Avarietyof?uorescentandluminescentmaterialsintheformofmolecules,their complexes,andnanoparticlesareavailableforimplementationasreportingunits intosensingtechnologies. Increasingdemandsfromtheseapplicationareasrequire developmentofnew?uorescencereportersbasedonassociationandaggregationof ?uorescencedyesandontheirincorporationintodifferentnanostructures. Inter- tionsbetweenthesedyesandtheirincorporatingmatricesleadtonewspectroscopic effectsthatcanbeactivelyusedforoptimizingthesensordesign. Oneofthese effects is a spectacular formation of J-aggregates with distinct and very sharp excitationandemissionbands. Byincorporationintonanoparticles,organicdyes offer dramatically increased brightness together with improvement of chemical stabilityandphotostability. Moreover,certaindyescanformnanoparticlesth- selvessothattheirspectroscopicpropertiesareimproved. Semiconductorquantum dotsaretheothertypeofnanoparticles thatpossessuniqueandveryattractive photophysicalandspectroscopicproperties. Manyinterestingandnotfullyund- stoodphenomenaareobservedinclusterscomposedofonlyseveralatomsofnoble metals.Inconjugatedpolymers,strongelectronicconjugationbetweenelementary chromophoricunitsresultsindramaticeffectsinquenchingandinconformati- dependentspectroscopicbehavior. Possessingsuchpowerfulanddiversearsenaloftools,wehavetoexplorethem innovelsensingandimagingtechnologiesthatcombineincreasedbrightnessand sensitivityinanalytedetectionwithsimplicityandlowcostofproduction. The present book overviews the pathways for achieving this goal. In line with the discussion on monomeric ?uorescence reporters in the accompanying book (Vol. 8ofthisseries),aninsightfulanalysisofphotophysicalmechanismsbehind the ?uorescence response of composed and nanostructured materials is made. Based on the progress in understanding these mechanisms, their realization in differentchemicalstructuresisoverviewed. vii viii Preface Demonstratingtheprogressinaninterdisciplinary?eldofresearchanddev- opment,thisbookisprimarilyaddressedtospecialistswithdifferentbackground- physicists, organic and analytical chemists, and photochemists - to those who developandapplynew?uorescencereporters. Itwillalsobeusefultospecialists inbioanalysisandbiomedicaldiagnostics. Kyiv,Ukraine AlexanderP.Demchenko June2010 Contents PartI GeneralAspects NanocrystalsandNanoparticlesVersusMolecularFluorescent LabelsasReportersforBioanalysisandtheLifeSciences: ACriticalComparison ...3 UteResch-Genger,MarkusGrabolle,RolandNitschke, andThomasNann OptimizationoftheCouplingofTargetRecognition andSignalGeneration ...41 AnaB. Descalzo,ShengchaoZhu,TobiasFischer,andKnutRurack CollectiveEffectsIn?uencingFluorescenceEmission ...107 AlexanderP. Demchenko PartII EncapsulatedDyesandSupramolecularConstructions FluorescentJ-AggregatesandTheirBiologicalApplications ...135 MykhayloYu. LosytskyyandValeriyM. Yashchuk Conjugates,Complexes,andInterlockedSystems BasedonSquarainesandCyanines ...159 LeonidD. Patsenker,AnatoliyL. Tatarets,OleksiiP. Klochko, andEwaldA. Terpetschnig PartIII Dye-DopedNanoparticlesandDendrimers Dye-DopedPolymericParticlesforSensingandImaging ...193 SergeyM. Borisov,TorstenMayr,Gu..nterMistlberger,andIngoKlimant ix x Contents Silica-BasedNanoparticles:DesignandProperties ...229 SongLiang,CarrieL. John,ShupingXu,JiaoChen,YuhuiJin, QuanYuan,WeihongTan,andJuliaX. Zhao LuminescentDendrimersasLigandsandSensors ofMetalIons ...253 GiacomoBergamini,EnricoMarchi,andPaolaCeroni ProspectsforOrganicDyeNanoparticles ...285 HiroshiYao PartIV LuminescentMetalNanoclusters Few-AtomSilverClustersasFluorescentReporters ...307 IsabelD?'ezandRobinH. A. Ras LuminescentQuantumClustersofGoldasBio-Labels ...333 M. A. HabeebMuhammedandT. Pradeep PartV ConjugatedPolymers Structure,EmissiveProperties,andReportingAbilities ofConjugatedPolymers ...357 MaryA. Reppy OpticalReportingbyConjugatedPolymers viaConformationalChanges ...389 RozalynA. SimonandK. PeterR. Nilsson FluorescenceReportingBasedonFRETBetweenConjugated PolyelectrolyteandOrganicDyeforBiosensorApplications ...417 Kan-YiPuandBinLiu Index ...455 PartI GeneralAspects NanocrystalsandNanoparticlesVersus MolecularFluorescentLabelsasReporters forBioanalysisandtheLifeSciences: ACriticalComparison UteResch-Genger,MarkusGrabolle,RolandNitschke,andThomasNann Abstract At the core of photoluminescence techniques are suitable ?uorescent labels and reporters, the spectroscopic properties of which control the limit of detection,thedynamicrange,andthepotentialformultiplexing.

