Nucleic Acid Aptamers: Selection, Characterization, and Application PDF
Preview Nucleic Acid Aptamers: Selection, Characterization, and Application
Methods in Molecular Biology 2570 Günter Mayer Marcus M. Menger Editors Nucleic Acid Aptamers Selection, Characterization, and Application Second Edition M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. Nucleic Acid Aptamers Selection, Characterization, and Application Second Edition Edited by Günter Mayer Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany Marcus M. Menger Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Potsdam, Germany Editors Gu¨nterMayer MarcusM.Menger LifeandMedicalSciencesInstitute BranchBioanalyticsandBioprocesses (LIMES) FraunhoferInstituteforCellTherapyandImmunology UniversityofBonn Potsdam,Germany Bonn,Germany ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-2694-8 ISBN978-1-0716-2695-5 (eBook) https://doi.org/10.1007/978-1-0716-2695-5 ©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerScience+BusinessMedia,LLC,part ofSpringerNature2023 Thisworkissubjecttocopyright.AllrightsaresolelyandexclusivelylicensedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,reproductionon microfilmsorinanyotherphysicalway,andtransmissionorinformation storageand retrieval,electronicadaptation, computersoftware,orbysimilar ordissimilar methodologynow knownorhereafter developed. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. CoverIllustrationCaption:CoverartdepictsthecrystalstructureofthemodifiedDNAaptamerSL1067boundtoits targetIL-1α.SL1067isuniformlysubstitutedatalldUpositionswith5-(2-naphthylcarboxamide)-deoxyuridine(2Nap- dU).Inthisimage,thehydrophobicnaphthylgroupsof2Nap-dUarehighlightedyellow,whiletheremainderofthe aptamerisshowninorangeandtheIL-1αproteinispresentedindeepblue.©SomaLogic ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface Inthepastdecades,theaptamerfieldhasseenaplethora ofselectionprocedures,adiverse setofbiophysicalmethodstocharacterizeaptamers’structures,kineticandthermodynamic properties, and various applications being adapted to the aptamer compound class. In this regard,andasitspredecessor from2015,thisbookissubdividedintothreepartsreflecting thesetopicsandthusprovidesrecentprotocolscoveringtheselection,characterization,and applicationofaptamers. TheselectionpartcomprisesChapters1,2,3,4,5,6,and7andprovidesprotocolsfor automation-assisted SELEX procedures (Chapter 1) and ligand-assisted identification of cell-bindingaptamers(Chapter2).Chapters3and 4describeprotocolsfor theimplemen- tationofemulsionPCR(ePCR)forclick-SELEXapproaches(Chapter3)andthegeneration ofchemicallymodifiedDNAlibraries(Chapter4).InChapter5,theidentificationofsmall molecule binding RNA aptamers by Capture-SELEX is described. Bioinformatic-assisted protocolsforaptamerdiscoveryinlargenucleicacidpopulations(Chapter6)andinlibraries obtained from so-called doped-SELEX procedures (Chapter 7) conclude Part I of this methodscollection. The second part (Chapters 8, 9, 10, 11, 12, and 13) depicts methods to characterize aptamers’interactionandstructuralpropertiesbybiophysicalapproaches.Isothermaltitra- tion calorimetry (ITC) for determining thermodynamic parameters of aptamers-target interaction is described in Chapter8. Chapter9 providesa protocol for measuringcircular dichroism (CD) spectra to gain structural information on aptamers, for example, the formation of G-quadruplex structures. Microscale thermophoresis (MST) as additional method to measure aptamer-target interaction properties in solution is described in Chapter10.Chapter11coverssurfaceplasmonresonance(SPR)studiesusingimmobilized ligands, and in Chapter 12, FRET-based protocols for aptamer characterization are given. The second part of the book concludes with protocols describing the characterization and application of aptamers, here