Skip to main content

Advertisement

Log in

Single-molecule localization to study cytoskeletal structures, membrane complexes, and mechanosensors

  • Review
  • Published:
Biophysical Reviews Aims and scope Submit manuscript

Abstract

In the last decades, a promising breakthrough in fluorescence imaging was represented by the advent of super-resolution microscopy (SRM). Super-resolution techniques recently became a popular method to study sub-cellular structures, providing a successful approach to observe cytoskeletal and focal adhesion proteins. Among the SR techniques, single-molecule localization microscopy plays a significant role due to its ability to unveil structures and molecular organizations in biological systems. Furthermore, since they provide information at the molecular level, these techniques are increasingly being used to study the stoichiometry and interaction between several membrane channel proteins and their accessory subunits. The aim of this review is to describe the single-molecule localization-based techniques and their applications relevant to cytoskeletal structures and membrane complexes in order to provide as future prospective an overall picture of their correlation with the mechanosensor channel expression and activity.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Aguet F, Upadhyayula S, Gaudin R, Chou YY, Cocucci E, He K, Chen BC, Mosaliganti K, Pasham M, Skillern W, Legant WR, Liu TL, Findlay G, Marino E, Danuser G, Megason S, Betzig E, Kirchhausen T (2016) Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy. Mol Biol Cell 27:3418–3435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ann L. McEvoy HH, Mark Bates, Evgenia Platonova, Paula J. Cranfill, Michelle A. Baird, Michael W. Davidson, Helge Ewers, Jan Liphardt, Robert E. Campbell (2012) A photoconvertible fluorescent protein for use in multiple imaging modalities. 12:1–15

  • Baker SM, Buckheit RW 3rd, Falk MM (2010) Green-to-red photoconvertible fluorescent proteins: tracking cell and protein dynamics on standard wide-field mercury arc-based microscopes. BMC Cell Biol 11:15

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Balint S, Verdeny Vilanova I, Sandoval Alvarez A, Lakadamyali M (2013) Correlative live-cell and superresolution microscopy reveals cargo transport dynamics at microtubule intersections. Proc Natl Acad Sci U S A 110:3375–3380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bartoi T, Augustinowski K, Polleichtner G, Grunder S, Ulbrich MH (2014) Acid-sensing ion channel (ASIC) 1a/2a heteromers have a flexible 2:1/1:2 stoichiometry. Proc Natl Acad Sci U S A 111:8281–8286

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–1645

    Article  CAS  PubMed  Google Scholar 

  • Bierwagen J, Testa I, Fölling J, Wenzel D, Jakobs S, Eggeling C, Hell SW (2010) Far-field autofluorescence nanoscopy. Nano Lett 10:4249–4252

    Article  CAS  PubMed  Google Scholar 

  • Birchler JA, Veitia RA (2012) Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A 109:14746–14753

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cella Zanacchi F, Lavagnino Z, Perrone Donnorso M, Del Bue A, Furia L, Faretta M, Diaspro A (2011) Live-cell 3D super-resolution imaging in thick biological samples. Nat Methods 8:1047–1049

    Article  PubMed  CAS  Google Scholar 

  • Cella Zanacchi F, Manzo C, Alvarez AS, Derr ND, Garcia-Parajo MF, Lakadamyali M (2017) A DNA origami platform for quantifying protein copy number in super-resolution. Nat Methods 14:789–792

    Article  CAS  Google Scholar 

  • Cella Zanacchi F, Manzo C, Magrassi R, Derr ND, Lakadamyali M (2019) Quantifying protein copy number in super resolution using an imaging-invariant calibration. Biophys J 116:2195–2203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen BC, Legant WR, Wang K, Shao L, Milkie DE, Davidson MW, Janetopoulos C, Wu XS, Hammer JA 3rd, Liu Z, English BP, Mimori-Kiyosue Y, Romero DP, Ritter AT, Lippincott-Schwartz J, Fritz-Laylin L, Mullins RD, Mitchell DM, Bembenek JN, Reymann AC, Bohme R, Grill SW, Wang JT, Seydoux G, Tulu US, Kiehart DP, Betzig E (2014) Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346:1257998

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen Y, Liu W, Zhang Z, Zheng C, Huang Y, Cao R, Zhu D, Xu L, Zhang M, Zhang YH, Fan J, Jin L, Xu Y, Kuang C, Liu X (2018) Multi-color live-cell super-resolution volume imaging with multi-angle interference microscopy. Nat Commun 9:4818

