Super-resolution microscopy : methods and protocols

264 Pages·2017·8.085 MB·English

by  Erfle, Holger

Methods in
Molecular Biology 1663
Holger Erfl e Editor
Super-
Resolution
Microscopy
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences,
University ofHertfordshire,
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Super-Resolution Microscopy
Methods and Protocols
Edited by
fl
Holger Er e
High-Content Analysis of the Cell (HiCell) and Advanced Biological Screening Facility,
BioQuant, Heidelberg University, Heidelberg, Germany
Editor
HolgerErfle
High-ContentAnalysisoftheCell(HiCell)
andAdvancedBiologicalScreeningFacility
BioQuant,HeidelbergUniversity
Heidelberg,Germany
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7264-7 ISBN978-1-4939-7265-4 (eBook)
DOI10.1007/978-1-4939-7265-4
LibraryofCongressControlNumber:2017950493
©SpringerScience+BusinessMediaLLC2017
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Preface
Super-resolution microscopy also known as nanoscopy opens a new avenue in the success
storyoffluorescencemicroscopyinmodern biologybysurpassingAbbe’sdiffractionlimit.
It bridges the resolution gap to electron microscopy by resolving structures at the low
nanometer scale. In addition, it maintains the advantages of optical fluorescence micros-
copylikesimplesamplepreparationallowingbreakthroughdiscoveriesindiversedirections
oflifesciences.
Thisbookaimstoprovideacurrentoverviewoftheadvancedtechnologiesandmethods
insuper-resolution microscopyaddressingnovicesas wellas experiencedusersinthisfield.
Westartwithamini-review,followedbyamanuscriptonhowtointroducesuper-resolution
microscopyintoacorefacility,andpresentanup-to-datesetofprotocols.
As thereisnosinglegoldstandard forfluorescence-based super-resolution microscopy
available,wetrywiththecollectionofchaptersathandtocoverawiderangeoftechnologies
and methods. From the technological side we include the two major streams currently
pursuedinsuper-resolutionimaging:ensembletechniquesandsingle-moleculelocalization
techniques. Further, we include chapters describing methods to establish correlations
between fluorescence-based super-resolution imaging and other imaging techniques like
confocalmicroscopy,atomicforcemicroscopy(AFM)andelectronmicroscopy.
The chapters offer state-of-the-art, reproducible and comprehensive protocols on a
widerangeoftopicsinsuper-resolutionmicroscopy.
Heidelberg,Germany HolgerErfle
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 Super-ResolutionMicroscopyTechniquesandTheirPotential
forApplicationsinRadiationBiophysics ................................... 1
JanPhilippEberle,AlexanderRapp,MatthiasKrufczik,
MarionEryilmaz,ManuelGunkel,HolgerErfle,andMichaelHausmann
2 ManagingtheIntroductionofSuper-ResolutionMicroscopy
intoaCoreFacility...................................................... 15
JeffreyA.KamykowskiandBrianStorrie
