Table Of ContentM M Edited by
eeting the need for an up-to-date and detailed primer on all aspects of the topic, this
ready reference reflects the incredible expansion in the application of FRET and its deri- e Igor Medintz and Niko Hildebrandt
d
vative techniques over the past decade, especially in the biological sciences. This wide
i
diversity is equally mirrored in the range of expert contributors. n
t
The book itself is clearly subdivided into four major sections. The first provides some z FRET –
background, theory, and key concepts, while the second section focuses on some com- •
mon FRET techniques and applications, such as in vitro sensing and diagnostics, the de- H
termination of protein, peptide and other biological structures, as well as cellular biosen-
i
sing with genetically encoded fluorescent indicators. The third section looks at recent deve- ld Förster Resonance
lopments, beginning with the use of fluorescent proteins, followed by a review of FRET e
usage with semiconductor quantum dots, along with an overview of multistep FRET. b
r
The text concludes with a detailed and greatly updated series of supporting tables on a
FRET pairs and Förster distances, together with some outlook and perspectives on FRET. n
Written for both the FRET novice and for the seasoned user, this is a must-have re- d Energy Transfer
t
source for office and laboratory shelves.
(
E
d
s
Dr. Igor L. Medintz obtained his B.S. and M.S in Forensic Science, follo- .) From Theory to Applications
wed by a Ph.D. degree in Molecular Biology in 1998 at the City University
of New York. He carried out research as a postdoctoral fellow at the Uni-
versity of California Berkeley as well as at U.S. Naval Research Laboratory
(NRL) in Washington, D.C. Since 2004, he has been a Research Biologist
at NRL where he focuses on developing chemistries to interface nanoma-
terials with biology and understanding how nanoparticles engage in diffe-
rent types of energy transfer.
FF
öR
rE
s
tT
e
r–
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Professor Niko Hildebrandt obtained a Diploma in Medical Physics in e
2001 at the University of Applied Sciences Berlin and a Ph.D. degree in s
Physical Chemistry in 2007 at the University of Potsdam, where he also o
n
carried out postdoctoral research until 2008. From 2008 to 2010 he was
a
head of the group NanoPolyPhotonics at the Fraunhofer Institute for Ap-
n
plied Polymer Research in Potsdam. Since 2010 he has been Full Professor
c
at Université Paris-Sud, where he is leading the group of NanoBioPhotonics
e
(www.nbp.ief.u-psud.fr) at the Institut d’Electronique Fondamentale with
E
a research focus on time-resolved FRET spectroscopy and imaging for
n
multiplexed nanobiosensing.
e
r
g
y
T
r
a
n
s
f
e
r
ISBN 978-3-527-32816-1
www.wiley-vch.de 9 783527 328161
Editedby
IgorMedintz
NikoHildebrandt
FRET-FörsterResonance
EnergyTransfer
RelatedTitles
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V
Contents
Preface XV
ListofContributors XIX
PartOne Background,Theory,andConcepts 1
1 HowIRememberTheodorFo€rster 3
HerbertDreeskamp
2 RememberingRobertCleggandElizabethJares-ErijmanandTheir
ContributionstoFRET 9
ThomasM.Jovin
2.1 BiographicalSketchofBobClegg 10
2.2 BiographicalSketchofEliJares-Erijman 11
2.3 ThePervasiveInfluenceofGregorioWeber 12
2.4 ContributionsbyBobCleggtoFRET 12
2.5 ContributionsbyEliJares-ErijmantoFRET 16
2.6 AFinalThought 18
References 19
3 Fo€rsterTheory 23
B.WiebvanderMeer
3.1 Introduction 23
3.2 Pre-F€orster 23
3.3 BottomLine 25
3.4 9000-Form,9-Form,andPracticalExpressionsoftheR6Equation 26
0
3.5 OverlapIntegral 28
3.6 Zones 31
3.7 TransferMechanisms 33
3.8 Kappa-SquaredBasics 34
3.9 IdealDipoleApproximation 35
3.10 ResonanceasanAll-or-NothingEffect 36
3.11 DetailsAbouttheAll-or-NothingApproximationofResonance 39
VIjContents
3.12 ClassicalTheoryCompleted 41
3.13 OscillatorStrength–EmissionSpectrumRelation
fortheDonor 42
3.14 OscillatorStrength–AbsorptionSpectrumRelation
fortheAcceptor 43
3.15 QuantumMechanicalTheory 44
3.16 TransferinaRandomSystem 47
3.17 DetailsforTransferinaRandomSystem 48
3.18 ConcentrationDepolarization 51
3.19 FRETTheory1965–2012 52
References 59
4 OptimizingtheOrientationFactorKappa-SquaredforMoreAccurate
