Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Porous microwells for geometry-selective, large-scale microparticle arrays

Abstract

Large-scale microparticle arrays (LSMAs) are key for material science and bioengineering applications. However, previous approaches suffer from trade-offs between scalability, precision, specificity and versatility. Here, we present a porous microwell-based approach to create large-scale microparticle arrays with complex motifs. Microparticles are guided to and pushed into microwells by fluid flow through small open pores at the bottom of the porous well arrays. A scaling theory allows for the rational design of LSMAs to sort and array particles on the basis of their size, shape, or modulus. Sequential particle assembly allows for proximal and nested particle arrangements, as well as particle recollection and pattern transfer. We demonstrate the capabilities of the approach by means of three applications: high-throughput single-cell arrays; microenvironment fabrication for neutrophil chemotaxis; and complex, covert tags by the transfer of an upconversion nanocrystal-laden LSMA.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Porous microwells for microparticle arrays.
Figure 2: Scaling analysis and characteristic-specific positioning.
Figure 3: Advanced assembly techniques.
Figure 4: Post-assembly techniques.
Figure 5: Application of large-scale microwell arrays.

Similar content being viewed by others

References

  1. Chung, S. E. et al. One-step pipetting and assembly of encoded chemical-laden microparticles for high-throughput multiplexed bioassays. Nat. Commun. 5, 3468 (2014).

    Article  Google Scholar 

  2. Pregibon, D. C., Toner, M. & Doyle, P. S. Multifunctional encoded particles for high-throughput biomolecule analysis. Science 315, 1393–1396 (2007).

    Article  CAS  Google Scholar 

  3. Walt, D. R. Techview: molecular biology. Bead-based fiber-optic arrays. Science 287, 451–452 (2000).

    Article  CAS  Google Scholar 

  4. Rissin, D. M. et al. Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations. Nat. Biotechnol. 28, 595–599 (2010).

    Article  CAS  Google Scholar 

  5. Eng, G. et al. Assembly of complex cell microenvironments using geometrically docked hydrogel shapes. Proc. Natl Acad. Sci. USA 110, 4551–4556 (2013).

    Article  CAS  Google Scholar 

  6. Hui, E. E. & Bhatia, S. N. Micromechanical control of cell-cell interactions. Proc. Natl Acad. Sci. USA 104, 5722–5726 (2007).

    Article  CAS  Google Scholar 

  7. Lee, J. et al. Universal process-inert encoding architecture for polymer microparticles. Nat. Mater. 13, 524–529 (2014).

    Article  CAS  Google Scholar 

  8. Han, S. et al. Lithographically encoded polymer microtaggant using high-capacity and error-correctable QR code for anti-counterfeiting of drugs. Adv. Mater. 24, 5924–5929 (2012).

    Article  CAS  Google Scholar 

  9. Bae, H. J. et al. Biomimetic microfingerprints for anti-counterfeiting strategies. Adv. Mater. 27, 2083–2089 (2015).

    Article  CAS  Google Scholar 

  10. Curtis, J. E., Koss, B. A. & Grier, D. G. Dynamic holographic optical tweezers. Opt. Commun. 207, 169–175 (2002).

    Article  CAS  Google Scholar 

  11. Hoogenboom, J. P., Vossen, D. L. J., Faivre-Moskalenko, C., Dogterom, M. & van Blaaderen, A. Patterning surfaces with colloidal particles using optical tweezers. Appl. Phys. Lett. 80, 4828–4830 (2002).

    Article  CAS  Google Scholar 

  12. Xin, H. B., Xu, R. & Li, B. J. Optical trapping, driving, and arrangement of particles using a tapered fibre probe. Sci. Rep.-Uk 2, 818 (2012).

    Article  Google Scholar 

  13. Chiou, P. Y., Ohta, A. T. & Wu, M. C. Massively parallel manipulation of single cells and microparticles using optical images. Nature 436, 370–372 (2005).

    Article  CAS  Google Scholar 

  14. Grzybowski, B. A., Stone, H. A. & Whitesides, G. M. Dynamic self-assembly of magnetized, millimetre-sized objects rotating at a liquid–air interface. Nature 405, 1033–1036 (2000).

    Article  CAS  Google Scholar 

  15. Tasoglu, S. et al. Guided and magnetic self-assembly of tunable magnetoceptive gels. Nat. Commun. 5, 4702 (2014).

    Article  CAS  Google Scholar 

  16. Tasoglu, S., Diller, E., Guven, S., Sitti, M. & Demirci, U. Untethered micro-robotic coding of three-dimensional material composition. Nat. Commun. 5, 3124 (2014).

