 281–283

      • phosphate diester route, 134, 284

      • phosphate triester route, 134, 284

      • phosphite triester route, 134–135

      • polyacrylamide gel electrophoresis, PAGE, 292–293, E27

      • purification of oligomers, 292

      • solid phase synthesis, 281, 289, 301

      • strategy, 280–281

  • oligonucleotide, 16–17, 638

    • aptamer, 354

    • chain convention, 28, 280

    • enzymatic synthesis, 311–314

    • flexibility

      • molecular dynamic analysis, E41

      • NMR, E8

    • gapmer, 358, 359, 364, 633

    • immune response, 381

    • immunomodulatory effects, 379–382

    • insertions, 319, 470

    • modified phosphates, 299–300

    • modified sugars, 298

    • reagents & therapeutics, 296–297

    • replacement of sugar-phosphate backbone, 360

    • sequencing

      • NMR, E8

    • splice-switching, 367–369

    • steric block, 368, 369

    • structure

      • crystal-packing effects, E18

      • NMR analysis, E10

    • sugar-modified, 354–357

    • synthesis, 12

    • synthesis of modified, 297–304

    • therapeutic, 298, 354, 356

    • triplex-forming oligonucleotide, TFO, 511

  • oligoribonucleotide

    • chemical synthesis, 294–297

      • base protection, 294

      • chain assembly, 296

      • deprotection, 296–297

      • hydroxyl protection – ACE, 296

      • hydroxyl protection – TBDMS, 295

      • hydroxyl protection – TOM, 295

      • orthogonal protection, 294

    • enzymatic assembly, 312–313

      • ligation, 312

      • transcription, 312

  • oncogene, 212

  • ONT sequencing, 334–335

  • open complex, 225

  • open reading frame, ORF, 172, 190, 235, 242, 638

  • operon

    • gene cluster, 175, 197, 638

  • optical rotatory dispersion, ORD, 28

  • origin recognition complex, ORC, 200, 638

  • orotidine 5′-monophosphate decarboxylase, ODCase, 109

  • orthologues, 174, 638

  • orthophosphoric acid, 119

  • osmometry, E32

  • 2′-O-substituted ribose sugars, 355

  • oxaliplatin, 430

  • Oxford Nanopore Technologies, ONT, 188, 332

  • oxidative bisulfite sequencing, oxBS-Seq, 341

  • 8-oxodAdo

    • 8-oxo-7,8-dihydro-2′-deoxyadenosine, 455

  • 8-oxoguanosine, 424, 465

  • ozone layer, 446, 452–453

  • PacBio single-molecule real-time, SMRT, sequencing, 332–334

  • Pacific Bioscience, PacBio, 332

  • packaging

    • DNA (see DNA packaging), 178–179, 182

    • RNA, pRNA, 274

  • paired-end reads, 190

  • palladium-catalysed couplings

    • modified nucleoside synthesis, 108, 109, 112, 144

  • paralogues, 175, 639

  • PAR-CLIP method, 590

  • parental strand, 198, 639

  • PARIS, psoralen analysis of RNA interactions and structures, 450

  • pattern recognition receptors, 379, 639

  • Patterson function, E18

  • PCR, polymerase chain reaction, 90, 194, 305–306, 342, 244

  • pentamidine, 490

  • pentose sugar, 22

  • peptide nucleic acid, PNA

    • modified backbone oligomers, 301–302, 360, 639

  • per-acylation method, 282–283

  • personalized medicine, 16, 192, 639

  • Pfizer/BioNTech, 353, 387, 389–390

  • phage, 186, 639

  • pharmacophore, 352, 639

  • phase, E18

  • phase problem, E18

  • phenotypes, 192, 639

  • phenyl, 491

  • phosphatase, 184, 309–310, 639

    • alkaline phosphatase, 310

  • phosphate

    • esters & anhydrides, 118–127

    • modifications in NA therapeutics, 358–359

    • triesters, 127

  • phosphate diester, 30

    • 2′,3′-cyclic phosphate, 125, 126

    • cyclic phosphate hydrolysis, 126

    • hydrolysis, 125, 423

    • in-line displacement, 123, 468

  • phosphate ester

    • diesters, 120

    • enzyme catalysis, 123

    • formal relationships, 133

    • hydrolysis, 120–122

    • hydroperoxide radical cleavage, 453

    • monoesters, 120

    • rates of hydrolysis, 123

    • structure, 22–23

    • triesters, 127

  • phosphate diester, 285–286

    • anionic, 575

    • linkage, 4, 32, 66, 280, 310, 358, 639

  • phosphate monoester

    • structure, 123–124

    • synchronous mechanism, 124

    • synthesis, 135–137

  • phosphate triester, 127, 281

    • DNA alkylation, 456–457

  • phospholipid bicelles, E10

  • phosphonacetate, 359

  • phosphoramidite

    • chemistry, 285, 288–289

    • synthesis, 135, 287, 639

  • phosphoric acid anhydrides

    • structure, 119

  • phosphorodiamidate morpholino oligomer, PMO, 302, 360, 639

