Principles of Fluorescence Spectroscopy

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950 INDEX Single-molecule detection [cont'd] photophysics, 768–770 resonance energy transfer, 773–775 single-molecule orientation and rotational motions, 775–779 imaging of dipole radiation patterns, 778–779 orientation imaging of R6G and GFP, 777–778 time-resolved studies of single molecules, 779–780 Single-molecule detection (SMD), 342–343 Single-particle detection, 85 Single-photon counting, 103. See also Time-correlated single-photon counting Single-photon-counting avalanche photodiode (SPAD), 755, 763 Single-photon excitation, green fluorescent protein, 171 Single-stranded DNA binding protein, 552–554 Singlet state, 334 Site-directed mutagenesis, azurins, 538–539. See also Genetically engineered proteins Skeletal muscle troponin C, 490–492 Skilling-Jaynes entropy function, 148 Smoluchowski model, 281, 344, 345–346, 347 SNAFL, 640–641 SNARF, 640–641 Sodium analyte recognition probes, 645–647 Sodium-binding benzofuran isophthalate (SBFI), 645, 647 Sodium Green, 16, 17, 646, 647 Sodium probes, 17, 635–636, 643, 645–647 Soleillet's rule, depolarization factor multiplication, 436–437 Sol gels, 634 Solvent effects on emission spectra, 205–235, 533–534 additional factors, 219–223 changes in non-radiative decay rates, 222–223 excited-state intramolecular photon transfer, 221–222 locally excited and internal charge transfer states, 219–221 biochemical examples calmodulin, hydrophobic surface exposure, 226–227 cyclodextrin binding using dansyl probe, 227–228 fatty acid binding proteins, 226 with solvent-sensitive probes, 226–229 development of advanced solvent-sensitive probes, 228–229 Lippert equation, 208–213 application of, 212–213 derivation of, 210–212 Lippert-Mataga equation, 208–210 Lippert plots, specific solvent effects, 215–216 mixtures, effects of, 229–231 overview, 205–208 polarity surrounding membrane-bound fluorophore, 206–207 probe–probe interactions, 225–226 Prodan phase transitions in membranes, 217–219 specific, 213–215 spectral shift mechanisms, 207–208 summary of, 231–232 temperature effects, 216–217 tryptophan, 533–534 viscosity effects, 223–225 shear stress on membrane viscosity, 225 Solvent relaxation, 12. See also Relaxation dynamics; Solvent effects on emission spectra vs. rotational isomer formation, 253–255 Solvent-sensitive probes, 226–229 Soybean peroxidase (SBP), 595 SPA (N-sulfopropylacridinium), 631 Species-associated spectra (SAS), 269–270 Spectral diffusion in single-molecule detection, 767 Spectral karyotyping, 730–732 Spectral observables, sensors, 624–626 Spectral overlap, two-state model, 661 Spectral relaxation, 239, 596–598. See also Relaxation dynamics Spectral response, PMTs, 45–46 Spectral shift mechanisms, solvent effects on emission spectra, 207–208 Spectrofluorometer, 3, 27–29 for high throughput, 29–30 ideal, 30 schematics of, 28 Spectroscopy fluorescence correlation, 757, 797–832 general principles (See Principles of fluorescence) Sperm whale myoglobin, 584 Sphere of action, 285–286 Spin-labeled naphthalene derivative, 314 Spin-labeled PC, 298 Spin–orbit coupling, quenching, 278 Spotted DNA microarrays, 732–734 SPQ [6-methoxy-N-(3-sulfopropyl)quinolinium] chloride sensors, 171–172, 631–632 quenching, 279 Squirrel cage, 46 Stains, DNA, 712–715 energy-transfer stains, 715 fragment sizing by flow cytometry, 715 high-affinity bis, 713–715 Standard lamp, correction factors obtained with, 53 Standards corrected emission spectra, 52–53 emission spectra correction, 52–53 quantum yield, 54–55 Staphylococcal nuclease, 346, 347, 536, 558, 560, 564–565 anisotropy, 588 frequency-domain lifetime measurements, 171 intensity decay of, 583 Staphylococcus aureus metalloprotease, 550–551 Static quenching, 11, 65, 277. See also Quenching combined with dynamic quenching, 282–283 examples, 283–284 theory of, 280, 282 Steady-state and time-resolved fluorescence principles, 14–15 Steady-state anisotropy calculation of, 367 DPH in DPMC vesicles, 302 proteins, tryptophan position and, 551 Steady-state intensity, 15 Steady-state measurements continuous relaxation model, 238 light sources, 31–34 vs. time-resolved measurements, 97 Steric shielding, quenching, 281, 286–288 Stern-Volmer equation, 278, 283–284 derivation of, 280–281 deviations from, 284–285 Stern-Volmer plots, 549–550 Stern-Volmer plots, modified, 288–289 Stern-Volmer quenching, 11 Stern-Volmer quenching constant, 18, 279 Steroid analogs, 80 Steroid binding protein (SBP), 286
