1932

Abstract

In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently, single-molecule methods have been used to image, localize, and track individually labeled macromolecules in the cytoplasm of living cells, allowing investigations of intermolecular kinetics under physiologically relevant conditions. In this review, we illuminate the particular advantages of single-molecule techniques when studying kinetics in living cells and discuss solutions to specific challenges associated with these methods.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-biochem-013118-110801
2019-06-20
2024-06-21
Loading full text...

Full text loading...

/deliver/fulltext/biochem/88/1/annurev-biochem-013118-110801.html?itemId=/content/journals/10.1146/annurev-biochem-013118-110801&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Moerner WE, Shechtman Y, Wang Q 2015. Single-molecule spectroscopy and imaging over the decades. Faraday Discuss 184:9–36
    [Google Scholar]
  2. 2. 
    Ha T. 2014. Single-molecule methods leap ahead. Nat. Methods 11:101015–18
    [Google Scholar]
  3. 3. 
    Sahl SJ, Moerner WE 2013. Super-resolution fluorescence imaging with single molecules. Curr. Opin. Struct. Biol. 23:5778–87
    [Google Scholar]
  4. 4. 
    Hell SW, Sahl SJ, Bates M, Zhuang X, Heintzmann R et al. 2015. The 2015 super-resolution microscopy roadmap. J. Phys. D 48:44443001
    [Google Scholar]
  5. 5. 
    Liu Z, Lavis LD, Betzig E 2015. Imaging live-cell dynamics and structure at the single-molecule level. Mol. Cell. 58:4644–59
    [Google Scholar]
  6. 6. 
    Pi J, Jin H, Yang F, Chen ZW, Cai J 2014. In situ single molecule imaging of cell membranes: linking basic nanotechniques to cell biology, immunology and medicine. Nanoscale 6:2112229–49
    [Google Scholar]
  7. 7. 
    Barden AO, Goler AS, Humphreys SC, Tabatabaei S, Lochner M et al. 2015. Tracking individual membrane proteins and their biochemistry: the power of direct observation. Neuropharmacology 98:22–30
    [Google Scholar]
  8. 8. 
    Elf J, Li G-W, Xie XS 2007. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316:58281191–94
    [Google Scholar]
  9. 9. 
    Jones DL, Leroy P, Unoson C, Fange D, Ćurić V et al. 2017. Kinetics of dCas9 target search in Escherichia coli. . Science 357:63581420–24
    [Google Scholar]
  10. 10. 
    Reyes-Lamothe R, Sherratt DJ, Leake MC 2010. Stoichiometry and architecture of active DNA replication machinery in Escherichia coli. . Science 328:5977498–501
    [Google Scholar]
  11. 11. 
    Liao Y, Li Y, Schroeder JW, Simmons LA, Biteen JS 2016. Single-molecule DNA polymerase dynamics at a bacterial replisome in live cells. Biophys. J. 111:122562–69
    [Google Scholar]
  12. 12. 
    Balleza E, Kim JM, Cluzel P 2018. Systematic characterization of maturation time of fluorescent proteins in living cells. Nat. Methods 15:147–51
    [Google Scholar]
  13. 13. 
    Mahmutovic A, Fange D, Berg OG, Elf J 2012. Lost in presumption: stochastic reactions in spatial models. Nat. Methods 9:121163–66
    [Google Scholar]
  14. 14. 
    Friedman N, Cai L, Xie XS 2006. Linking stochastic dynamics to population distribution: an analytical framework of gene expression. Phys. Rev. Lett. 97:16168302
    [Google Scholar]
  15. 15. 
    Xu H, Sepúlveda LA, Figard L, Sokac AM, Golding I 2015. Combining protein and mRNA quantification to decipher transcriptional regulation. Nat. Methods 12:8739–42
    [Google Scholar]
  16. 16. 
    Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M et al. 2010. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329:5991533–38
    [Google Scholar]
  17. 17. 
    Sepúlveda LA, Xu H, Zhang J, Wang M, Golding I 2016. Measurement of gene regulation in individual cells reveals rapid switching between promoter states. Science 351:62781218–22
    [Google Scholar]
  18. 18. 
    So L-H, Ghosh A, Zong C, Sepúlveda LA, Segev R, Golding I 2011. General properties of transcriptional time series in Escherichia coli. Nat. Genet. 43:6554–60
    [Google Scholar]
  19. 19. 
    Jones D, Elf J 2018. Bursting onto the scene? Exploring stochastic mRNA production in bacteria. Curr. Opin. Microbiol. 45:124–30
    [Google Scholar]
  20. 20. 
    Battich N, Stoeger T, Pelkmans L 2015. Control of transcript variability in single mammalian cells. Cell 163:71596–610
    [Google Scholar]
  21. 21. 
    Golding I. 2018. Infection by bacteriophage lambda: an evolving paradigm for cellular individuality. Curr. Opin. Microbiol. 43:9–13
    [Google Scholar]
  22. 22. 