3 Live-CellSTEDImagingwiththeHyPer2Biosensor........................ 21
NataliaM.MishinaandVsevolodV.Belousov
4 Diffraction-UnlimitedFluorescenceImagingwithanEasySTED
RetrofittedConfocalMicroscope ......................................... 29
Andre´ KlaussandCarstenHille
5 Two-PhotonSTEDMicroscopyforNanoscaleImaging
ofNeuralMorphologyInVivo ........................................... 45
MirelleJ.T.terVeer,ThomasPfeiffer,andU.ValentinNa€gerl
6 STEDImagingofGolgiDynamicswithCer-SiR:ATwo-Component,
Photostable,High-DensityLipidProbeforLiveCells....................... 65
RomanS.Erdmann,DerekToomre,andAlannaSchepartz
7 Four-ChannelSuper-ResolutionImagingby3-DStructuredIllumination ..... 79
UlrikeEngel
8 CorrelativeSIM-STORMMicroscopy..................................... 95
O.Burri,T.Laroche,R.Guiet,andA.Seitz
9 CorrelativeSuper-ResolutionFluorescenceImagingandAtomic
ForceMicroscopyfor theCharacterizationofBiologicalSamples ............. 105
PatriciaBondia,SantiagoCasado,andCristinaFlors
10 QuantitativeSingle-MoleculeLocalizationMicroscopy(qSMLM)
ofMembraneProteinsBasedonKineticAnalysis
ofFluorophoreBlinkingCycles........................................... 115
FranziskaFricke,JoelBeaudouin,SebastianMalkusch,
RolandEils,andMikeHeilemann
11 Two-ColorSingle-MoleculeTrackinginLiveCells ......................... 127
SiegfriedHa€nselmannandDirk-PeterHerten
12 FullyAutomatedTargetedConfocalandSingle-Molecule
LocalizationMicroscopy................................................. 139
JanPhilippEberle,WalterMuranyi,HolgerErfle,andManuelGunkel
vii
viii Contents
13 BrainSliceStainingandPreparationforThree-Dimensional
Super-ResolutionMicroscopy ............................................ 153
ChristopherL.German,ManasaV.Gudheti,AnnetteE.Fleckenstein,
andErikM.Jorgensen
14 CorrelativeIn-ResinSuper-ResolutionFluorescenceandElectron
MicroscopyofCulturedCells ............................................ 163
ErrinJohnsonandRainerKaufmann
15 SynthesisofJaneliaFluorHaloTagandSNAP-TagLigands
andTheirUseinCellularImagingExperiments ............................ 179
JonathanB.Grimm,TimothyA.Brown,BrianP.English,
Timothe´eLionnet,andLukeD.Lavis
16 MeasuringNanometerDistancesBetweenFluorescent
LabelsStep-by-Step..................................................... 189
SusannaMariaFru€handIngmarSchoen
17 CorrelativeSingle-MoleculeLocalizationMicroscopy
andConfocalMicroscopy................................................ 205
ChristianSoeller,YufengHou,IsuruD.Jayasinghe,
DavidBaddeley,andDavidCrossman
18 CorrelativeFluorescenceSuper-ResolutionLocalizationMicroscopy
andPlatinumReplicaEMonUnroofedCells .............................. 219
KemA.SochackiandJustinW.Taraska
19 InSituSuper-ResolutionImagingofGenomicDNA
withOligoSTORMandOligoDNA-PAINT ............................... 231
BrianJ.Beliveau,AlistairN.Boettiger,GuyNir,BogdanBintu,
PengYin,XiaoweiZhuang,andC.-tingWu
20 Super-ResolutionHighContentScreeningandAnalysis..................... 253
