Nucleic Acid and Peptide Aptamers: Methods and Protocols

404 Pages·2009·5.47 MB·English

by  Shawn K. Piasecki

M M B TM
ETHODS IN OLECULAR IOLOGY
SeriesEditor
JohnM.Walker
SchoolofLifeSciences
UniversityofHertfordshire
Hatfield,Hertfordshire,AL109AB,UK
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M M B TM
ETHODS IN OLECULAR IOLOGY
Nucleic Acid and Peptide Aptamers
Methods and Protocols
Edited by
Gu¨nter Mayer
University of Bonn, Germany
Editor
Gu¨nterMayer
UniversityofBonn
Bonn,Germany
[email protected]
SeriesEditor
JohnM.Walker
UniversityofHertfordshire
Hatfield,Herts.
UK
ISSN1064-3745 e-ISSN1940-6029
ISBN978-1-934115-89-3 e-ISBN978-1-59745-557-2
DOI10.1007/978-1-59745-557-2
LibraryofCongressControlNumber:2008938954
#HumanaPress,apartofSpringerScienceþBusinessMedia,LLC2009
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Preface
Afterthedecipheringofthehumangenomeandthoseofotherorganisms,theinvestigation
of the function of gene products and their orchestral interplay is now one of the most
important challenges in the life sciences. In this regard, specific ligands are required that
allow the sensitive detection and functional assignment of gene products, favourably in the
native context, which can be a model organism or at least cultured cells. Darwinian-like
evolutionary methods, which enablethe identification of such ligands, are described in this
volumeoftheHumanaPressMethodsinMolecularBiologySeries,entitledNucleicAcidand
PeptideAptamers.Theidentifiedactivecompoundsaccordingtotheprotocolsdescribedin
Nucleic Acid and Peptide Aptamers harbour information about both their active
conformation and the blueprint for their own synthesis. This feature allows the
simultaneous screening of up to 1016 different molecules in one test tube by the
application of appropriate selection schemes and the rapid synthetic access to adapt the
ligands for certain purposes. Selection procedures can be performed solely in vitro,
allowing themostconvenientcontrolof theselectionprocess andthus retaining controlof
thecharacteristicsoftheidentifiedligands.Targetmoleculescanbeeithersmallcompounds
(ormetabolites),proteins,nucleicacidsorevencomplextargetssuchaslivingcells.
Thepresentprotocolcollectioncoversmethodsrelatedtothetwomajorclassesofmolecules
employed for in vitro selection procedures: Nucleic acids and peptides/proteins. The 22
chapters of Nucleic Acid and Peptide Aptamers highlight important methodologies in the
field of evolutionary molecular biology approaches. The collection allows researchers not
only to identify ligands for their target molecules but also describes protocols for the
application of these ligands in certain research issues. These ligands, unless they are of
nucleic acid or of peptidic nature, can act as potent inhibitors and enable the functional
investigationand/orthedetectionofthetargetmolecule.Thisvolumeismeanttosupport
students,postdoctoralfellows,andseniorscientistintheireffortstoinvestigatebiomolecules
by using specific nucleic acid and/or peptide aptamers and offers guidelines for their
identificationandapplication.
Chapter 1 (by Ellington) describes the synthesis of nucleic acid libraries and methods to
investigating their diversity. In the following Chapters 2–6 protocols for the application of
differentinvitroselectionmethodstargetingdistinctmoleculesareillustratedindetail.These
protocolscoverthemodificationofproteinswithbiotin,enablingaccesstostreptavidin–biotin
chemistry for the separation step during the selection process (by Ho¨ver and Mayer) and
protocols for the identification of aptamers by capillary electrophoresis (by Mosing and
Bowser), a method that circumvents any protein modification prior selection. Chapters 4–6
describetheselectionofaptamerstargetingsmallmolecules(byPiganeau),complextargets(by
Franciscis)andribonucleicacids(byToulme´).Protocolsforthecharacterizationofaptamersby
state-of-the-artmethodscanbefoundintheChapters7(byWernerandHahn),describingthe
applicationoffluorescencecorrelationspectroscopyfordeterminingthedissociationconstant
ofanaptamer-targetinteraction.OnthesubjectofstructuralinvestigationsChapters8and9,
byWakemanandWinklerandBateyetal.,respectively,giveprotocolsfortheapplicationofin-
line probing of RNA structures and the growth and analysis of crystals to determine the
v
vi Preface
secondary and tertiary structure of RNA molecules by X-ray crystallography. Applications of
aptamersarehighlightedintheChapters10–14.Thesechaptersgiveinsighthowaptamerscan
be adapted to different assay formats, covering locked nucleic acids (by Erdmann), the
application of aptamers for diagnostic purposes (by Gronewold and by Lu et al.), the use of
aptamerstocontrolgeneexpression(byWeigandandSuess)andasmolecularprobesforthe
identification of small molecule inhibitors of protein function with aptamer inherited
properties (by Yamazaki and Famulok). The nucleic acid aptamer part is then closed by a
Chapter15byTavitianetal.describingprotocolsallowingtheinvivoimagingofaptamers.
