Principles of Fluorescence Spectroscopy

PRINCIPLES OF FLUORESCENCE SPECTROSCOPY 947
comparison with resonance energy transfer, 331–334
distance dependence, 332–333
encounter complexes and quenching efficiency, 333–334
by dabcyl, 722
energy transfer, 519
energy transfer, χ 0 changes from, 480
fractional accessibility, 288–290
experimental considerations, 289–290
Stern-Volmer plots, modified, 288–289
by gold, molecular beacons, 723–724
on gold surfaces, 313–314
molecular beacon by gold colloids, 313–314
molecular beacon by gold surface, 314
intramolecular, 314–317
DNA dynamics, 314–315
electron transfer in flavoprotein, 315–316
sensors based on photoinduced electron transfer, 316, 318
of lanthanides, 523
mechanisms of, 334–336
electron-exchange, 335
intersystem crossing, 334–335
photoinduced electron transfer, 335–336
molecular biology applications, 310–313
molecular beacons by guanine, 311
release of quenching upon hybridization, 310, 311
substrate binding to ribozymes, 311–312
molecular information from fluorescence, 18–19
of phosphorescence, 317–318
photoinduced electron transfer, 336–341
examples of, 338–340
in linked donor–acceptor pairs, 340–341
photoinduced electron transfer quenching in biomolecules, 341–342
DNA bases and nucleotides, 341–342
quenching of indole by imidazolium, 341
proteins
anisotropy decays, 431–432
tryptophan position and, 550
proteins, applications to, 290–300
colicin E1 folding, 292–293
conformational changes and tryptophan accessibility, 291
effects of quenchers on proteins, 292
endonuclease III, 290–291
multiple decay time quenching, 291–292
quenchers, 278
quenching-resolved emission spectra, 301–304
fluorophore mixtures, 301–302
Tet repressor, 302–304
self-, metal-enhanced fluorescence, 853–854
sensing applications, 305–310
amplified, 309–310
chloride-sensitive fluorophores, 306
chloride-sensitive green fluorescent protein, 307–309
intracellular chloride imaging, 306–307
simulated intensity decay, 101
single-molecule photoinduced electron transfer, 342–343
sphere of action, 285–286
static, theory of, 282
static and dynamic, 282–283
examples of, 283–284
steric shielding and charge effects, 286–288
DNA-bound probe accessibility, 286–287
ethenoadenine derivatives, 287–288
Stern-Volmer equation, deviations from, 284–285
transient effects, 343–348
experimental studies, 346–348
proteins, distance-dependent quenching in, 348
tryptophan fluorescence, by phenylalanine, 537
Quenching, advanced topics, 293–301
membranes, 293–300
boundary lipid, 298
lipid-water partitioning effects, 298–300
localization of membrane-bound tryptophan residues, 294–295
in micelles, 300
oxygen diffusion, 293–294
partitioning, 298–300
membranes, applications to
localized quenchers, 295–296
parallax and depth-dependent quenching, 296–298
membranes, diffusion in, 300–301
lateral, 300–301
probe accessibility to water- and lipid-soluble quenchers, 286–287
quenching efficiency, 281, 333, 543
Quenching constants, 309, 348, 548–549
Quenching efficiency, 281, 333, 542
encounter complexes, 333–334
Quin-2, 648, 649
fluorescence-lifetime imaging microscopy, 744–745
Quinine, 2, 7
chloride sensors, 631
Quinine sulfate, 51–52, 53, 56, 196, 197
Quinolinium, 279
R
R0 . See Förster distance
Rac activation, 459, 460
Radiating plasmon model, 856, 868
Radiation boundary condition (RBC) model, 344–346
Radiation patterns, 778–779
Radiative decay, 842–843
Radiative decay engineering, 841–870
introduction, 841–843
Jablonski diagram, 842–843
optical properties of metal colloids, 845–846
surface plasmon-coupled emission, 861–870
Radiative decay rate, 223, 537
Radiative transfer, 366
Radio-frequency amplifiers, frequency-domain lifetime
measurements, 167
Raman notch filter, 39
Raman scatter, 39, 42, 43, 289
Rapid diffusion limit, 467
Ras in single-molecule detection, 24
rATP, 725
Rayleigh scatter, 42, 59, 289, 766
Reaction coordinate, 238
Reaction kinetics, 758–759, 799
Receptors, membrane-bound, 813–815
Red and near-IR dyes, 74–75
Red-edge excitation shifts, 257–259
energy transfer, 259
membranes, 258–259
Red fluorescent protein, 81
Red shift, solvent effects on, 533–534
Reflectivity in surface-plasmon resonance, 862–863
Refractive index, 50, 208, 209