Biomolecular dynamics and binding studies in the living cell

Physics of Life Reviews

Volumn 11, Issue 1, 2014, Pages 1-30

  Diekmann, Stephan ^a   Hoischen, Christian ^a  

^a Molecular Biology   (Germany)

Author keywords

Dynamics; Fluorescence microscopy; Live cell imaging; Protein protein interaction; Proximity

Indexed keywords

BIOMOLECULAR DYNAMICS; LIVE-CELL IMAGING; MOLECULAR INFORMATION; MOLECULAR PROPERTIES; MULTI-PROTEIN COMPLEX; PHYSICO-CHEMICAL DATA; PROTEIN-PROTEIN INTERACTIONS; PROXIMITY;

DYNAMICS; FLUORESCENCE MICROSCOPY; MOLECULAR ORIENTATION;

PROTEINS;

PHOTOPROTEIN; PROTEIN;

ANIMAL; BIOPHYSICS; CELL SURVIVAL; DYNAMICS; FLUORESCENCE MICROSCOPY; HUMAN; LIVE CELL IMAGING; METABOLISM; METHODOLOGY; NANOTECHNOLOGY; PROTEIN BINDING; PROTEIN-PROTEIN INTERACTION; PROXIMITY; REVIEW;

DYNAMICS; FLUORESCENCE MICROSCOPY; LIVE CELL IMAGING; PROTEIN-PROTEIN INTERACTION; PROXIMITY;

ANIMALS; BIOPHYSICS; CELL SURVIVAL; HUMANS; LUMINESCENT PROTEINS; NANOTECHNOLOGY; PROTEIN BINDING; PROTEINS;

EID: 84896704404     PISSN: 15710645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plrev.2013.11.011     Document Type: Review

References (229)