Thepeptideaptamerpartcommenceswithprotocolsthatdescribedifferentmethodsforthe
identification of peptide aptamers. These chapters also include detailed explanations of the
constructionofsuitablepeptidelibrariesfortheselectionprocess.Chapter16byArndtetal.
describestheuseofphagedisplayandcomplementationassaysfortheidentificationofpeptides
that interfere with protein-protein interactions. Chapter 17 by Takahashi and Roberts
introducethemRNAdisplaymethodologyandstrategiesbasedonthewell-knownandwide
spread used yeast ‘‘two hybrid’’ system for the specific enrichment of peptide aptamers and
ligand-regulatedpeptideaptamerscanbefoundinChapter18(byMiller).Lopez-Ochoaetal.
givedetailsforthehigh-throughputidentificationandcharacterizationofpeptideaptamersin
Chapter19.Arecentlydescribedvariantofpeptideaptamers,namelyMicrobodies,whichare
embedded in a certain three-dimensional, highly stable scaffold, is introduced in Chapter 20
(byBlind).Chapters21and22illustratehowpeptideaptamerscanbeusedtoidentifysmall
molecules(byColas)andfortheapplicationofpeptidesasdrugcarriers(byBeck-Sickinger).
Theprotocolsgivenhereinrepresentastate-of-the-artcollectionofmethodologiesforthe
isolation, characterizationandapplicationofbothpeptideandnucleicacidaptamers andwill
allowresearcherstoapplythesecompoundstoaddressdistinctresearchissues.
Gu¨nterMayer,PhD.
Contents
Preface.................................................................. v
Contributors............................................................. ix
PART I: NUCLEIC ACID APTAMERS
1. NucleicAcidPoolPreparationandCharacterization ......................... 3
ShawnK.Piasecki,BradleyHall,andAndrewD.Ellington
2. InVitroSelectionofssDNAAptamersUsingBiotinylatedTargetProteins ....... 19
Gu¨nterMayerandThomasHo¨ver
3. IsolatingAptamersUsingCapillaryElectrophoresis–SELEX(CE–SELEX) ....... 33
ReneeK.MosingandMichaelT.Bowser
4. InVitroSelectionofAllostericRibozymes ................................ 45
NicolasPiganeau
5. Cell-SpecificAptamersforTargetedTherapies............................. 59
LauraCerchia,PalomaH.Giangrande,JamesO.McNamara,
andVittoriodeFranciscis
6. AptamersTargetingRNAMolecules .................................... 79
MargueriteWatrin,EricDausse,IsabelleLebars,BernardRayner,
AnthonyBugaut,andJean-JacquesToulme´
7. FluorescenceCorrelationSpectroscopy(FCS)-BasedCharacterisation
ofAptamerLigandInteraction ........................................ 107
ArneWernerandUlrichHahn
8. StructuralProbingTechniquesonNaturalAptamers ....................... 115
CatherineA.WakemanandWadeC.Winkler
9. DeterminingStructuresofRNAAptamersandRiboswitchesbyX-Ray
Crystallography.................................................... 135
AndreaL.Edwards,AndrewD.Garst,andRobertT.Batey
10. LockedNucleicAcidAptamers........................................ 165
JanBarciszewski,MichaelMedgaard,TroelsKoch,JensKurreck,
andVolkerA.Erdmann
11. ScreeningofNovelInhibitorsofHIV-1ReverseTranscriptasewithaReporter
RibozymeAssay ................................................... 187
