Nucleic Acids in Chemistry and Biology, ed. G. M. Blackburn, M. Egli, M. J. Gait, and J. K. Watts, The Royal Society of Chemistry, 4th edn, 2022, pp. 648-670.
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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