1. Alcala J.R., Gratton E., Prendergast F.G. Resolvability of fluorescence lifetime distributions using phase fluorometry. Biophys J 1987, 51:587-596.
2. Ando R., Hama H., Yamamoto-Hino M., Mizuno H., Miyawaki A. An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc Natl Acad Sci USA 2002, 99:12651-12656.
3. Anthony N., Guo P., Berland K. Principles of fluorescence for quantitative fluorescence microscopy. FLIM microscopy in biology and medicine 2010, 35-63. CRC Press, London. A. Periasamy, R.M. Clegg (Eds.).
4. Axelrod D., Koppel D.E., Schlessinger J., Elson E., Webb W.W. Mobility measurement by analysis of fluorescence photo-bleaching recovery kinetics. Biophys J 1976, 16:1055-1069.
5. Bacart J., Corbel C., Jockers R., Bach S., Couturier C. The BRET technology and its application to screening assays. Biotechnol J 2008, 3:311-324.
6. Bacia K., Schwille P. A dynamic view of cellular processes by in vivo fluorescence auto- and cross-correlation spectroscopy. Methods 2003, 29:74-85.
7. Bacia K., Schwille P. Practical guidelines for dual-color fluorescence cross-correlation spectroscopy. Nat Protoc 2007, 2:2842-2856.
8. Bacskai B.J., Skoch J., Hickey G.A., Allen R., Hyman B.T. Fluorescence resonance energy transfer determinations using multi-photon fluorescence lifetime imaging microscopy to characterize amyloid-beta plaques. J Biomed Opt 2003, 8:368-375.
9. Bailey E.A., Rollefson G.K. The determination of the fluorescence lifetimes of dissolved substances by a phase shift method. J Chem Phys 1953, 21:1315-1322.
10. Bancaud A., Huet S., Rabut G., Ellenberg J. Fluorescence perturbation techniques to study mobility and molecular dynamics of proteins in live cells: FRAP, photo-activation, photo-conversion, and FLIP. Live cell imaging: a laboratory manual 2009, Cold Spring Harbor Press, New York, USA. J. Swedlow, R. Goldman, D. Spector (Eds.).
11. Bantscheff M., Schirle M., Sweetman G., Rick J., Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 2007, 389:1017-1031.
12. Brasselet S., Moerner W.E. Fluorescence behavior of single-molecule pH-sensors. Single Mol 2000, 1:17-23.
13. Beaudouin J., Mora-Bermudez F., Klee T., Daigle N., Ellenberg J. Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins. Biophys J 2006, 90:1878-1894.
14. Berney C., Danuser G. FRET or no FRET: A quantitative comparison. Biophys J 2003, 84:3992-4010.
15. Betzig E., Patterson G.H., Sougrat R., Lindwasser O.W., Olenych S., Bonifacino J.S., et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 2006, 313:1642-1645.
16. Binz H.K., Amstutz P., Kohl A., Stumpp M.T., Briand C., Forrer P., et al. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat Biotechnol 2004, 22:575-582.
17. Birks F.B., Little W.A. Photo-fluorescence decay times of organic phosphors. Proc Phys Soc A 1953, 66:921-928.
18. Boch J., Scholze H., Schornack S., Landgraf A., Hahn S., Kay S., et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 2009, 326:1509-1512.
19. Brunger A.T., Strop P., Vrljic M., Bowen M., Chu S., Weninger K.R. Macromolecular models by single-molecule FRET. NATO science for peace and security series B: physics and biophysics 2013, 1-19. J.D. Puglisi, M.V. Margaris (Eds.).
20. Carrero G., McDonald D., Crawford E., de Vries G., Hendzel M.J. Using FRAP and mathematical modeling to determine the in vivo kinetics of nuclear proteins. Methods 2003, 29:14-28.
21. Carroll C.W., Silva M.C., Godek K.N., Jansen L.E., Straight A.F. Centromere assembly requires the direct recognition of CENP-A nucleosomes by CENP-N. Nat Cell Biol 2009, 11:896-902.
22. Chen D., Huang S. Nucleolar components involved in ribosome biogenesis cycle between the nucleolus and nucleoplasm in interphase cells. J Cell Biol 2001, 153:169-176.
23. Chen H., Farkas E.R., Webb W.W. Chapter 1: In vivo applications of fluorescence correlation spectroscopy. Methods Cell Biol 2008, 89:3-35.
24. Clegg R.M. Fluorescence resonance energy transfer. Fluorescence imaging spectroscopy and microscopy, vol 137 1996, 179-251. John Wiley & Sons Inc., New York. X.F. Wang, B. Herman (Eds.).
25. Cisse I., Okumus B., Joo C., Ha T. Fueling protein DNA interactions inside porous nanocontainers. Proc Natl Acad Sci USA 2007, 104:12646-12650.
26. Clegg R.M. Fluorescence lifetime-resolved imaging: what, why, how - a prologue. FLIM microscopy in biology and medicine 2010, 3-34. CRC Press, London. A. Periasamy, R.M. Clegg (Eds.).
27. Coffman V.C., Wu J.Q. Counting protein molecules using quantitative fluorescence microscopy. Trends Biochem Sci 2012, 37:499-506.
28. Coffman V.C., Wu P., Parthun M.R., Wu J.Q. CENP-A exceeds microtubule attachment sites in centromere clusters of both budding and fission yeast. J Cell Biol 2011, 195:563-572.
29. Cole N.B., Smith C.L., Sciaky N., Terasaki M., Edidin M., Lippincott-Schwartz J. Diffusional mobility of Golgi proteins in membranes of living cells. Science 1996, 273:797-801.
30. Cox S., Rosten E., Monypenny J., Jovanovic-Talisman T., Burnette D.T., Lippincott-Schwartz J., et al. Bayesian localization microscopy reveals nanoscale podosome dynamics. Nat Methods 2011, 9:195-200.
31. Cremer T., Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2001, 2:292-301.
32. Cremer C., Kaufmann R., Gunkel M., Pres S., Weiland Y., Müller P., et al. Superresolution imaging of biological nanostructures by spectral precision distance microscopy. Biotechnol J 2011, 6:1037-1051.