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chichili GR, Rodgers W (2007) Clustering of membrane raft proteins by the actin cytoskeleton. J Biol Chem 282:36682–36691

    Article  CAS  PubMed  Google Scholar 

  • Chmyrov A, Keller J, Grotjohann T, Ratz M, d’Este E, Jakobs S, Eggeling C, Hell SW (2013) Nanoscopy with more than 100,000 ‘doughnuts. Nat Methods 10:737

    Article  CAS  PubMed  Google Scholar 

  • Dempsey GTVJ, Chen KH, Bates M, Zhuang X (2011) Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat Methods 8:1027–1036

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deschout H, Cella Zanacchi F, Mlodzianoski M, Diaspro A, Bewersdorf J, Hess ST, Braeckmans K (2014a) Precisely and accurately localizing single emitters in fluorescence microscopy. Nat Methods 11:253–266

    Article  CAS  PubMed  Google Scholar 

  • Deschout H, Shivanandan A, Annibale P, Scarselli M, Radenovic A (2014b) Progress in quantitative single-molecule localization microscopy. Histochem Cell Biol 142:5–17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dmitriy M, Chudakov SLKAL (2007) Tracking intracellular protein movements using photoswitchable fluorescent proteins PS-CFP2 and Dendra2. Nat Protoc 2:2024–2032

    Article  CAS  Google Scholar 

  • Dmitriy M, Chudakov VVV, Staroverov DB, Souslova EA, Lukyanov S, Lukyanov KA (2004) Photoswitchable cyan fluorescent protein for protein tracking. Nat Biotechnol 22:1453–1439

    Article  CAS  Google Scholar 

  • Durisic N, Godin AG, Wever CM, Heyes CD, Lakadamyali M, Dent JA (2012) Stoichiometry of the human glycine receptor revealed by direct subunit counting. J Neurosci 32:12915–12920

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Durisic N, Laparra-Cuervo L, Sandoval-Alvarez A, Borbely JS, Lakadamyali M (2014) Single-molecule evaluation of fluorescent protein photoactivation efficiency using an in vivo nanotemplate. Nat Methods 11:156–162

    Article  CAS  PubMed  Google Scholar 

  • Encell LP, Friedman Ohana R, Zimmerman K, Otto P, Vidugiris G, Wood MG, Los GV, McDougall MG, Zimprich C, Karassina N, Learish RD, Hurst R, Hartnett J, Wheeler S, Stecha P, English J, Zhao K, Mendez J, Benink HA, Murphy N, Daniels DL, Slater MR, Urh M, Darzins A, Klaubert DH, Bulleit RF, Wood KV (2012) Development of a dehalogenase-based protein fusion tag capable of rapid, selective and covalent attachment to customizable ligands. Curr Chem Genomics 6:55–71

    Article  PubMed  PubMed Central  Google Scholar 

  • Endesfelder U, Malkusch S, Fricke F, Heilemann M (2014) A simple method to estimate the average localization precision of a single-molecule localization microscopy experiment. Histochem Cell Biol 141:629–638

    Article  CAS  PubMed  Google Scholar 

  • Ester MK, H.P Kriegel; Sander, J.; Xu, X.; (1996) A density based algorithm for discovering clusters in large spatial database with noise. Proceed of 2nd international conference on knowledge discovery and data mining 34:226-231

  • Fedor V, Subach GHP, Manley S, Gillette JM, Lippincott-Schwartz J, Verkhusha VV (2009) Photoactivatable mCherry for high-resolution two-color fluorescence microscopy. Nat Methods 6:153–159

    Article  CAS  Google Scholar 

  • Fletcher DA, Mullins RD (2010) Cell mechanics and the cytoskeleton. Nature 463:485–492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fricke F, Beaudouin J, Eils R, Heilemann M (2015) One, two or three? Probing the stoichiometry of membrane proteins by single-molecule localization microscopy. Sci Rep 5:14072

    Article  PubMed  PubMed Central  Google Scholar 

  • Frost NA, Shroff H, Kong H, Betzig E, Blanpied TA (2010) Single-molecule discrimination of discrete perisynaptic and distributed sites of actin filament assembly within dendritic spines. Neuron 67:86–99

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gallagher SS, Sable JE, Sheetz MP, Cornish VW (2009) An in vivo covalent TMP-tag based on proximity-induced reactivity. ACS Chem Biol 4:547–556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Galland R, Grenci G, Aravind A, Viasnoff V, Studer V, Sibarita JB (2015) 3D high- and super-resolution imaging using single-objective SPIM. Nat Methods 12:641–644