K.Soliman
Index ...................................................................... 261
Contributors
DAVIDBADDELEY (cid:1) DepartmentofCellBiology,YaleUniversity,NewHaven,CT,USA;
AucklandBioengineeringInstitute,UniversityofAuckland,Auckland,NewZealand
JOELBEAUDOUIN (cid:1) DepartmentforBioinformaticsandFunctionalGenomics,Bioquantand
InstituteofPharmacyandMolecularBiotechnology,HeidelbergUniversity,Heidelberg,
Germany;InstitutdeBiologieStructurale,Universite´ GrenobleAlpes,CentreNationalde
laRechercheScientifique,Commissariata` l’EnergieAtomiqueetauxEnergies
Alternatives,F-38000Grenoble,France;DivisionofTheoreticalBioinformatics,German
CancerResearchCenter(DKFZ),Heidelberg,Germany
BRIAN J.BELIVEAU (cid:1) DepartmentofGenetics,HarvardMedicalSchool,Boston,MA,USA;
WyssInstituteforBiologicallyInspiredEngineering,HarvardUniversity,Boston,MA,
USA;DepartmentofSystemsBiology,HarvardMedicalSchool,Boston,MA,USA
VSEVOLOD V.BELOUSOV (cid:1) Shemyakin-OvchinnikovInstituteofBioorganicChemistry,
Moscow,Russia
BOGDANBINTU (cid:1) HowardHughesMedicalInstitute,Cambridge,MA,USA;Department
ofPhysics,HarvardUniversity,Cambridge,MA,USA
ALISTAIRN.BOETTIGER (cid:1) DepartmentofDevelopmentalBiology,StanfordUniversity,
Stanford,CA,USA;HowardHughesMedicalInstitute,Cambridge,MA,USA;
DepartmentofChemistryandChemicalBiology,HarvardUniversity,
Cambridge,MA,USA
PATRICIABONDIA (cid:1) MadridInstituteforAdvancedStudiesinNanosciences(IMDEA
Nanoscience),Madrid,Spain;NanobiotechnologyUnitAssociatedtotheNationalCenter
forBiotechnology(CSIC),Madrid,Spain
TIMOTHYA.BROWN (cid:1) JaneliaResearchCampus,HowardHughesMedicalInstitute,
Ashburn,VA,USA
O.BURRI (cid:1) FacultyofLifeSciences(SV),BioImagingandOpticsPlatform(BIOP),
EcolePolytechniqueFe´de´raledeLausanne(EPFL),Lausanne,Switzerland
SANTIAGOCASADO (cid:1) MadridInstituteforAdvancedStudiesinNanoscience(IMDEA
Nanoscience),Madrid,Spain
DAVIDCROSSMAN (cid:1) DepartmentofPhysiology,UniversityofAuckland,Auckland,New
Zealand
JANPHILIPPEBERLE (cid:1) High-ContentAnalysisoftheCell(HiCell)andAdvancedBiological
ScreeningFacility,BioQuant,HeidelbergUniversity,Heidelberg,Germany
ROLAND EILS (cid:1) DepartmentforBioinformaticsandFunctionalGenomics,Bioquantand
InstituteofPharmacyandMolecularBiotechnology,HeidelbergUniversity,Heidelberg,
Germany;DivisionofTheoreticalBioinformatics,GermanCancerResearchCenter
(DKFZ),Heidelberg,Germany
ULRIKEENGEL (cid:1) NikonImagingCenteratHeidelbergUniversityandCentrefor
OrganismalStudies(COS),HeidelbergUniversity,Heidelberg,Germany
BRIAN P.ENGLISH (cid:1) JaneliaResearchCampus,HowardHughesMedicalInstitute,
Ashburn,VA,USA
ROMANS.ERDMANN (cid:1) DepartmentofCellBiology,YaleUniversitySchoolofMedicine,
NewHaven,CT,USA;DepartmentofChemistry,YaleUniversity,NewHaven,CT,USA
ix
x Contributors
HOLGERERFLE (cid:1) High-ContentAnalysisoftheCell(HiCell)andAdvancedBiological
ScreeningFacility,BioQuant,HeidelbergUniversity,Heidelberg,Germany