33. Daddysman M.K., Fecko C.J. Revisiting point FRAP to quantitatively characterize anomalous diffusion in live cells. J Phys Chem 2013, 117:1241-1251.
34. Dedecker P., Hotta J.-I., Flors C., Sliwa M., Uji-I H., Roeffaers M.B.J., et al. Subdiffraction imaging through the selective donut-mode depletion of thermally stable photoswitchable fluorophores: Numerical analysis and application to the fluorescent protein Dronpa. J Am Chem Soc 2007, 129:16132-16141.
35. Denk W., Strickler J., Webb W.W. Two-photon laser scanning fluorescence microscopy. Science 1990, 248:73-76.
36. Depry C., Mehta S., Zhang J. Multiplexed visualization of dynamic signaling networks using genetically encoded fluorescent protein-based biosensors. Pflugers Arch - Eur J Physiol 2013, 465:373-381.
37. Diekmann S. Microscopic techniques. An introduction to molecular biotechnology 2011, 197-209. Wiley VCH, Weinheim. M. Wink (Ed.).
38. Digman M.A., Gratton E. Analysis of diffusion and binding in cells using the RICS approach. Microsc Res Tech 2009, 72:323-332.
39. Digman M.A., Sengupta P., Wiseman P.W., Brown C.M., Horwitz A.R., Gratton E. Fluctuation correlation spectroscopy with a laser-scanning microscope: exploiting the hidden time structure. Biophys J 2005, 88:L33-L66.
40. Digman M.A., Caiolfa V.R., Zamai M., Gratton E. The phasor approach to fluorescence lifetime imaging analysis. Biophys J 2008, 94:L14-L16.
41. Dreier B., Honegger A., Hess C., Nagy-Davidescu G., Mittl P.R., Grütter M.G., et al. Development of a genetic adenovirus delivery system based on structure-guided design of bispecific trimeric DARP in adapters. Proc Natl Acad Sci USA 2013, 110:E869-E877.
42. Dundr M., Hoffmann-Rohrer U., Hu Q., Grummt I., Rothblum L.I., Phair R.D., et al. A kinetic framework for a mammalian RNA polymerase in vivo. Science 2002, 298:1623-1626.
43. Dundr M., McNally J.G., Cohen J., Misteli T. Quantification of GFP-fusion proteins in single living cells. J Struct Biol 2002, 140:92-99.
44. Dunn G.A., Dobbie I.M., Monypenny J., Holt M.R., Zicha D. Fluorescence localization after photobleaching (FLAP): a new method for studying protein dynamics in living cells. J Microsc 2002, 205:109-112.
45. Easwaran H.P., Leonhardt H., Cardoso M.C. Cell cycle markers for live cell analyses. Cell Cycle 2005, 4:453-455.
46. Egner A., Geisler C., von Middendorff C., Bock H., Wenzel D., Medda R., et al. Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters. Biophys J 2007, 93:3285-3290.
47. Elangovan M., Wallrabe H., Chen Y., Day R.N., Barroso M., Periasamy A. Characterisation of one- and two-photon-excitation fluorescence resonance energy transfer microscopy. Methods 2003, 29:58-73.
48. Ellenberg J., Siggia E.D., Moreira J.E., Smith C.L., Presley J.F., Worman H.J., et al. Nuclear membrane dynamics and reassembly in living cells: targeting of an inner nuclear membrane protein in interphase and mitosis. J Cell Biol 1997, 138:1193-1206.
49. Erdel F., Müller-Ott K., Baum M., Wachsmuth M., Rippe K. Dissecting chromatin interactions in living cells from protein mobility maps. Chromosom Res 2011, 19:99-115.
50. Eskat A., Deng W., Hofmeister A., Rudolphi S., Emmerth S., Hellwig D., et al. Step-wise assembly, maturation and dynamic behavior of the human CENP-P/O/R/Q/U kinetochore sub-complex. PLoS ONE 2012, 7:e44717.
51. Fereidouni F., Esposito A., Blab G.A., Gerritsen H.C. A modified phasor approach for analyzing time-gated fluorescence lifetime images. J Microsc 2011, 244:248-258.
52. Fernandez-Suarez M., Ting A.Y. Fluorescent probes for super-resolution imaging in living cells. Nat Rev Mol Cell Biol 2008, 9:929-943.
53. Ficz G., Heintzmann R., Arndt-Jovin D.J. Polycomb group protein complexes exchange rapidly in living Drosophila. Development 2005, 132:3963-3976.
54. Folling J., Bossi M., Bock H., Medda R., Wurm C.A., Hein B., et al. Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat Methods 2008, 5:943-945.
55. Förster T. Intermolecular energy migration and fluorescence. Ann Phys 1948, 2:55-75.
56. Förster T. Delocalised excitation and excitation transfer. Modern quantum chemistry, vol 3 1965, 93-137. Academic Press Inc., New York. O. Sinanoglu (Ed.).
57. Fonseca J.P., Steffen P.A., Müller S., Lu J., Sawicka A., Seiser C., et al. In vivo polycomb kinetics and mitotic chromatin binding distinguish stem cells from differentiated cells. Genes Dev 2012, 26:857-871.
58. Gambin Y., Deniz A.A. Multicolor single-molecule FRET to explore protein folding and binding. Mol BioSyst 2010, 6:1540-1547.
59. Geißler R., Scholze H., Hahn S., Streubel J., Bonas U., Behrens S.E., et al. Transcriptional activators of human genes with programmable DNA-specificity. PLoS ONE 2011, 6:e19509.
60. Gerritsen H.C., Bader A., Agronskaia S. Laser scanning confocal FLIM microscopy. FLIM microscopy in biology and medicine 2010, 143-163. CRC Press, London. A. Periasamy, R.M. Clegg (Eds.).
61. Ghosh I., Hamilton A.D., Regan L. Leucine zipper assisted protein reassembly: Application to the Green Fluorescent Protein. J Am Chem Soc 2000, 122:5658-5659.
62. Giunta S., Belotserkovskaya R., Jackson S.P. DNA damage signaling in response to double-strand breaks during mitosis. J Cell Biol 2010, 190:197-207.
63. Goeppert-Mayer M. Über Elementarakte mit zwei Quantensprüngen. Annu Phys 1931, 9:273-295.
64. Griffin B.A., Adams S.R., Tsien R.Y. Specific covalent labeling of recombinant protein molecules inside live cells. Science 1998, 281:269-272.
