Microfluidic mixer designed for performing single-molecule kinetics with confocal detection on timescales from milliseconds to minutes

Nature Protocols

Volumn 8, Issue 8, 2013, Pages 1459-1474

  Wunderlich, Bengt ^a   Nettels, Daniel ^a   Benke, Stephan ^a   Clark, Jennifer ^a   Weidner, Sascha ^a   Hofmann, Hagen ^a   Pfeil, Shawn H ^b,c   Schuler, Benjamin ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c WEST CHESTER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMETICONE; SILICON;

ANISOTROPY; ARTICLE; CALIBRATION; CHEMICAL REACTION KINETICS; CLINICAL PROTOCOL; CONFOCAL MICROSCOPY; CONFORMATIONAL TRANSITION; EQUIPMENT DESIGN; EXPERIMENTAL DESIGN; FILTER; FLOW RATE; FLUORESCENCE RESONANCE ENERGY TRANSFER; HYDRODYNAMICS; MICROFLUIDICS; MICROTECHNOLOGY; MIXER; PRIORITY JOURNAL; PROCESS DESIGN; PROTEIN FOLDING;

CALIBRATION; EQUIPMENT DESIGN; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MICROFLUIDICS; MICROTECHNOLOGY; PROTEIN FOLDING; SILICON; TEMPERATURE;

EID: 84880295113     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2013.082     Document Type: Article

References (58)

