Analytical_Techniques_In_DNA_251

236 Index

P Rough draft WGS, 171
ROX acceptor dye, 14, 17
Phase domain, fluorescence lifetime, 21, 23i,
23–25 S

Photobleaching, 113, 115, 116, 136 Sample collection, 33
Photoresist (PR) resin, 62 Sample purification, 32
Photostable fluorescent dyes, 110
PHRAP assembler, 164 ESI-MS, 87
PHRED automated sequencer, 162, 164 integrated, 77–80
Physical mapping applications, 160, 160i, 161 UV-MALDI, 86–87
Planar CE chip technology, 62 Sanger, Fred, 3
Plasmid Bluescript, 37, Sanger sequencing method, 3
Plasmid clones, 163, 166 compared to Maxam-Gilbert, 3–4
Plasmid preparation, 31 MALDI-TOF-MS alternative, 91
PMMA (polymethylmethacrylate)-based Separation, 6–8, 64, 99
Sequence tagged connectors (STCs), 162
microchips, 35 Sequence tagged sites (STSs), 162
Polyacrylamide gel electrophoresis (PAGE), 2, 3 Sequence-ready genomic frameworks, 159–163
Sequencing by hybridization (SBH), 178
size-based separation, 6–7 biochemistry, 190–191
Polymerase chain reaction (PCR), 5, 30 optimality, 191–192
performance optimization, 187–189
and ancient DNA analysis, 196, 203–204 probing scheme, 181–183
BAC libraries, 162 reconstruction, 183–187
bacterial colony sequencing, 38 Sequencing ladder analysis, MALDI-TOF-MS,
clinical samples, 52–56
fluorescence incorporation, 122 91
in forensic DNA analysis, 223, 224 Short tandem repeats (STRs), 96, 217
gap closure, 168 Shotgun sequencing, 163, 166
integrated amplification, 74 Simple sequence repeats (SSRs), 163
sample preparation, 33 Single nucleotide polymorphisms (SNPs),
transcription for MALDI-TOF-MS, 94
and UV-MALDI analysis, 87 96–97
Polymethylmethacrylate (PMMA) multiplexing, 100, 100i, 102
primer-extension-based analysis, 97, 98i
microchannels, 135, 136 Single-channel, sequencing, 64–65
Polymorphisms, MALDI TOF-MS, 96–97 Single-molecule sequencing, 108
Primer oligo base extension (PROBE) assay, 97 detection, 110–113
Production sequencing, 163–164 future strategies, 146–147
Purification (integrated), 75–80 hydrodynamic focusing sample stream,

Q 128–134
identification, 113–121
Quantum yield, 14, 20 incorporation and degradation, 121–128
microchannels, 134–146
R procedure, 108–109, 109i
submicrometer capillaries, 134–146
“Racetrack effect,” 66 Size-exclusion columns (SEC), 38, 45, 47,
Radioactive labeling, 9, 13
Radioisotope sequencing, 1 54
Read-out, definition, 178 Slab-gel sequencing, 6–7
Resequencing, MALDI TOF-MS, 92
Restriction fragment length polymorphisms compared to CGE, 32
lifetimes, 22
(RFLPs), 96, 217 Small-volume solutions, 41
Revised Cambridge Reference Sequence (RCRS), Soft tissue, as ancient DNA source, 201
Solvent evaporation, 35
222, 225 SpectruMedix analysis system, 36
Rhodamine dyes, 19, 38, 113, 125 Submicrometer capillaries, single-molecule

and oxazine, 138 sequencing, 134–146
Robotics, 33

Index 237

T U

TAMRA acceptor dye, 14, 15t, 16 UV detection, clinical samples, 53, 54
Target, definition, 178
Temperature lowering, 108 V
The PinPoint™ assay, 99
Thermo aquaticus (Taq) polymerase, 6, 199 Very large scale integration (VLSI) processing,
ThermoSequenase (Amersham Life Science), 62, 65

38, 41 W
Ti:sapphire laser, 116
TIGR (Institute for Genomic Research) Watson/Crick-complementary binding, 178, 190
Whole genome sequencing, 163–172
Assembler, 164 Whole-Genome Shotgun (WGS), 167, 170
TIGR (Institute for Genomic Research),
Y
H. influenzae genome, 167, 168
Time domain, fluorescence lifetime, 21–22, 22i Yeast artificial chromosome (YAC), 159
Time-correlated single photon counting (TCSPC),

116–121
Time-resolved identification, 140–141, 144
Tunneling microscopy, 108
Two-photon excitation (TPE), 115, 116