    Yu J, Xiao J, Ren X, Lao K, Xie XS 2006. Probing gene expression in live cells, one protein molecule at a time. Science 311:57671600–3
    [Google Scholar]
  23. 23. 
    Cai L, Friedman N, Xie XS 2006. Stochastic protein expression in individual cells at the single molecule level. Nature 440:358–62
    [Google Scholar]
  24. 24. 
    Golding I, Paulsson J, Zawilski SM, Cox EC 2005. Real-time kinetics of gene activity in individual bacteria. Cell 123:61025–36
    [Google Scholar]
  25. 25. 
    Choi PJ, Cai L, Frieda K, Sunney Xie X 2008. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322:5900442–46
    [Google Scholar]
  26. 26. 
    Uphoff S, Lord ND, Okumus B, Potvin-Trottier L, Sherratt DJ, Paulsson J 2016. Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation. Science 351:62771094–97
    [Google Scholar]
  27. 27. 
    Hammar P, Leroy P, Mahmutovic A, Marklund EG, Berg OG, Elf J 2012. The lac repressor displays facilitated diffusion in living cells. Science 336:60881595–98
    [Google Scholar]
  28. 28. 
    Hammar P, Walldén M, Fange D, Persson F, Baltekin O et al. 2014. Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation. Nat. Genet. 46:4405–8
    [Google Scholar]
  29. 29. 
    Sanamrad A, Persson F, Lundius EG, Fange D, Gynnå AH, Elf J 2014. Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid. PNAS 111:3111413–18
    [Google Scholar]
  30. 30. 
    Bakshi S, Choi H, Mondal J, Weisshaar JC 2014. Time-dependent effects of transcription- and translation-halting drugs on the spatial distributions of the Escherichia coli chromosome and ribosomes. Mol. Microbiol. 94:4871–87
    [Google Scholar]
  31. 31. 
    Stracy M, Lesterlin C, Garza de Leon F, Uphoff S, Zawadzki P, Kapanidis AN 2015. Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid. PNAS 112:32E4390–99
    [Google Scholar]
  32. 32. 
    Bakshi S, Dalrymple RM, Li W, Choi H, Weisshaar JC 2013. Partitioning of RNA polymerase activity in live Escherichia coli from analysis of single-molecule diffusive trajectories. Biophys. J. 105:122676–86
    [Google Scholar]
  33. 33. 
    Izeddin I, Récamier V, Bosanac L, Cissé II, Boudarene L et al. 2014. Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus. eLife 3:e02230
    [Google Scholar]
  34. 34. 
    Normanno D, Boudarène L, Dugast-Darzacq C, Chen J, Richter C et al. 2015. Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher. Nat. Commun. 6:7357
    [Google Scholar]
  35. 35. 
    Cooperman BS, Kapanidis AN 2016. In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria. Nucleic Acids Res 45:2926–37
    [Google Scholar]
  36. 36. 
    Kleine Borgmann LAK, Ries J, Ewers H, Ulbrich MH, Graumann PL 2013. The bacterial SMC complex displays two distinct modes of interaction with the chromosome. Cell Rep 3:51483–92
    [Google Scholar]
  37. 37. 
    English BP, Hauryliuk V, Sanamrad A, Tankov S, Dekker NH, Elf J 2011. Single-molecule investigations of the stringent response machinery in living bacterial cells. PNAS 108:31E365–73
    [Google Scholar]
  38. 38. 
    Winther KS, Roghanian M, Gerdes K 2018. Activation of the stringent response by loading of RelA-tRNA complexes at the ribosomal A-site. Mol. Cell. 70:195–105.e4
    [Google Scholar]
  39. 39. 
    Li W, Bouveret E, Zhang Y, Liu K, Wang JD, Weisshaar JC 2016. Effects of amino acid starvation on RelA diffusive behavior in live Escherichia coli. Mol. . Microbiol 99:3571–85
    [Google Scholar]
  40. 40. 
    Kudrin P, Dzhygyr I, Ishiguro K, Beljantseva J, Maksimova E et al. 2018. The ribosomal A-site finger is crucial for binding and activation of the stringent factor RelA. Nucleic Acids Res 46:41973–83
    [Google Scholar]
  41. 41. 
    Marklund EG, Mahmutovic A, Berg OG, Hammar P, van der Spoel D et al. 2013. Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models. PNAS 110:4919796–801
    [Google Scholar]
  42. 42. 
    Gebhardt JCM, Suter DM, Roy R, Zhao ZW, Chapman AR et al. 2013. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat. Methods 10:5421–26
    [Google Scholar]
  43. 43. 
    Swinstead EE, Miranda TB, Paakinaho V, Baek S, Goldstein I et al. 2016. Steroid receptors reprogram FoxA1 occupancy through dynamic chromatin transitions. Cell 165:3593–605
    [Google Scholar]
  44. 44. 
