Abstract
The appropriate functioning of living cells depends on a variety of dynamic processes that necessitate delicate motion, transportation, association, and disassociation in time and space. Different dynamic patterns such as directed motion, normal diffusion, and restricted diffusion take part at different length scales, and their identification serves as a tool for exploring biochemical processes. Here we describe single-particle tracking which is a powerful method that allows the characterization of dynamic processes on the single-molecule or single-particle level with nanometer spatial and sub-second temporal precision. In particular, we describe the cell preparation procedures, microscopy imaging, and image analysis processes for following telomere dynamics in living mammalian cells.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Lichtman JW, Conchello J-A (2005) Fluorescence microscopy. Nat Methods 2(12):910–919
Lippincott-Schwartz J, Patterson GH (2003) Development and use of fluorescent protein markers in living cells. Science 300(5616):87–91. doi:10.1126/science.1082520
Saxton MJ (2008) Single-particle tracking: connecting the dots. Nat Methods 5(8):671–672
Mueller F, Mazza D, Stasevich TJ, McNally JG (2010) FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know? Curr Opin Cell Biol 22:403–411. doi:10.1016/j.ceb.2010.03.002
Schwille P, Haupts U, Maiti S, Webb WW (1999) Molecular dynamics in living cells observed by fluorescence correlation spectroscopy with one- and two-photon excitation. Biophys J 77:2251–2265. doi:10.1016/S0006-3495(99)77065-7
Weidemann T, Wachsmuth M, Ta K, Müller G, Waldeck W, Langowski J (2003) Counting nucleosomes in living cells with a combination of fluorescence correlation spectroscopy and confocal imaging. J Mol Biol 334:229–240. doi:10.1016/j.jmb.2003.08.063
Thompson RE, Larson DR, Webb WW (2002) Precise nanometer localization analysis for individual fluorescent probes. Biophys J 82(5):2775–2783
Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR (2003) Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization. Science 300(5628):2061–2065. doi:10.1126/science.1084398
Saxton MJ, Jacobson K (1997) Single-particle tracking: applications to membrane dynamics. Annu Rev Biophys Biomol Struct 26(1):373–399. doi:10.1146/annurev.biophys.26.1.373
Barkai E, Garini Y, Metzler R (2012) Strange kinetics of single molecules in living cells. Physics Today 65(8):29–35
Metzler R, Klafter J (2004) The restaurant at the end of the random walk: recent developments in the description of anomalous transport by fractional dynamics. J Phys Math Gen 37(31):R161
Weiss M, Elsner M, Kartberg F, Nilsson T (2004) Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells. Biophys J 87(5):3518–3524
Bronstein I, Israel Y, Kepten E, Mai S, Shav-Tal Y, Barkai E, Garini Y (2009) Transient anomalous diffusion of telomeres in the nucleus of mammalian cells. Phys Rev Lett 103:1–4. doi:10.1103/PhysRevLett.103.018102
Platani M, Goldberg I, Lamond AI, Swedlow JR (2002) Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 4(7):502–508
Golding I, Cox EC (2004) RNA dynamics in live Escherichia coli cells. Proc Natl Acad Sci USA 101(31):11310–11315. doi:10.1073/pnas.0404443101
Banks DS, Fradin C (2005) Anomalous diffusion of proteins due to molecular crowding. Biophys J 89(5):2960–2971
Saxton MJ (1994) Anomalous diffusion due to obstacles: a Monte Carlo study. Biophys J 66(2 part 1):394–401
Metzler R, Klafter J (2000) The random walk’s guide to anomalous diffusion: a fractional dynamics approach. Physics Reports 339(1):1–77
Saxton MJ (2007) A biological interpretation of transient anomalous subdiffusion. I. Qualitative model. Biophys J 92(4):1178–1191
Mattern KA, Swiggers SJJ, Nigg AL, Löwenberg B, Houtsmuller AB, Zijlmans JMJM (2004) Dynamics of protein binding to telomeres in living cells: implications for telomere structure and function. Mol Cell Biol 24:5587–5594
Molenaar C, Wiesmeijer K, Verwoerd NP, Khazen S, Eils R, Tanke HJ, Dirks RW (2003) Visualizing telomere dynamics in living mammalian cells using PNA probes. EMBO J 22:6631–6641
Brody Y, Neufeld N, Bieberstein N, Causse SZ, Böhnlein E-M, Neugebauer KM, Darzacq X, Shav-Tal Y (2011) The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLoS Biol 9:e1000573. doi:10.1371/journal.pbio.1000573
Acknowledgements
This work was partially supported by the Israel Science Foundation grants No. 985/08, 1729/08, 1793/07, and 507/07 and the Wolfson Foundation grant 2008.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Berger, I.B., Kepten, E., Garini, Y. (2013). Single-Particle Tracking for Studying the Dynamic Properties of Genomic Regions in Live Cells. In: Shav-Tal, Y. (eds) Imaging Gene Expression. Methods in Molecular Biology, vol 1042. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-526-2_10
Download citation
DOI: https://doi.org/10.1007/978-1-62703-526-2_10
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-525-5
Online ISBN: 978-1-62703-526-2
eBook Packages: Springer Protocols