Manufacturing of Ultra-Thin X-ray-Compatible COC Microfluidic Devices for Optimal In Situ Macromolecular Crystallography Experiments
Abstract
:1. Introduction
2. Materials and Methods
2.1. Photo-Lithographic Master Fabrication
2.2. COC Device Fabrication
2.3. Sample Loading and Crystallization
2.4. Data Acquisition, Processing, and Structure Determination
3. Results and Discussion
3.1. COC Devices for Diffusion-Based Crystallization
3.2. Sample Injection, Crystal Formation, and Diffraction Studies
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Pinker, F.; Brun, M.; Morin, P.; Deman, A.-L.; Chateaux, J.-F.; Oliéric, V.; Stirnimann, C.; Lorber, B.; Terrier, N.; Ferrigno, R.; et al. ChipX: A novel microfluidic chip for counter-diffusion crystallization of biomolecules and in situ crystal analysis at room temperature. Cryst. Growth Des. 2013, 13, 3333–3340. [Google Scholar] [CrossRef]
- Dhouib, K.; Malek, C.K.; Pfleging, W.; Gauthier-Manuel, B.; Duffait, R.; Thuillier, G.; Ferrigno, R.; Jacquamet, L.; Ohana, J.; Ferrer, J.-L.; et al. Microfluidic chips for the crystallization of biomacromolecules by counter-diffusion and on-chip crystal X-ray analysis. Lab Chip 2009, 9, 1412–1421. [Google Scholar] [CrossRef] [PubMed]
- Emamzadah, S.; Petty, T.J.; De Almeida, V.; Nishimura, T.; Joly, J.; Ferrer, J.-L.; Halazonetis, T.D. Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction. Acta Crystallogr. Sect. D Biol. Crystallogr. 2009, 65, 913–920. [Google Scholar] [CrossRef]
- Guha, S.; Perry, S.L.; Pawate, A.S.; Kenis, P.J.A. Fabrication of X-ray compatible microfluidic platforms for protein crystallization. Sens. Actuators B Chem. 2012, 174, 1–9. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ghazal, A.; Lafleur, J.P.; Mortensen, K.; Kutter, J.P.; Arleth, L.; Jensen, G.V. Recent advances in X-ray compatible microfluidics for applications in soft materials and life sciences. Lab Chip 2016, 16, 4263–4295. [Google Scholar] [CrossRef] [Green Version]
- Tsao, C.W. Polymer microfluidics: Simple, low-cost fabrication process bridging academic lab research to commercialized production. Micromachines 2016, 7, 225. [Google Scholar] [CrossRef] [Green Version]
- Kojic, S.P.; Stojanovic, G.M.; Radonic, V. Novel cost-effective microfluidic chip based on hybrid fabrication and its comprehensive characterization. Sensors 2019, 19, 1719. [Google Scholar] [CrossRef] [Green Version]
- Vakili, M.; Vasireddi, R.; Gwozdz, P.V.; Monteiro, D.C.F.; Heymann, M.; Blick, R.H.; Trebbin, M. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography. Rev. Sci. Instrum. 2020, 91, 085108. [Google Scholar] [CrossRef]
- Aghvami, S.A.; Opathalage, A.; Zhang, Z.; Ludwig, M.; Heymann, M.; Norton, M.; Wilkins, N.; Fraden, S. Rapid prototyping of cyclic olefin copolymer (COC) microfluidic devices. Sens. Actuators B Chem. 2017, 247, 940–949. [Google Scholar] [CrossRef]
- Whitesides, G.M. The origins and the future of microfluidics. Nature 2006, 442, 368–373. [Google Scholar] [CrossRef]
- Sackmann, E.K.; Fulton, A.L.; Beebe, D.J. The present and future role of microfluidics in biomedical research. Nature 2014, 507, 181–189. [Google Scholar] [CrossRef] [PubMed]
- Vasireddi, R.; Kruse, J.; Vakili, M.; Kulkarni, S.; Keller, T.F.; Monteiro, D.C.F.; Trebbin, M. Solution blow spinning of polymer/nanocomposite micro-/nanofibers with tunable diameters and morphologies using a gas dynamic virtual nozzle. Sci. Rep. 2019, 9, 14297. [Google Scholar] [CrossRef] [Green Version]
- Rezvani, S.; Shi, N.; Squires, T.M.; Schmidt, C.F. Microfluidic device for chemical and mechanical manipulation of suspended cells. J. Phys. D Appl. Phys. 2018, 51, 045403. [Google Scholar] [CrossRef]
- Trautmann, A.; Roth, G.-L.; Nujiqi, B.; Walther, T.; Hellmann, R. Towards a versatile point-of-care system combining femtosecond laser generated microfluidic channels and direct laser written microneedle arrays. Microsyst. Nanoeng. 2019, 5, 6. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Miserere, S.; Mottet, G.; Taniga, V.; Descroix, S.; Viovy, J.-L.; Malaquin, L. Fabrication of thermoplastics chips through lamination based techniques. Lab Chip 2012, 12, 1849–1856. [Google Scholar] [CrossRef]