    Liao Y, Schroeder JW, Gao B, Simmons LA, Biteen JS 2015. Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair. PNAS 112:50E6898–906
    [Google Scholar]
  45. 45. 
    Chen J, Zhang Z, Li L, Chen B-C, Revyakin A et al. 2014. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell 156:61274–85
    [Google Scholar]
  46. 46. 
    Persson F, Lindén M, Unoson C, Elf J 2013. Extracting intracellular diffusive states and transition rates from single-molecule tracking data. Nat. Methods 10:3265–69
    [Google Scholar]
  47. 47. 
    Bisson-Filho AW, Hsu Y-P, Squyres GR, Kuru E, Wu F et al. 2017. Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division. Science 355:6326739–43
    [Google Scholar]
  48. 48. 
    Yang X, Lyu Z, Miguel A, McQuillen R, Huang KC, Xiao J 2017. GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell wall synthesis. Science 355:6326744–47
    [Google Scholar]
  49. 49. 
    Loffreda A, Jacchetti E, Antunes S, Rainone P, Daniele T et al. 2017. Live-cell p53 single-molecule binding is modulated by C-terminal acetylation and correlates with transcriptional activity. Nat. Commun. 8:1313
    [Google Scholar]
  50. 50. 
    Volkov IL, Lindén M, Aguirre Rivera J, Ieong K-W, Metelev M et al. 2018. tRNA tracking for direct measurements of protein synthesis kinetics in live cells. Nat. Chem. Biol. 14:618–26
    [Google Scholar]
  51. 51. 
    Ha T. 2016. Probing nature's nanomachines one molecule at a time. Biophys. J. 110:51004–7
    [Google Scholar]
  52. 52. 
    Crawford R, Torella JP, Aigrain L, Plochowietz A, Gryte K et al. 2013. Long-lived intracellular single-molecule fluorescence using electroporated molecules. Biophys. J. 105:112439–50
    [Google Scholar]
  53. 53. 
    Plochowietz A, Crawford R, Kapanidis AN 2014. Characterization of organic fluorophores for in vivo FRET studies based on electroporated molecules. Phys. Chem. Chem. Phys. 16:2512688–94
    [Google Scholar]
  54. 54. 
    Plochowietz A, Farrell I, Smilansky Z, Cooperman BS, Kapanidis AN 2017. In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria. Nucleic Acids Res 45:2926–37
    [Google Scholar]
  55. 55. 
    Kim SB, Awais M, Sato M, Umezawa Y, Tao H 2007. Integrated molecule-format bioluminescent probe for visualizing androgenicity of ligands based on the intramolecular association of androgen receptor with its recognition peptide. Anal. Chem. 79:51874–80
    [Google Scholar]
  56. 56. 
    Suzuki K, Kimura T, Shinoda H, Bai G, Daniels MJ et al. 2016. Five colour variants of bright luminescent protein for real-time multicolour bioimaging. Nat. Commun. 7:13718
    [Google Scholar]
  57. 57. 
    Jun Y-W, Sheikholeslami S, Hostetter DR, Tajon C, Craik CS, Alivisatos AP 2009. Continuous imaging of plasmon rulers in live cells reveals early-stage caspase-3 activation at the single-molecule level. PNAS 106:4217735–40
    [Google Scholar]
  58. 58. 
    Leduc C, Si S, Gautier J, Soto-Ribeiro M, Wehrle-Haller B et al. 2013. A highly specific gold nanoprobe for live-cell single-molecule imaging. Nano Lett 13:41489–94
    [Google Scholar]
  59. 59. 
    de Wit G, Danial JSH, Kukura P, Wallace MI 2015. Dynamic label-free imaging of lipid nanodomains. PNAS 112:4012299–303
    [Google Scholar]
  60. 60. 
    Andrecka J, Ortega Arroyo J, Lewis K, Cross RA, Kukura P 2016. Label-free imaging of microtubules with sub-nm precision using interferometric scattering microscopy. Biophys. J. 110:1214–17
    [Google Scholar]
  61. 61. 
    Watanabe N, Mitchison TJ 2002. Single-molecule speckle analysis of actin filament turnover in lamellipodia. Science 295:55571083–86
    [Google Scholar]
  62. 62. 
    Deich J, Judd EM, McAdams HH, Moerner WE 2004. Visualization of the movement of single histidine kinase molecules in live Caulobacter cells. PNAS 101:4515921–26
    [Google Scholar]
  63. 63. 
    Lommerse PHM, Snaar-Jagalska BE, Spaink HP, Schmidt T 2005. Single-molecule diffusion measurements of H-Ras at the plasma membrane of live cells reveal microdomain localization upon activation. J. Cell Sci. 118:Part 91799–1809
    [Google Scholar]
  64. 64. 
