Aptamers for Analytical Applications: Affinity Acquisition and Method Design

414 Pages·2019·16.67 MB·English

by  Yiyang Dong

AptamersforAnalyticalApplications
Aptamers for Analytical Applications
AffinityAcquisitionandMethodDesign
EditedbyYiyangDong
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vii
Contents
AbouttheAuthor xv
Foreword xvii
Preface xix
1 IntroductionofSELEXandImportantSELEXVariants 1
YiyangDong,ZhuoWang,SaiWang,YehuiWu,YufanMa,andJiahuiLiu
1.1 SELEX 1
1.2 NegativeSELEXandItsAnalogs 3
1.3 One-RoundSELEX 5
1.4 CE-SELEX 6
1.5 MicrofluidicSELEX 8
1.6 Cell-SELEX 10
1.7 InSilico-SELEX 12
1.8 Post-SELEXandInChemico-SELEX 14
1.9 Auto-SELEX 17
1.10 Primer-FreeSELEX 17
1.11 GenomicSELEX 18
1.12 Photo-SELEX 19
1.13 qPCR-SELEX 19
1.14 Perspectives 20
References 21
2 InChemicoModificationofNucleotidesforBetter
Recognition 27
PrzemyslawJurek,MartaMatusiewicz,MaciejMazurek,andFilipJelen
2.1 Introduction 27
2.1.1 BeyondATGC 27
2.1.2 TheScopeofThisChapter 29
2.2 ModifiedFunctionalNucleicAcids 30
2.2.1 The“Hows” 30
2.2.1.1 Post-SELEXOptimization 30
2.2.1.2 In-lineModifications 30
2.2.2 The“Whys” 31
2.2.2.1 TheHurdles 31
viii Contents
2.2.2.2 TheGains 32
2.2.3 The“Ifs” 33
2.3 BackboneModifications 35
2.3.1 2′-OHModifications 36
2.3.2 PhosphodiesterBondModifications 36
2.3.3 XenoNucleicAcids 38
2.3.3.1 TNA 39
2.3.3.2 FANAs 39
2.3.3.3 HNA,CeNA,LNA,ANA 39
2.3.3.4 OtherModifications 40
2.4 NucleobaseModifications 40
2.4.1 GeneralInformation 40
2.4.2 ModifiedAptamersandCatalysts 42
2.4.2.1 IntroductionofCationicMoieties 42
2.4.2.2 CatalystswithProtein-likeSidechains 43
2.4.2.3 Nucleobase-linkedNucleobases 44
2.4.2.4 GlycansTargetingwithBoronicAcids 44
2.4.2.5 “ClickChemistry”–BasedVersatileApproach 45
2.4.2.6 NonenzymaticSelection–X-aptamers 45
2.4.2.7 SlowOff-rateModifiedAptamers 46
2.5 AptamerswithExpandedGeneticAlphabet 48
2.5.1 GACTZPAptamers 48
2.5.2 AptamerswithaHydrophobicFifthBase 50
2.6 Summary 52
2.A Appendix 52
References 68
3 ImmobilizationofAptamersonSubstrates 85
AnnalisaDeGirolamo,MaureenMcKeague,MichelangeloPascale,
MarinaCortese,andMariaC.DeRosa
3.1 Introduction 85
3.2 MethodsforImmobilizationofAptamers 87
3.2.1 PhysicalAdsorption 87
3.2.2 CovalentBinding 88
3.2.2.1 CovalentImmobilizationofActivatedAptamersonaFunctionalized
Surface 88
3.2.2.2 CovalentImmobilizationofModifiedAptamersonActivated
Surfaces 92
3.2.2.3 CovalentImmobilizationbyEntrapment 95
3.2.2.4 CovalentImmobilizationbyElectrografting 97
3.2.3 Self-assembledMonolayers 98
3.2.4 Avidin–BiotinBinding(AffinityCoupling) 100
3.2.5 ElectrochemicalAdsorption 101
3.2.6 Hybridization 101
3.3 ImmobilizationofAptamersonSubstratesforDiagnostic
Applications 102
3.3.1 FlatGold 102
3.3.1.1 SurfacePlasmonResonanceDetection 109
Contents ix
3.3.1.2 ElectrochemicalDetection 109
3.3.2 SolidPhase 111
3.3.2.1 OpticalDetection 112
3.3.2.2 SampleCleanup 114
3.3.3 Nanomaterials 115
3.4 FuturePerspectivesonNewSubstratesandNewImmobilization
Chemistries 116
3.5 Conclusions 117
References 119
4 CharacterizationofAptamer–LigandComplexes 127
RebecaMiranda-Castro,Noemíde-los-Santos-Álvarez,and
MaríaJ.Lobo-Castañón
4.1 Introduction 127
4.2 EquilibriumCharacterization:Thermodynamics 128
4.2.1 BasicPrinciples 128
4.2.2 Separation-BasedMethods 133
4.2.2.1 EquilibriumDialysisandRelatedTechniques 133
4.2.2.2 High-PerformanceLiquidChromatography 135
4.2.2.3 Electrophoresis 136
4.2.3 DirectMethods 137
4.2.3.1 IsothermalTitrationCalorimetry 138
4.2.3.2 Fluorescence-BasedMethods 140
4.3 KineticCharacterization 146
4.3.1 HeterogeneousMethods 148
4.3.1.1 SurfacePlasmonResonance 148
4.3.1.2 ElectrochemicalImpedanceSpectroscopy 152
4.3.2 HomogeneousMethods 154
4.3.2.1 RotatingDropletElectrochemistry 154
4.3.2.2 CapillaryElectrophoresis 157
4.3.2.3 Nanopore-BasedStudies 159
4.4 ConcludingRemarks 162
Acknowledgments 163
References 164
5 UtilizationofAptamersforSamplePreparationinAnalytical
Methods 173
ZhiyongYanandYangLiu
5.1 Introduction 173
5.2 SubstrateMaterialsDevelopedforImmobilizationofAptamers 175
5.3 UtilizationofAptamersforSamplePreparationinSPE 177
5.3.1 AptamersUtilizedinAffinityColumnforSPE 181
5.3.2 AptamersUtilizedinOtherSPE 182
5.4 AptamersUtilizedinSPME 182
5.4.1 AptamersUtilizedinFiberSPME 183
5.4.2 AptamersUtilizedinSBSE 184
5.4.3 AptamersUtilizedinOtherFormatsofSPME 185
x Contents
5.5 AptamersUtilizedinOtherAffinityChromatography 185
5.6 AptamersUtilizedinMicrofluidicSeparationSystem 187
5.7 AptamersUtilizedinMagneticSeparationSystem 189
5.7.1 AptamersUtilizedinMagneticSolid-PhaseExtraction(MSPE) 190
5.7.2 AptamersUtilizedinOtherMagneticSeparationFormats 190
5.8 AptamersUtilizedinCE 191
5.9 AptamersUtilizedinOtherSampleSeparationMethods 192
5.10 ConclusionandOutlook 192
References 192
6 DevelopmentofAptamer-BasedColorimetricAnalytical
Methods 205
SubashC.B.Gopinath,ThangavelLakshmipriya,M.K.MdArshad,and
ChunHongVoon
6.1 Introduction 205
6.2 AptamerGenerationforColorimetricAssay 206
6.3 Aptasensor 206
6.4 Aptamer-AuNP-BasedColorimetricAssays 207
6.5 ApplicationsofAuNP-Aptamer-BasedColorimetricAssays 211
6.6 Conclusions 213
References 213
7 Enzyme-LinkedAptamerAssay(ELAA) 219
YiyangDongandSaiWang
7.1 Introduction 219
7.2 Enzyme-LinkedImmunosorbentAssay 219
7.3 AnalyticalMeritsofAptamervsAntibody 221
7.4 Enzyme-LinkedAptamerAssay(ELAA) 223
7.5 ComparisonofDirect-CompetitiveELAA(dc-ELAA),
Indirect-CompetitiveELAA(ic-ELAA),andELISA 225
7.6 Conclusion 226
References 227
8 DevelopmentofAptamer-BasedFluorescenceSensors 229
SeyedM.Taghdisi,RezvanYazdian-Robati,MonaAlibolandi,
MohammadRamezani,andKhalilAbnous
8.1 Introduction 229
8.2 Fluorescent-Dye-BasedAptasensors 230
8.3 Nanoparticle-BasedAptasensors 231
8.3.1 FluorescentAptasensorsBasedonGoldNanoparticles 231
8.3.2 FluorescentAptasensorsBasedonCarbonNanomaterials 234
8.3.3 FluorescentAptasensorsBasedonSilicaNanoparticles 236
8.3.4 FluorescentAptasensorsBasedonSilverNanoparticles 238
8.3.5 FluorescentAptasensorsBasedonDNAStructures 239
8.3.5.1 FluorescentAptasensorsBasedonDNANanostructures 239
8.3.5.2 FluorescentAptasensorsBasedonTriple-HelixMolecularSwitch
(THMS) 240
Contents xi
8.4 Conclusion 241
Acknowledgment 241
SuggestedWebsites 242
References 242
9 DevelopmentofAptamer-BasedElectrochemical
Methods 247
Jian-guoXu,LiYao,LinCheng,ChaoYan,andWeiChen