SatokoYamazakiandMichaelFamulok
12. AptamersasArtificialGeneRegulationElements.......................... 201
BeatrixSuessandJuliaE.Weigand
vii
viii Contents
13. AptamersandBiosensors ............................................ 209
ThomasM.A.Gronewold
14. Nanoparticles/DipStick............................................. 223
YiLu,JuewenLiuandDebapriyaMazumdar
15. InVivoImagingofOligonucleotidicAptamers ........................... 241
BertrandTavitian,Fre´de´ricDuconge´,Rapha¨elBoisgard,andFre´de´ricDolle´
PART II: PEPTIDE APTAMERS
16. SelectionofPeptidesInterferingwithProtein–ProteinInteraction ............ 263
AnnetteGaida,UrsB.Hagemann,DinahMattay,ChristinaRa¨uber,
KristianM.Mu¨ller,andKatjaM.Arndt
17. InVitroSelectionofProteinandPeptideLibrariesUsingmRNADisplay....... 293
TerryT.TakahashiandRichardW.Roberts
18. Ligand-RegulatedPeptideAptamers ................................... 315
RussellA.Miller
19. IsolationofPeptideAptamerstoTargetProteinFunction................... 333
LuisaLopez-Ochoa,TaraE.Nash,JorgeRamirez-Prado,
andLindaHanley-Bowdoin
20. MicrobodiesTM.................................................... 361
Hans-UlrichSchmoldt,MatinDaneschdar,HaraldKolmar,
andMichaelBlind
21. PeptideAptamersforSmallMoleculeDrugDiscovery...................... 373
CarineBardou,ChristopheBorie,MarcBickle,BrianB.Rudkin,
andPierreColas
22. SynthesisandApplicationofPeptidesasDrugCarriers ..................... 389
RobertRennert,InesNeundorf,andAnnetteG.Beck-Sickinger
Index................................................................ 405
Contributors
KATJAM.ARNDT (cid:2) InstituteofBiologyIII,Albert-Ludwigs-UniversityofFreiburg,
Freiburg,Germany
JANBARCISZEWSKI (cid:2) InstituteofBioorganicChemistryofthePolishAcademyofSciences,
Poznan,Poland
CARINEBARDOU (cid:2) AptanomicsS.A.,Lyon,France;Imaxio,Lyon,France
ROBERTT.BATEY (cid:2) DepartmentofChemistryandBiochemistry,UniversityofColorado,
Boulder,CO,USA
ANNETTEG.BECK-SICKINGER (cid:2) InstituteofBiochemistry,FacultyofBiosciences,
PharmacyandPsychology,LeipzigUniversity,Leipzig,Germany
MARCBICKLE (cid:2) AptanomicsS.A.,Lyon,France
MICHAELBLIND (cid:2) NascaCellTechnologiesAG,Munich,Germany
RAPHAE¨LBOISGARD (cid:2) InsermU803,Laboratoired0ImagerieMole´culaire
Expe´rimentale,ServicehospitalierFre´de´ricjoliot,Intitutd0ImagerieBiome´dicale,
CEA,Orsay,France
CHRISTOPHEBORIE (cid:2) AptanomicsS.A.,Lyon,France
MICHAELT.BOWSER (cid:2) UniversityofMinnesota,Minneapolis,MN,USA
ANTHONYBUGAUT (cid:2) DepartmentofChemistry,UniversityofCambridge,Cambridge,
UK
LAURACERCHIA (cid:2) Istitutoperl’EndocrinologiaeOncologiaSperimentale
‘‘G.Salvatore,’’Naples,Italy
PIERRECOLAS (cid:2) AptanomicsS.A.,Lyon,France
MATINDANESCHDAR (cid:2) Institutfu¨rBiochemieundOrganischeChemie,TUDarmstadt,
Darmstadt,Germany
ERICDAUSSE (cid:2) INSERM,InstitutEurope´endeChimieetBiologie,Pessac,France;
Universite´ VictorSegalen,Bordeaux,France
VITTORIODEFRANCISCIS (cid:2) Istitutoperl’EndocrinologiaeOncologiaSperimentale
‘‘G.Salvatore,’’Naples,Italy