  • phosphorodithioate, PS2, 300, 639

  • 5-phosphoribosylamine

    • purine biosynthesis, 156

  • phosphorothioate, PS, 299–300, 397, 640

    • antisense application, 358

    • backbone analogues, 300

  • phosphorylation, 5, 137, 158, 162, 609, 640

    • dependent steps in transcription, 184

  • phosphoryl chloride, 135

  • phosphoryl transfer

    • mechanisms, 122–123

    • nucleophilic attack, 128-130

  • phosphotriester, 286–287

  • photochemistry

    • photolyases, 555

  • photochemistry of nucleic acids, 446–453

  • photolithography

    • DNA synthesis on chip, 293

  • photolyase, 463

  • phylogenetic analysis, 191–192

  • phylogenies, 192

  • physical mapping, 190, 640

  • physical properties

    • nucleoside & nucleotide, 24–27

  • ping-pong pathway, 268

  • pivalyloxymethyl, PivOM, 295

  • Piwi–Argonaute–Zwille, PAZ, domain, 588–589

  • Piwi-interacting RNAs, piRNAs, 266–268, 640

    • initiator piRNA, 268

    • pachytene piRNAs, 267

    • piRNA cluster, 268

    • trailing piRNAs, 267, 268

  • Piwi proteins, 266, 588

  • plasmid, 10, 55, 187, 640

  • platform potential, 353, 640

  • ploidy, 185, 640

  • pneumococci, 2

  • pneumonia, 2

  • polyacrylamide, E27

  • polyacrylamide gel electrophoresis, PAGE

    • DNA sequencing, 292–293, 633

    • oligonucleotide analysis, 292, E27

    • reptation

      • DNA movement, E27

  • polyadenylate-binding protein, PABPC, 236

  • polyadenylation, 228, 236, 576, 640

  • polycomb repressive complex 2, PRC2, 269

  • polycyclic aromatic chromophore, 483

  • polymerase, 640

    • core, 225

    • DNA, 204–205, 304–305

    • RNA, 195–196, 225–227

    • switching, 208, 640

  • polymerase chain reaction, PCR, 305, 314, 405, 639

    • error-prone PCR, 320

    • gene synthesis, 12

    • overlap PCR, 317

    • recursive PCR, 316

  • polymorphic sequences, 192, 640

  • polymorphism

    • analysis, 192

  • polynucleotide, 28, 640

  • polynucleotide kinase

    • oligonucleotide 5′-phosphorylation, 309

  • polyphenylalanine, 13

  • polyphosphate ester

    • monoalkyl ester synthesis, 138

    • nucleoside, 137, 141–145

    • P1,P2-dialkyl ester synthesis, 138

    • structure, 137

  • polyploid, 185, 640

  • polytene, 185, 640

  • polyuridylic acid, 13

  • post-source decay, PSD, E12

  • post-transcriptional silencing, 263

  • Poulter reaction, 141

  • precision medicine, 16

  • pre-initiation complex, PIC, 195, 226, 251, 563, 641

  • premature termination codons, PTC, 254

  • pre-messenger ribonucleoprotein particles, pre-mRNPs, 227

  • prime editing guide RNA, pegRNA, 396–397, 639

  • primer, 304, 641

  • pre-miRNA, 265

  • processivity, 307

    • clamp, 206, 641

  • proflavine, 483

  • prokaryotes, 171, 275, 641

  • promoter, 225, 641

    • alternative, 174

    • region, 225

    • RNA polymerase II, 567

    • transcription initiation, 173

  • propeller twist

    • helical structure, 41–44

  • propidium, 483

  • 5-propynyl-dU, 297

  • protecting group in synthesis, 280

    • permanent, 281

    • temporary, 281

  • protection of telomere protein, Pot1, 540

  • protein engineering

    • modified protein production, 254

  • proteins

    • α-helix motifs, 534, 537–538

    • β-ribbons, 534, 538

    • β-sheets, 534, 538

    • binding, 4E-BP, 254

    • binding RNA

      • dsRNA recognition, 579

    • biosynthesis, 13

    • counter-ion interactions, 530

    • fusion, 212, 395, 609, 633

    • helix–turn–helix motif, 534–535

    • homeodomain, sequence-specific induced fit, 535

    • interaction with nucleic acids, 528–533

    • leucine zipper, 535–536, 549

    • loops, 534, 540

    • met repressor protein, 538

    • nanopores, 334

    • nucleases

      • structure-selective, 555

    • nucleic acid binding

      • forces, 528–533

      • water, 531–532

    • nucleic acid complexes

      • base-stacking, 532, 576

      • dipolar forces, 532

      • dispersive forces, 532–533

      • electrostatic forces, 532, 545–547, 575

      • enthalpy, 543, 577

      • entropic forces, 530, 543, 577

      • hydrogen bonds, 528–530, 547

      • hydrophobic effect, 531, 576

      • kinetics & thermodynamics, 543–551, 576–577

      • non-specific interactions, 544

      • salt bridges, 530

      • salt effects, 545