    Article  CAS  Google Scholar 

  17. Heo, J. et al. Ultra-high-aspect-orthogonal and tunable three dimensional polymeric nanochannel stack array for BioMEMS applications. Nanoscale 6, 9681–9688 (2014).

    Article  CAS  Google Scholar 

  18. Le Goff, G. C., Lee, J., Gupta, A., Hill, W. A. & Doyle, P. S. High-throughput contact flow lithography. Adv. Sci. 2, 1500149 (2015).

    Article  Google Scholar 

  19. Hamrock, B. J., Jacobson, B. O. & Schmid, S. R. Fundamentals of Machine Elements (WCB/McGraw-Hill, 1999).

    Google Scholar 

  20. Guo, M. Y. & Wyss, H. M. Micromechanics of soft particles. Macromol. Mater. Eng. 296, 223–229 (2011).

    Article  CAS  Google Scholar 

  21. Wyss, H. M., Franke, T., Mele, E. & Weitz, D. A. Capillary micromechanics: measuring the elasticity of microscopic soft objects. Soft Matter 6, 4550–4555 (2010).

    Article  CAS  Google Scholar 

  22. Tominaga, T. et al. Effect of substrate adhesion and hydrophobicity on hydrogel friction. Soft Matter 4, 1033–1040 (2008).

    Article  CAS  Google Scholar 

  23. Pregibon, D. C. & Doyle, P. S. Optimization of encoded hydrogel particles for nucleic acid quantification. Anal. Chem. 81, 4873–4881 (2009).

    Article  CAS  Google Scholar 

  24. Choi, N. W. et al. Multiplexed detection of mRNA using porosity-tuned hydrogel microparticles. Anal. Chem. 84, 9370–9378 (2012).

    Article  CAS  Google Scholar 

  25. Chung, S. E., Park, W., Shin, S., Lee, S. A. & Kwon, S. Guided and fluidic self-assembly of microstructures using railed microfluidic channels. Nat. Mater. 7, 581–587 (2008).

    Article  CAS  Google Scholar 

  26. Chung, S. E., Jung, Y. & Kwon, S. Three-dimensional fluidic self-assembly by axis translation of two-dimensionally fabricated microcomponents in railed microfluidics. Small 7, 796–803 (2011).

    Article  CAS  Google Scholar 

  27. Dendukuri, D. et al. Modeling of oxygen-inhibited free radical photopolymerization in a PDMS microfluidic device. Macromolecules 41, 8547–8556 (2008).

    Article  CAS  Google Scholar 

  28. Cruz, F. C. et al. New technologies for examining the role of neuronal ensembles in drug addiction and fear. Nat. Rev. Neurosci. 14, 743–754 (2013).

    Article  CAS  Google Scholar 

  29. Di Carlo, D., Wu, L. Y. & Lee, L. P. Dynamic single cell culture array. Lab. Chip 6, 1445–1449 (2006).

    Article  CAS  Google Scholar 

  30. Rettig, J. R. & Folch, A. Large-scale single-cell trapping and imaging using microwell arrays. Anal. Chem. 77, 5628–5634 (2005).

    Article  CAS  Google Scholar 

  31. Hughes, A. J. et al. Single-cell western blotting. Nat. Methods 11, 749–U794 (2014).

    Article  CAS  Google Scholar 

  32. Phillipson, M. & Kubes, P. The neutrophil in vascular inflammation. Nat. Med. 17, 1381–1390 (2011).

    Article  CAS  Google Scholar 

  33. Ridley, A. J. et al. Cell migration: Integrating signals from front to back. Science 302, 1704–1709 (2003).

    Article  CAS  Google Scholar 

  34. Sadik, C. D., Kim, N. D. & Luster, A. D. Neutrophils cascading their way to inflammation. Trends Immunol. 32, 452–460 (2011).

    Article  CAS  Google Scholar 

  35. Ng, L. G. et al. Visualizing the neutrophil response to sterile tissue injury in mouse dermis reveals a three-phase cascade of events. J. Invest. Dermatol. 131, 2058–2068 (2011).

    Article  CAS  Google Scholar 

  36. Kress, H. et al. Cell stimulation with optically manipulated microsources. Nat. Methods 6, 905–909 (2009).

    Article  CAS  Google Scholar 

  37. Boneschansker, L., Yan, J., Wong, E., Briscoe, D. M. & Irimia, D. Microfluidic platform for the quantitative analysis of leukocyte migration signatures. Nat. Commun. 5, 4787 (2014).

