Subject Index 461
DNA (contd)
chain terminators 168
chips 184
circular 46–49
copying 223–235
cross-links 301, 330
double strand cleavage 314
drug intercalation 314, 350
duplex stability 195
elongation 234
expression chips 187
fingerprinting 181
footprinting 203–204, 297
helix
melting curve 428
helix-coil transition
circular dichroism 431
helix distortion by
BPDE-adduct 309
hybridisation 172
inserts 171
intergenic 215
intrastrand linking 303
isomorphous geometry 18
knotted 49
melting
multi-phase 429
melting curve 428
methylation & gene
expression 230
microarrays 185
nicked 47, 440
palindromic sequence 174, 175
primary structure 24
profiles 182
recombinant 170
repetitious 216
replication 223, 231
replication initiation 234
replication priming 233
satellite 216
secondary structure 24
semi-conservative replication 232
sequence determination 168–170
sequencing 168, 169
single molecule
single molecule force
spectroscopy 449
sticky ends 174
supercoiling 26
superhelical 46–47, 440
topology 232
transcription 223
triple-stranded 49–52
vector 170
zig-zag structure 31
DNA alkylation
biological consequences 323–325
chloroacetaldehyde,
etheno-derivatives 302
demethylation 326
‘hard’ alkylating agents, (SN1 agents),
primary carcinogens 301, 306,
308, 325, 327
phosphate triester 325
‘soft’ alkylating agents,
(SN2 agents) 301, 327
tolerance of 326
DNA annealing 66
DNA breathing 66, 359
DNA cation binding
counter-ion condensation 343
entropic release of counter-ions
non-polyelectrolyte contribution 343
polyelectrolyte contribution 343
DNA cellular content
by species 68
DNA cleavage
chain breaks by radicals 323
hydrogen atom abstraction 314, 323
superoxide radical 316
DNA conformation 24–32
average rise (Dz)26
helix parameters 29
helix rotation ()26
tilt angle ()26
DNA cross-link
intrastrand 303, 317
interstrand cross-links, ICLs 330
DNA cross-linking
azinomycin B 310, 311
DNA damage
chlorofluorocarbons, CFCs 321, 322
ozone barrier 316, 321
DNA enzymes
topoisomerase I 48, 416
topoisomerase II 49, 416
DNA footprinting
Fe-EDTA complex 297
DNA glycohydrolase
inhibition by nucleoside analogues 329
mechanisms 329
DNA helix
average parameters 29–30
energy of bending 401
energy of twisting 401
sequence-dependent modulation 33–36
DNA hydration 30, 346
DNA intercalation 347–360
bisintercalators 355
decrease in linear charge density 353
ethidium, propidium, proflavin 348
free energy of binding 354
neighbour exclusion principle 353
nonclassical threading 358–360
polycyclic aromatic hydrocarbons 347
solvent accessible surface 355
thermodynamic parameters 359
DNA intercalators
structures 349DNA ligase
gene manipulation 176
DNA methylation
in vivo 306
phosphate triesters 301
DNA microarray
analysis 187
DNA mutation 236–237
DNA packaging
eukaryotic 217, 408–409
in archaea and eubacteria 409–410
DNA photodimer
intrastrand 317
photoreversion 317, 326
DNA photoproduct
psoralen 319
DNA polymerase
erroneous activity 331
nucleotide polymerisation 124, 220
proofreading, DNA pol III 237, 330,
332, 410
DNA polymerase I 168, 235, 330, 332
DNA polymerase III 234, 332
DNA promoter 263
DNA properties
intrinsic viscosity 350
DNA protein recognition
representative motifs 391–397
DNA quadruplex 52–55
DNA recognition motifs 390–397
DNA recombination 238–248
DNA renaturation 65
DNA repair 325–333
accurate repair 324
adaptive Adaresponse 327
base pair mismatch 330
cross-link repair 330
endonucleases
APE1 405–406
error-prone 332
excision repair 328, 329
human DNA glycosylases 327, 328
mechanisms 331
phosphate triesters 327
photodimer repair 330, 332
post-replication repair 332
preferential repair 331
recombination repair 238, 239
replication bypass 317, 319
SOS repair 332
translesion synthesis 318
DNA structure
anisomorphic 40
A-tract 44
cruciforms 40, 41, 42
Dickerson dodecamer 27, 346, 347, 362
anthramycin complex 312
G-tract 44
hairpin loops 40
helical twist 33