MARIONERYILMAZ (cid:1) Kirchhoff-InstituteforPhysics,HeidelbergUniversity,Heidelberg,
Germany
ANNETTEE.FLECKENSTEIN (cid:1) SchoolofDentistry,UniversityofUtah,SaltLakeCity,UT,USA
CRISTINAFLORS (cid:1) MadridInstituteforAdvancedStudiesinNanoscience
(IMDEANanoscience),Madrid,Spain;NanobiotechnologyUnitAssociated
totheNationalCenter forBiotechnology(CSIC),Madrid,Spain
FRANZISKAFRICKE (cid:1) InstituteofPhysicalandTheoreticalChemistry,Goethe-University
Frankfurt,FrankfurtamMain,Germany
SUSANNAMARIAFRu€H (cid:1) LaboratoryofAppliedMechanobiology,ETHZurich,Zurich,
Switzerland
CHRISTOPHERL.GERMAN (cid:1) SchoolofDentistry,UniversityofUtah,SaltLakeCity,UT,USA
JONATHANB.GRIMM (cid:1) JaneliaResearchCampus,HowardHughesMedicalInstitute,
Ashburn,VA,USA
MANASAV.GUDHETI (cid:1) DepartmentofBiology,UniversityofUtah,SaltLakeCity,UT,USA;
Vutara,SaltLakeCity,UT,USA
R.GUIET (cid:1) FacultyofLifeSciences(SV),BioImagingandOpticsPlatform (BIOP),
EcolePolytechniqueFe´de´raledeLausanne(EPFL),Lausanne,Switzerland
MANUELGUNKEL (cid:1) High-ContentAnalysisoftheCell(HiCell)andAdvancedBiological
ScreeningFacility,BioQuant,HeidelbergUniversity,Heidelberg,Germany
SIEGFRIEDH€aNSELMANN (cid:1) Physikalisch-ChemischesInstitutandCellNetworksCluster,
HeidelbergUniversity,Heidelberg,Germany
MICHAELHAUSMANN (cid:1) Kirchhoff-InstituteforPhysics,HeidelbergUniversity,Heidelberg,
Germany
MIKEHEILEMANN (cid:1) InstituteofPhysicalandTheoreticalChemistry,Goethe-University
Frankfurt,FrankfurtamMain,Germany;SingleMoleculeBiology,Bioquant,Heidelberg
University,Heidelberg,Germany;InstituteforAnatomyandCellBiology,Heidelberg
University,Heidelberg,Germany
DIRK-PETERHERTEN (cid:1) Physikalisch-ChemischInstitutandCellNetworksCluster,Heidelberg
University,Heidelberg,Germany
CARSTENHILLE (cid:1) DepartmentofPhysicalChemistry/AppliedLaserSensinginComplex
Biosystems(ALSComBi),InstituteofChemistry,UniversityofPotsdam,Potsdam,
Germany
YUFENG HOU (cid:1) InstituteofExperimentalMedicalResearch,OsloUniversityHospital
Ulleva˚l,UniversityofOslo,Oslo,Norway;DepartmentofPhysiology,Universityof
Auckland,Auckland,NewZealand
ISURU D.JAYASINGHE (cid:1) SchoolofBiomedicalSciences,UniversityofLeeds,Leeds,UK
ERRINJOHNSON (cid:1) SirWilliamDunnSchoolofPathology,UniversityofOxford,Oxford,UK
ERIKM.JORGENSEN (cid:1) DepartmentofBiology,UniversityofUtah,SaltLakeCity,UT,USA;
HowardHughesMedicalInstitute,SilverSprings,MD,USA
JEFFREYA.KAMYKOWSKI (cid:1) DigitalMicroscopyLaboratory,DepartmentofPhysiology
andBiophysics,UniversityofArkansasforMedicalSciences,LittleRock,AR,USA
RAINERKAUFMANN (cid:1) DivisionofStructuralBiology,WellcomeTrustCentreforHuman
Genetics,UniversityofOxford,Oxford,UK;DepartmentofBiochemistry,University
ofOxford,Oxford,UK
ANDRE´ KLAUSS (cid:1) DepartmentofPhysicalChemistry/AppliedLaserSensinginComplex
Biosystems(ALSComBi),InstituteofChemistry,UniversityofPotsdam,Potsdam,
Germany
Contributors xi