65. Gu Y., Di W.L., Kelsell D.P., Zicha D. Quantitative fluorescence resonance energy transfer (FRET) measurement with acceptor photo-bleaching and spectral un-mixing. J Microsc 2004, 215:162-173.
66. Guillot P.V., Xie S.Q., Hollinshead M., Pombo A. Fixation-induced redistribution of hyperphosphorylated RNA polymerase II in the nucleus of human cells. Exp Cell Res 2004, 295:460-468.
67. Gurskaya N.G., Verkhusha V.V., Shcheglov A.S., Staroverov D.B., Chepurnykh T.V., Fradkov A.F., et al. Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nat Biotechnol 2006, 24:461-465.
68. Gustafsson M.G.L. Nonlinear structured-illumination microscopy: widefield fluorescence imaging with theoretically unlimited resolution. Proc Natl Acad Sci USA 2005, 102:13081-13086.
69. Ha T., Enderle T., Ogletree D.F., Chemla D.S., Selvin P.R., Weiss S. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc Natl Acad Sci USA 1996, 93:6264-6268.
70. Ha T. Single molecule fluorescence resonance energy transfer. Methods 2001, 25:78-86.
71. Harada Y., Funatsu T., Murakami K., Nonoyama Y., Ishihama A., Yanagida T. Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys J 1999, 76:709-715.
72. Haugland R.P., Yguerabide J., Stryer L. Dependence of the kinetics of singlet-singlet energy transfer of spectral overlap. Proc Natl Acad Sci USA 1969, 63:23-30.
73. Haustein E., Schwille P. Ultrasensitive investigations of biological systems by fluorescence correlation spectroscopy. Methods 2003, 29:153-166.
74. Hebert B., Costantino S., Wiseman P.W. Spatiotemporal image correlation spectroscopy (STICS) theory, verification, and application to protein velocity mapping in living CHO cells. Biophys J 2005, 88:3601-3614.
75. Heilemann M., van de Linde S., Mukherjee A., Sauer M. Super-resolution imaging with small organic fluorophores 13. Angew Chem, Int Ed Engl 2009, 48:6903-6908.
76. Hell S.W. Far-field optical nanoscopy. Science 2007, 316:1153-1158.
77. Heinze K.G., Koltermann A., Schwille P. Simultaneous two-photon excitation of distinct labels for dual-color fluorescence cross-correlation analysis. Proc Natl Acad Sci USA 2000, 97:10377-10382.
78. Hellwig D., Münch S., Orthaus S., Hoischen C., Hemmerich P., Diekmann S. Live.cell imaging reveals sustained centromere binding of CENP-T via CENP-A and CENP-B. J Biophotonics 2008, 1:245-254.
79. Hellwig D., Hoischen C., Ulbricht T., Diekmann S. Acceptor-photobleaching FRET analysis of core kinetochore and NAC proteins in living human cells. Eur Biophys J 2009, 38:781-791.
80. Hellwig D., Emmerth S., Ulbricht T., Döring V., Hoischen C., Martin R., et al. Dynamics of CENP-N kinetochore binding during the cell cycle. J Cell Sci 2011, 124:3871-3883.
81. Hemmerich P., Weidtkamp-Peters S., Hoischen C., Schmiedeberg L., Erliandri I., Diekmann S. Dynamics of inner kinetochore assembly and maintenance in living cells. J Cell Biol 2008, 180:1101-1114.
82. Hemmerich P., Schmiedeberg L., Diekmann S. Dynamic as well as stable protein interactions contribute to genome function and maintenance. Chromosom Res 2011, 19:131-151.
83. Henderson J.N., Remington S.J. The kindling fluorescent protein: a transient photo-switchable marker. Physiology (Bethesda) 2006, 21:162-170.
84. Hess S.T., Girirajan T.P.K., Mason M.D. Ultra-high resolution imaging by fluorescence photo-activation localization microscopy. Biophys J 2006, 91:4258-4272.
85. Heun P., Taddei A., Gasser S.M. From snapshots to moving pictures: new perspectives on nuclear organization. Trends Cell Biol 2001, 11:519-525.
86. Hinde E., Digman M.A., Hahn K.M., Gratton E. Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM. Proc Natl Acad Sci USA 2013, 110:135-140.
87. Hoffmann C., Gaietta G., Bünemann M., Adams S.R., Oberdorff-Maass S., Behr B., et al. A FIAsH-based FRET approach to determine G protein-coupled receptor activation in living cells. Nat Methods 2005, 2:171-176.
88. Hoffmann C., Gaietta G., Zürn A., Adams S.R., Terrillon S., Ellisman M.H., et al. Fluorescent labeling of tetracystein-tagged proteins in intact cells. Nat Protoc 2010, 5:1666-1677.
89. Hofmann M., Eggeling C., Jakobs S., Hell S.W. Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. Proc Natl Acad Sci USA 2005, 102:17565-17569.
90. Houtsmuller A.B. Fluorescence recovery after photo-bleaching: Application to nuclear proteins. Adv Biochem Eng Biotechnol 2005, 95:177-199.
91. Houtsmuller A.B., Vermeulen W. Macromolecular dynamics in living cell nuclei revealed by fluorescence redistribution after photo-bleaching. Histochem Cell Biol 2001, 115:13-21.
92. Hu C.-D., Chinenov Y., Kerppola T.K. Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol Cell 2002, 9:789-798.
93. Huang B., Bates M., Zhuang X. Super-resolution fluorescence microscopy. Annu Rev Biochem 2009, 78:993-1016.
94. Hwang W.Y., Fu Y., Reyon D., Maeder M.L., Tsai S.Q., Sander J.D., et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 2013, 31:227-229.
95. Iizuka R., Yamagishi-Shirasaki M., Funatsu T. Kinetic study of de novo chromophore maturation of fluorescent proteins. Anal Biochem 2011, 414:173-178.
96. Ishihama Y., Tadakuma H., Tani T., Funatsu T. The dynamics of pre-mRNAs and poly(A) + RNA at speckles in living cells revealed by iFRAP studies. Exp Cell Res 2008, 314:748-762.
