Subject Index 467
double strand break 416
DNA-binding by protein loops
Rel & Stat proteins 396
DNA-protein binding
kinetic aspects 402–404
helix-turn-helix motif 385, 392
homeodomain, sequence-specific
induced fit 386, 404
interaction with nucleic acids 384–422
leucine zipper 392–393, 403
met repressor protein 394
nucleases
structure-selective 407
nucleic acid binding
water 398–399
nucleic acid binding
forces 387–391
nucleic acid complexes
base stacking 390
dipolar forces 390
dispersion forces 390–391
electrostatic forces 384–386
entropic forces 390
hydrogen bonds 387–389
hydrophobic effect 389–390
kinetics & thermodynamics 398–404
non-specific interactions 398–402
salt bridges 389, 398–400
salt effects 400–401
specificity 404–407
structure & specificity 399–400
oligonucleotide/oligosaccharide
binding fold, OB 397
polymerases 409–412
polymerases
DNA-directed DNA 409–411
polymerases
DNA-directed RNA 410–412
RNA interactions and
assemblies 416–421
RNA polymerase
‘futile’ cycle 412
two metal mechanism 413
synthesis
mitochondria 274
mRNA 273
TATA-binding 391–392
transport
tRNA aminoacyl synthetases 417, 419
zinc-bearing motifs
steroid & nuclear receptors 393
zinc fingers 393
pseudodeoxyuridine
UDG inhibition 329
pseudogenes
defective mammalian genes 215
pseudoknot
secondary & tertiary structure 289
pseudorotation at phosphorus
trigonal bipyramid 102, 106
pseudorotation cycle
sugar pucker 20
pseudouridine,
synthesis 88
UDGase inhibitor 271
purine base
structure 14
purine nucleoside
chemical synthesis 79
purine nucleoside phosphorylase,
PNP 84
purine nucleotide biosynthesis 116–118
committed step 117
de novopathways 116
salvage pathways 119
purine photoproduct
adenine photoproducts 320
8-oxoguanine 320, 328
purine-pyrimidine tracts
unusual DNA structure 40
pyrimidine
base 14
pyrimidine analogue, dP
mutational base 192
pyrimidine nucleoside
synthesis 82
pyrimidine nucleotide biosynthesis
de novopathways 119
salvage pathways 120
pyrimidine oligomers
degradation of apurinic acid 296
pyrimidine photoproduct
cell death 318
cis-syn-thymine photodimer 237,
316, 317
pyrimidine(6–4)pyrimidone
photoproduct 317
thymine photohydrate 316quadruplex DNA
ligand binding 375
selective ligands 378Raman spectroscopy 433
recA protein
single strand DNA binding 332
recombinant DNA
hybrid DNA for cloning 8, 170
recursive PCR
gene synthesis & detection 178, 179
repair
damaged DNA 325–333
replication
bypass 332
DNA 231
fork 232
origin 233, 234
pre-priming complex 234
rolling circle 286
repressor proteinlexA, multifunctional 332
restriction endonuclease
sequence-specific DNA
cleavage 173, 176
restriction enzyme
DNA specificity 402–403
palindromic sites 175, 402
restriction enzyme cleavage
markers 222
retrotransposon
repetitious DNA 216, 281
retrovirus
inhibitor 129
(+)-strand RNA virus 220
reverse transcriptase
intron insertion 124, 281
RNA sequencing 170
reverse-splicing reaction
intron insertion 282
ribonuclease A
mechanism 106
ribonucleoside
periodate cleavage 297
ribonucleotide reductase
mechanism 121–122
ribosomal factory
eukaryotic/prokaryotic comparison 276
ribosome
30S subunit 276, 278
50S subunit 276, 278
70S, A-site 278
70S, E-site 278
70S, P-site 278
internal re-entry sites, IRES 288
mRNA tunnel 278
RNA-protein recognition 387
riboswitches
native aptamer role 203
ribothymidine
structure 14
ribozyme
catalytic mechanism 287
hairpin 286
hammerhead 286
RNA self-splicing 266, 285–286
RISC, RNAi–induced silencing
complex gene silencing 283
RNA
2 -O-methylation 282
base modification 271
bulges 61–62, 386
capping 263
catalytic 266
catalytic 285
coaxial stacking 198
cross-linking 300
duplex 263, 282, 288
duplexes 193
editing
deaminase Apobec-1 270