- Vakili, M.; Merkens, S.; Gao, Y.; Gwodz, P.V.; Vasireddi, R.; Sharpnack, L.; Meyer, A.; Blick, R.H.; Trebbin, M. 3D micromachined polyimide mixing devices for in situ x-ray imaging of solution-based block copolymer phase transitions. Langmuir 2019, 35, 10435–10445. [Google Scholar] [CrossRef]
- Sui, S.; Perry, S.L. Microfluidics: From crystallization to serial time-resolved crystallography. Struct. Dynam. 2017, 4, 032202. [Google Scholar] [CrossRef]
- Steigert, J.; Haeberle, S.; Brenner, T.; Müller, C.; Steinert, C.P.; Koltay, P.; Gottschlich, N.; Reinecke, H.; Rühe, J.; Zengerle, R.; et al. Rapid prototyping of microfluidic chips in COC. J. Micromech. Microeng. 2007, 17, 333–341. [Google Scholar] [CrossRef]
- de Wijn, R.; Hennig, O.; Roche, J.; Engilberge, S.; Rollet, K.; Fernandez-Millan, P.; Brillet, K.; Betat, H.; Mörl, M.; Roussel, A.; et al. A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography. IUCrJ 2019, 6, 454–464. [Google Scholar] [CrossRef]
- Nunes, P.S.; Ohlsson, P.D.; Ordeig, O.; Kutter, J.P. Cyclic olefin polymers: Emerging materials for lab-on-a-chip applications. Microfluid. Nanofluidics 2010, 9, 145–161. [Google Scholar] [CrossRef]
- Greaves, E.D.; Manz, A. Toward on-chip X-ray analysis. Lab Chip 2005, 5, 382–391. [Google Scholar] [CrossRef] [PubMed]
- Chaussavoine, I.; Beauvois, A.; Mateo, T.; Vasireddi, R.; Douri, N.; Priam, J.; Liatimi, Y.; Lefrançois, S.; Tabuteau, H.; Davranche, M.; et al. The microfluidic laboratory at Synchrotron SOLEIL. J. Synchrotron Radiat. 2020, 27, 230–237. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Weinhausen, B.; Köster, S. Microfluidic devices for X-ray studies on hydrated cells. Lab Chip 2013, 13, 212–215. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lieske, J.; Cerv, M.; Kreida, S.; Komadina, D.; Fischer, J.; Barthelmess, M.; Fischer, P.; Pakendorf, T.; Yefanov, O.; Mariani, V.; et al. On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies. IUCrJ 2019, 6, 714–728. [Google Scholar] [CrossRef] [Green Version]
- Monteiro, D.C.F.; Von Stetten, D.; Stohrer, C.; Sans, M.; Pearson, A.R.; Santoni, G.; Van Der Linden, P.; Trebbin, M. 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow. J. Synchrotron Radiat. 2019, 26, 406–412. [Google Scholar] [CrossRef]
- Gavira, J.A.; Rodriguez-Ruiz, I.; Martinez-Rodriguez, S.; Basu, S.; Teychené, S.; McCarthy, A.A.; Mueller-Dieckman, C. Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips. Acta Crystallogr. Sect. D Struct. Biol. 2020, 76, 751–758. [Google Scholar] [CrossRef]
- Junius, N.; Jaho, S.; Sallaz-Damaz, Y.; Borel, F.; Salmon, J.-B.; Budayova-Spano, M. A microfluidic device for both on-chip dialysis protein crystallization and in situ X-ray diffraction. Lab Chip 2020, 20, 296–310. [Google Scholar] [CrossRef] [Green Version]
- Hansen, C.L.; Skordalakes, E.; Berger, J.M.; Quake, S.R. A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion. Proc. Natl. Acad. Sci. USA 2002, 99, 16531–16536. [Google Scholar] [CrossRef] [Green Version]
- Chavas, L.M.G.; Gourhant, P.; Guimaraes, B.G.; Isabet, T.; Legrand, P.; Lener, R.; Montaville, P.; Sirigu, S.; Thompson, A. PROXIMA-1 beamline for macromolecular crystallography measurements at Synchrotron SOLEIL. J. Synchrotron Radiat. 2021, 28, 970–976. [Google Scholar] [CrossRef]
- Zeldin, O.B.; Gerstel, M.; Garman, E.F. RADDOSE-3D: Time- and space-resolved modelling of dose in macromolecular crystallography. J. Appl. Crystallogr. 2013, 46, 1225–1230. [Google Scholar] [CrossRef]
- Kabsch, W. Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. 2010, 66, 133–144. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Vonrhein, C.; Flensburg, C.; Keller, P.; Sharff, A.; Smart, O.; Paciorek, W.; Womack, T.; Bricogne, G. Data processing and analysis with the autoPROC toolbox. Acta Crystallogr. Sect. D Biol. Crystallogr. 2011, 67, 293–302. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Evans, P. Scaling and assessment of data quality. Acta Crystallogr. Sect. D Biol. Crystallogr. 2006, 62, 72–82. [Google Scholar] [CrossRef] [PubMed]