    Article  CAS  PubMed  Google Scholar 

  • Gautier A, Juillerat A, Heinis C, Correa IR Jr, Kindermann M, Beaufils F, Johnsson K (2008) An engineered protein tag for multiprotein labeling in living cells. Chem Biol 15:128–136

    Article  CAS  PubMed  Google Scholar 

  • George N, Pick H, Vogel H, Johnsson N, Johnsson K (2004) Specific labeling of cell surface proteins with chemically diverse compounds. J Am Chem Soc 126:8896–8897

    Article  CAS  PubMed  Google Scholar 

  • Giannone G, Hosy E, Levet F, Constals A, Schulze K, Sobolevsky AI, Rosconi MP, Gouaux E, Tampe R, Choquet D, Cognet L (2010) Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density. Biophys J 99:1303–1310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gibson TJ, Seiler M, Veitia RA (2013) The transience of transient overexpression. Nat Methods 10:715–721

    Article  CAS  PubMed  Google Scholar 

  • Gottlieb PA, Sachs F (2012) Piezo1: properties of a cation selective mechanical channel. Channels 6:214–219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grimm JB, English BP, Chen J, Slaughter JP, Zhang Z, Revyakin A, Patel R, Macklin JJ, Normanno D, Singer RH, Lionnet T, Lavis LD (2015) A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat Methods 12:244–250 243 p following 250

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gunewardene MS, Subach FV, Gould TJ, Penoncello GP, Gudheti MV, Verkhusha VV, Hess ST (2011) Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cells. Biophys J 101:1522–1528

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gurskaya NGVV, Shcheglov AS, Staroverov DB, Chepurnykh TV, Fradkov AF, Lukyanov S, Lukyanov KA (2006) Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nat Biotechnol 24:461–465

    Article  CAS  PubMed  Google Scholar 

  • Hao Chang MZ, Ji W, Chen J, Zhang Y, Liu B, Lu J, Zhang J, Xu P, Xu T (2012) A unique series of reversibly switchable fluorescent proteins with beneficial properties for various applications. PNAS 109:4455–4460

    Article  PubMed  PubMed Central  Google Scholar 

  • Harder Z, Zunino R, McBride H (2004) Sumo1 conjugates mitochondrial substrates and participates in mitochondrial fission. Current Biology : CB 14:340–345

    Article  CAS  PubMed  Google Scholar 

  • Hell SW, Wichmann J (1994) Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt Lett 19:780–782

    Article  CAS  PubMed  Google Scholar 

  • Hermanson G (2013) Bioconjugate techniques: Elsevier

  • Hertel F, Mo GC, Duwe S, Dedecker P, Zhang J (2016) RefSOFI for mapping nanoscale organization of protein-protein interactions in living cells. Cell Rep 14:390–400

    Article  CAS  PubMed  Google Scholar 

  • Hess ST, Girirajan TP, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91:4258–4272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hoffmann C, Gaietta G, Zurn A, Adams SR, Terrillon S, Ellisman MH, Tsien RY, Lohse MJ (2010) Fluorescent labeling of tetracysteine-tagged proteins in intact cells. Nat Protoc 5:1666–1677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hofmann M, Eggeling C, Jakobs S, Hell SW (2005) Breaking the diffraction<p>barrier in fluorescence microscopy at low light intensities by using reversibly<p>photoswitchable proteins. Proc Natl Acad Sci U S A 102:17565–17569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jörg Wiedenmann SI, Oswald F, Schmitt F, Röcker C, Salih A, Spindler K-D, Nienhaus GU (2004) EosFP, a fluorescent marker protein with UV-inducible green-to-red fluorescence conversion. PNAS 101:15905–15910

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Kanchanawong P, Shtengel G, Pasapera AM, Ramko EB, Davidson MW, Hess HF, Waterman CM (2010) Nanoscale architecture of integrin-based cell adhesions. Nature 468:580–584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Keppler A, Gendreizig S, Gronemeyer T, Pick H, Vogel H, Johnsson K (2003) A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat Biotechnol 21:86–89

    Article  CAS  PubMed  Google Scholar 

  • Kindermann M, Sielaff I, Johnsson K (2004) Synthesis and characterization of bifunctional probes for the specific labeling of fusion proteins. Bioorg Med Chem Lett 14:2725–2728