    Hendrix J, Flors C, Dedecker P, Hofkens J, Engelborghs Y 2008. Dark states in monomeric red fluorescent proteins studied by fluorescence correlation and single molecule spectroscopy. Biophys. J. 94:104103–13
    [Google Scholar]
  65. 65. 
    Weber W, Helms V, McCammon JA, Langhoff PW 1999. Shedding light on the dark and weakly fluorescent states of green fluorescent proteins. PNAS 96:116177–82
    [Google Scholar]
  66. 66. 
    Landgraf D, Okumus B, Chien P, Baker TA, Paulsson J 2012. Segregation of molecules at cell division reveals native protein localization. Nat. Methods 9:5480–82
    [Google Scholar]
  67. 67. 
    Dersch S, Graumann PL 2017. The ultimate picture—the combination of live cell superresolution microscopy and single molecule tracking yields highest spatio-temporal resolution. Curr. Opin. Microbiol. 43:55–61
    [Google Scholar]
  68. 68. 
    Eun Y-J, Kapoor M, Hussain S, Garner EC 2015. Bacterial filament systems: toward understanding their emergent behavior and cellular functions. J. Biol. Chem. 290:2817181–89
    [Google Scholar]
  69. 69. 
    Hensel Z, Feng H, Han B, Hatem C, Wang J, Xiao J 2012. Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis. Nat. Struct. Mol. Biol. 19:8797–802
    [Google Scholar]
  70. 70. 
    Okumus B, Landgraf D, Lai GC, Bakhsi S, Arias-Castro JC et al. 2016. Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells. Nat. Commun. 7:11641
    [Google Scholar]
  71. 71. 
    Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD 2014. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159:3635–46
    [Google Scholar]
  72. 72. 
    Liu H, Dong P, Ioannou MS, Li L, Shea J et al. 2018. Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling. PNAS 115:2343–48
    [Google Scholar]
  73. 73. 
    Manley S, Gillette JM, Patterson GH, Shroff H, Hess HF et al. 2008. High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat. Methods 5:2155–57
    [Google Scholar]
  74. 74. 
    Niu L, Yu J 2008. Investigating intracellular dynamics of FtsZ cytoskeleton with photoactivation single-molecule tracking. Biophys. J. 95:42009–16
    [Google Scholar]
  75. 75. 
    Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M et al. 2016. Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli. Nat. Commun. 7:12568
    [Google Scholar]
  76. 76. 
    Uphoff S, Reyes-Lamothe R, Garza de Leon F, Sherratt DJ, Kapanidis AN 2013. Single-molecule DNA repair in live bacteria. PNAS 110:208063–68
    [Google Scholar]
  77. 77. 
    Badrinarayanan A, Reyes-Lamothe R, Uphoff S, Leake MC, Sherratt DJ 2012. In vivo architecture and action of bacterial structural maintenance of chromosome proteins. Science 338:6106528–31
    [Google Scholar]
  78. 78. 
    Beattie TR, Kapadia N, Nicolas E, Uphoff S, Wollman AJ et al. 2017. Frequent exchange of the DNA polymerase during bacterial chromosome replication. eLife 6:e21763
    [Google Scholar]
  79. 79. 
    Holden SJ, Pengo T, Meibom KL, Fernandez C, Collier J, Manley S 2014. High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization. PNAS 111:124566–71
    [Google Scholar]
  80. 80. 
    Ho HN, van Oijen AM, Ghodke H 2018. The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage. Nat. Commun. 9:11570
    [Google Scholar]
  81. 81. 
    Liu Z, Xing D, Su QP, Zhu Y, Zhang J et al. 2014. Super-resolution imaging and tracking of protein-protein interactions in sub-diffraction cellular space. Nat. Commun. 5:4443
    [Google Scholar]
  82. 82. 
    Los GV, Encell LP, McDougall MG, Hartzell DD, Karassina N et al. 2008. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem. Biol. 3:6373–82
    [Google Scholar]
  83. 83. 
    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. 21:186–89
    [Google Scholar]
  84. 84. 
    Zhao ZW, Roy R, Gebhardt JCM, Suter DM, Chapman AR, Xie XS 2014. Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. PNAS 111:2681–86
    [Google Scholar]
  85. 85. 
    Ke N, Landgraf D, Paulsson J, Berkmen M 2016. Visualization of periplasmic and cytoplasmic proteins with a self-labeling protein tag. J. Bacteriol. 198:71035–43
    [Google Scholar]
  86. 86. 
    Banaz N, Makela J, Uphoff S 2018. Choosing the right label for single-molecule tracking in live bacteria: side-by-side comparison of photoactivatable fluorescent protein and Halo tag dyes. J. Phys. D 52:064002
  87. 87. 
    Barlag B, Beutel O, Janning D, Czarniak F, Richter CP et al. 2016. Single molecule super-resolution imaging of proteins in living Salmonella enterica using self-labelling enzymes. Sci. Rep. 6:31601
    [Google Scholar]
  88. 88. 
