Nucleic Acid Aptamers: Selection, Characterization, and Application

283 Pages·2022·10.601 MB·English

by  Günter Mayer, Marcus M. Menger

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
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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
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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