FREDERICDOLLE (cid:2) GroupoedeRadiochimie,Laboratoired0ImagerieMole´culaire
Expe´rimentale,ServicehospitalierFre´de´ricjoliot,Intitutd0ImagerieBiome´dicale,
CEA,Orsay,France
FREDERICDUCONGE (cid:2) InsermU803,Laboratoired0ImagerieMole´culaire
Expe´rimentale,ServicehospitalierFre´de´ricjoliot,Intitutd0ImagerieBiome´dicale,
CEA,Orsay,France
ANDREAL.EDWARDS (cid:2) DepartmentofChemistryandBiochemistry,University
ofColorado,Boulder,CO,USA
ANDREWD.ELLINGTON (cid:2) DepartmentofChemistryandBiochemistry,InstituteforCell
andMolecularBiology,UniversityofTexasatAustin,Austin,TX,USA
ix
x Contributors
VOLKERA.ERDMANN (cid:2) InstituteforChemistryandBiochemistry,FreeUniversity
Berlin,Berlin,Germany
MICHAELFAMULOK (cid:2) LifeandMedicalSciences,ProgramUnitChemicalBiology
andMedicinalChemistry,UniversityofBonn,Bonn,Germany
ANNETTEGAIDA (cid:2) InstituteofBiologyIII,Albert-Ludwigs-UniversityofFreiburg,
Freiburg,Germany
ANDREWD.GARST (cid:2) DepartmentofChemistryandBiochemistry,University
ofColorado,Boulder,CO,USA
PALOMAH.GIANGRANDE (cid:2) DepartmentofInternalMedicine,DivisionofCardiology,
UniversityofIowa,IowaCity,IA,USA
THOMASM.A.GRONEWOLD (cid:2) BiosensorGmbH,Bonn,Germany
URSB.HAGEMANN (cid:2) InstituteofBiologyIII,Albert-Ludwigs-UniversityofFreiburg,
Freiburg,Germany
ULRICHHAHN (cid:2) DepartmentofChemistry,InstituteforBiochemistryandMolecular
Biology,UniversityofHamburg,Hamburg,Germany
BRADLEYHALL (cid:2) DepartmentofChemistryandBiochemistry,InstituteforCell
andMolecularBiology,UniversityofTexasatAustin,Austin,TX,USA
LINDAHANLEY-BOWDOIN (cid:2) DepartmentofMolecularandStructuralBiochemistry,
NorthCarolinaStateUniversity,Raleigh,NC,USA
THOMASHo¨ VER (cid:2) LifeandMedicalSciences,ProgramUnitChemicalBiology
andMedicinalChemistry,UniversityofBonn,Bonn,Germany
TROELSKOCH (cid:2) SantarisPharma,Horshølm,Denmark
HARALDKOLMAR (cid:2) Institutfu¨rBiochemieundOrganischeChemie,TUDarmstadt,
Darmstadt,Germany
JENSKURRECK (cid:2) InstituteforChemistryandBiochemistry,FreeUniversityBerlin,
Berlin,Germany;InstituteofIndustrialGenetics,UniversityofStuttgart,Stuttgart,
Germany
ISABELLELEBARS (cid:2) CNRS–Universite´ Bordeaux,InstitutEurope´endeChimie
etBiologie,Pessac,France
JUEWENLIU (cid:2) DepartmentofChemistry,UniversityofIllinoisUrbana-Champaign,
Urbana,IL,USA
LUISALOPEZ-OCHOA (cid:2) DepartmentofMolecularandStructuralBiochemistry,North
CarolinaStateUniversity,Raleigh,NC,USA
YILU (cid:2) DepartmentofChemistry,UniversityofIllinoisUrbana-Champaign,Urbana,
IL,USA
DINAHMATTAY (cid:2) InstituteofBiologyIII,Albert-Ludwigs-UniversityofFreiburg,
Freiburg,Germany
GU¨ NTERMAYER (cid:2) LifeandMedicalSciences,ProgramUnitChemicalBiology
andMedicinalChemistry,UniversityofBonn,Bonn,Germany
DEBAPRIYAMAZUMDAR (cid:2) DepartmentofChemistry,UniversityofIllinois
Urbana-Champaign,Urbana,IL,USA
JAMESO.MCNAMARA (cid:2) DepartmentofInternalMedicine,DivisionofCardiology,
UniversityofIowa,IowaCity,IA,USA
MICHAELMEDGAARD (cid:2) SantarisPharma,Horshølm,Denmark
RUSSELLA.MILLER (cid:2) ClinicalResearchBuilding,UniversityofPennsylvania,
Philadelphia,PA,USA