97. Ishikawa-Ankerhold H.C., Ankerhold R., Drummen G.P.C. Advanced fluorescence microscopy techniques - FRAP, FLIP, FLAP, FRET and FLIM. Molecules 2012, 17:4047-4132.
98. Jares-Erijman E.A., Jovin T.M. FRET imaging. Nat Biotechnol 2003, 21:1387-1395.
99. Johnston K., Joglekar A., Hori T., Suzuki A., Fukagawa T., Salmon E.D. Vertebrate kinetochore protein architecture: protein copy number. J Cell Biol 2010, 189:937-943.
100. Joo C., Balci H., Ishitsuka Y., Buranachai C., Ha T. Advances in single-molecule fluorescence methods for molecular biology. Annu Rev Biochem 2008, 77:51-76.
101. Kapanidis A.N., Weiss S. Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules. J Chem Phys 2002, 117:10953-10964.
102. Kapanidis A.N., Laurence T.A., Lee N.K., Margeat E., Kong X., Weiss S. Alternating laser excitation of single molecules. Acc Chem Res 2005, 38:523-533.
103. Karpova T.S., Baumann C.T., He L., Wu X., Grammer A., Lipsky P., et al. Fluorescence resonance energy transfer from cyan to yellow fluorescent protein detected by acceptor photo-bleaching using confocal microscopy and a single laser. J Microsc 2003, 209:56-57.
104. Kato H., Jiang J., Zhou B.-R., Rozendaal M., Feng H., Ghirlando R., et al. A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Science 2013, 340:1110-1113.
105. Kenworthy A. Imaging protein-protein interactions using fluorescence resonance energy transfer microscopy. Methods 2001, 24:289-296.
106. Keppler A., Gendreizig S., Gronemeyer T., Pick H., Vogel H., Johansson K. A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat Biotechnol 2003, 21:86-89.
107. Kerppola T.K. Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells. Annu Rev Biophys 2008, 37:465-487.
108. Kerppola T.K. Visualization of molecular interactions using bimolecular fluorescence complementation analysis: characteristics of protein fragment complementation. Chem Soc Rev 2009, 38:2876-2886.
109. Kimura H., Hieda M., Cook P.R. Measuring histone and polymerase dynamics in living cells. Methods Enzymol 2004, 375:381-393.
110. Klein T.M., Wolf E.D., Wu R., Sanford J.C. High-velocity micro-projectiles for delivering nucleic acids into living cells. Nature 1987, 327:70-73.
111. König K. Multiphoton microscopy in life sciences. J Microsc 2000, 200:83-104.
112. Kohl T., Haustein E., Schwille P. Determining protease activity in vivo by fluorescence cross-correlation analysis. Biophys J 2005, 89:2770-2782.
113. Kollner M., Wolfrum J. How many photons are necessary for fluorescence-lifetime measurements?. Chem Phys Lett 1996, 200:199-204.
114. Koppel D.E., Axelrod D., Schlessinger J., Elson E.L., Webb W.W. Dynamics of fluorescence marker concentration as a probe of mobility. Biophys J 1976, 16:1315-1329.
115. Kurzawa L., Morris M.C. Cell cycle markers and biosensors. ChemBioChem 2010, 11:1037-1047.
116. Lakowicz J.R., Szmacinski H., Nowaczyk K., Berndt K.W., Johnson M. Fluorescence lifetime imaging. Anal Biochem 1992, 202:316-330.
117. Lakowicz J.R. Principles of fluorescence spectroscopy 1999, 692. Plenum Publishing Corp., New York. 2nd ed.
118. Lam A.J., St-Pierre F., Gong Y., Marshall J.D., Cranfill P.J., Baird M.A., et al. Improving FRET dynamic range with bright green and red fluorescent proteins. Nat Methods 2012, 9:1005-1012.
119. Cnp1 deposition occurs during G2 in fission yeast. Open Biol 2012, 2:120078.
120. Lawrimore J., Bloom K.S., Salmon E.D. Point centromeres contain more than a single centromerespecific Cse4 (CENP-A) nucleosome. J Cell Biol 2011, 195:573-582.
121. Leake M.C., Chandler J.H., Wadhams G.H., Bai F., Berry R.M., Armitage J.P. Stoichiometry and turnover in single, functioning membrane protein complexes. Nature 2006, 443:355-358.
122. Lenser T., Weisshart K., Ulbricht T., Klement K., Hemmerich P. Fluorescence fluctuation microscopy to reveal 3D architecture and function in the cell nucleus. Methods Cell Biol 2010, 98:2-33.
123. Levi V., Gratton E. Chromatin dynamics during interphase explored by single-particle tracking. Chromosom Res 2008, 16:439-449.
124. Li G.W., Xie X.S. Central dogma at the single-molecule level in living cells. Nature 2011, 475:308-315.
125. Lippincott-Schwartz J., Altan-Bonnet N., Patterson G.H. Photo-bleaching and photo-activation: following protein dynamics in living cells. Nat Cell Biol Suppl 2003, 7-14.
126. Ma H.T., Poon R.Y. Synchronisation of HeLa cells. Methods Mol Biol 2011, 761:151-161.
127. Madsen P., Celis J.E. S-phase patterns of cyclin (PCNA) antigen staining resemble topographical patterns of DNA synthesis. A role for cyclin in DNA replication?. FEBS Lett 1985, 193:5-11.
128. Magde D., Elson E.L., Webb W.W. Fluorescence correlation spectroscopy. II. An experimental realization. Biopolymers 1974, 13:29-61.
129. Mali P., Yang L., Esvelt K.M., Aach J., Guell M., DiCarlo J.E., et al. RNA-guided human genome engineering via Cas9. Science 2013, 339:823-826.
130. Marguerat S., Schmidt A., Codlin S., Chen W., Aebersold R., Bähler J. Quantitative analysis of fission yeast transcriptomes and proteasomes in proliferating and quiescent cells. Cell 2012, 151:671-683.
131. Martin B.R., Giepmans B.N.G., Adams S.R., Tsien R.Y. Mammalian cell-based optimization of the biarsenical-binding tetracysteine motif for improved fluorescence and affinity. Nat Biotechnol 2005, 23:1308-1314.
132. Matsuda A., Shao L., Boulanger J., Kervrann C., Carlton P.M., Kner P., et al. Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones. PLoS ONE 2010, 5:12768.
