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Abstract:

Diffusion is one of the main transport processes that occur inside cells determining the spatial and time distribution of relevant action molecules. In most cases these molecules not only diffuse but also interact with others as they get transported. When these interactions occur faster than diffusion the resulting transport can be characterized by "effective diffusion coefficients" that depend on both the reaction rates and the "free" diffusion coefficients. Fluorescence correlation spectroscopy (FCS) gives information on effective rather than free diffusion coefficients under this condition. In the present paper we investigate what coefficients can be drawn from FCS experiments for a wide range of values of the ratio of reaction to diffusion time scales, using different fitting functions. We find that the effective coefficients can be inferred with relatively small errors even when the condition of fast reactions does not exactly hold. Since the diffusion time scale depends on the size of the observation volume and the reaction time scale depends on concentrations, we also discuss how by changing either one or the other property one can switch between the two limits and extract more information on the system under study. © 2013 American Physical Society.

Registro:

Documento: Artículo
Título:From free to effective diffusion coefficients in fluorescence correlation spectroscopy experiments
Autor:Ipiña, E.P.; Dawson, S.P.
Filiación:Departamento de Física, FCEN-UBA, Pabellón i, 1428 Buenos Aires, Argentina
Palabras clave:Diffusion time; Effective diffusion coefficients; Fast reaction; Fitting functions; Fluorescence Correlation Spectroscopy; Other properties; Time distribution; Transport process; Experiments; Fluorescence spectroscopy; Molecules; Reaction rates; Time measurement; Diffusion; biopolymer; article; biological model; chemical model; chemistry; computer simulation; diffusion; metabolism; methodology; spectrofluorometry; Biopolymers; Computer Simulation; Diffusion; Models, Biological; Models, Chemical; Spectrometry, Fluorescence
Año:2013
Volumen:87
Número:2
DOI: http://dx.doi.org/10.1103/PhysRevE.87.022706
Título revista:Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
Título revista abreviado:Phys. Rev. E Stat. Nonlinear Soft Matter Phys.
ISSN:15393755
CODEN:PLEEE
CAS:Biopolymers
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15393755_v87_n2_p_Ipina

Referencias:

  • Berg, H.C., (1993) Random Walks in Biology, , Princeton University Press, Princeton, NJ
  • Wagner, J., Keizer, J., (1994) Biophys. J., 67, p. 447. , BIOJAU 0006-3495 10.1016/S0006-3495(94)80500-4
  • Pando, B., Dawson, S.P., Mak, D.-O.D., Pearson, J.E., (2006) Proc. Natl. Acad. Sci., 103, p. 5338. , http://www.pnas.org/content/103/14/5338.full.pdf+html, PNASA6 0027-8424 10.1073/pnas.0509576103
  • Strier, D.E., Dawson, S.P., (2000) J. Chem. Phys., 112, p. 825. , JCPSA6 0021-9606 10.1063/1.480650
  • Smith, G., (1996) Biophys. J., 71, p. 3064. , BIOJAU 0006-3495 10.1016/S0006-3495(96)79500-0
  • Duffy, A., Sneyd, J., Dale, P., (2001) SIAM J. Appl. Math., 58, p. 1178. , SMJMAP 0036-1399 10.1137/S0036139996305074
  • Strier, D.E., Chernomoretz, A., Dawson, S.P., Slow time evolution of two-time-scale reaction-diffusion systems: The physical origin of nondiffusive transport (2002) Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 65 (4), pp. 046233/1-046233/14. , http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype= pdf&id=PLEEE8000065000004046233000001&idtype=cvips, DOI 10.1103/PhysRevE.65.046233, 046233
  • Axelrod, D., Koppel, D.E., Schlessinger, J., Elson, E., Webb, W.W., (1976) Biophys. J., 16, p. 1055. , BIOJAU 0006-3495 10.1016/S0006-3495(76)85755-4
  • Jacobson, K., Wojcieszyn, J., The translational mobility of substances within the cytoplasmic matrix (1984) Proceedings of the National Academy of Sciences of the United States of America, 81 (21), pp. 6747-6751. , DOI 10.1073/pnas.81.21.6747
  • Gribbon, P., Hardingham, T.E., (1998) Biophys. J., 75, p. 1032. , BIOJAU 0006-3495 10.1016/S0006-3495(98)77592-7
  • Magde, D., Elson, E., Webb, W.W., (1972) Phys. Rev. Lett., 29, p. 705. , PRLTAO 0031-9007 10.1103/PhysRevLett.29.705
  • Berland, K., So, P., Gratton E, E., (1995) Biophys. J, 68, p. 694. , BIOJAU 0006-3495 10.1016/S0006-3495(95)80230-4
  • Krichevsky, O., Bonnet, G., (2002) Rep. Prog. Phys., 65, p. 251. , RPPHAG 0034-4885 10.1088/0034-4885/65/2/203
  • Schwille, P., Haupts, U., Maiti, S., Webb, W.W., (1999) Biophys. J, 77, p. 2251. , BIOJAU 0006-3495 10.1016/S0006-3495(99)77065-7
  • Elson, E.L., Fluorescence correlation spectroscopy measures molecular transport in cells (2001) Traffic, 2 (11), pp. 789-796. , DOI 10.1034/j.1600-0854.2001.21107.x
  • Kim, S.A., Schwille, P., Intracellular applications of fluorescence correlation spectroscopy: Prospects for neuroscience (2003) Current Opinion in Neurobiology, 13 (5), pp. 583-590. , DOI 10.1016/j.conb.2003.09.002
  • Grunwald, D., Cardoso, M.C., Leonhardt, H., Buschmann, V., Diffusion and binding properties investigated by Fluorescence correlation Spectroscopy (FCS) (2005) Current Pharmaceutical Biotechnology, 6 (5), pp. 381-386. , DOI 10.2174/138920105774370616
  • Bismuto, E., Gratton, E., Lamb, D.C., (2001) Biophys. J., 81, p. 3510. , BIOJAU 0006-3495 10.1016/S0006-3495(01)75982-6
  • 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 (2005) Biophysical Journal, 88 (5), pp. L33-L36. , DOI 10.1529/biophysj.105.061788
  • Haustein, E., Schwille, P., Fluorescence correlation spectroscopy: Novel variations of an established technique (2007) Annual Review of Biophysics and Biomolecular Structure, 36, pp. 151-169. , DOI 10.1146/annurev.biophys.36.040306.132612
  • Sprague, B.L., Pego, R.L., Stavreva, D.A., McNally, J.G., Analysis of binding reactions by fluorescence recovery after photobleaching (2004) Biophysical Journal, 86 (6), pp. 3473-3495. , DOI 10.1529/biophysj.103.026765
  • Sprague, B.L., McNally, J.G., FRAP analysis of binding: Proper and fitting (2005) Trends in Cell Biology, 15 (2), pp. 84-91. , DOI 10.1016/j.tcb.2004.12.001, PII S0962892404003332
  • Sigaut, L., Ponce, M.L., Colman-Lerner, A., Dawson, S.P., (2010) Phys. Rev. e, 82, p. 051912. , PLEEE8 1539-3755 10.1103/PhysRevE.82.051912
  • Abu-Arish, A., Porcher, A., Czerwonka, A., Dostatni, N., Fradin, C., (2010) Biophys. J., 99, p. 33. , BIOJAU 0006-3495 10.1016/j.bpj.2010.05.031
  • Gregor, T., Wieschaus, E.F., McGregor, A.P., Bialek, W., Tank, D.W., Stability and Nuclear Dynamics of the Bicoid Morphogen Gradient (2007) Cell, 130 (1), pp. 141-152. , DOI 10.1016/j.cell.2007.05.026, PII S0092867407006630
  • Gregor, T., Tank, D.W., Wieschaus, E.F., Bialek, W., Probing the Limits to Positional Information (2007) Cell, 130 (1), pp. 153-164. , DOI 10.1016/j.cell.2007.05.025, PII S0092867407006629
  • (2010) Computer Code Matlab, , version 7.10.0 (R2010a) (The MathWorks Inc., Natick, MA
  • Sigaut, L., (2011), Ph.D. thesis, Departamento de Fisica, FCEN, Universidad de Buenos Aires; Sigaut, L., Pearson, J.E., Colman-Lerner, A., Ponce Dawson, S., (unpublished); Banks, D.S., Fradin, C., Anomalous diffusion of proteins due to molecular crowding (2005) Biophysical Journal, 89 (5), pp. 2960-2971. , DOI 10.1529/biophysj.104.051078
  • Thompson, N.L., Navaratnarajah, P., Wang, X., (2011) J. Phys. Chem. B, 115, p. 120. , JPCBFK 1520-6106 10.1021/jp1069708
  • Charier, S., Meglio, A., Alcor, D., Cogne-Laage, E., Allemand, J.-F., Jullien, L., Lemarchand, A., Reactant concentrations from fluorescence correlation spectroscopy with tailored fluorescent probes. An example of local calibration-free pH measurement (2005) Journal of the American Chemical Society, 127 (44), pp. 15491-15505. , DOI 10.1021/ja053909w
  • Estrada, L., Roberti, M., Simoncelli, S., Levi, V., Aramendía, P., Martínez, O., (2012) J. Phys. Chem. B, 116, p. 2306. , JPCBFK 1520-6106 10.1021/jp209467t
  • Driever, W., Nussleinvolhard, C., (1988) Cell, 54, p. 83. , CELLB5 0092-8674 10.1016/0092-8674(88)90182-1

Citas:

---------- APA ----------
Ipiña, E.P. & Dawson, S.P. (2013) . From free to effective diffusion coefficients in fluorescence correlation spectroscopy experiments. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 87(2).
http://dx.doi.org/10.1103/PhysRevE.87.022706
---------- CHICAGO ----------
Ipiña, E.P., Dawson, S.P. "From free to effective diffusion coefficients in fluorescence correlation spectroscopy experiments" . Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 87, no. 2 (2013).
http://dx.doi.org/10.1103/PhysRevE.87.022706
---------- MLA ----------
Ipiña, E.P., Dawson, S.P. "From free to effective diffusion coefficients in fluorescence correlation spectroscopy experiments" . Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, vol. 87, no. 2, 2013.
http://dx.doi.org/10.1103/PhysRevE.87.022706
---------- VANCOUVER ----------
Ipiña, E.P., Dawson, S.P. From free to effective diffusion coefficients in fluorescence correlation spectroscopy experiments. Phys. Rev. E Stat. Nonlinear Soft Matter Phys. 2013;87(2).
http://dx.doi.org/10.1103/PhysRevE.87.022706