- Evans, P.R.; Murshudov, G.N. How good are my data and what is the resolution? Acta Crystallogr. Sect. D Biol. Crystallogr. 2013, 69, 1204–1214. [Google Scholar] [CrossRef]
- Winn, M.D.; Ballard, C.C.; Cowtan, K.D.; Dodson, E.J.; Emsley, P.; Evans, P.R.; Keegan, R.M.; Krissinel, E.B.; Leslie, A.G.W.; McCoy, A.; et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. Sect. D Biol. Crystallogr. 2011, 67, 235–242. [Google Scholar] [CrossRef] [Green Version]
- French, G.S.; Wilson, K.S. On the treatment of negative intensity observations. Acta Crystallogr. Sect. A Cryst. Phys. Diffr. Theor. Gen. Crystallogr. 1978, 34, 517–525. [Google Scholar] [CrossRef]
- Vagin, A.; Teplyakov, A. MOLREP: An automated program for molecular replacement. J. Appl. Crystallogr. 1997, 30, 1022–1025. [Google Scholar] [CrossRef]
- Bricogne, G.; Blanc, E.; Brandl, M.; Flensburg, C.; Keller, P.; Paciorek, W.; Roversi, P.; Sharff, A.; Smart, O.S.; Vonrhein, C.; et al. BUSTER, Version 2.10.3.; Global Phasing Ltd.: Cambridge, UK, 2017. [Google Scholar]
- Emsley, P.; Lohkamp, B.; Scott, W.G.; Cowtan, K. Features and development of Coot. Acta Crystallogr. Sect. D Biol. Crystallogr. 2010, 66, 486–501. [Google Scholar] [CrossRef] [Green Version]
- Williams, C.J.; Headd, J.J.; Moriarty, N.W.; Prisant, M.G.; Videau, L.L.; Deis, L.N.; Verma, V.; Keedy, D.A.; Hintze, B.J.; Chen, V.B.; et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2018, 27, 293–315. [Google Scholar] [CrossRef]
- Chaussavoine, I.; Isabet, T.; Lener, R.; Montaville, P.; Vasireddi, R.; Chavas, L.M.G. Implementation of wedged-serial protein crystallography. J. Synchrotron Radiat. 2022, 29, 439–446. [Google Scholar] [CrossRef]
- Owen, R.L.; Rudino-Pinera, E.; Garman, E.F. Experimental determination of the radiation dose limit for cryocooled protein crystals. Proc. Natl. Acad. Sci. USA 2006, 103, 4912–4917. [Google Scholar] [CrossRef] [PubMed] [Green Version]
DATA COLLECTION | |
---|---|
Space group | P43212 |
Unit cell parameters (Å, °) | a = b = 79.61, c = 37.88, α = β = γ = 90 |
Resolution (Å) | 56.28–1.83 (1.86–1.83) |
No. of observed reflections | 306,732 (4445) |
No. of unique reflections | 11,146 (525) |
Completeness (%) | 100 (99.4) |
Rmerge | 0.111 (0.578) |
Rmeas | 0.113 (0.614) |
Rpim | 0.021 (0.2) |
〈I/σ(I)〉 | 22.2 (2.8) |
CC1/2 | 0.999 (0.884) |
Multiplicity | 27.5 (8.5) |
Wilson B factor (Å2) | 28.68 |
REFINEMENT | |
Rfree | 0.19 |
Rwork | 0.17 |
r.m.s.d., bond lengths/angles (Å, °) | 0.008/0.92 |
Ramachandran (favored/allowed, %) | 99.21/0.79 |
Average B factor (Å2) | |
Overall | 29.18 |
For protein residues | 27.73 |
For water | 44.52 |
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Vasireddi, R.; Gardais, A.; Chavas, L.M.G. Manufacturing of Ultra-Thin X-ray-Compatible COC Microfluidic Devices for Optimal In Situ Macromolecular Crystallography Experiments. Micromachines 2022, 13, 1365. https://doi.org/10.3390/mi13081365
Vasireddi R, Gardais A, Chavas LMG. Manufacturing of Ultra-Thin X-ray-Compatible COC Microfluidic Devices for Optimal In Situ Macromolecular Crystallography Experiments. Micromachines. 2022; 13(8):1365. https://doi.org/10.3390/mi13081365
Chicago/Turabian StyleVasireddi, Ramakrishna, Antonin Gardais, and Leonard M. G. Chavas. 2022. "Manufacturing of Ultra-Thin X-ray-Compatible COC Microfluidic Devices for Optimal In Situ Macromolecular Crystallography Experiments" Micromachines 13, no. 8: 1365. https://doi.org/10.3390/mi13081365
APA StyleVasireddi, R., Gardais, A., & Chavas, L. M. G. (2022). Manufacturing of Ultra-Thin X-ray-Compatible COC Microfluidic Devices for Optimal In Situ Macromolecular Crystallography Experiments. Micromachines, 13(8), 1365. https://doi.org/10.3390/mi13081365