Rapid droplet-based mixing for single-molecule spectroscopy.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
Oct 2023
Oct 2023
Historique:
received:
27
02
2023
accepted:
02
08
2023
pubmed:
26
9
2023
medline:
26
9
2023
entrez:
25
9
2023
Statut:
ppublish
Résumé
Probing non-equilibrium dynamics with single-molecule spectroscopy is important for dissecting biomolecular mechanisms. However, existing microfluidic rapid-mixing systems for this purpose are incompatible with surface-adhesive biomolecules, exhibit undesirable flow dispersion and are often demanding to fabricate. Here we introduce droplet-based microfluidic mixing for single-molecule spectroscopy to overcome these limitations in a wide range of applications. We demonstrate its robust functionality with binding kinetics of even very surface-adhesive proteins on the millisecond timescale.
Identifiants
pubmed: 37749213
doi: 10.1038/s41592-023-01995-9
pii: 10.1038/s41592-023-01995-9
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1479-1482Subventions
Organisme : Novo Nordisk Fonden (Novo Nordisk Foundation)
ID : #NNF18OC0033926
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Lerner, E. et al. Toward dynamic structural biology: two decades of single-molecule Förster resonance energy transfer. Science 359, eaan1133 (2018).
doi: 10.1126/science.aan1133
pubmed: 29348210
pmcid: 6200918
Schuler, B. Single-molecule FRET of protein structure and dynamics—a primer. J. Nanobiotechnology 11, S2 (2013).
doi: 10.1186/1477-3155-11-S1-S2
pubmed: 24565277
pmcid: 4029180
Capretto, L., Cheng, W., Hill, M. & Zhang, X. Micromixing within microfluidic devices. Top. Curr. Chem. 304, 27–68 (2011).
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).
doi: 10.1103/PhysRevLett.80.3863
Lipman, E. A., Schuler, B., Bakajin, O. & Eaton, W. A. Single-molecule measurement of protein folding kinetics. Science 301, 1233–1235 (2003).
doi: 10.1126/science.1085399
pubmed: 12947198
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).
doi: 10.1063/1.3125643
pubmed: 19485532
Gambin, Y. et al. Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. Nat. Methods 8, 239–241 (2011).
doi: 10.1038/nmeth.1568
pubmed: 21297620
pmcid: 3071799
Wunderlich, B. et al. Microfluidic mixer designed for performing single-molecule kinetics with confocal detection on timescales from milliseconds to minutes. Nat. Protoc. 8, 1459–1474 (2013).
doi: 10.1038/nprot.2013.082
pubmed: 23845960
Zijlstra, N. et al. Rapid microfluidic dilution for single-molecule spectroscopy of low-affinity biomolecular complexes. Angew. Chem. Int. Ed. 56, 7126–7129 (2017).
doi: 10.1002/anie.201702439
Dingfelder, F. et al. Rapid microfluidic double-jump mixing device for single-molecule spectroscopy. J. Am. Chem. Soc. 139, 6062–6065 (2017).
doi: 10.1021/jacs.7b02357
pubmed: 28394601
Vogler, E. A. Protein adsorption in three dimensions. Biomaterials 33, 1201–1237 (2012).
doi: 10.1016/j.biomaterials.2011.10.059
pubmed: 22088888
Zhang, H. & Chiao, M. Anti-fouling coatings of poly(dimethylsiloxane) devices for biological and biomedical applications. J. Med. Biol. Eng. 35, 143–155 (2015).
doi: 10.1007/s40846-015-0029-4
pubmed: 25960703
pmcid: 4414934
Taylor, G. I. Dispersion of soluble matter in solvent flowing slowly through a tube. Proc. R. Soc. Lond. A 219, 186–203 (1953).
doi: 10.1098/rspa.1953.0139
Wunderlich, B., Nettels, D. & Schuler, B. Taylor dispersion and the position-to-time conversion in microfluidic mixing devices. Lab Chip 14, 219–228 (2014).
doi: 10.1039/C3LC51002F
pubmed: 24195996
Anna, S. L., Bontoux, N. & Stone, H. A. Formation of dispersions using ‘flow focusing’ in microchannels. Appl. Phys. Lett. 82, 364–366 (2003).
doi: 10.1063/1.1537519
Song, H., Bringer, M. R., Tice, J. D., Gerdts, C. J. & Ismagilov, R. F. Experimental test of scaling of mixing by chaotic advection in droplets moving through microfluidic channels. Appl. Phys. Lett. 83, 4664–4666 (2003).
doi: 10.1063/1.1630378
pubmed: 17940580
Baret, J.-C. Surfactants in droplet-based microfluidics. Lab Chip 12, 422–433 (2012).
doi: 10.1039/C1LC20582J
pubmed: 22011791
Qin, D., Xia, Y. & Whitesides, G. M. Soft lithography for micro- and nanoscale patterning. Nat. Protoc. 5, 491–502 (2010).