133. Mazza D., Abernathy A., Golob N., Morisaki T., McNally J.G. A benchmark for chromatin binding measurements in live cells. Nucleic Acids Res 2012, 40:e119.
134. McKeague M., DeRosa M.C. Challenges and opportunities for small molecule aptamer development. J Nucl Acids 2012, 2012:748913.
135. McNally J.G. Quantitative FRAP in analysis of molecular binding dynamics in vivo. Methods Cell Biol 2008, 85:329-351.
136. Mejillano M.R., Shivanna B.D., Himes R.H. Studies on the nocodazole-induced GTPase activity of tubulin. Arch Biochem Biophys 1996, 336:130-138.
137. Michelman-Ribeiro A., Mazza D., Rosales T., Stasevich T.J., Boukari H., Rishi V., et al. Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy. Biophys 2009, 97:337-346.
138. Mikuni S., Kinjo M. Fluorescence correlation spectroscopy and fluorescence cross correlation spectroscopy for cell biology. Tanpak Kakusan Koso 2006, 51:1998-2005.
139. Miller J.C., Tan S., Qiao G., Barlow K.A., Wang J., Xia D.F., et al. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 2011, 29:143-148.
140. Moerner W.E., Fromm D.P. Methods of single-molecule fluorescence spectroscopy and microscopy. Rev Sci Instrum 2003, 74:3597-3619.
141. Mueller F., Wach P., McNally J.G. Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved fluorescence recovery after photo-bleaching. Biophys J 2008, 94:3323-3339.
142. Mueller F., Mazza D., Stasevich T.J., McNally J.G. FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?. Curr Opin Cell Biol 2010, 22:403-411.
143. Mueller F., Karpova T.S., Mazza D., McNally J.G. Monitoring dynamic binding of chromatin proteins in vivo by fluorescence recovery after photo-bleaching. Methods Mol Biol 2012, 833:153-176.
144. Mueller F., Morisake T., Mazza D., McNally J.G. Minimizing the impact of photoswitching of fluorescent proteins on FRAP analysis. Biophys J 2012, 102:1656-1665.
145. Müller K.P., Erdel F., Caudron-Herger M., Marth C., Fodor B.D., Richter M., et al. Multiscale analysis of dynamics and interactions of heterochromatin protein 1 by fluorescence fluctuation microscopy. Biophys J 2009, 97:2876-2885.
146. Newman R.H., Fosbrink M.D., Zhang J. Genetically and codable fluorescent biosensors for tracking signaling dynamics in living cells. Chem Rev 2011, 111:3614-3666.
147. Oida T., Sako Y., Kusumi A. Fluorescence lifetime imaging microscopy (flimscopy). Methodology development and application to studies of endosome fusion in single cells. Biophys J 1993, 64:676-685.
148. Opazo F., Levy M., Byrom M., Schäfer C., Geisler C., Groemer T.W., et al. Aptamers as potential tools for super-resolution microscopy. Nat Methods 2012, 9:938-939.
149. Orthaus S., Biskup C., Hoffmann B., Hoischen C., Ohndorf S., Benndorf K., et al. Assembly of the inner kinetochore proteins CENP-A and CENP-B in living human cells. ChemBioChem 2008, 9:77-92.
150. Orthaus S., Klement K., Happel N., Hoischen C., Diekmann S. Linker histone H1 is present in centromeric chromatin of living human cells next to inner kinetochore proteins. Nucleic Acids Res 2009, 37:3391-3406.
151. Patterson G.H., Knobel S.M., Sharif W.D., Kain S.R., Piston D.W. Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. Biophys J 1997, 73:2782-2790.
152. Patterson G.H., Lippincott-Schwartz J. A photoactivatable GFP for selective photolabeling of proteins and cells. Science 2002, 297:1873-1877.
153. Pelet S., Previte M.J.R., So P.T.C. Comparing the quantification of Förster resonance energy transfer measurement accuracies based on intensity, spectral, and lifetime imaging. J Biomed Opt 2006, 11:034017.
154. Periasamy A. Methods in cellular imaging 2001, 434. Oxford University Press, New York.
155. Periasamy A., Clegg R.M. FLIM microscopy in biology and medicine 2010, CRC Press, London.
156. Peters R., Peters J., Tews K.H., Bahr W. A microfluorimetric study of translational diffusion in erythrocyte membranes. Biochim Biophys Acta 1974, 367:282-294.
157. Peters R., Brünger A., Schulten K. Continuous fluorescence microphotolysis: a sensitive method for study of diffusion processes in single cells. Proc Natl Acad Sci USA 1981, 78:962-966.
158. Phair R.D., Gorski S.A., Misteli T. Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy. Methods Enzymol 2004, 375:393-414.
159. Plachta N., Bollenbach T., Pease S., Fraser S.E., Pantazis P. Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nat Cell Biol 2011, 13:117-123.
160. Pfleger K.D.G., Eidne K.A. Illuminating insights into protein-protein interactions using bioluminiscence resonance energy transfer (BRET). Nat Methods 2006, 3:165-174.
161. Prendergast L., van Vuuren C., Kaczmarczyk A., Doering V., Hellwig D., Quinn N., et al. Premitotic assembly of human CENPs-T and -W switches centromeric chromatin to a mitotic state. PLoS Biol 2011, 9:e1001082.
162. Reits E.A., Neefjes J.J. From fixed to FRAP: Measuring protein mobility and activity in living cells. Nat Cell Biol 2001, 3:E145-E147.
163. Renz M., Langowski J. Dynamics of the CapG actin-binding protein in the cell nucleus studied ba FRAP and FCS. Chromosom Res 2008, 16:427-437.
164. Ries J.J., Schwille P.P. Fluorescence correlation spectroscopy. BioEssays 2012, 34:361-368.
165. Rigler R., Mets U., Widengren J., Kask P. Fluorescence correlation spectroscopy with high count rate and low background: analysis of translational diffusion. Eur Biophys J 1993, 22:169-175.