    Article  CAS  PubMed  Google Scholar 

  • Kobertz WR (2014) Stoichiometry of the cardiac IKs complex. Proc Natl Acad Sci U S A 111:5065–5066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kolomeisky AB (2013) Motor proteins and molecular motors: how to operate machines at the nanoscale. J Phys Condensed matter : Institut Phys J 25:463101

    Article  CAS  Google Scholar 

  • Kolomeisky AB, Fisher ME (2007) Molecular motors: a theorist’s perspective. Annu Rev Phys Chem 58:675–695

    Article  CAS  PubMed  Google Scholar 

  • Konstantin A. Lukyanov DMC, Sergey Lukyanov and Vladislav V. Verkhusha (2005) Innovation: photoactivatable fluorescent proteins. Nat Rev Mol Cell Biol 6:885–891

    Article  CAS  PubMed  Google Scholar 

  • Levet F, Hosy E, Kechkar A, Butler C, Beghin A, Choquet D, Sibarita JB (2015) SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data. Nat Methods 12:1065–1071

    Article  CAS  PubMed  Google Scholar 

  • Los GV, Encell LP, McDougall MG, Hartzell DD, Karassina N, Zimprich C, Wood MG, Learish R, Ohana RF, Urh M, Simpson D, Mendez J, Zimmerman K, Otto P, Vidugiris G, Zhu J, Darzins A, Klaubert DH, Bulleit RF, Wood KV (2008) HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem Biol 3:373–382

    Article  CAS  PubMed  Google Scholar 

  • Lu CH, Tang WC, Liu YT, Chang SW, Wu FCM, Chen CY, Tsai YC, Yang SM, Kuo CW, Okada Y, Hwu YK, Chen P, Chen BC (2019) Lightsheet localization microscopy enables fast, large-scale, and three-dimensional super-resolution imaging. Commun Biol 2:177

    Article  PubMed  PubMed Central  Google Scholar 

  • Lukinavicius G, Umezawa K, Olivier N, Honigmann A, Yang G, Plass T, Mueller V, Reymond L, Correa IR Jr, Luo ZG, Schultz C, Lemke EA, Heppenstall P, Eggeling C, Manley S, Johnsson K (2013) A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat Chem 5:132–139

    Article  CAS  PubMed  Google Scholar 

  • Manley S, Gillette JM, Patterson GH, Shroff H, Hess HF, Betzig E, Lippincott-Schwartz J (2008) High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat Methods 5:155–157

    Article  CAS  PubMed  Google Scholar 

  • Mark A. Rizzo MWD, and David W. Piston (2009) Fluorescent protein tracking and detection: applications using fluorescent proteins in living cells

  • Martinac B (2014) The ion channels to cytoskeleton connection as potential mechanism of mechanosensitivity. Biochim Biophys Acta 1838:682–691

    Article  CAS  PubMed  Google Scholar 

  • Mingshu Zhang HC, Zhang Y, Yu J, Wu L, Ji W, Chen J, Liu B, Lu J, Liu Y, Zhang J, Xu PXT (2012) Rational design of true monomeric and bright photoactivatable fluorescent proteins. Nat Methods 9:727–729

    Article  PubMed  CAS  Google Scholar 

  • Mortensen KI, Churchman LS, Spudich JA, Flyvbjerg H (2010) Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat Methods 7:377–381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nakajo K, Ulbrich MH, Kubo Y, Isacoff EY (2010) Stoichiometry of the KCNQ1 - KCNE1 ion channel complex. Proc Natl Acad Sci U S A 107:18862–18867

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nicovich PR, Owen DM, Gaus K (2017) Turning single-molecule localization microscopy into a quantitative bioanalytical tool. Nat Protoc 12:453–460

    Article  CAS  PubMed  Google Scholar 

  • Nozaki T, Imai R, Tanbo M, Nagashima R, Tamura S, Tani T, Joti Y, Tomita M, Hibino K, Kanemaki MT, Wendt KS, Okada Y, Nagai T, Maeshima K (2017) Dynamic organization of chromatin domains revealed by super-resolution live-cell imaging. Mol Cell 67:282

    Article  CAS  PubMed  Google Scholar 

  • Odell ID, Cook D (2013) Immunofluorescence techniques. J Investig Dermatol 133:e4

    Article  CAS  PubMed  Google Scholar 

  • Pan L, Yan R, Li W, Xu K (2018) Super-resolution microscopy reveals the native ultrastructure of the erythrocyte cytoskeleton. Cell Rep 22:1151–1158