PRINCIPLES OF FLUORESCENCE SPECTROSCOPY 951 Steroids, quenching, 284, 286–287 Stilbene, 223–224, 309, 310 Stokes, G.G., 6, 7 Stokes-Einstein equation, 281 Stokes shift, 6–7, 119 advanced solvent-sensitive probes, 228–229 dielectric constant and refractive index effects, 207, 208 emission spectra and, 17–18 in protein labeling, 69–70 solvent effects, 208–210, 222 Stratum corneum, 751 Stray light, 36–37 Streak camera fluorescence-lifetime imaging microscopy, literature references, 754 Streak cameras, 125–128 Streptavidin, 565–566, 678 Streptococcal protein G, 244 Stretched exponentials, time-domain lifetime measurements, 144 Stroboscopic sampling, 124–125 Structural analogs of biomolecules, 80 Structural motifs tryptophan spectral properties and, 561–562 Structure protein (See Conformation; Protein folding) steric shielding and quenching, 286–288 Stryryl, 72 Substrate binding to ribozymes, 311–312 Subtilisin, 583 Subtilisin Carlsberg, 395–396 Succinimide, 278, 279, 281 Succinyl fluorescein, 707, 708 Sudan III, 633 Sulfa antibiotic sulfamethazine (SHZ), 660 Sulfonyl chlorides, 68 Sulforhodamine, 656, 657 Sulforhodamine, 865, 866 Sulfur dioxide, 279, 632 Support materials, oxygen sensors, 627, 628, 629 Support plane analysis, 134 Surface-bound assays, 867 Surface plasmon-coupled emission (SPCE), 861–870 applications of, 867–868 expected properties, 865 experimental demonstration, 865–867 future developments, 868–870 phenomenon of, 861 surface-plasmon resonance, 861–865 theory, 863–865 Surface-plasmon resonance (SPR), 861–865 Suspension arrays, multiplexed microbead, 726–727, 728 Syber Green, 720 Synchrotron radiation, 114 Syto 14, 189, 190 T TAMRA, 724, 726 Taqman, 720 Temperature effects excited-state lifetime, 221 LE and ICT states of Prodan, 216–217 metal–ligand complexes, 685 room-temperature phosphorescence of proteins, 599 rotational motions of proteins, 368, 369 solvent relaxation, 216–217 Terbium, 3, 87, 523–524 energy transfer, 467, 521 as fluorophores, 679 Förster distances, 468 Terbium probes, 87 p-Terphenyl, 120, 133, 134, 178 resolution of two widely spaced lifetimes, 178–180 Tetraethylorthosilicate (TEOS), 634 Tetrahydrorhodamine, 454 Tetramethylrhodamine-labeled lipid (TMR-POPE), 764 Tetramethylrhodamine-labeled nucleotide, 808–809 Tetramethylrhodamine (TMR), 313, 314, 707, 729, 769 RET imaging of fibronectin, 516 Tetraoctylammonium hydroxide (TOAH), 634 Tet repressor, 145, 302–304 Texas Red, 41, 69, 70, 72, 707 Texas Red-PE, 72 T-format anisotropy measurement, 29, 363–364 Thallium, 279 Theory anisotropy, 355–358 anisotropy decay, 414–415 energy transfer for donor–acceptor pair, 445–448 homotransfer and heterotransfer, 450–451 orientation factor, 448–449 transfer rate dependence on distance, overlap integral, and orientation factor, 449–450 energy-transfer sensing, 636–637 frequency-domain lifetime measurements, 161–163 global analysis of data, 162–163 least-squares analysis of intensity decays, 161–162 phase-sensitive detection, 195–197 examples of PSDF and phase suppression, 196–197 quenching, 278–282 relaxation dynamics, time-dependent, 250–251 representative literature references, 504 Thermophilic β-glycosidase, 594 Thiazole dyes, DNA technology, 715 Thiazole orange, 74–75 Thin-film filters, 39–40 Thiocyanate, 279, 631 Three-decay time model, 178, 179 Three-dimensional imaging of cells, 618–619 Three-photon excitation, cross-sections for, 609 Thymidine kinase, 497 TICT (twisted internal charge transfer), 207, 220, 221, 627, 645 Time-correlated single-photon counting (TCSPC), 103–107, 241 convolution integral, 106–107 detectors color effects in, 119–121 DNA sequencing, 123–124 dynode chain PMTs, 118 microchannel plate PMTs, 117–118 multi-detector and multidimensional, 121–124 timing effects of monochromators, 121 electronics, 114–117 amplifiers, 115 analyte-to-digital converter (ADC), 115 constant fraction discriminators, 114–115 delay lines, 116
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Principles of Fluorescence Spectros
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Joseph R. Lakowicz Center for Fluor
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Preface The first edition of Princi
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x GLOSSARY OF ACRONYMS DNS dansyl o
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xii GLOSSARY OF ACRONYMS TRES time-
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xiv GLOSSARY OF MATHEMATICAL TERMS
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xvi CONTENTS 2.9.4. Conversion betw
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xviii CONTENTS 6. Solvent and Envir
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xx CONTENTS 10.4.4. Alignment of Po
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xxii CONTENTS 14.7.1. Simulations o
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xxiv CONTENTS 19.12. New Approaches
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xxvi CONTENTS 25.3. Optical Propert
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2 INTRODUCTION TO FLUORESCENCE Figu
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6 INTRODUCTION TO FLUORESCENCE inst
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10 INTRODUCTION TO FLUORESCENCE Fig
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12 INTRODUCTION TO FLUORESCENCE ns,
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14 INTRODUCTION TO FLUORESCENCE 1.7
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24 INTRODUCTION TO FLUORESCENCE due
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28 INSTRUMENTATION FOR FLUORESCENCE
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3 Fluorescence probes represent the
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PRINCIPLES OF FLUORESCENCE SPECTROS
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98 TIME-DOMAIN LIFETIME MEASUREMENT