SOMAmers, using DNA PAINT (Chapter 13). This chapter alsoprovidesagreatbridgetothethirdpart(Chapters14,15,16,17,18,19,and20)ofthe bookthatdiscussesapplicationprotocolsofaptamers. The application of aptamers in field-effect transistors to detect small molecules is described in Chapter 14, methods for the impedimetric detection of protein targets using aptamers are covered by Chapter 15, and protocols for measuring viral RNA binding to small molecules are topics of Chapter 16. Chapter 17 describes the expression of circular RNA aptamers being used in mammalian cells. The application of aptamers in enyzme- linked oligonucelotide assays (ELONA) is shown in Chapter 18. The combination of aptamers with fluorogenic RNAs as biosensors is explained in Chapter 19. Chapter 20 concludesthethirdpartofthebookbyexplicatingRAPTER,anautomatedelectrochemical analysisdetectionsystem. Wearegratefultoallcontributors,whomadethis bookpossibleandwereverypatient withusastherealizationtookquiteawhile.Additionally,wethankthecompanySomaLo- v vi Preface gic, Inc. (USA) for permission to use the crystal structure image of the modified DNA aptamerSL1067 boundtoitstarget IL‑1α ascoverart.Finally,we thinkthat thisrenewed protocolcollectioncoversmanystate-of-the-arttechniquesintheaptamerfieldand,hope- fully, will be an obliging resource for scientists identifying, characterizing, and using aptamers. Bonn,Germany Gu¨nterMayer Potsdam,Germany MarcusM.Menger Contents Preface ..................................................................... v Contributors................................................................. ix PART I SELECTION 1 AutomatedssDNASELEXUsingHistidine-TaggedTargetProteins.......... 3 StefanBreuersandGu¨nterMayer 2 DiscoveryofAptamersAgainstCellSurfaceMarkers UsingLigand-GuidedSelection...... ....... ....... ........ ....... ........ 13 NicoleWilliams,RutikaPatel,andPrabodhikaMallikaratchy 3 ImplementationofEmulsionPCRforAmplificationofClick-Modified DNADuringSELEX....... ........ ....... ....... ........ ....... ........ 39 MoujabChoukeife,AnnaJonczyk,andGu¨nterMayer 4 PreparationofChemicallyModifiedDNALibraryforSELEXvia IncorporationofCLB-dUTPinPrimerExtensionReaction........ .. ...... .. 45 MagdaPuchała,MartaRadzin´ska,JoannaGuzdek, AgnieszkaSok-Grochowska,AleksandraAdamowicz-Skrzypkowska, PawełPie˛ta,PrzemysławJurek,andMonikaCzarnecka 5 RNACapture-SELEXonStreptavidinMagneticBeads ....... ....... ........ 63 LeonKrausandBeatrixSuess 6 TheBioinformaticsofAptamers:HT-SELEXAnalysiswithAptaSUITE ....... 73 JanHoinkaandTeresaM.Przytycka 7 ImprovementofAptamersbyHigh-ThroughputSequencing ofDoped-SELEX.......... ........ ....... ....... ........ ....... ........ 85 Fre´de´ricDuconge´ PART II CHARACTERIZATION 8 AnalysisofAptamer-SmallMoleculeBindingInteractions UsingIsothermalTitrationCalorimetry ..... ....... ..... ... ..... .. ........ 105 SladjanaSlavkovicandPhilipE.Johnson 9 DeterminationofAptamerStructureUsingCircular DichroismSpectroscopy .... ........ ....... ....... ........ ....... ........ 119 YannickKerler,StephanSass,CarstenHille, andMarcusM.Menger 10 Immobilization-FreeDeterminationofDissociationConstants IndependentofLigandSizeUsingMicroScaleThermophoresis ...... ........ 129 WiebkeSabrowski,WalterF.M.St¨ocklein, andMarcusM.Menger vii viii Contents 11 Label-FreeDeterminationoftheKineticParametersofProtein-Aptamer InteractionbySurfacePlasmonResonance.......... ........ ....... ........ 141 NicoDreymann,AnjaM¨oller,andMarcusM.Menger 12 ProbingofFluorogenicRNAAptamersviaSupramolecularFo¨rster ResonanceEnergyTransfer withaUniversalFluorescent NucleobaseAnalog ........ ........ ....... ....... ........ ....... ........ 155 ChristianSteinmetzgerandClaudiaH¨obartner PART III APPLICATION 13 Slow-Off-Rate-ModifiedAptamerLabelingforFluorescence MicroscopyandDNA-PAINT....... ....... ....... ........ ....... ...... .. 177 SebastianStraussandRalfJungmann 14 Aptamer–Field-EffectTransistorsforSmall-MoleculeSensing inComplexEnvironments .......... ....... ....... ........ ....... ........ 187 NakoNakatsuka 15 Aptasensor forImpedimetricDetectionofLysozyme......... ....... ........ 197 EceEksin,HuseyinSenturk,andArzumErdem 16 BiophysicalAnalysisofSmallMoleculeBinding toViralRNAStructures .... ........ ....... ....... ...... .. ...... .... ..... 205 Liang-YuanChiu,JesseDavila-Calderon, ZhengguoCai, andBlantonS.Tolbert 17 DesigningandExpressingCircularRNAAptamerstoRegulate MammalianCellBiology.... ........ ....... ....... ........ ....... ........ 223 JacobL.LitkeandSamieR.Jaffrey 18 Enzyme-LinkedOligonucleotideAssay(ELONA) ........... ....... ........ 235 MiguelMoreno,AnaGarcı´a-Sacrista´n,M.ElenaMartı´n, andVı´ctorM.Gonza´lez 19 High-ThroughputDevelopmentandOptimizationofRNA-Based FluorogenicBiosensorsofSmallMoleculesUsingDroplet-Based Microfluidics....... ....... ........ .. .... ........ ........ ....... ........ 243 ClaireHusser,Ste´phanieBaudrey,andMichaelRyckelynck 20 RoboticAPTamer-EnabledElectrochemicalReader(RAPTER)System forAutomatedAptamer-MediatedElectrochemicalAnalysis.......... ........ 271 YoungLo,ShaolinLiang,WaljitS.Dhillo,AnthonyE.G.Cass, andJulianA.Tanner Index ...................................................................... 281 Contributors ALEKSANDRAADAMOWICZ-SKRZYPKOWSKA • PureBiologicsSA,Wrocław,Poland STE´PHANIEBAUDREY • Universite´deStrasbourg,CNRS,ArchitectureetRe´activite´del’ARN, UPR9002,Strasbourg,France STEFANBREUERS • LifeandMedicalSciencesInstitute(LIMES),UniversityofBonn,Bonn, Germany;CenterofAptamerResearchandDevelopment,UniversityofBonn,Bonn, Germany ZHENGGUOCAI • DepartmentofChemistry,DukeUniversity,Durham,NC,USA ANTHONYE.G.CASS • DepartmentofChemistry,ImperialCollegeLondon,London,UK LIANG-YUANCHIU • DepartmentofChemistry,CaseWesternReserveUniversity,Cleveland, OH,USA MOUJAB CHOUKEIFE • LifeandMedicalSciencesInstitute(LIMES),UniversityofBonn, Bonn,Germany MONIKACZARNECKA • PureBiologicsSA,Wrocław,Poland JESSE DAVILA-CALDERON • DepartmentofChemistry,CaseWesternReserveUniversity, Cleveland,OH,USA WALJITS.DHILLO • SectionofEndocrinologyandInvestigativeMedicine,ImperialCollege London,London,UK NICODREYMANN • FraunhoferInstituteforCellTherapyandImmunology,Branch BioanalysisandBioprocesses(IZI-BB),Potsdam,Germany;InstituteforBiochemistryand Biology,UniversityofPotsdam,Potsdam,Germany FRE´DE´RIC DUCONGE´ • CEA,FundamentalResearchDivision(DRF),InstitutofBiology Franc¸oisJacob(Jacob),MolecularImagingResearchCenter,Fontenay-aux-Roses,France; NeurodegenerativeDiseasesLaboratory,CNRSCEAUMR9199,Fontenay-aux-Roses, France;Paris-SaclayUniversity,Fontenay-aux-Roses,France ECEEKSIN • FacultyofPharmacy,AnalyticalChemistryDepartment,EgeUniversity, Bornova,Izmir,Turkey ARZUM ERDEM • FacultyofPharmacy,AnalyticalChemistryDepartment,EgeUniversity, Bornova,Izmir,Turkey ANAGARCI´A-SACRISTA´N • AptusBiotechSL,Madrid,Spain VI´CTORM.GONZA´LEZ • AptusBiotechSL,Madrid,Spain;GrupodeApta´meros, DepartamentodeBioquı´mica-Investigaci(cid:1)on,IRYCIS-HospitalUniversitarioRam(cid:1)ony Cajal,Madrid,Spain JOANNAGUZDEK • PureBiologicsSA,Wrocław,Poland CARSTENHILLE • PhysicalChemistry,InstituteofChemistry,UniversityofPotsdam, Potsdam,Germany;TechnicalUniversityofAppliedSciencesWildau,Wildau,Germany CLAUDIAHO¨BARTNER • InstituteofOrganicChemistry,JuliusMaximiliansUniversity Wu¨rzburg,Wu¨rzburg,Germany;Center forNanosystemsChemistry(CNC),Julius MaximiliansUniversityWu¨rzburg,Wu¨rzburg,Germany JANHOINKA • NationalCenter forBiotechnologyInformation,NationalLibraryof Medicine,NIH,Bethesda,MD,USA CLAIREHUSSER • Universite´deStrasbourg,CNRS,ArchitectureetRe´activite´del’ARN, UPR9002,Strasbourg,France ix
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