Avarietyof?uorescentandluminescentmaterialsintheformofmolecules,their complexes,andnanoparticlesareavailableforimplementationasreportingunits intosensingtechnologies. Increasingdemandsfromtheseapplicationareasrequire developmentofnew?uorescencereportersbasedonassociationandaggregationof ?uorescencedyesandontheirincorporationintodifferentnanostructures. Inter- tionsbetweenthesedyesandtheirincorporatingmatricesleadtonewspectroscopic effectsthatcanbeactivelyusedforoptimizingthesensordesign. Oneofthese effects is a spectacular formation of J-aggregates with distinct and very sharp excitationandemissionbands. Byincorporationintonanoparticles,organicdyes offer dramatically increased brightness together with improvement of chemical stabilityandphotostability. Moreover,certaindyescanformnanoparticlesth- selvessothattheirspectroscopicpropertiesareimproved. Semiconductorquantum dotsaretheothertypeofnanoparticles thatpossessuniqueandveryattractive photophysicalandspectroscopicproperties. Manyinterestingandnotfullyund- stoodphenomenaareobservedinclusterscomposedofonlyseveralatomsofnoble metals.Inconjugatedpolymers,strongelectronicconjugationbetweenelementary chromophoricunitsresultsindramaticeffectsinquenchingandinconformati- dependentspectroscopicbehavior. Possessingsuchpowerfulanddiversearsenaloftools,wehavetoexplorethem innovelsensingandimagingtechnologiesthatcombineincreasedbrightnessand sensitivityinanalytedetectionwithsimplicityandlowcostofproduction. The present book overviews the pathways for achieving this goal. In line with the discussion on monomeric ?uorescence reporters in the accompanying book (Vol. 8ofthisseries),aninsightfulanalysisofphotophysicalmechanismsbehind the ?uorescence response of composed and nanostructured materials is made. Based on the progress in understanding these mechanisms, their realization in differentchemicalstructuresisoverviewed. vii viii Preface Demonstratingtheprogressinaninterdisciplinary?eldofresearchanddev- opment,thisbookisprimarilyaddressedtospecialistswithdifferentbackground- physicists, organic and analytical chemists, and photochemists - to those who developandapplynew?uorescencereporters. Itwillalsobeusefultospecialists inbioanalysisandbiomedicaldiagnostics. Kyiv,Ukraine AlexanderP.Demchenko June2010 Contents PartI GeneralAspects NanocrystalsandNanoparticlesVersusMolecularFluorescent LabelsasReportersforBioanalysisandtheLifeSciences: ACriticalComparison ...3 UteResch-Genger,MarkusGrabolle,RolandNitschke, andThomasNann OptimizationoftheCouplingofTargetRecognition andSignalGeneration ...41 AnaB. Descalzo,ShengchaoZhu,TobiasFischer,andKnutRurack CollectiveEffectsIn?uencingFluorescenceEmission ...107 AlexanderP. Demchenko PartII EncapsulatedDyesandSupramolecularConstructions FluorescentJ-AggregatesandTheirBiologicalApplications ...135 MykhayloYu. LosytskyyandValeriyM. Yashchuk Conjugates,Complexes,andInterlockedSystems BasedonSquarainesandCyanines ...159 LeonidD. Patsenker,AnatoliyL. Tatarets,OleksiiP. Klochko, andEwaldA. Terpetschnig PartIII Dye-DopedNanoparticlesandDendrimers Dye-DopedPolymericParticlesforSensingandImaging ...193 SergeyM. Borisov,TorstenMayr,Gu..nterMistlberger,andIngoKlimant ix x Contents Silica-BasedNanoparticles:DesignandProperties ...229 SongLiang,CarrieL. John,ShupingXu,JiaoChen,YuhuiJin, QuanYuan,WeihongTan,andJuliaX. Zhao LuminescentDendrimersasLigandsandSensors ofMetalIons ...253 GiacomoBergamini,EnricoMarchi,andPaolaCeroni ProspectsforOrganicDyeNanoparticles ...285 HiroshiYao PartIV LuminescentMetalNanoclusters Few-AtomSilverClustersasFluorescentReporters ...307 IsabelD?'ezandRobinH. A. Ras LuminescentQuantumClustersofGoldasBio-Labels ...333 M. A. HabeebMuhammedandT. Pradeep PartV ConjugatedPolymers Structure,EmissiveProperties,andReportingAbilities ofConjugatedPolymers ...357 MaryA. Reppy OpticalReportingbyConjugatedPolymers viaConformationalChanges ...389 RozalynA. SimonandK. PeterR. Nilsson FluorescenceReportingBasedonFRETBetweenConjugated PolyelectrolyteandOrganicDyeforBiosensorApplications ...417 Kan-YiPuandBinLiu Index ...455 PartI GeneralAspects NanocrystalsandNanoparticlesVersus MolecularFluorescentLabelsasReporters forBioanalysisandtheLifeSciences: ACriticalComparison UteResch-Genger,MarkusGrabolle,RolandNitschke,andThomasNann Abstract At the core of photoluminescence techniques are suitable ?uorescent labels and reporters, the spectroscopic properties of which control the limit of detection,thedynamicrange,andthepotentialformultiplexing.