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100 TIME-DOMAIN LIFETIME MEASUREMEN
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5 In the preceding chapter we descr
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6 Solvent polarity and the local en
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238 DYNAMICS OF SOLVENT AND SPECTRA
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278 QUENCHING OF FLUORESCENCE 8.1.
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280 QUENCHING OF FLUORESCENCE Figur
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282 QUENCHING OF FLUORESCENCE ly ev
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290 QUENCHING OF FLUORESCENCE relat
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298 QUENCHING OF FLUORESCENCE σ ar
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320 QUENCHING OF FLUORESCENCE 47. R
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322 QUENCHING OF FLUORESCENCE 113.
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328 QUENCHING OF FLUORESCENCE P8.3.
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330 QUENCHING OF FLUORESCENCE P8.11
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332 MECHANISMS AND DYNAMICS OF FLUO
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10 Measurements of fluorescence ani
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444 ENERGY TRANSFER Figure 13.1. Fl
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446 ENERGY TRANSFER wavelength is e
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448 ENERGY TRANSFER Table 13.1. Cal
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450 ENERGY TRANSFER Figure 13.6. Ab
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452 ENERGY TRANSFER safe for many p
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454 ENERGY TRANSFER Figure 13.12. P
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456 ENERGY TRANSFER Figure 13.16. E
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458 ENERGY TRANSFER Figure 13.21. R
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460 ENERGY TRANSFER Figure 13.24. R
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462 ENERGY TRANSFER tiple acceptors
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464 ENERGY TRANSFER Figure 13.29. A
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466 ENERGY TRANSFER Figure 13.33. F
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468 ENERGY TRANSFER Table 13.3. Rep
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470 ENERGY TRANSFER 55. Clegg RM. 1
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472 ENERGY TRANSFER Tong AK, Jockus
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474 ENERGY TRANSFER Figure 13.39. O
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14 In the previous chapter we descr
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578 TIME-RESOLVED PROTEIN FLUORESCE
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608 MULTIPHOTON EXCITATION AND MICR
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19 Fluorescence sensing of chemical
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676 NOVEL FLUOROPHORES Figure 20.1.
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678 NOVEL FLUOROPHORES Figure 20.7.
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680 NOVEL FLUOROPHORES Figure 20.12
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698 NOVEL FLUOROPHORES 33. Acherman
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700 NOVEL FLUOROPHORES 103. Demas J
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702 NOVEL FLUOROPHORES 176. Montalt
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21 During the past 20 years there h
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22 Fluorescence microscopy is one o
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758 SINGLE-MOLECULE DETECTION Figur
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766 SINGLE-MOLECULE DETECTION small
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770 SINGLE-MOLECULE DETECTION Table
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786 SINGLE-MOLECULE DETECTION face
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788 SINGLE-MOLECULE DETECTION TCSPC
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790 SINGLE-MOLECULE DETECTION 53. H
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792 SINGLE-MOLECULE DETECTION Ke PC
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794 SINGLE-MOLECULE DETECTION Polar
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862 RADIATIVE-DECAY ENGINEERING: SU
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Appendix I Corrected Emission Spect
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Appendix II Fluorescence Lifetime S
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890 APPENDIX III P ADDITIONAL READI
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892 APPENDIX III P ADDITIONAL READI
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894 ANSWERS TO PROBLEMS A1.4. A. Th
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896 ANSWERS TO PROBLEMS Energy tran
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