    Wombacher R, Heidbreder M, van de Linde S, Sheetz MP, Heilemann M et al. 2010. Live-cell super-resolution imaging with trimethoprim conjugates. Nat. Methods 7:9717–19
    [Google Scholar]
  89. 89. 
    Lukinavičius G, Umezawa K, Olivier N, Honigmann A, Yang G et al. 2013. A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat. Chem. 5:2132–39
    [Google Scholar]
  90. 90. 
    Zheng Q, Lavis LD 2017. Development of photostable fluorophores for molecular imaging. Curr. Opin. Chem. Biol. 39:32–38
    [Google Scholar]
  91. 91. 
    Lavis LD. 2017. Chemistry is dead. Long live chemistry!. Biochemistry 56:5165–70
    [Google Scholar]
  92. 92. 
    Grimm JB, English BP, Chen J, Slaughter JP, Zhang Z et al. 2015. A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat. Methods 12:3244–50
    [Google Scholar]
  93. 93. 
    Zhen CY, Tatavosian R, Huynh TN, Duc HN, Das R et al. 2016. Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin. eLife 5:e17667
    [Google Scholar]
  94. 94. 
    Rhodes J, Mazza D, Nasmyth K, Uphoff S 2017. Scc2/Nipbl hops between chromosomal cohesin rings after loading. eLife Sci 6:e30000
    [Google Scholar]
  95. 95. 
    Hussain S, Wivagg CN, Szwedziak P, Wong F, Schaefer K et al. 2018. MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis. eLife Sci 7:e32471
    [Google Scholar]
  96. 96. 
    Hughes LD, Rawle RJ, Boxer SG 2014. Choose your label wisely: water-soluble fluorophores often interact with lipid bilayers. PLOS ONE 9:2e87649
    [Google Scholar]
  97. 97. 
    Fernández-Suárez M, Ting AY 2008. Fluorescent probes for super-resolution imaging in living cells. Nat. Rev. Mol. Cell Biol. 9:12929–43
    [Google Scholar]
  98. 98. 
    Saurabh S, Perez AM, Comerci CJ, Shapiro L, Moerner WE 2016. Super-resolution imaging of live bacteria cells using a genetically directed, highly photostable fluoromodule. J. Am. Chem. Soc. 138:3310398–401
    [Google Scholar]
  99. 99. 
    Virant D, Traenkle B, Maier J, Kaiser PD, Bodenhöfer M et al. 2018. A peptide tag-specific nanobody enables high-quality labeling for dSTORM imaging. Nat. Commun. 9:1930
    [Google Scholar]
  100. 100. 
    Plass T, Milles S, Koehler C, Szymański J, Mueller R et al. 2012. Amino acids for Diels–Alder reactions in living cells. Angew. Chem. Int. Ed. Engl. 51:174166–70
    [Google Scholar]
  101. 101. 
    Nikić I, Plass T, Schraidt O, Szymański J, Briggs JAG et al. 2014. Minimal tags for rapid dual-color live-cell labeling and super-resolution microscopy. Angew. Chem. Int. Ed. Engl. 53:82245–49
    [Google Scholar]
  102. 102. 
    Lajoie MJ, Rovner AJ, Goodman DB, Aerni H-R, Haimovich AD et al. 2013. Genomically recoded organisms expand biological functions. Science 342:6156357–60
    [Google Scholar]
  103. 103. 
    Cheng M, Zhang W, Yuan J, Luo W, Li N et al. 2014. Single-molecule dynamics of site-specific labeled transforming growth factor type II receptors on living cells. Chem. Commun. 50:9414724–27
    [Google Scholar]
  104. 104. 
    Kipper K, Lundius EG, Ćurić V, Nikić I, Wiessler M et al. 2017. Application of noncanonical amino acids for protein labeling in a genomically recoded Escherichia coli. ACS Synth. . Biol 6:2233–55
    [Google Scholar]
  105. 105. 
    Devaraj NK, Hilderbrand S, Upadhyay R, Mazitschek R, Weissleder R 2010. Bioorthogonal turn-on probes for imaging small molecules inside living cells. Angew. Chem. Int. Ed. Engl. 49:162869–72
    [Google Scholar]
  106. 106. 
    Ha T, Enderle T, Ogletree DF, Chemla DS, Selvin PR, Weiss S 1996. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. PNAS 93:136264–68
    [Google Scholar]
  107. 107. 
    Sakon JJ, Weninger KR 2010. Detecting the conformation of individual proteins in live cells. Nat. Methods 7:3203–5
    [Google Scholar]
  108. 108. 
    König I, Zarrine-Afsar A, Aznauryan M, Soranno A, Wunderlich B et al. 2015. Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells. Nat. Methods 12:8773–79
    [Google Scholar]
  109. 109. 