      • specificity, 574, 583, 589–598

      • structure & specificity, 574–575

    • oligonucleotide/oligosaccharide binding fold, OB, 540

    • polymerases, 560–563

      • DNA-directed DNA, 560–561

      • DNA-directed RNA, 561–563

    • replacement, 390–391

    • RNA polymerase

      • ‘futile’ cycle, 562

    • synthesis

      • mitochondria, 242

      • mRNA, 242

    • TATA-binding, 539

    • transport, 236

    • tRNA aminoacyl synthetases, 249–250

    • zinc-bearing motifs

      • steroid and nuclear receptors, 537

      • zinc fingers, 536–537, 586–587

  • protonation states, E19

  • proton sponge effect, 373, 641

  • proton-wire mechanism, 248

  • protospacer-adjacent motif, PAM, 393, 641

  • pseudodeoxyuridine, dΨ

    • UDGase inhibition, 465, E43

  • pseudogenes

    • defective mammalian genes, 175, 641

  • pseudogenization, 272

  • pseudoknot

    • secondary & tertiary structure, 252, 641

  • pseudorotation cycle

    • sugar pucker, 29

  • pseudouridine, Ψ, 101

    • base-pairing, 239

    • in RNA modification, 238–240, 261–262

    • structure, 238

    • synthesis, 104

    • therapeutic uses, 354, 361, 387

    • vaccine incorporation, 621

  • pseudouridylation, 262

  • psoriasis, 449

  • PU.1 transcription factor, 498–500

  • Pumilio/feminizing-3, PUF, domain, 587–588, 622

  • purification, 314

  • purine base

    • modified by radiation, 455

    • structure, 22, 30, 641

  • purine nucleoside

    • chemical synthesis, 64

  • purine nucleoside phosphorylase, PNP, 108, 152

  • purine nucleotide biosynthesis, 147–149

    • committed step, 148

    • de novo pathways, 147–149

    • salvage pathways, 149

  • purine photoproduct

    • adenine photoproducts, 450

    • 8-oxoguanine, 450

  • purine photoproducts, 450–452

  • purine-pyrimidine tracts

    • unusual DNA structure, 50

  • pyridine, 491, 496

  • pyrimidine

    • 5-modified, 361

    • base modified by radiation, 453–454

    • structure, 22, 30, 641

  • pyrimidine analogue, dP

    • mutational base, 321

  • pyrimidine nucleoside

    • synthesis, 40

  • pyrimidine nucleotide biosynthesis

    • de novo pathways, 149–150

    • salvage pathways, 150

  • pyrimidine photoproduct

    • cell death, 448

    • cis–syn-thymine photodimer, 447

    • cyclobutane photodimer, 447, 448

    • pyrimidine(6-4)pyrimidone photoadducts, 448

    • spore photoproduct, 448

    • thymine photohydrate, 446

  • pyrroleamidine, 493

  • pyrrolo[1,4]benzodiazepines, P[1,4]Bs, 440–442

  • quadruplex DNA, 61, 511–518, 541–542, 641, E36

    • completed Phase II trials, 515

    • ligand binding, 513–514

    • structure in genome, 513

  • quantum mechanics, QM, E40

    • Hamiltonian, E43

  • quantum mechanics/molecular mechanics, QM/MM, 123, E42–44

    • DNA repair, E43–44

  • Quarfloxin, 515

  • quindoline compounds, 513

  • quinocarcin, 442

  • quinoline compounds, 501

  • radius of gyration, Rg, E32, E33, E40

  • reaction coordinate, E40, E43

  • reactive oxygen species, ROS, 445, 453

  • real space, E16

  • recA protein

    • single strand DNA binding, 564

  • reciprocal lattice point, E16

  • reciprocal space, E15

  • recoding, 242, 252

  • recombinant DNA

    • hybrid DNA for cloning, 10, 641

  • recombinase, 214, 641

  • recombination see DNA recombination; genetic recombination

  • recombinational exchange, 174, 642

  • recursive PCR

    • gene synthesis & detection, 316

  • remdesivir, 105, 163, 165

  • repair

    • damaged DNA, 212–219

  • repeat A, repA, 269

  • repeat-containing RNA, 617

  • replication

    • bypass, 447, 449

    • DNA, 183, 198–211

    • elongation, 203–210

      • termination, 209

    • fork, 199, 642

      • barriers, RFBs, 209

      • collapse, 209

      • restart factors, 207

      • structure, 204–206

    • initiation zone, 201, 635

    • origin, 178, 638, 642

      • activation, 201–203

      • establishment, 200–201

      • licensing, 198

    • re-establishment of epigenetic states, 210

    • semi-conservative, 198, 644

    • stress, 203, 207

  • replicon, 200, 642

  • replisome, 200, 207, 642

  • reporter groups, 303

  • repression, 264, 506, 534, 556, 568, 642

  • Research Collaboratory for Structural Bioinformatics/Protein Data Bank,

    • RCSB/PDB, E16, E21