MATTHIASKRUFCZIK (cid:1) Kirchhoff-InstituteforPhysics,HeidelbergUniversity,Heidelberg,
Germany
T.LAROCHE (cid:1) FacultyofLifeSciences(SV),BioImagingandOpticsPlatform (BIOP),
EcolePolytechniqueFe´de´raledeLausanne(EPFL),Lausanne,Switzerland
LUKED.LAVIS (cid:1) JaneliaResearchCampus,HowardHughesMedicalInstitute,
Ashburn,VA,USA
TIMOTHE´ELIONNET (cid:1) JaneliaResearchCampus,HowardHughesMedicalInstitute,
Ashburn,VA,USA
SEBASTIANMALKUSCH (cid:1) InstituteofPhysicalandTheoreticalChemistry,Goethe-University
Frankfurt,FrankfurtamMain,Germany
NATALIA M.MISHINA (cid:1) Shemyakin-OvchinnikovInstituteofBioorganicChemistry,
Moscow,Russia
WALTERMURANYI (cid:1) DepartmentofInfectiousDiseasesandVirology,HeidelbergUniversity
Hospital,Heidelberg,Germany
U.VALENTIN N€aGERL (cid:1) InterdisciplinaryInstituteforNeuroscience,UMR5297CNRS,
Bordeaux,France;Universite´ deBordeoux,Bordeaux,France
GUYNIR (cid:1) DepartmentofGenetics,HarvardMedicalSchool,Boston,MA,USA
THOMASPFEIFFER (cid:1) InterdisciplinaryInstituteforNeuroscience,UMR5297CNRS,
Bordeaux,France;Universite´ deBordeoux,Bordeaux,France
ALEXANDERRAPP (cid:1) DepartmentofBiology,TechnicalUniversita€tDarmstadt,
Darmstadt,Germany
ALANNASCHEPARTZ (cid:1) DepartmentofChemistry,YaleUniversity,NewHaven,CT,USA;
DepartmentofMolecular,Cellular,andDevelopmentalBiology,YaleUniversity,
NewHaven,CT,USA
INGMARSCHOEN (cid:1) LaboratoryofAppliedMechanobiology,ETHZurich,Zurich,Switzerland
A.SEITZ (cid:1) FacultyofLifeSciences(SV),BioImagingandOpticsPlatform (BIOP),
EcolePolytechniqueFe´de´raledeLausanne(EPFL),Lausanne,Switzerland
KEMA.SOCHACKI (cid:1) NationalHeartLungandBloodInstitute,NationalInstitutes
ofHealth(NIH),Bethesda,MD,USA
CHRISTIAN SOELLER (cid:1) BiomedicalPhysics,UniversityofExeter,Exeter,UK;Department
ofPhysiology,UniversityofAuckland,Auckland,NewZealand
K.SOLIMAN (cid:1) CollegeofPharmacy,ArabAcademyofScienceandtechnologyandMaritime
Transport,Alexandria,Egypt;Go¨ttingenMedicalCenterNeuropediatricDivision,
Go¨ttingenUniversity,Go¨ttingen,Germany
BRIAN STORRIE (cid:1) DigitalMicroscopyLaboratory,DepartmentofPhysiologyandBiophysics,
UniversityofArkansasforMedicalSciences,LittleRock,AR,USA
JUSTINW.TARASKA (cid:1) NationalHeartLungandBloodInstitute,NationalInstitutes
ofHealth(NIH),Bethesda,MD,USA
MIRELLE J.T.TERVEER (cid:1) InterdisciplinaryInstituteforNeuroscience,UMR5297CNRS,
Bordeaux,France;Universite´ deBordeaux,Bordeaux,France
DEREKTOOMRE (cid:1) DepartmentofCellBiology,YaleUniversitySchoolofMedicine,
NewHaven,CT,USA
C.-TINGWU (cid:1) DepartmentofGenetics,HarvardMedicalSchool,Boston,MA,USA
PENG YIN (cid:1) WyssInstituteforBiologicallyInspiredEngineering,HarvardUniversity,
Boston,MA,USA;DepartmentofSystemsBiology,HarvardMedicalSchool,
Boston,MA,USA
XIAOWEIZHUANG (cid:1) HowardHughesMedicalInstitute,Cambridge,MA,USA;
DepartmentofChemistryandChemicalBiology,HarvardUniversity,Cambridge,
MA,USA;DepartmentofPhysics,HarvardUniversity,Cambridge,MA,USA