    Mo GCH, Ross B, Hertel F, Manna P, Yang X et al. 2017. Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution. Nat. Methods 14:4427–34
    [Google Scholar]
  110. 110. 
    Dertinger T, Colyer R, Iyer G, Weiss S, Enderlein J 2009. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). PNAS 106:5222287–92
    [Google Scholar]
  111. 111. 
    Dertinger T, Colyer R, Vogel R, Heilemann M, Sauer M et al. 2012. Superresolution optical fluctuation imaging (SOFI). Adv. Exp. Med. Biol. 733:17–21
    [Google Scholar]
  112. 112. 
    Jin D, Xi P, Wang B, Zhang L, Enderlein J, van Oijen AM 2018. Nanoparticles for super-resolution microscopy and single-molecule tracking. Nat. Methods 15:6415–23
    [Google Scholar]
  113. 113. 
    Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM 1998. Localization of ASH1 mRNA particles in living yeast. Mol. Cell. 2:4437–45
    [Google Scholar]
  114. 114. 
    Lim F, Downey TP, Peabody DS 2001. Translational repression and specific RNA binding by the coat protein of the Pseudomonas phage PP7. J. Biol. Chem. 276:2522507–13
    [Google Scholar]
  115. 115. 
    Golding I, Cox EC 2004. RNA dynamics in live Escherichia coli cells. PNAS 101:3111310–15
    [Google Scholar]
  116. 116. 
    Hocine S, Raymond P, Zenklusen D, Chao JA, Singer RH 2013. Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nat. Methods 10:2119–21
    [Google Scholar]
  117. 117. 
    Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH 2011. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 332:6028475–78
    [Google Scholar]
  118. 118. 
    Wu B, Chen J, Singer RH 2014. Background free imaging of single mRNAs in live cells using split fluorescent proteins. Sci. Rep. 4:3615
    [Google Scholar]
  119. 119. 
    Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N et al. 2016. Mapping translation “hot-spots” in live cells by tracking single molecules of mRNA and ribosomes. eLife 5:e10415
    [Google Scholar]
  120. 120. 
    Morisaki T, Lyon K, DeLuca KF, DeLuca JG, English BP et al. 2016. Real-time quantification of single RNA translation dynamics in living cells. Science 352:62921425–29
    [Google Scholar]
  121. 121. 
    Wu B, Eliscovich C, Yoon YJ, Singer RH 2016. Translation dynamics of single mRNAs in live cells and neurons. Science 352:62921430–35
    [Google Scholar]
  122. 122. 
    Tutucci E, Vera M, Biswas J, Garcia J, Parker R, Singer RH 2018. An improved MS2 system for accurate reporting of the mRNA life cycle. Nat. Methods 15:181–89
    [Google Scholar]
  123. 123. 
    Zhang J, Fei J, Leslie BJ, Han KY, Kuhlman TE, Ha T 2015. Tandem Spinach array for mRNA imaging in living bacterial cells. Sci. Rep. 5:17295
    [Google Scholar]
  124. 124. 
    Arora A, Sunbul M, Jäschke A 2015. Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers. Nucleic Acids Res 43:21e144
    [Google Scholar]
  125. 125. 
    Bratu DP, Cha B-J, Mhlanga MM, Kramer FR, Tyagi S 2003. Visualizing the distribution and transport of mRNAs in living cells. PNAS 100:2313308–13
    [Google Scholar]
  126. 126. 
    Catrina IE, Marras SAE, Bratu DP 2012. Tiny molecular beacons: LNA/2′-O-methyl RNA chimeric probes for imaging dynamic mRNA processes in living cells. ACS Chem. Biol. 7:91586–95
    [Google Scholar]
  127. 127. 
    Zhao D, Yang Y, Qu N, Chen M, Ma Z et al. 2016. Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2′-O-methyl RNA molecular beacons. Biomaterials 100:172–83
    [Google Scholar]
  128. 128. 
    Pitchiaya S, Heinicke LA, Park JI, Cameron EL, Walter NG 2017. Resolving subcellular miRNA trafficking and turnover at single-molecule resolution. Cell Rep 19:3630–42
    [Google Scholar]
  129. 129. 
    Fessl T, Adamec F, Polívka T, Foldynová-Trantírková S, Vácha F, Trantírek L 2012. Towards characterization of DNA structure under physiological conditions in vivo at the single-molecule level using single-pair FRET. Nucleic Acids Res 40:16e121
    [Google Scholar]
  130. 130. 
    Biteen JS, Thompson MA, Tselentis NK, Bowman GR, Shapiro L, Moerner WE 2008. Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP. Nat. Methods 5:11947–49
    [Google Scholar]
  131. 131. 
    Tokunaga M, Imamoto N, Sakata-Sogawa K 2008. Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat. Methods 5:2159–61
    [Google Scholar]
  132. 132. 