  • residual dipolar couplings, RDCs, E10

  • restriction endonuclease

    • sequence-specific DNA cleavage, 308, 310, 529, 543–545

  • restriction enzyme cleavage

    • markers, 551

  • restriction enzymes, 9, 642

    • DNA specificity, 551–555

      • palindromic sites, 551

  • retention time, E29

  • retrotransposons

    • repetitious DNA, 187, 234, 642

  • retrovirus, 234, 642

  • reverse-phase HPLC, E29

  • reverse-splicing reaction

    • intron insertion, 232

  • reverse transcriptase, 382

    • gene editing, 396–397

    • intron insertion, 158

    • RNA sequencing, 304, 307–308

  • reverse transcriptase, RT

    • RNA sequencing, 234, 336, 642

  • reverse transcription, 187, 234, 642

  • reversible small molecule-nucleic acid interactions

    • binding modes and sites of interaction, 479–480

    • interaction of small ions with NA, 481–482

    • water-nucleic acid interactions, 480–481

  • Rev responsive element, RRE, 579–581

  • ribonuclease A

    • bovine, 599

    • mechanism, 125, 131

  • ribonucleases, 599

  • ribonucleoprotein, RNP, 573, 584

  • ribonucleosides, 115

  • 5′-ribonucleotide, 23

  • ribonucleotide reductase

    • mechanism, 151–152

  • ribonucleotides, 22, 642

  • ribose 2′-hydroxyl, 21, 68, 574

  • ribosomal factory

    • eukaroyotic/prokaryotic comparison, 248

  • ribosomal frameshifting, 252

  • ribosomal pausing, 507

  • ribosomal proteins, 245

    • large subunit, 245

    • small subunit, 245

  • ribosome, 242, 244, 573, 577, 587, 597, 642, E21

    • 30S subunit, 246

    • 40S, A-site, 246

    • 50S subunit, 246, 248

    • 70S, E-site, 246

    • 70S, P-site, 246

    • internal re-entry sites, IRES, 251

    • mRNA tunnel, 246

    • RNA-protein recognition, 579

    • stalling, 252

  • riboswitches, 140, 642

    • native aptamer role, 274

  • ribothymidine

    • structure, 23, 85

  • ribozyme, 21, 642

    • activity, 509

    • catalytic mechanism, 130–131, 248

    • hairpin, 132

    • hammerhead, 132

    • RNA self-splicing, 66, 232–234

    • self-catalytic, 509

    • self-cleaving, 132–133

    • Varkud Satellite, VS, 132

  • rigosertib, 619

  • risdiplam, 619

  • R-loops, 363

  • RNA

    • alkylation, 460–462, 627

    • base modification, 237

    • bulges, 69

    • capping, 227–228

    • catalytic, 72, 235

    • coaxial stacking, 73

    • coding, 480

    • cross-linking, 617

    • double-stranded, 479

    • drugging, 510

    • duplex, 70, 73, 608

    • duplexes, 67

    • editing, 237, 643

      • deaminase Apobec-1, 241

    • epigenetic phenomena, 182–184, 460

      • export, 236

    • formaldehyde reaction, 427

    • guide strand, 372

    • helix, structure & function, 579–581

    • infectious mobile element, 233

    • insertion–deletion editing, 241

    • interference, RNAi, 370–371

    • 2′-O-methylation

      • translation, 261–262

    • misfolding, 76

    • modification, 237

    • nonsense-mediated decay, 254, 368, 609

    • polyadenylation, 228, 236, 576, 640

    • poly(A) tail, 228, 255, 388–389

    • primary structure, 65–66

    • protein binding

      • RNA binding single-stranded, 365, 607

      • RNA chaperones, 77, 559, 607, 629

      • RNA interactions, 573–598

    • processing, 227–235

    • quality control, 254–255

    • receptors, 255

    • removal, 255

    • short hairpin, shRNAs

      • ribose zippers, 74

    • slippery sequence, 252, 507

    • small nuclear, snRNA

      • apolipoprotein B, 241

    • small nucleolar RNA, snoRNA

      • deaminase reactions, 241

      • pairing arrangements, 239

      • pseudouridinylation, 239

    • tertiary folding, 232

    • tertiary structure, 72–74, 77

    • tertiary structure – metal ions, 74–76

      • misfolding, 76

    • thermodynamics, 70

    • translation, 242

    • transversional editing, 240

    • undruggable, 505

    • untranslated regions, UTRs, 73, 172, 263, 388, 512, 646

    • virus, 158–159, 251, 507

    • world, 13–14, 130

  • RNA analysis in situ

    • Southern blotting, 84

  • RNA binding domains, RBDs, 578–579, 584

  • RNA binding proteins, RBPs, 573, 589–598, 623

    • associated with human diseases, 608–614

    • hnRNPs, 611

    • inhibition of RBP-RNA interactions with small molecules, 614–621

    • lineage 28, LIN28, protein, 612–613, 614

    • mechanisms modulating specificity, 595