1. Selvin, P.R. & Ha, T. Single-Molecule Techniques: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 2008).
2. Dunkle, J.A. & Cate, J.H.D. Ribosome structure and dynamics during translocation and termination. Annual Review of Biophysics 39, 227-244 (2010).
3. Marshall, R.A., Aitken, C.E., Dorywalska, M. & Puglisi, J.D. Translation at the single-molecule level. Annu. Rev. Biochem. 77, 177-203 (2008).
4. Greenleaf, W.J., Woodside, M.T. & Block, S.M. High-resolution, single-molecule measurements of biomolecular motion. Annu. Rev. Biophys. Biomol. Struct. 36, 171-190 (2007). (Pubitemid 46998115)
5. Kapanidis, A.N. & Strick, T. Biology, one molecule at a time. Trends Biochem. Sci. 34, 234-243 (2009).
6. Ha, T., Kozlov, A.G. & Lohman, T.M. Single-molecule views of protein movement on single-stranded DNA. Annu. Rev. Biophys. 41, 295-319 (2012).
7. Smiley, R.D. & Hammes, G.G. Single-molecule studies of enzyme mechanisms. Chem. Rev. 106, 3080-3094 (2006).
8. Dittrich, P.S., Muller, B. & Schwille, P. Studying reaction kinetics by simultaneous FRET and cross-correlation analysis in a miniaturized continuous-flow reactor. Phys. Chem. Chem. Phys. 6, 4416-4420 (2004).
9. Zhuang, X.W. Single-molecule RNA science. in Annu. Rev. Biophys. Biomol. Struct. 34, 399-414 (2005).
10. Schuler, B. & Hofmann, H. Single-molecule spectroscopy of protein folding dynamics-expanding scope and timescales. Curr. Opin. Struct. Biol. 23, 36-47 (2013).
11. Nettels, D., Gopich, I.V., Hoffmann, A. & Schuler, B. Ultrafast dynamics of protein collapse from single-molecule photon statistics. Proc. Natl. Acad. Sci. USA 104, 2655-2660 (2007). (Pubitemid 46327935)
12. Soranno, A. et al. Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. Proc. Natl. Acad. Sci. USA 109, 17800-17806 (2012).
13. Neuweiler, H., Johnson, C.M. & Fersht, A.R. Direct observation of ultrafast folding and denatured state dynamics in single protein molecules. Proc. Natl. Acad. Sci. USA 106, 18569-74 (2009).
14. Sherman, E. & Haran, G. Fluorescence correlation spectroscopy of fast chain dynamics within denatured protein L. Chemphyschem. 12, 696-703 (2011).
15. Chung, H.S., Cellmer, T., Louis, J.M. & Eaton, W.A. Measuring ultrafast protein folding rates from photon-by-photon analysis of single-molecule fluorescence trajectories. Chem. Phys. http://dx.doi.org/10. 1016/j.chemphys.2012.08.005 (14 August 2012).
16. Schuler, B., Lipman, E.A. & Eaton, W.A. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419, 743-747 (2002). (Pubitemid 35177962)
17. Hoffmann, A. et al. Quantifying heterogeneity and conformational dynamics from single-molecule FRET of diffusing molecules: recurrence analysis of single particles (RASP). Phys. Chem. Chem. Phys. 13, 1857-1871 (2011).
18. Chung, H.S. et al. Extracting rate coefficients from single-molecule photon trajectories and FRET efficiency histograms for a fast-folding protein. J. Phys. Chem. A 115, 3642-3656 (2011).
19. Gopich, I.V. & Szabo, A. FRET efficiency distributions of multistate single molecules. J. Phys. Chem. B 114, 15221-15226 (2010).
20. Chung, H.S., Louis, J.M. & Eaton, W.A. Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories. Proc. Natl. Acad. Sci. USA 106, 11837-11844 (2009).
21. Chung, H.S., McHale, K., Louis, J.M. & Eaton, W.A. Single-molecule fluorescence experiments determine protein folding transition path times. Science 335, 981-984 (2012).
22. Rhoades, E., Gussakovsky, E. & Haran, G. Watching proteins fold one molecule at a time. Proc. Natl. Acad. Sci. USA 100, 3197-3202 (2003). (Pubitemid 36356560)
23. Rhoades, E., Cohen, M., Schuler, B. & Haran, G. Two-state folding observed in individual protein molecules. J. Am. Chem. Soc. 126, 14686-14687 (2004). (Pubitemid 39532128)
24. Pirchi, M. et al. Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein. Nat. Commun. 2, 493 (2011).
25. Kuzmenkina, E.V., Heyes, C.D. & Nienhaus, G.U. Single-molecule Förster resonance energy transfer study of protein dynamics under denaturing conditions. Proc. Natl. Acad. Sci. USA 102, 15471-15476 (2005). (Pubitemid 41528081)
26. Hofmann, H. et al. Single-molecule spectroscopy of protein folding in a chaperonin cage. Proc. Natl. Acad. Sci. USA 107, 11793-11798 (2010).
27. Gambin, Y. et al. Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. Nat. Methods 8, 239-241 (2011).
28. Lipman, E.A., Schuler, B., Bakajin, O. & Eaton, W.A. Single-molecule measurement of protein folding kinetics. Science 301, 1233-1235 (2003). (Pubitemid 37052211)
29. Borgia, A. et al. Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy. Nat. Commun. 2, 1195 (2012).
30. Hamadani, K.M. & Weiss, S. Nonequilibrium single-molecule protein folding in a coaxial mixer. Biophys. J. 95, 352-365 (2008).