FRETMeasurements 63
B.WiebvanderMeer,DanielM.vanderMeer,andStevenS.Vogel
4.1 Two-ThirdsorNotTwo-Thirds? 63
4.2 RelevantQuestions 65
4.3 HowtoVisualizeKappa-Squared? 65
4.4 Kappa-SquaredCanBeMeasuredinAtLeastOneCase 68
4.5 AveragingRegimes 70
4.6 DynamicAveragingRegime 72
4.7 WhatIstheMostProbableValueforKappa-Squaredinthe
DynamicRegime? 76
4.8 Optimistic,Conservative,andPracticalApproaches 83
4.9 ComparisonwithExperimentalResults 85
4.10 SmartSimulationsAreSuperior 90
4.11 StaticKappa-Squared 92
4.12 BeyondRegimes 101
4.13 Conclusions 102
References 103
5 HowtoApplyFRET:FromExperimentalDesigntoDataAnalysis 105
NikoHildebrandt
5.1 Introduction:FRET–MoreThanaFour-LetterWord! 105
5.2 FRET:Let’sgetstarted! 106
5.3 FRET:TheBasicConcept 107
5.4 FRET:InevitableMathematics 112
5.4.1 F€orsterDistance(orF€orsterRadius) 112
5.4.2 FRETEfficiency 113
5.4.2.1 DeterminationbyDonorQuenching 113
5.4.2.2 DeterminationbyAcceptorSensitization 113
5.4.2.3 DeterminationbyDonorQuenchingandAcceptorSensitization 114
5.4.2.4 DeterminationbyDonorPhotobleaching 115
5.4.2.5 DeterminationbyAcceptorPhotobleaching 115
5.4.3 FRETwithMultipleDonorsand/orAcceptors 116
ContentsjVII
5.5 FRET:TheExperiment 118
5.5.1 TheDonor–AcceptorFRETPair 118
5.5.2 F€orsterDistanceDetermination 119
5.5.3 TheMainFRETExperiment 122
5.5.3.1 Steady-StateFRETMeasurements 123
5.5.3.2 Time-ResolvedFRETMeasurements 130
5.5.3.3 InterpretationofTime-ResolvedFRETData 133
5.6 FRETbeyondF€orster 139
5.6.1 Time-ResolvedFRETwithLanthanide-BasedDonors 140
5.6.1.1 TerbiumtoQuantumDotFRETUsingTime-ResolvedDonor
QuenchingandAcceptorSensitizationAnalysis 141
5.6.2 BRETandCRET 147
5.6.3 EnergyTransfertoMetalNanoparticles(FRET,NSET,DMPET,
NPILM,etc.) 148
5.6.4 OtherTransferMechanisms 150
5.6.4.1 ElectronExchangeEnergyTransfer(DexterTransfer) 151
5.6.4.2 ChargeTransfer(MarcusTheory) 152
5.6.4.3 PlasmonCoupling 153
5.6.4.4 SingletOxygenDiffusion 154
5.7 SummaryandOutlook 155
References 156
6 MaterialsforFRETAnalysis:BeyondTraditionalDye–Dye
Combinations 165
KimE.Sapsford,BridgetWildt,AngelaMariani,AndrewB.Yeatts,
andIgorMedintz
6.1 Introduction 165
6.2 Bioconjugation 166
6.3 OrganicMaterials 171
6.3.1 Ultraviolet,Visible,andNear-Infrared
EmittingDyes 171
6.3.2 QuencherMolecules 173
6.3.3 EnvironmentallySensitiveFluorophores 175
6.3.4 Dye-ModifiedMicrospheres/Nanomaterials 179
6.3.5 DendrimersandPolymerMacromolecules 180
6.3.6 PhotochromicDyes 182
6.3.7 CarbonNanomaterials 186
6.4 BiologicalMaterials 188
6.4.1 NaturalFluorophores 188
6.4.2 NonnaturalAminoAcids 190
6.4.3 GreenFluorescentProteinandDerivatives 192
6.4.4 Light-HarvestingProteins 200
6.4.5 DNA-BasedMacrostructures/Nanotechnology 201
6.4.6 Enzyme-GeneratedBioluminescence 201
6.4.7 Enzyme-GeneratedChemiluminescence 209
VIIIjContents
6.5 InorganicMaterials 211
6.5.1 LuminescentLanthanideComplexesandDopedNano-/
Microparticles 212
6.5.2 LuminescentTransitionMetalComplexes 217
6.5.3 NobleMetalNanomaterials(Gold,Silver,andCopper) 219
6.5.4 Silicon-BasedMaterials 222
6.5.5 SemiconductorNanocrystals 223
6.6 Multi-FRETSystems 231
6.7 SummaryandOutlook 236
References 236
PartTwo CommonFRETTechniques/Applications 269
7 InVitroFRETSensing,Diagnostics,andPersonalizedMedicine 271
SamanthaSpindel,JessicaGranek,andKimE.Sapsford
7.1 Introduction 271
7.2 SmallOrganicMoleculesandSyntheticOrganic
Polymers 272
7.3 Carbohydrate–Lipid 273
7.4 TheBiotin–AvidinInteraction 273
7.5 ProteinsandPeptides 275
7.5.1 BindingProteins 275
7.5.2 AntigensandEpitope-BasedPeptideSequences 277
7.5.3 PeptideSequencesforEnzymaticSensing 279
7.6 Antibodies 282
7.7 NucleicAcid(DNA/RNA) 287
7.7.1 MolecularBeacons 288
7.7.2 PolymeraseChainReactionandFRET 289
7.7.2.1 FRETHybridizationProbes 290
7.7.2.2 TaqMan 291
7.7.2.3 ScorpionAssay 292
7.7.2.4 Others 294
7.7.3 IsothermalAmplificationReactionsandFRET 294
7.7.4 ClinicalApplicationsofNucleicAcidDetection
UsingFRET 295
7.7.4.1 DetectionofPathogens 295
7.7.4.2 PrognosticandDiagnosticApplications 296
7.7.4.3 PharmacogenomicsandPersonalizedMedicine 298
7.8 Aptamers 299
7.9 High-ThroughputandPoint-of-CareDevices 302
7.9.1 PoCTechnologyAdvances 302
7.9.2 PoCMaterialAdvances 304
7.10 Conclusions 305
References 305