    • muscleblind-like, MBNL, proteins, 613–614

    • serine–arginine rich, SR, 611

    • specificity, 590

    • structure and dynamics, 597

  • RNA Bind-n-Seq, RBNS, 595

  • RNA chaperone proteins

    • RNA folding, 76

  • RNAcompete, 593

  • RNA damage, 471

  • RNA–DNA duplexes

    • structure, 66–68, 77–79, 632

    • RNase H, 127

  • RNA-induced silencer complex, RISC, 264, 643

  • RNA interference, RNAi, 370–371, 643

    • clinical applications of, 378–379

    • genetic manipulation by silencing, 378

    • RNAi therapeutics, 373–377

      • chemical modification of siRNAs, 377–379

  • RNA mobile element

    • Alu, 235

    • L1, 235

    • retrotransposons, 187, 235

  • RNA motif

    • A-minor, 74, 75

    • kissing hairpin complex, 73

    • self-cleaving, 131, 132

    • –small molecule interactions, 505

    • tetraloop receptor, 73

  • RNA polymerase, 195–196, 225–227, 304, 307

    • transcription inhibition, 227

    • two metal mechanism, 562

    • yeast pol II structure, 562

  • RNA processing, 227–236, 643

  • RNA-recognition motif, RRM, 579, 643

  • RNase H induction

    • antisense activity, 363

  • RNA-seq, 193, 643

  • RNA splicing, 172, 228–235

    • exon omission, 365, 367

    • pre-mRNA splicing, 229–231

    • spliceosome, 230–231, 645, E21

  • RNA structure, 22, 65

    • A-platforms, 76

    • bulges, 69

    • conformational change, 576

    • general features, 68–69

    • hairpin loops, 68–69, 507

    • internal loop, 69

    • junctions, 69

    • motifs, 505–506

    • P456, 77

    • primary structure, 65–66

    • pseudoknot, 71, 507

    • R17 virus 55-mer, 68

    • secondary structure, 68–69

    • tertiary architecture, 77

    • viral function, 508

  • RNA-targeted BIoactive ligaNd Database, R-BIND, 505

  • RNA transcript

    • RNA processing, 225

  • RNA transport

    • from nucleus to cytoplasm, 236

  • Rosenberg, Barnett

    • cisplatin, 429

  • Rossmann fold, 605, 643

  • roundworm, 188, 643

  • RRM domains, 584–586

    • anti-parallel β-sheet, 584

  • rRNA, ribosomal RNA, 72, 642

    • base modifications, 238–239

    • expansion segments, ES, 504

    • gene clusters, 174

    • in translation, 242, 244

  • ruthenium, 431

  • S-adenosylmethionine, SAM, 165

  • saframycin, 440

  • salicyl chlorophosphite, 142

  • Sanger, Frederick

    • chain termination method, 328

    • DNA sequencing, 10, 326

  • Sanger sequencing, 10, 326, 328, 643

    • first generation sequencing, 328

    • improved, 328

  • sangivamycin

    • nucleoside analogue, synthesis, 112

  • SARS CoV-2, 386, 389, E21

  • satellite repeats

    • repetitious DNA, 177, 178, 643

  • scaffold protein, 250

  • scalar couplings, E8

  • scattering length, b, E19

  • second virial coefficient, E32, E33

  • seed region, 372

  • seed sequence, 369, 643

  • segmental duplication, 216, 643

  • selection methodologies

    • advances in, 406–407, 643

  • selection in vitro, SELEX

    • oligonucleotide selection, 109, 404, 409, 412, 418, 643

  • selective binding, 483

  • selenocysteine

    • UGA code for 21st amino acid, 243

  • semi-conservative replication, 198, 644

  • sequence errors, 342

  • sequence-specific recognition, 543

  • sequencing, 15–16, 644

    • automated fluorescent, 328

    • comparative analysis, 191–192

    • DNA, 188–194

    • DNA ladder, 432

    • genome, 188–192

    • Maxam Gilbert, 328

      • dimethyl sulfate reaction, 428

      • hydrazine reaction, 328

    • modified bases, 340–342

    • primary analysis, 190

    • read length, 328

    • RNA, 335–337

    • RNA-Seq, 16

    • Sanger, 326, 328

    • sequence by synthesis, 326

    • shotgun sequencing, 328–329, 644

    • triplet repeat sequences, 509

    • whole-transcriptome, 16

  • severe acute respiratory syndrome coronavirus

    • SARS-CoV-1, 158

    • SARS-CoV-2, 158

  • shapes of components

    • nucleoside & nucleotide, 29–32

  • Shine–Dalgarno sequence, 250, 644

  • short hairpin RNA, shRNA, 377, 644

  • shotgun sequencing, 188–190, 193

  • showdomycin

    • nucleoside analogue, 104

  • sibiromycin, 440

  • sickle cell anaemia, 12

  • sigma factor

    • prokaryotic transcription, 196, 225, 644

  • signal recognition particle, SRP, 234, 253

  • signal-to-noise ratio, 193

  • Signer, Rudolf, 4

  • SIL group, 296

  • silyl-Hilbert–Johnson method, 98

  • single-cell-seq, 193, 644

  • single molecule force spectroscopy, SMFS, E26

  • single-molecule localization microscopy, SMLM, E24

  • single-nucleotide polymorphism, SNP

    • DNA fingerprinting, 192, 644

  • single strand binding proteins, SSBs

    • DNA replication, 206, 211

  • single-stranded RNA, ssRNA, 584, 622

  • siRNA, small interfering RNA, 16, 100, 266, 372, 644

    • amyloidosis treatment, patisiran, 366, 373, 374

    • delivering in therapeutics, 373–374, 506–507

    • modification of linkages, 377–378

    • modification of siRNA architecture, 375–376

    • modification of termini, 378

    • sugar modification, 377

  • Siksnys, Virginijus, 391

  • site-directed mutagenesis, 319

  • site-specific recombination, 217, 219

  • size-exclusion chromatography, E30

  • skin cancer

    • ozone barrier, 446, 452

  • slow-off-rate modified aptamer, SOMAmer, 408, 410–411

  • small angle neutron scattering, SANS, E32

  • small angle X-ray scattering, SAXS, E32, E35

  • small molecule structure determination, E19

  • small nuclear ribonucleoproteins, snRNPs, 230

  • SMILing DNA, E4

  • Smith, Michael

    • site-directed mutagenesis, 319

  • SMRTbells, 333

  • SN 6999

    • DNA groove binding, 501

  • snoRNA, small nucleolar RNA, 178, 238–239, 260–262

    • C/D box snoRNAs, 260

    • H/ACA box snoRNAs, 261

  • snRNA, small nuclear RNA, 72, 644

    • splicesome component, 239–240

  • snRNPs, small nuclear ribonucleoproteins, 261, 610

  • sodium borohydride, 423

  • sofusbuvir, 164

  • solenoid

    • chromosome structure, 87, 90

  • solid-state NMR, E11

  • SOMAscan, 410

  • somatostatin, 11

  • Sonogashira reaction

    • modified base synthesis, 109, 112

  • Southern, Edwin

    • Southern blot, 84

    • DNA fractionation, 84, 344, 645

  • Sowa–Ouchi reaction, 137

  • substrate specificity

    • DNA enzymes, 551–555

  • spectroscopic properties

    • nucleoside & nucleotide, 27–28

  • Spiegelmer, 411, 412

  • spinal muscular atrophy, SMA, 610

  • spine of hydration

    • DNA structure, 39, 480, 645

  • 3′-splice site, 230

  • 5′-splice site, 230

  • splice-switching, 367–369

  • splicing, 172, 262, 365, 645

    • non-productive, 368, 638

    • optional exon usage, 365

  • splicing factor

    • SF3B1, 611

    • SRSF2, 612

    • U2AF1, 612

  • splint, 313

  • Sputnik V, 386

  • stavudine, d4T

    • antiviral nucleotide analogue, 158

  • Stec, Wojtek, 289

  • steric block oligonucleotide

    • cDNA block RNA recognition, 302, 368–369

  • Stille reaction, 114

  • STING, stimulator of interferon genes, 141

  • Stokes radius, E33

  • stop codon, 190, 242, 253–254, 645

  • streptomycin, 503

  • streptonigrin, 440

  • stress response, 138

  • structural biology, 17

  • structural dynamics, E22, E24

    • DNA motion, 85

    • gas phase, E15

    • macromolecular, E21

    • molecular mechanics, E39–40

    • molecular dynamics, E41

    • rapid motions, 86

  • structural polymorphism, 33

  • structure–activity relationships, SAR, 509

  • succinaldehyde, 434

  • sucrose density gradients, E32

  • sugar pucker, 29–30, 44

    • C2′-endo, 29, 33, 44, 115

    • C3′-endo, 30, 33, 44, 100, 115

  • suicide inhibitor, 153, 157

  • supercoiling

    • DNA, 37, 57–59, 179, 645, E27

    • energy of, 57

    • linkage, 56

    • linking number Lk, 56

    • super-helical density σ, 57

    • topological winding number Tw, 56

    • writhing number Wr, 56

  • Suzuki–Miyaura reaction, 109, 112, 114

  • SYBR gold, E27

  • symmetry, E18

  • synclinal, sc, 31

  • synperiplanar, 32

  • synthesis-dependent strand annealing, SDSA, 215, 645

  • synthetases

    • Class 1, 250

    • Class 2, 250

  • synthetic organophosphates, OP agents, 127

  • tallysomycin, 440

  • tandem copies, 587

  • target transcripts, 364

  • TATA binding protein, TBP

    • eukaryotic transcription, 195, 539, 547

  • taxonomy, 192, 645

  • T-cell leukaemia, 383

  • tegafur, prodrug, 434

  • telomerase

    • chromosome and lengthening, 210, 513, 645

    • inhibition, 513

  • telomere

    • eukaryotic chromosome, 178, 512, 645

    • protection of telomere protein, Pot1, 540

    • quaduplex structure, 511–512

  • telomere end-binding protein, TEBP, 540