    Ritter JG, Veith R, Veenendaal A, Siebrasse JP, Kubitscheck U 2010. Light sheet microscopy for single molecule tracking in living tissue. PLOS ONE 5:7e11639
    [Google Scholar]
  133. 133. 
    Abrahamsson S, Chen J, Hajj B, Stallinga S, Katsov AY et al. 2013. Fast multicolor 3D imaging using aberration-corrected multifocus microscopy. Nat. Methods 10:160–63
    [Google Scholar]
  134. 134. 
    Planchon TA, Gao L, Milkie DE, Davidson MW, Galbraith JA et al. 2011. Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat. Methods 8:417–23
    [Google Scholar]
  135. 135. 
    Gao L, Shao L, Chen B-C, Betzig E 2014. 3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy. Nat. Protoc. 9:51083–1101
    [Google Scholar]
  136. 136. 
    Chen B-C, Legant WR, Wang K, Shao L, Milkie DE et al. 2014. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346:62081257998
    [Google Scholar]
  137. 137. 
    Liu Z, Legant WR, Chen B-C, Li L, Grimm JB et al. 2014. 3D imaging of Sox2 enhancer clusters in embryonic stem cells. eLife 3:e04236
    [Google Scholar]
  138. 138. 
    Douglass KM, Sieben C, Archetti A, Lambert A, Manley S 2016. Super-resolution imaging of multiple cells by optimized flat-field epi-illumination. Nat. Photonics 10:11705–8
    [Google Scholar]
  139. 139. 
    Huang B, Jones SA, Brandenburg B, Zhuang X 2008. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nat. Methods 5:121047–52
    [Google Scholar]
  140. 140. 
    Kao HP, Verkman AS 1994. Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position. Biophys. J. 67:31291–1300
    [Google Scholar]
  141. 141. 
    Biteen JS, Goley ED, Shapiro L, Moerner WE 2012. Three-dimensional super-resolution imaging of the midplane protein FtsZ in live Caulobacter crescentus cells using astigmatism. ChemPhysChem 13:41007–12
    [Google Scholar]
  142. 142. 
    Izeddin I, El Beheiry M, Andilla J, Ciepielewski D, Darzacq X, Dahan M 2012. PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking. Opt. Express 20:54957–67
    [Google Scholar]
  143. 143. 
    Pavani SRP, Thompson MA, Biteen JS, Lord SJ, Liu N et al. 2009. Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. PNAS 106:92995–99
    [Google Scholar]
  144. 144. 
    Backlund MP, Joyner R, Weis K, Moerner WE 2014. Correlations of three-dimensional motion of chromosomal loci in yeast revealed by the double-helix point spread function microscope. Mol. Biol. Cell 25:223619–29
    [Google Scholar]
  145. 145. 
    von Diezmann A, Shechtman Y, Moerner WE 2017. Three-dimensional localization of single molecules for super-resolution imaging and single-particle tracking. Chem. Rev. 117:117244–75
    [Google Scholar]
  146. 146. 
    Backlund MP, Lew MD, Backer AS, Sahl SJ, Moerner WE 2014. The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging. ChemPhysChem 15:4587–99
    [Google Scholar]
  147. 147. 
    Testa I, Schönle A, von Middendorff C, Geisler C, Medda R et al. 2008. Nanoscale separation of molecular species based on their rotational mobility. Opt. Express 16:2521093–104
    [Google Scholar]
  148. 148. 
    Gustavsson A-K, Petrov PN, Lee MY, Shechtman Y, Moerner WE 2018. 3D single-molecule super-resolution microscopy with a tilted light sheet. Nat. Commun. 9:1123
    [Google Scholar]
  149. 149. 
    Shtengel G, Galbraith JA, Galbraith CG, Lippincott-Schwartz J, Gillette JM et al. 2009. Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. PNAS 106:93125–30
    [Google Scholar]
  150. 150. 
    Taute KM, Gude S, Tans SJ, Shimizu TS 2015. High-throughput 3D tracking of bacteria on a standard phase contrast microscope. Nat. Commun. 6:8776
    [Google Scholar]
  151. 151. 
    Levi V, Ruan Q, Gratton E 2005. 3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells. Biophys. J. 88:42919–28
    [Google Scholar]
  152. 152. 
    Balzarotti F, Eilers Y, Gwosch KC, Gynnå AH, Westphal V et al. 2016. Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science 355:6325606–12
    [Google Scholar]
  153. 153. 
    Sage D, Kirshner H, Pengo T, Stuurman N, Min J et al. 2015. Quantitative evaluation of software packages for single-molecule localization microscopy. Nat. Methods 12:8717–24
    [Google Scholar]
  154. 154. 
    Chenouard N, Smal I, de Chaumont F, Maška M, Sbalzarini IF et al. 2014. Objective comparison of particle tracking methods. Nat. Methods 11:3281–89
    [Google Scholar]
  155. 155. 
    Garza de Leon F, Sellars L, Stracy M, Busby SJW, Kapanidis AN 2017. Tracking low-copy transcription factors in living bacteria: the case of the lac repressor. Biophys. J. 112:71316–27
    [Google Scholar]
  156. 156. 
    Vestergaard CL, Blainey PC, Flyvbjerg H 2014. Optimal estimation of diffusion coefficients from single-particle trajectories. Phys. Rev. E 89:2022726
    [Google Scholar]
  157. 157. 
    Gonzalez RC, Wintz P 1977. Digital Image Processing Reading, MA: Addison-Wesley
    [Google Scholar]
  158. 158. 
    Lindeberg T. 1998. Feature detection with automatic scale selection. Int. J. Comput. Vis. 30:279–116
    [Google Scholar]
  159. 159. 
    Kong H, Akakin HC, Sarma SE 2013. A generalized Laplacian of Gaussian filter for blob detection and its applications. IEEE Trans. Cybern. 43:61719–33
    [Google Scholar]
  160. 160. 
    Magnusson KEG, Jalden J 2012. A batch algorithm using iterative application of the Viterbi algorithm to track cells and construct cell lineages. 9th IEEE International Symposium on Biomedical Imaging382–85 New York: IEEE
    [Google Scholar]
  161. 161. 
    Sergé A, Bertaux N, Rigneault H, Marguet D 2008. Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes. Nat. Methods 5:8687–94
    [Google Scholar]
  162. 162. 
    Smith CS, Stallinga S, Lidke KA, Rieger B, Grunwald D 2015. Probability-based particle detection that enables threshold-free and robust in vivo single molecule tracking. Mol. Biol. Cell 26:3893–4181
    [Google Scholar]
  163. 163. 
    Loy G, Zelinsky A 2003. Fast radial symmetry for detecting points of interest. IEEE Trans. Pattern Anal. Mach. Intell. 25:8959–73
    [Google Scholar]
  164. 164. 
    Olivo-Marin J-C. 2002. Extraction of spots in biological images using multiscale products. Pattern Recognit 35:91989–96
    [Google Scholar]
  165. 165. 
    Mortensen KI, Churchman LS, Spudich JA, Flyvbjerg H 2010. Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat. Methods 7:5377–81
    [Google Scholar]
  166. 166. 
    Rieger B, Stallinga S 2014. The lateral and axial localization uncertainty in super-resolution light microscopy. ChemPhysChem 15:4664–70
    [Google Scholar]
  167. 167. 
    Lindén M, Ćurić V, Amselem E, Elf J 2017. Pointwise error estimates in localization microscopy. Nat. Commun. 8:15115
    [Google Scholar]
  168. 168. 
    Jaqaman K, Loerke D, Mettlen M, Kuwata H, Grinstein S et al. 2008. Robust single-particle tracking in live-cell time-lapse sequences. Nat. Methods 5:8695–702
    [Google Scholar]
  169. 169. 
    Venkataramanan L, Sigworth FJ 2002. Applying hidden Markov models to the analysis of single ion channel activity. Biophys. J. 82:41930–42
    [Google Scholar]
  170. 170. 
    Kohavi R. 1995. A study of cross-validation and bootstrap for accuracy estimation and model selection. Proceedings of the 14th International Joint Conference on Artificial Intelligence, Vol. 2 CS Mellish 1137–43 Denver: Int. Joint Conf. Artif. Intell.
    [Google Scholar]
  171. 171. 
    Monnier N, Barry Z, Park HY, Su K-C, Katz Z et al. 2015. Inferring transient particle transport dynamics in live cells. Nat. Methods 12:9838–40
    [Google Scholar]
  172. 172. 
    Kaipio J, Somersalo E 2007. Statistical inverse problems: discretization, model reduction and inverse crimes. J. Comput. Appl. Math. 198:2493–504
    [Google Scholar]
  173. 173. 
    Lindén M, Ćurić V, Boucharin A, Fange D, Elf J 2016. Simulated single molecule microscopy with SMeagol. Bioinformatics 32:152394–95
    [Google Scholar]
  174. 174. 
    Minton AP. 2006. How can biochemical reactions within cells differ from those in test tubes?. J. Cell Sci. 119:142863–69
    [Google Scholar]
  175. 175. 
    Lawson MJ, Camsund D, Larsson J, Baltekin Ö, Fange D, Elf J 2017. In situ genotyping of a pooled strain library after characterizing complex phenotypes. Mol. Syst. Biol. 13:10947
    [Google Scholar]
  176. 176. 
    Marklund E, Amselem E, Kipper K, Zheng X, Johansson M 2018. Direct observation of rotation-coupled protein diffusion along DNA on the microsecond timescale. bioRxiv. https://doi.org/10.1101/401414
    [Crossref] [Google Scholar]
/content/journals/10.1146/annurev-biochem-013118-110801
Loading
/content/journals/10.1146/annurev-biochem-013118-110801
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error