    Article  CAS  PubMed  Google Scholar 

  • Patterson JS (2008) Fluorescent proteins for photoactivation experiments. Methods Cell Biol 85:45–61

    Article  PubMed  CAS  Google Scholar 

  • Patterson GH, Lippincott-Schwartz J (2002) A photoactivatable GFP for selective photolabeling of proteins and cells. Science 297:1873–1877

    Article  CAS  PubMed  Google Scholar 

  • Patterson G, Davidson M, Manley S, Lippincott-Schwartz J (2010) Superresolution imaging using single-molecule localization. Annu Rev Phys Chem 61:345–367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pavan MaP M (2007) Dominant sets and pairwise clustering. IEEE Trans Pattern Anal Mach Intell 29:167–172

    Article  Google Scholar 

  • Pennacchietti F, Vascon S, Nieus T, Rosillo C, Das S, Tyagarajan SK, Diaspro A, Del Bue A, Petrini EM, Barberis A, Zanacchi FC (2017) Nanoscale molecular reorganization of the inhibitory postsynaptic density is a determinant of GABAergic synaptic potentiation. J Neurosci 37:1747–1756

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Plant LD, Xiong D, Dai H, Goldstein SA (2014) Individual IKs channels at the surface of mammalian cells contain two KCNE1 accessory subunits. Proc Natl Acad Sci U S A 111:E1438–E1446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pollard TD, Cooper JA (2009) Actin, a central player in cell shape and movement. Science 326:1208–1212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ratz M, Testa I, Hell SW, Jakobs S (2015) CRISPR/Cas9-mediated endogenous protein tagging for RESOLFT super-resolution microscopy of living human cells. Sci Rep 5:9592

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ricci MA, Manzo C, Garcia-Parajo MF, Lakadamyali M, Cosma MP (2015) Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell 160:1145–1158

    Article  CAS  PubMed  Google Scholar 

  • Ries J, Kaplan C, Platonova E, Eghlidi H, Ewers H (2012) A simple, versatile method for GFP-based super-resolution microscopy via nanobodies. Nat Methods 9:582–584

    Article  CAS  PubMed  Google Scholar 

  • Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793–795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ryoko Ando HM, Miyawak A (2004) Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting. Science 306:1370–1373

    Article  PubMed  CAS  Google Scholar 

  • Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32:347–355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Satoshi Habuchi HT, Anna B. Kochaniak, Atsushi Miyawaki , Antoine M. van Oijen (2008) mKikGR, a monomeric photoswitchable fluorescent protein. PLoS One 3:1–9

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schnell U, Dijk F, Sjollema KA, Giepmans BN (2012) Immunolabeling artifacts and the need for live-cell imaging. Nat Methods 9:152–158

    Article  CAS  PubMed  Google Scholar 

  • Schnitzbauer J, Strauss MT, Schlichthaerle T, Schueder F, Jungmann R (2017) Super-resolution microscopy with DNA-PAINT. Nat Protoc 12:1198–1228

    Article  CAS  PubMed  Google Scholar 

  • Sednev M (2015) A practical guide to dSTORM: super-resolution imaging with standard fluorescent probes

  • Sednev MV, Belov VN, Hell SW (2015) Fluorescent dyes with large stokes shifts for super-resolution optical microscopy of biological objects: a review. Methods Appl Fluoresc 3:042004

    Article  PubMed  CAS  Google Scholar 

  • Sheetz MP (1983) Membrane skeletal dynamics: role in modulation of red cell deformability, mobility of transmembrane proteins, and shape. Semin Hematol 20:175–188

    CAS  PubMed  Google Scholar 

  • Shroff H, Galbraith CG, Galbraith JA, White H, Gillette J, Olenych S, Davidson MW, Betzig E (2007) Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc Natl Acad Sci U S A 104:20308–20313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shroff HGC, Galbraith JA, Betzig E (2008) Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat Methods 5:417–423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sigal YM, Zhou R, Zhuang X (2018) Visualizing and discovering cellular structures with super-resolution microscopy. Science 361:880–887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Siyuan Wang JRM, Graham T. Dempsey, X. Sunney Xie, and Xiaowei Zhuang, PNAS (2014) Characterization and development of photoactivatable fluorescent proteins for single-molecule–based superresolution imaging. PNAS (23):8452–8457

