466 Subject Index
oligonucleotide (contd)
gapmer 196
immune response 196
insertions 189
mixmer 196
reagents & therapeutics 193–202
sequencing
NMR 435
steric block 193, 194
structure
crystal-packing effects 439
NMR analysis 437
synthesis of modified 158–165
therapeutic 193
uptake with cationic lipids 195
oligonucleotide alignment
filamentous phase Pf1
NMR analysis 438
phospholipid bicelles
NMR analysis 438
oligonucleotide probes 172
oligoribonucleotide
chemical synthesis 153–155
synthesis
base protection 154
chain assembly 155
deprotection 155, 156
enzymatic 157
hydroxyl protection – ACE 155
hydroxyl protection – TBDMS 154
hydroxyl protection – TOM 155
enzymatic synthesis
ligation 157
transcription 157
oncogene
Ha-ras-1 proto-oncogene 325
open reading frame, ORF
epigenetic phenomena 281
operon
gene cluster 210
oriC
replication origin 234
8-oxo-2-deoxyguanosine
mutational nucleoside analogue 191
packaging
DNA 408–409
palindrome
metoperator 394
palladium-catalysed couplings
modified nucleoside synthesis 91,
94, 95
peptide nucleic acids, PNA
modified backbone oligomers 163, 164
phosphate
esters & anhydrides 100–110
phosphate diester
2 ,3-cyclic phosphate 286
cyclic phosphate hydrolysis 105
hydrolysis 104
‘in-line’ displacement 106
phosphate ester
diesters 100
formal relationships 107
hydrolysis 101
hydroperoxide radical cleavage 322
monoesters 101
rates of hydrolysis 105
structure 14
triesters 100, 327
phosphate monoester
structure 106
synthesis 110
phosphate triester
alkyl triester hydrolysis 103
aryl triester hydrolysis 104
DNA alkylation 325
phosphonoacetyl aspartate, PALA
pyrimidine biosynthesis inhibitor 120
phosphoramidite
synthesis 147
5-phosphoribosylamine
purine biosynthesis 117
phosphoric acid anhydrides
structure 100
phosphorodiamidate modified
oligonucleotides
backbone analogues 164
phosphorothioate
antisense application 196
backbone analogues 160
protection of mutagenised
DNA 189–190
5 -phosphorylation
in gene synthesis 177
phosphoryl transfer
mechanisms 102
photochemistry of nucleic
acids 316–322
photolithography
DNA synthesis on chip 185
photo-SELEX
oligonucleotide selection 202
physical properties
nucleoside & nucleotide 16–19
plasmids
DNA insertion vector 170
plastid
eukaryotic organelle 218
polyacrylamide gel electrophoresis
DNA sequencing 168
oligodeoxyribonucleotide
synthesis 153
oligonucleotide analysis 443
reptation
DNA movement 443
Polymerase
fidelity 191
polymerase chain reaction,
PCR 170–174error-prone 191
gene synthesis 178
polymerases
DNA 409–410
polymerases
RNA 410–412
polymorphism
analysis 188
polynucleotide kinase
oligonucleotide 5-phosphorylation 176
polyphosphate ester
monoalkyl ester synthesis 112
nucleoside 113
P^1 ,P^2 -dialkyl ester synthesis 112
structure 111
Pribnow box
prokaryotic transcription 224, 225
promoter
alternative 211
region 224
RNA polymerase II 228
transcription initiation 210
propeller twist
helical structure 33, 371, 390
protein
nucleic acid interactions 384–390
transport
signal recognition particle, SRP 280
protein engineering
modified protein production 190
proteins
-helix motifs 384, 392–394
‘ridge’ 394
aminoacyl tRNAGlu synthetase
class I, structure 420
binding RNA
dsRNA recognition 417
binding single-stranded DNA 396–397
binding single-stranded RNA 417, 418
-ribbon 384, 394–395
DNA binding
co-operative features 401
DNA duplex manipulation 413–416
DNA gyrase 416
DNA helicases 413
relationship to F1ATPase 414
DNA photodimer repair
photolyase 407
DNA pumps
bacterial infection 413, 415
plasmid-transfer in conjugation 415
DNA recognition specificity
direct readout 398
indirect readout 398, 401
DNA target selectivity
sliding, hopping, inter-segmental
transfer 404
DNA topoisomerase I
single strand break 416
DNA topoisomerase II