9.1 Introduction 247
9.2 ClassificationofElectrochemicalAptasensors 247
9.3 AmperometricAptasensors 248
9.3.1 CovalentLabels 248
9.3.1.1 EnzymeLabels 248
9.3.1.2 OtherCovalentlyLinkedRedoxSpecies 250
9.3.2 Non-covalentLabels 256
9.3.2.1 IntercalatedRedoxSpecies 256
9.3.2.2 CationicRedoxSpecies 260
9.3.3 Label-FreeAptasensors 263
9.4 PotentiometricAptasensors 265
9.5 ImpedimetricAptasensors 266
9.6 ElectrochemiluminescenceAptasensors 268
9.7 Conclusion 268
References 269
10 DevelopmentofAptamer-BasedLateralFlowAssay
Methods 273
MiriamJauset-Rubio,MohammadS.El-Shahawi,AbdulazizS.Bashammakh,
AbdulrahmanO.Alyoubi,andCiaraK.O’Sullivan
10.1 Introduction 273
10.2 DevelopmentofAptamer-BasedLateralFlowAssay–Strategy 275
10.2.1 AnalogiesandDifferencesComparedtoLateralflowImmunoassays
(LFIAs) 275
10.2.2 FundamentalAssayConsiderations 276
10.2.3 FundamentalAnalyticalConsiderations 277
10.3 LateralFlowAptamerAssays 278
10.3.1 SandwichAssay 278
10.3.2 CompetitiveAssay 281
10.3.3 SignalAmplification 283
10.4 SummaryandPerspectives 291
References 294
11 DevelopmentofAptamer-BasedNon-labelingMethods 301
HuajieGu,LilingHao,andZhoupingWang
11.1 Introduction 301
11.2 SurfacePlasmonResonance(SPR)-BasedAptasensor 302
11.2.1 Introduction 302
xii Contents
11.2.2 ThePrincipleofSPRTechnique 302
11.2.3 TheClassificationofSPRBiosensors 303
11.2.3.1 SPRBiosensorsBasedonAngularModulation 303
11.2.3.2 SPRBiosensorsBasedonWavelengthModulation 304
11.2.3.3 SPRBiosensorsBasedonAmplitudeModulation 304
11.2.3.4 SPRBiosensorsBasedonPhaseModulation 304
11.2.4 TheApplicationofAptamer-BasedSPRTechnique 304
11.2.4.1 DeterminationoftheAffinityofAptamers 305
11.2.4.2 DetectionAnalyteConcentrations 305
11.2.5 SummaryandProspectsofSPRAptasensors 310
11.3 QuartzCrystalMicrobalance(QCM)-BasedAptasensor 311
11.3.1 Introduction 311
11.3.2 ThePrincipleofQCMTechnique 311
11.3.3 TheApplicationofAptamer-BasedQCMTechnique 312
11.3.3.1 DeterminationoftheAffinityofAptamers 312
11.3.3.2 DetectionofAnalyteConcentrations 313
11.3.4 SummaryandProspectofQCMAptasensors 318
11.4 IsothermalTitrationCalorimetry(ITC) 319
11.4.1 Introduction 319
11.4.2 ThePrincipleofITCTechnique 319
11.4.3 ThermodynamicParametersObtainedfromITCExperiment 320
11.4.4 ApplicationofITCinAssociationBetweenAptamerandTarget 322
11.4.4.1 InteractionBetweentheAptamerDomainofthePurineRiboswitch
andLigands 322
11.4.4.2 InteractionBetweentheCocaine-BindingAptamerandQuinine 324
11.4.4.3 AffinityTestbyITCAfterSystemicEvolutionofLigandsby
EXponentialEnrichment(SELEX) 327
11.4.5 Summary 329
11.5 MicroScaleThermophoresis(MST) 329
11.5.1 Introduction 329
11.5.2 ThePrincipleofMSTTechnique 330
11.5.3 ApplicationofMSTinAssociationBetweenAptamerandTarget 332
11.5.3.1 InteractionBetweenSteroidHormonesandAptamers 332
11.5.3.2 AffinityTestbyMSTAfterSystemicEvolutionofLigandsby
EXponentialEnrichment(SELEX) 333
11.5.4 Summary 335
References 335
12 ChallengesofSELEXandDemeritsofAptamer-Based
Methods 345
HaiyunLiuandJinghuaYu
12.1 Introduction 345
12.2 ChallengesofSELEX 347
12.2.1 AptamerDegradation 347
12.2.2 Purification 348
12.2.3 BindingAffinity(K ) 348
d
12.2.4 TargetImmobilization 349