  • temozolomide

    • anticancer drug, 439, 464, 466

  • template strand, 226, 227, 645

  • tenofovir, 165

  • tenofovir alafenamide, 165

  • termination

    • prokaryotic transcription, 226

  • TET-assisted bisulfite sequencing, TAB-Seq, 341

  • tetranucleotide hypothesis

    • DNA history, 4

  • tetraplex DNA, 61

  • tetrazomine

    • antibiotic, 442

  • therapeutic oligonucleotides

    • antisense, 363–365

  • thermophiles, 237

  • thermostable DNA polymerase

    • DNA sequencing, 305

  • thiazole, 491

  • thiazole orange, 516

  • 6-thioguanine, 114

    • anticancer agent, 155

  • thiophene, 491

  • thiophene-N-methylbenzimidazole, BI, 496

  • thiophosphoramidate morpholino, TMO, 360

  • thiopurines, 155–156

  • 4-thiouridine, 4sU, 432, 590

  • thymidine, Thd

    • ribothymidine in tRNA, 23, 66, 85, 423

  • thymidine kinase, TK

    • drug activation, 160

  • thymidylate kinase, 160

  • thymidylate synthase

    • drug target, 151–152, 157

  • thymine, Thy

    • base structure, 4, 22

  • thymine photodimers, 35, 447–448, 469, 471

  • thymus nucleic acid, 3

  • time-of-flight MS, TOF, E11

  • TmPyP4

    • 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)porphyrin, 514

  • Todd, (Lord) Alexander, 5, 118, 122

  • toll-like receptors, TLRs, 379, 381, 645

  • topoisomerases, 57–58, 155, 207, 646

  • topologically-associated domains, TADs, 180, 186

  • total correlation spectroscopy, TOCSY, E8

  • toyocamycin

    • nucleoside analogue, 112

  • trans-acting factors, 230, 646

  • transcript, 175, 646

  • transcription, 171–172, 646

    • bubble, 561

    • cis-acting regulatory sequences, 171–172, 212, 630

    • DNA–RNA heteroduplex formation, 77–78

    • elongation, 225, 226

    • enhancers, 173, 195

    • eukaryotic, 195–196

    • genomic organization, 197

    • initiation, 196, 225–226

    • prokaryotic, 196–197

    • proofreading, 165, 250, 350, 560

    • RNA polymerase ‘bubble,’ 561

    • silencers, 367

    • template strand, 226, 227

    • termination, 225, 226–227

    • unit, 171–172, 646

    • in vitro transcription, 311

  • transcriptional noise, 272

  • transcriptional silencing, 266

  • transcriptional start site, 174, 195, 641

  • transcriptional stop site, 174, 646

  • transcription factors, 195, 409, 533, 567–568, 646

    • general transcription factors, 226

    • zinc-bearing, 536

  • transcriptome

    • methylated, 460

    • RNA sequencing, 335, 338––340, 574, 646

  • transcriptome-wide analyses, 589

  • transduction, 314, 384, 646

  • trans-esterification reactions, 230

  • transfection, 314, 646

  • transferability, E40

  • transformation

    • gene cloning, 314, 432, 646

  • transgene, 383, 646

  • transient protection, 282–283

  • transition state, 646, E7

    • analogue, 466

  • translation, 172, 242–255, 646

    • elongation, 252

    • elongation factor, 245

    • ‘in-frame,’ 252

    • initiation, 245, 246, 251, 388

    • initiation complex, 246

    • initiation eukaryotic vs. viral, 253

    • initiation factor, 250

    • peptidyl transfer reaction, 246

    • recycling factor, 245

    • release factor, 245

    • termination, 253–254

  • translocation, 216, 246, 646

  • transport

    • RNA, 236

  • transposable elements

    • repetitious DNA, 177, 187–188, 234, 646

  • transposase, 187, 646

  • transposon

    • expression, 266

    • - mediated recombination, 217, 219

  • transthyretin, TTR, 390

  • 4-triazolo-pyrimidine, 112

  • tricycloDNA, 357

  • trimethylsilyl triflate, 98

  • tripartite recognition motif, TRM, 587–588

  • triple-helical DNA

    • structure, 59, 60

    • via synthetic oligonucleotide for gene expression block, 511

  • triple-stranded RNA

    • structure, 72–74

  • triplet code

    • protein biosynthesis, 9

  • tRNA, transfer RNA, 9, 21, 646

    • acceptor stem, 249, 250

    • adaptor molecule, 13

    • aminoacylation, 249–250, 606, 627

    • anticodon loop, 242

    • A-site, 246

    • base modifications, 237–238

    • cloverleaf structure, 69

    • cognate amino acid, 242, 605

    • cognate synthetase recognition, 250

    • D-loop, 424

    • E-site, 246

    • L-shape tertiary fold, 77

    • P-site, 246

    • ribosomal translocation, 244, 246

    • secondary structure, 72

    • TψC loop, 249