    Article  CAS  Google Scholar 

  • Sydor AM, Czymmek KJ, Puchner EM, Mennella V (2015) Super-resolution microscopy: from single molecules to supramolecular assemblies. Trends Cell Biol 25:730–748

    Article  CAS  PubMed  Google Scholar 

  • Syeda R, Florendo MN, Cox CD, Kefauver JM, Santos JS, Martinac B, Patapoutian A (2016) Piezo1 channels are inherently mechanosensitive. Cell Rep 17:1739–1746

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Testa I, Wurm CA, Medda R, Rothermel E, von Middendorf C, Folling J, Jakobs S, Schonle A, Hell SW, Eggeling C (2010) Multicolor fluorescence nanoscopy in fixed and living cells by exciting conventional fluorophores with a single wavelength. Biophys J 99:2686–2694

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsutsui H, , Karasawa S, , Shimizu H, , Nukina N, Miyawaki A (2005) Semi-rational engineering of a coral fluorescent protein into an efficient highlighter. EMBO Rep 6:233–238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ulbrich MH, Isacoff EY (2007) Subunit counting in membrane-bound proteins. Nat Methods 4:319–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Uttamapinant C, White KA, Baruah H, Thompson S, Fernandez-Suarez M, Puthenveetil S, Ting AY (2010) A fluorophore ligase for site-specific protein labeling inside living cells. Proc Natl Acad Sci U S A 107:10914–10919

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Valm AM, Cohen S, Legant WR, Melunis J, Hershberg U, Wait E, Cohen AR, Davidson MW, Betzig E, Lippincott-Schwartz J (2017) Applying systems-level spectral imaging and analysis to reveal the organelle interactome. Nature 546:162–167

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van den Berg J, Galbiati H, Rasmussen A, Miller S, Poolman B (2016) On the mobility, membrane location and functionality of mechanosensitive channels in Escherichia coli. Sci Rep 6:32709

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Verdeny-Vilanova I, Wehnekamp F, Mohan N, Sandoval Alvarez A, Borbely JS, Otterstrom JJ, Lamb DC, Lakadamyali M (2017) 3D motion of vesicles along microtubules helps them to circumvent obstacles in cells. J Cell Sci 130:1904–1916

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vicidomini G, Bianchini P, Diaspro A (2018) STED super-resolved microscopy. Nat Methods 15:173–182

    Article  CAS  PubMed  Google Scholar 

  • Vira S, Mekhedov E, Humphrey G, Blank PS (2010) Fluorescent-labeled antibodies: balancing functionality and degree of labeling. Anal Biochem 402:146–150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Voeltz GK, Prinz WA, Shibata Y, Rist JM, Rapoport TA (2006) A class of membrane proteins shaping the tubular endoplasmic reticulum. Cell 124:573–586

    Article  CAS  PubMed  Google Scholar 

  • Watanabe S, Mizukami S, Hori Y, Kikuchi K (2010) Multicolor protein labeling in living cells using mutant beta-lactamase-tag technology. Bioconjug Chem 21:2320–2326

    Article  CAS  PubMed  Google Scholar 

  • Wombacher R, Cornish VW (2011) Chemical tags: applications in live cell fluorescence imaging. J Biophotonics 4:391–402

    Article  CAS  PubMed  Google Scholar 

  • Xu K, Babcock HP, Zhuang X (2012) Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat Methods 9:185–188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu K, Zhong G, Zhuang X (2013) Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science 339:452–456

    Article  CAS  PubMed  Google Scholar 

  • Zhang W, Cheng LE, Kittelmann M, Li J, Petkovic M, Cheng T, Jin P, Guo Z, Gopfert MC, Jan LY, Jan YN (2015) Ankyrin Repeats Convey Force to Gate the NOMPC Mechanotransduction Channel. Cell 162:1391–1403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou XX, Lin MZ (2013) Photoswitchable fluorescent proteins: ten years of colorful chemistry and exciting applications. Curr Opin Chem Biol 17:682–690

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

The authors acknowledge the Nanoscopy group and the Nikon imaging center at the Istituto Italiano di Tecnologia.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to R. Magrassi or F. Cella Zanacchi.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain studies with human participants or animals.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Magrassi, R., Scalisi, S. & Cella Zanacchi, F. Single-molecule localization to study cytoskeletal structures, membrane complexes, and mechanosensors. Biophys Rev 11, 745–756 (2019). https://doi.org/10.1007/s12551-019-00595-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12551-019-00595-2

Keywords

Navigation