166. Rizzo M., Springer G., Granada B., Piston D. An improved cyan fluorescent protein variant useful for FRET. Nat Biotechnol 2004, 22:445-449.
167. Rossow M.J., Sasaki J.M., Digman M.A., Gratton E. Raster image correlation spectroscopy in live cells. Nat Protoc 2010, 5:1761-1774.
168. Rothbauer U., Zolghadr K., Tillib S., Nowak D., Schermelleh L., Gahl A., et al. Targeting and tracing antigens in live cells with fluorescent nanobodies. Nat Methods 2006, 3:887-889.
169. Rothbauer U., Zolghadr K., Muyldermans S., Schepers A., Cardoso M.C., Leonhardt H. A versatile nanotrap for biochemical and functional studies with fluorescent fusion proteins. Mol Cell Proteomics 2008, 7:282-289.
170. Rothenberg E., Ha T. Single-molecule FRET analysis of helicase functions. Methods Mol Biol 2010, 587:29-43.
171. Roy R., Hohng S., Ha T. A practical guide to single-molecule FRET. Nat Methods 2008, 5:507-516.
172. Rust M.J., Bates M., Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 2006, 3:793-795.
173. Sakaue-Sawano A., Kurokawa H., Morimura T., Hanyu A., Hama H., Osawa H., et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 2008, 132:487-498.
174. Schäfer B., Gemeinhardt H., Greulich K.O. Direct microscopic observation of the time course of single molecule DNA restriction reactions. Angew Chem, Int Ed Engl 2001, 40:4663-4666.
175. Schuler B., Eaton W.A. Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 2008, 18:16-26.
176. Schmiedeberg L., Weisshart K., Diekmann S., Meyer zu Hoerste G., Hemmerich P. High- and low-mobility populations of HP1 in heterochromatin of mammalian cells. Mol Biol Cell 2004, 15:2819-2833.
177. Schwanhäusser B., Busse D., Li N., Dittmar G., Schuchhardt J., Wolf J., et al. Global quantification of mammalian gene expression control. Nature 2013, 473:337-342.
178. Schwille P.P., Bieschke J., Oehlenschläger F. Kinetic investigations by fluorescence correlation spectroscopy: the analytical and diagnostic potential of diffusion studies. Biophys Chem 1997, 66:211-282.
179. Shaner N.C., Steinbach P.A., Tsien R.Y. A guide to choosing fluorescent proteins. Nat Methods 2005, 2:905-909.
180. Shivaraju M., Unruh J.R., Slaughter B.D., Mattingly M., Berman J., Gerton J.L. Cell-cycle-coupled structural oscillation of centromeric nucleosomes in yeast. Cell 2012, 150:304-316.
181. Siebrasse J.P., Grunwald D., Kubitscheck U. Single-molecule tracking in eukaryotic cell nuclei. Anal Bioanal Chem 2007, 387:41-44.
182. Sjollema K.A., Schnell U., Kuipers J., Kalicharan R., Giepmans B.N. Correlated light microscopy and electron microscopy. Methods Cell Biol 2012, 111:157-173.
183. Solarczyk K.J., Zarebski M., Dobrucki J.W. Inducing local damage by visible light to study chromatin repair. DNA Repair 2012, 11:996-1002.
184. Somanathan S., Suchyna T.M., Siegel A.J., Berezney R. Targeting of PCNA to sites of DNA replication in the mammalian cell nucleus. J Cell Biochem 2001, 81:56-67.
185. Sporbert A., Domaing P., Leonhardt H., Cardoso M.C. PCNA acts as a stationary loading platform for transiently interacting Okazaki fragment maturation proteins. Nucleic Acids Res 2005, 33:3521-3528.
186. Sprague B.L., McNally J.G. FRAP analysis of binding: proper and fitting. Trends Cell Biol 2005, 15:84-91.
187. Sprague B.L., Pego R.L., Stavreva D.A., McNally J.G. Analysis of binding reactions by fluorescence recovery after photobleaching. Biophys J 2004, 86:3473-3495.
188. Spring B.Q., Clegg R.M. Frequency domain FLIM. FLIM microscopy in biology and medicine 2010, 115-142. CRC Press, London. A. Periasamy, R.M. Clegg (Eds.).
189. Sprouse R.O., Karpova T.S., Mueller F., Dasgupta A., McNally J.G., Auble D.T. Regulation of TATA-binding protein dynamics in living yeast cells. Proc Natl Acad Sci USA 2008, 105:13304-13308.
190. Stasevich T.J., McNally J.G. Assembly of the transcription machinery: ordered and stable, random and dynamic, or both?. Chromosoma 2011, 120:533-545.
191. Stasevich T.J., Mueller F., Michelman-Ribeiro A., Rosales T., Knutson J.R., McNally J.G. Cross-validating FRAP and FCS to quantify the impact of photo-bleaching on in vivo binding estimates. Biophys J 2010, 99:3093-3101.
192. Steffen P.A., Fonseca J.P., Ringrose L. Epigenetics meets mathematics: towards a quantitative understanding of chromatin biology. Bioessays 2012, 34:901-913.
193. Stevenson D.J., Gunn-Moore F.J., Campbell P., Dholakia K. Single cell optical transfection. J R Soc Interface 2010, 7:863-871.
194. Stryer L. Fluorescence energy transfer as a spectroscopic ruler. Annu Rev Biochem 1978, 47:819-846.
195. Stryer L., Haugland R.P. Energy transfer: a spectroscopic ruler. Proc Natl Acad Sci USA 1967, 58:719-726.
196. Suhling K., Siegel J., Phillips D., French P.M., Leveque-Fort S., Webb S.E.D., et al. Imaging the environment of green fluorescent protein. Biophys J 2002, 83:3589-3595.
197. Thompson R.E., Larson D.R., Webb W.W. Precise nanometer localization analysis for individual fluorescent probes. Biophys J 2002, 82:2775-2783.
198. Tramier M., Zahid M., Mevel J.C., Masse M.J., Coppey-Moisan M. Sensitivity of CFP/YFP and GFP/mCherry pairs to donor photo-bleaching on FRET determination by fluorescence lifetime imaging microscopy in living cells. Microsc Res Tech 2006, 69:933-939.
199. Treanor B., Lanigan P.M., Suhling K., Schreiber T., Munro I., Neil M.A.A., et al. Imaging fluorescence lifetime heterogeneity applied to GFP-tagged MHC protein at an immunological synapse. J Microsc 2005, 217:36-43.