31. Brody, J.P., Yager, P., Goldstein, R.E. & Austin, R.H. Biotechnology at low Reynolds numbers. Biophys. J. 71, 3430-3441 (1996). (Pubitemid 26422384)
32. Knight, J.B., Vishwanath, A., Brody, J.P. & Austin, R.H. Hydrodynamic focusing on a silicon chip: mixing nanoliters in microseconds. Phys. Rev. Lett. 80, 3863-3866 (1998). (Pubitemid 128629864)
33. Zimmerman, W.B.J. Multiphysics Modeling with Finite Element Methods, (World Scientific Publishing, 2006).
34. Hoffmann, A. et al. Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy. Proc. Natl. Acad. Sci. USA 104, 105-110 (2007). (Pubitemid 46067992)
35. Kane, A.S. et al. Microfluidic mixers for the investigation of rapid protein folding kinetics using synchrotron radiation circular dichroism spectroscopy. Anal. Chem. 80, 9534-9541 (2008).
36. Liu, K., Tian, Y., Burrows, S.M., Reif, R.D. & Pappas, D. Mapping vortex-like hydrodynamic flow in microfluidic networks using fluorescence correlation spectroscopy. Analytica. Chimica. Acta. 651, 85-90 (2009).
37. Benninger, R.K. et al. Quantitative 3D mapping of fluidic temperatures within microchannel networks using fluorescence lifetime imaging. Anal. Chem. 78, 2272-2278 (2006).
38. Pfeil, S.H., Wickersham, C.E., Hoffmann, A. & Lipman, E.A. A microfluidic mixing system for single-molecule measurements. Rev. Sci. Instrum. 80, 055105 (2009).
39. Lemke, E.A. et al. Microfluidic device for single-molecule experiments with enhanced photostability. J. Am. Chem. Soc. 131, 13610-13612 (2009).
40. Gambin, Y., Simonnet, C., VanDelinder, V., Deniz, A. & Groisman, A. Ultrafast microfluidic mixer with three-dimensional flow focusing for studies of biochemical kinetics. Lab Chip 10, 598-609 (2010).
41. McDonald, J.C. & Whitesides, G.M. Poly(dimethylsiloxane) as a material for fabricating microfluidic devices. Acc. Chem. Res. 35, 491-499 (2002).
42. Hofmann, H. et al. Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy. Proc. Natl. Acad. Sci. USA 109, 16155-16160 (2012).
43. Arbour, T.J. & Enderlein, J. Application of dual-focus fluorescence correlation spectroscopy to microfluidic flow-velocity measurement. Lab Chip 10, 1286-1292 (2010).
44. Roder, H., Maki, K. & Cheng, H. Early events in protein folding explored by rapid mixing methods. Chem. Rev. 106, 1836-1861 (2006). (Pubitemid 43840532)
45. Cooksey, G.A., Plant, A.L. & Atencia, J. A vacuum manifold for rapid world-to-chip connectivity of complex PDMS microdevices. Lab Chip 9, 1298-1300 (2009).
46. Nettels, D. et al. Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proc. Natl. Acad. Sci. USA 106, 20740-20745 (2009).
47. Kawahara, K. & Tanford, C. Viscosity and density of aqueous solutions of urea and guanidine hydrochloride. J. Biol. Chem. 241, 3228-3232 (1966).
48. CRC Handbook of Chemistry and Physics, (CRC Press, 2013).
49. Sisamakis, E., Valeri, A., Kalinin, S., Rothwell, P.J. & Seidel, C.A.M. Accurate single-molecule FRET studies using multiparameter fluorescence detection. Methods Enzymol. 475, 455-514 (2010).
50. Schuler, B. Application of single-molecule Förster resonance energy transfer to protein folding. Methods Mol. Biol. 350, 115-138 (2007).
51. Gösch, M., Blom, H., Holm, J., Heino, T. & Rigler, R. Hydrodynamic flow profiling in microchannel structures by single-molecule fluorescence correlation spectroscopy. Anal. Chem. 72, 3260-3265 (2000). (Pubitemid 30482501)
52. Dimitriadis, G. et al. Microsecond folding dynamics of the F13W G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump. Proc. Natl. Acad. Sci. USA 101, 3809-3814 (2004). (Pubitemid 38381060)
53. Arora, P., Oas, T.G. & Myers, J.K. Fast and faster: a designed variant of the B-domain of protein A folds in 3 microsec. Protein Sci. 13, 847-853 (2004). (Pubitemid 38429208)
54. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. & Ban, N. The structure of a cytolytic α-helical toxin pore reveals its assembly mechanism. Nature 459, 726-730 (2009).
55. Eifler, N. et al. Cytotoxin ClyA from Escherichia coli assembles to a 13-meric pore independent of its redox-state. EMBO J. 25, 2652-2661 (2006). (Pubitemid 44012247)
56. Schuler, B., Müller-Späth, S., Soranno, A. & Nettels, D. Application of confocal single-molecule FRET to intrinsically disordered proteins. Methods Mol. Biol. 896, 21-45 (2012).
57. Dittrich, P.S. & Schwille, P. Spatial two-photon fluorescence cross-correlation spectroscopy for controlling molecular transport in microfluidic structures. Anal. Chem. 74, 4472-4479 (2002). (Pubitemid 35006436)
58. Taylor, G. Conditions under which dispersion of a solute in a stream of solvent can be used to measure molecular diffusion. Proc. Royal Soc. London A 225, 473-477 (1954).