    • variable loop, 249

  • tRNA translocation

    • hybrid states model, 246

  • tropism, 384

  • tubercidin

    • nucleoside analogue, 112

  • tuberculosis, TB, 503

  • two-step mechanisms, 125, 127

  • UDP-galactose, 139

  • UDP-glucose, 139

  • UDP-hexoses

    • synthesis, 139

  • UDP-N-acetylglucosamine, 139

  • UFC radiation, 452

  • ultraviolet absorption, E2–3

    • extinction coefficient of bases, 27, E36

    • hypochromicity, E2, E36

    • purines & pyrimidines, E2

  • unequal sibling-chromsome exchange, 216

  • upstream open reading frame, uORF, 370

  • uracil, U, Ura, 4, 22

  • uridine, U, Urd, 387, 423

  • uridine, 2′-deoxy, dUrd

    • DNA damage & repair, 464

  • uridine, 2′-deoxy-2′,2′-difluorouridine

    • TDG glycosylase inhibition, 465

  • uridine, 2′-deoxy-5-fluoro-

    • error-prone PCR, 321

    • thymidylate synthase inhibition, 109

  • US Environmental Protection Agency, EPA

    • ToxCast programme, 433

  • US Food and Drug Administration, FDA, 418, 618, 632

  • UV melting, E36–37

  • valganciclovir, 161

  • Van der Waals

    • 3.4 Å base-pair separation, 37, 38

    • DNA models, 43, 67

    • minor groove contacts, 63, 491, 493, 497

  • van der Waals forces

    • in protein DNA interactions, 532

  • Varicella-zoster virus, VZV, 109

  • vascular endothelial growth factor-A, VEGF-A, 415

  • Vaxzevria, 385

  • vinyl chloride, 433

  • 5-vinyl-2′-deoxyuridine

    • antiviral agent, 160

  • 6-vinylpurine, 114

  • viral replication, 507

  • viral Rev protein, 579, 580

  • viral RNA

    • structure, 251

  • viral RNA function

    • bacteriophage packaging motor, 273

  • viral vectors

    • adeno-associated, AAV, 383–385

    • integrating, 382–383, 384

    • non-integrating, 383

  • viroids

    • virus replication, 55

  • virus

    • adeno-associated, AAV, 383–384

    • DNA, 159–162

    • eukaryotic, 186

    • genome, 186

    • lentivirus, 382

    • life cycle, 186

    • replication-deficient, 382, 642

    • RNA, 158–159, 251, 507

    • viral replication, 507

  • virus capsid shell

    • viral protein envelope, 273

  • Vorbrüggen, Helmut

    • glycosylation, 98, 118

  • Wallace rule

    • calculation of Tm, 84

  • water, 531–532

    • bulk water, 531

    • buried water molecules, 531

    • ordered water, 531

  • Watson, James

    • DNA structure, 7

  • Watson–Crick base-pairing, 8, 26–27, 32

    • adenines pairing with thymine photodimer, 64–65

    • structure of pairing, 448

    • DNA polymerase fidelity, 560

    • human mismatch repair, 470

    • in RNA tertiary structure, 77

    • rules, 351–352, 527, 647

    • in triplex DNA, 511

  • Weissman, Drew, 387

  • whole-genome duplication, WGD, 185

  • Wilkins, Maurice

    • DNA structure, 7

  • wobble base pairing, 26–27, 46, 460, 647

  • writhing DNA

    • unusual DNA structure, 49

  • writing, 15, 458

  • writing DNA

    • unusual DNA structure, 49

  • Wyman’s concept

    • median ligand activity, 482

  • wyosine

    • fluorescence, E4

    • minor tRNA base, 22, 107

  • xanthine oxidase

    • allopurinol therapy for gout, 153–154

  • xeno nucleic acids, XNAs, 301, 354, 407, 408, 647

  • xeroderma pigmentosum

    • nucleotide excision, 469

    • repair deficiency, 452, 473

  • X-linked X-inactive specific transcript, XIST, 269

  • X-ray, 453

    • Cambridge Crystallographic Data Centre (CCDC), E25

    • crystallography, E16–19

    • diffraction principle of, 12,

    • fibre diffraction, E20

      • dyad in diffraction pattern, antiparallel strands, E15

    • molecular replacement, MR, E18

    • multiple isomorphous replacement, MIR

      • 5-bromodeoxyuridine, E18

    • single crystal diffraction, E22

    • single-wavelength anomalous dispersion, SAD, E16

    • structure factor equation, E23

  • X-ray free-electron laser, XFEL, E16

  • X-ray photons, E21

  • Yoshikawa phosphorylation, 142

  • Yoshikawa reaction

    • nucleotide synthesis, 137

  • Zachau, Heinz

    • tRNA structure, 9

  • Z-DNA

    • left-handed DNA structure, 12, 33, 39–40

  • Zamecnik, Paul, 13, 16, 140, 362

  • zero-mode waveguides, ZMW, 333

  • zidovudine, AZT

    • anti-HIV therapy nucleoside analogue, 158–159

  • zip-code family of targeting proteins, 236

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