doi: 10.1038/nprot.2009.234
pubmed: 20203666
Harinarayana, V. & Shin, Y. C. Two-photon lithography for three-dimensional fabrication in micro/nanoscale regime: a comprehensive review. Opt. Laser Technol. 142, 107180 (2021).
doi: 10.1016/j.optlastec.2021.107180
Dogan, J., Schmidt, T., Mu, X., Engström, Å. & Jemth, P. Fast association and slow transitions in the interaction between two intrinsically disordered protein domains. J. Biol. Chem. 287, 34316–34324 (2012).
doi: 10.1074/jbc.M112.399436
pubmed: 22915588
pmcid: 3464538
Dyson, H. J. & Wright, P. E. Role of intrinsic protein disorder in the function and interactions of the transcriptional coactivators CREB-binding protein (CBP) and p300. J. Biol. Chem. 291, 6714–6722 (2016).
doi: 10.1074/jbc.R115.692020
pubmed: 26851278
pmcid: 4807259
Altman, R. B. et al. Cyanine fluorophore derivatives with enhanced photostability. Nat. Methods 9, 68–71 (2011).
doi: 10.1038/nmeth.1774
pubmed: 22081126
pmcid: 3433158
Dogan, J., Jonasson, J., Andersson, E. & Jemth, P. Binding rate constants reveal distinct features of disordered protein domains. Biochemistry 54, 4741–4750 (2015).
doi: 10.1021/acs.biochem.5b00520
pubmed: 26153298
Borgia, A. et al. Extreme disorder in an ultrahigh-affinity protein complex. Nature 555, 61–66 (2018).
doi: 10.1038/nature25762
pubmed: 29466338
pmcid: 6264893
Sottini, A. et al. Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes. Nat. Commun. 11, 5736 (2020).
doi: 10.1038/s41467-020-18859-x
pubmed: 33184256
pmcid: 7661507
Charmet, J., Arosio, P. & Knowles, T. P. J. Microfluidics for protein biophysics. J. Mol. Biol. 430, 565–580 (2018).
doi: 10.1016/j.jmb.2017.12.015
pubmed: 29289566
Yang, T. et al. Droplet-based microfluidic temperature-jump platform for the rapid assessment of biomolecular kinetics. Anal. Chem. 94, 16675–16684 (2022).
doi: 10.1021/acs.analchem.2c03009
pubmed: 36395420
Abate, A. R., Hung, T., Mary, P., Agresti, J. J. & Weitz, D. A. High-throughput injection with microfluidics using picoinjectors. Proc. Natl Acad. Sci. USA 107, 19163–19166 (2010).
doi: 10.1073/pnas.1006888107
pubmed: 20962271
pmcid: 2984161
Hofmann, H. et al. Single-molecule spectroscopy of protein folding in a chaperonin cage. Proc. Natl Acad. Sci. USA 107, 11793–11798 (2010).
doi: 10.1073/pnas.1002356107
pubmed: 20547872
pmcid: 2900638
Dunlop, P. J. & Stokes, R. H. The diffusion coefficients of sodium and potassium iodides in aqueous solution at 25°
Zosel, F., Soranno, A., Buholzer, K. J., Nettels, D. & Schuler, B. Depletion interactions modulate the binding between disordered proteins in crowded environments. Proc. Natl Acad. Sci. USA 117, 13480–13489 (2020).
doi: 10.1073/pnas.1921617117
pubmed: 32487732
pmcid: 7306994
Schilling, J., Schöppe, J. & Plückthun, A. From DARPins to LoopDARPins: novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display. J. Mol. Biol. 426, 691–721 (2014).
doi: 10.1016/j.jmb.2013.10.026
pubmed: 24513107
Cull, M. G. & Schatz, P. J. in Methods in Enzymology Vol. 326, 430–440 (Academic Press, 2000).
Soranno, A. et al. Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. Proc. Natl Acad. Sci. USA 111, 4874–4879 (2014).
doi: 10.1073/pnas.1322611111
pubmed: 24639500
pmcid: 3977265
Müller-Späth, S. et al. Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc. Natl Acad. Sci. USA 107, 14609–14614 (2010).
doi: 10.1073/pnas.1001743107
pubmed: 20639465
pmcid: 2930438
Holmstrom, E. D. et al. in Methods in Enzymology Vol. 611 (ed. Rhoades, E.) 287–325 (Academic Press, 2018).
Hellenkamp, B. et al. Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. Nat. Methods 15, 669–676 (2018).
doi: 10.1038/s41592-018-0085-0
pubmed: 30171252
pmcid: 6121742
Hess, D. et al. Exploring mechanism of enzyme catalysis by on-chip transient kinetics coupled with global data analysis and molecular modeling. Chem 7, 1066–1079 (2021).
doi: 10.1016/j.chempr.2021.02.011