200. Tschernyschkow S., Herda S., Gruenert G., Döring V., Görlich D., Hofmeister A., et al. Rule-based modeling and simulations of the inner kinetochore structure. Prog Biophys Mol Biol 2013, [online].
201. Tsien R.Y. The green fluorescent protein. Annu Rev Biochem 1998, 67:509-544.
202. Tsukamoto T., Hashiguchi N., Janicki S.M., Tumbar T., Belmont A.S., et al. Visualization of gene activity in living cells. Nat Cell Biol 2000, 2:871-878.
203. Uttamapinant C., White K.A., Baruah H., Thompson S., Fernandez-Suarez M., Puthenveetil S., et al. A fluorophore ligase for site-specific protein labeling inside living cells. Proc Natl Acad Sci USA 2010, 107:10914-10919.
204. Vamosi G., Baudendistal N., von der Lieth C.W., Szaloki N., Mocsár G., Müller G., Brázda P., et al. Conformation of the c-Fos/C-Jun complex in vivo: a combined FRET, FCCS and MD-modeling study. Biophys J 2008, 94:2859-2868.
205. van Munster E.B., Gadella T.W. phiFLIM: A new method to avoid aliasing in frequency domain fluorescence lifetime imaging microscopy. J Microsc 2004, 213:29-38.
206. van Munster E.B., Kremers G.J., Adjobo-Hermans M.J., Gadella T.W. Fluorescence resonance energy transfer (FRET) measurement by gradual acceptor photo-bleaching. J Microsc 2005, 218:253-262.
207. van Rheenen J., Langeslag M., Jalink K. Correcting confocal acquisition to optimize imaging of fluorescence resonance energy transfer by sensitized emission. Biophys J 2004, 86:2517-2529.
208. van Royen M.E., Farla P., Mattern K.A., Geverts B., Trapman J., Houtsmuller A.B. Fluorescence recovery after photobleaching (FRAP) to study nuclear protein dynamics in living cells. Methods Mol Biol 2009, 464:363-385.
209. Vassilev L.T., Tovar C., Chen S., Knezevic D., Zhao X., Sun H., et al. Selective small-molecule inhibitor reveals critical mitotic functions of human CDSK1. Proc Natl Acad Sci USA 2006, 103:10660-10665.
210. Venetta B.D. Microscope phase fluorometer for determining the fluorescence lifetimes of fluorochromes. Rev Sci Instrum 1959, 30:450-457.
211. Vogelsang J., Cordes T., Forthmann C., Steinhauer C., Tinnefeld P. Controlling the fluorescence of ordinary oxazine dyes for single-molecule switching and super-resolution microscopy. Proc Natl Acad Sci USA 2009, 106:8107-8112.
212. Wachsmuth M., Weidemann T., Müller G., Hoffmann-Rohrer U.W., Knoch T.A., Waldeck W., et al. Analysing intracellular binding and diffusion with continuous fluorescence photo-bleaching. Biophys J 2003, 84:3353-3363.
213. Wallrabe H., Periasamy A. Imaging protein molecules using FRET and FLIM microscopy. Curr Opin Biotechnol 2005, 16:19-27.
214. Wallrabe H., Chen Y., Periasamy A., Barroso M. Issues in confocal microscopy for quantitative FRET analysis. Microsc Res Tech 2006, 69:196-206.
215. Wang B.G., König K., Halbhuber K.J. Two-photon microscopy of deep intravital tissues and its merits in clinical research. J Microsc 2010, 238:1-20.
216. Wang X.F., Uchida T., Minami S. A fluorescence lifetime distribution measurement system based on phase-resolved detection using an image sissector tube. Appl Spectrosc 1989, 43:840-845.
217. Weber G. Resolution of the fluorescence lifetimes in a heterogeneous system by phase and modulation measurements. J Phys Chem 1981, 85:949-953.
218. Weidemann T., Wachsmuth M., Knoch T.A., Müller G., Waldeck W., Langowski J. Counting nucleosomes in living cells with a combination of fluorescence correlation spectroscopy and confocal imaging. J Mol Biol 2003, 334:229-240.
219. Weidtkamp-Peters S., Felekyan S., Bleckmann A., Simon R., Becker W., Kühnemuth R., et al. Multiparameter fluorescence image spectroscopy to study molecular interactions. Photochem Photobiol Sci 2009, 8:470-480.
220. White J., Stelzer E. Photo-bleaching GFP reveals protein dynamics inside live cells. Trends Cell Biol 1999, 9:61-65.
221. Wieland G., Orthaus S., Ohndorf S., Diekmann S., Hemmerich P. Functional complementation of human centromere protein A (CENP-A) by Cse4p from Saccharomyces cerevisiae. Mol Cell Biol 2004, 24:6620-6630.
222. Wood A.J., Lo T.W., Zeitler B., Pickle C.S., Ralston E.J., Lee A.H., et al. Targeted genome editing across species using ZFNs and TALENs. Science 2011, 333:307.
223. Wouters F.S., Esposito A. Quantitative analysis of fluorescence lifetime imaging made easy. HFSP J 2008, 2:7-11.
224. Wouters F.S., Bastiaens P.I., Wirtz K.W., Jovin T.M. FRET microscopy demonstrates molecular association of non-specific lipid transfer protein (nsL-TP) with fatty acid oxidation enzymes in peroxisomes. EMBO J 1998, 17:7179-7189.
225. Wu J.Q., Pollard T.D. Counting cytokinesis proteins globally and locally in fission yeast. Science 2005, 310:310-314.
226. Zeug A., Woehler A., Neher E., Ponimaskin E.G. Quantitative intensity-based FRET approaches - a comparative snapshot. Biophys J 2012, 103:1821-1827.
227. Zhang F., Cong L., Lodato S., Kosuri S., Church G.M., Arlotta P. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol 2011, 29:149-153.
228. Zimmer M. Green fluorescent protein (GFP): Applications, structure, and related photo-physical behavior. Chem Rev 2002, 102:759-781.
229. Zolghadr K., Mortusewicz O., Rothbauer U., Kleinhans R., Goehler H., Wanker E.E., et al. A fluorescent two-hybrid assay for direct visualization of protein interactions in living cells. Mol Cell Proteomics 2008, 7:2279-2287.