    Article  CAS  Google Scholar 

  38. Lin, F. et al. Neutrophil migration in opposing chemoattractant gradients using microfluidic chemotaxis devices. Ann. Biomed. Eng. 33, 475–482 (2005).

    Article  Google Scholar 

  39. Heit, B., Tavener, S., Raharjo, E. & Kubes, P. An intracellular signaling hierarchy determines direction of migration in opposing chemotactic gradients. J. Cell Biol. 159, 91–102 (2002).

    Article  CAS  Google Scholar 

  40. Weiner, O. D. et al. Spatial control of actin polymerization during neutrophil chemotaxis. Nat. Cell Biol. 1, 75–81 (1999).

    Article  CAS  Google Scholar 

  41. Wang, F. et al. Simultaneous phase and size control of upconversion nanocrystals through lanthanide doping. Nature 463, 1061–1065 (2010).

    Article  CAS  Google Scholar 

  42. Wang, F. & Liu, X. G. Upconversion multicolor fine-tuning: Visible to near-infrared emission from lanthanide-doped NaYF4 nanoparticles. J. Am. Chem. Soc. 130, 5642–5643 (2008).

    Article  CAS  Google Scholar 

  43. Meruga, J. M. et al. Red-green-blue printing using luminescence-upconversion inks. J. Mater Chem. C 2, 2221–2227 (2014).

    Article  CAS  Google Scholar 

  44. Xia, Y. N. & Whitesides, G. M. Soft lithography. Annu. Rev. Mater Sci. 28, 153–184 (1998).

    Article  CAS  Google Scholar 

  45. Rogers, J. A., Paul, K. E. & Whitesides, G. M. Quantifying distortions in soft lithography. J. Vac. Sci. Technol. B 16, 88–97 (1998).

    Article  CAS  Google Scholar 

  46. Ogunniyi, A. O., Story, C. M., Papa, E., Guillen, E. & Love, J. C. Screening individual hybridomas by microengraving to discover monoclonal antibodies. Nat. Protoc. 4, 767–782 (2009).

    Article  CAS  Google Scholar 

  47. Lee, W. C. et al. Multivariate biophysical markers predictive of mesenchymal stromal cell multipotency. Proc. Natl Acad. Sci. USA 111, E4409–E4418 (2014).

    Article  CAS  Google Scholar 

  48. Shepherd, R. F. et al. Stop-flow lithography of colloidal, glass, and silicon microcomponents. Adv. Mater. 20, 4734–4739 (2008).

    Article  CAS  Google Scholar 

  49. Martínez-Sala, R. Sound attenuation by sculpture. Nature 378, 241 (1995).

    Article  Google Scholar 

Download references

Acknowledgements

We gratefully acknowledge funding from the National Science Foundation grants CMMI-1120724, a Samsung Scholarship to J.J.K., and National Institutes of Health (GM092804). This work was supported in part by the MRSEC Program of the National Science Foundation under award number DMR-1419807. Microfabrication was performed at BioMEMS Resource Center (EB002503) and MTL, MIT. The modulus measurement was performed in G. McKinley’s and A. S. Myerson’s laboratories at MIT. We thank B. Hamza and E. J. Lim of the BioMEMS Resource Center for fabrication of Si wafer and insightful discussion, and L. C. Hsiao and H. Burak Eral for the modulus measurement.

Author information

Authors and Affiliations

Authors

Contributions

J.J.K. and K.W.B. equally contributed to this work. J.J.K. designed the research, conducted the majority of the experiments, conducted a scaling analysis, and interpreted data. K.W.B. conceived the project, obtained preliminary results, and interpreted data. J.J.K. and E.R. designed and demonstrated the biological studies. P.S.D. and D.I. designed the research, supervised the study, and interpreted data. J.J.K., P.S.D. and D.I. wrote the manuscript, and all authors commented on the manuscript.

Corresponding authors

Correspondence to Daniel Irimia or Patrick S. Doyle.

Ethics declarations

Competing interests

Two provisional US patent applications were filed on 1 November 2013 and 17 August 2016, respectively.

Supplementary information

Supplementary Information

Supplementary Information (PDF 4223 kb)

Supplementary Movie 1

Supplementary Movie 1 (MOV 1273 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kim, J., Bong, K., Reátegui, E. et al. Porous microwells for geometry-selective, large-scale microparticle arrays. Nature Mater 16, 139–146 (2017). https://doi.org/10.1038/nmat4747

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmat4747

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing