Nanoscale tweezers for single-cell biopsies
Source abstract
Abstract
Much of the functionality of multicellular systems arises from the spatial organization and dynamic behaviours within and between cells. Current single-cell genomic methods only provide a transcriptional 'snapshot' of individual cells. The real-time analysis and perturbation of living cells would generate a step change in single-cell analysis. Here we describe minimally invasive nanotweezers that can be spatially controlled to extract samples from living cells with single-molecule precision. They consist of two closely spaced electrodes with gaps as small as 10-20 nm, which can be used for the dielectrophoretic trapping of DNA and proteins. Aside from trapping single molecules, we also extract nucleic acids for gene expression analysis from living cells without affecting their viability. Finally, we report on the trapping and extraction of a single mitochondrion. This work bridges the gap between single-molecule/organelle manipulation and cell biology and can ultimately enable a better understanding of living cells.
Source: europepmc · Quality: candidate unverified · Source record ↗
Research context
OpenAlex topics: Microfluidic and Bio-sensing Technologies · Advanced biosensing and bioanalysis techniques · Microfluidic and Capillary Electrophoresis Applications
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (45)
Show source-provided references
1. Tseng, F.-G. & Santra, T. S. Essentials of Single-cell Analysis: Concepts, Applications and Future Prospects (Springer, Berlin, 2016).
2. Borland, L. M., Kottegoda, S., Phillips, K. S. & Allbritton, N. L. Chemical analysis of single cells. Annu. Rev. Anal. Chem. 1, 191–227 (2008).10.1146/annurev.anchem.1.031207.113100 ↗
3. Trouillon, R., Passarelli, M. K., Wang, J., Kurczy, M. E. & Ewing, A. G. Chemical analysis of single cells. Anal. Chem. 85, 522–542 (2013).10.1021/ac303290s ↗
4. Higgins, S. G. & Stevens, M. M. Extracting the contents of living cells. Science 356, 379–380 (2017).10.1126/science.aan0228 ↗
5. Gawad, C., Koh, W. & Quake, S. R. Single-cell genome sequencing: current state of the science. Nat. Rev. Genet. 17, 175–188 (2016).10.1038/nrg.2015.16 ↗
6. Blainey, P. C. & Quake, S. R. Dissecting genomic diversity, one cell at a time. Nat. Methods 11, 19–21 (2014).10.1038/nmeth.2783 ↗
7. Park, M. C., Hur, M. C., Cho, H. S., Park, S. H. & Suh, K. Y. High-throughput single-cell quantification using simple microwell-based cell docking and programmable time-course live-cell imaging. Lab Chip 11, 79–86 (2011).10.1039/C0LC00114G ↗
8. Mu, X., Zheng, W. F., Sun, J. S., Zhang, W. & Jiang, X. Y. Microfluidics for manipulating cells. Small 9, 9–21 (2013).10.1002/smll.201200996 ↗
9. Wang, J., Trouillon, R., Dunevall, J. & Ewing, A. G. Spatial resolution of single-cell exocytosis by microwell-based individually addressable thin film ultramicroelectrode arrays. Anal. Chem. 86, 4515–4520 (2014).10.1021/ac500443q ↗
10. Kimmerling, R. J. et al. A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages. Nat. Commun. 7, 10220 (2016).10.1038/ncomms10220 ↗
11. Gao, J., Riahi, R., Sin, M. L. Y., Zhang, S. F. & Wong, P. K. Electrokinetic focusing and separation of mammalian cells in conductive biological fluids. Analyst 137, 5215–5221 (2012).10.1039/c2an35707k ↗
12. Fu, A. Y., Spence, C., Scherer, A., Arnold, F. H. & Quake, S. R. A microfabricated fluorescence-activated cell sorter. Nat. Biotechnol. 17, 1109–1111 (1999).10.1038/15095 ↗
13. Liu, L., Cheung, T. H., Charville, G. W. & Rando, T. A. Isolation of skeletal muscle stem cells by fluorescence-activated cell sorting. Nat. Protoc. 10, 1612–1624 (2015).10.1038/nprot.2015.110 ↗
14. Norregaard, K. et al. Manipulation and motion of organelles and single molecules in living cells. Chem. Rev. 117, 4342–4375 (2017).10.1021/acs.chemrev.6b00638 ↗
15. Zhang, H. & Liu, K. K. Optical tweezers for single cells. J. R. Soc. Interface 5, 671–690 (2008).10.1098/rsif.2008.0052 ↗
16. Ashkin, A., Schütze, K., Dziedzic, J. M., Euteneuer, U. & Schliwa, M. Force generation of organelle transport measured in vivo by an infrared laser trap. Nature 348, 346–348 (1990).10.1038/348346a0 ↗
17. Wang, Y. et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512, 155–160 (2015).10.1038/nature13600 ↗
18. McConnell, M. J. et al. Mosaic copy number variation in human neurons. Science 342, 632–637 (2013).10.1126/science.1243472 ↗
19. Cai, X. et al. Single-cell, genome-wide sequencing identifies clonal somatic copy-number variation in the human brain. Cell Rep. 8, 1280–1289 (2014).10.1016/j.celrep.2014.07.043 ↗
20. Villani, A. C. et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356, eaah4573 (2017).10.1126/science.aah4573 ↗
21. Macaulay, I. C. et al. Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells. Cell Rep. 14, 966–977 (2016).10.1016/j.celrep.2015.12.082 ↗
22. Lan, F., Demaree, B., Ahmed, N. & Abate, A. R. Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding. Nat. Biotechnol. 35, 640–646 (2017).10.1038/nbt.3880 ↗
23. Regev, A. et al. The human cell atlas. eLife 6, 27041 (2017).10.7554/eLife.27041 ↗
24. Guillaume-Gentil, O. et al. Tunable single-cell extraction for molecular analyses. Cell 166, 506–516 (2016).10.1016/j.cell.2016.06.025 ↗
25. Actis, P. Sampling from single cells. Small Methods 2, 1700300 (2018).10.1002/smtd.201700300 ↗
26. Guillaume-Gentil, O. et al. Force-controlled manipulation of single cells: from AFM to FluidFM. Trends Biotechnol. 32, 381–388 (2014).10.1016/j.tibtech.2014.04.008 ↗
27. Li, X., Tao, Y. L., Lee, D. H., Wickramasinghe, H. K. & Lee, A. P. In situ mRNA isolation from a microfluidic single-cell array using an external AFM nanoprobe. Lab Chip 17, 1635–1644 (2017).10.1039/C7LC00133A ↗
28. Seger, R. A. et al. Voltage controlled nano-injection system for single-cell surgery. Nanoscale 4, 5843–5846 (2012).10.1039/c2nr31700a ↗
29. Actis, P. et al. Compartmental genomics in living cells revealed by single-cell nanobiopsy. ACS Nano 8, 546–553 (2014).10.1021/nn405097u ↗
30. Tóth, E. N. et al. Single-cell nanobiopsy reveals compartmentalization of mRNA in neuronal cells. J. Biol. Chem. 293, 4940–4951 (2018).10.1074/jbc.M117.800763 ↗
31. Kim, H., Okano, K., Osada, T., Ikai, A. & Yasuda, K. Development of mRNA analysis system in single living cells by atomic force microscopy. Biophys. J. 88, 154A–154A (2005).10.1529/biophysj.104.055319 ↗
32. Osada, T., Uehara, H., Kim, H. & Ikai, A. Advances in Clinical Chemistry, Vol. 38, Ch. 3 (Elsevier, London, 2004).
33. Osada, T., Uehara, H., Kim, H. & Ikai, A. mRNA analysis of single living cells. J. Nanobiotechnol. 1, 2 (2003).10.1186/1477-3155-1-2 ↗
34. Nawarathna, D., Turan, T. & Wickramasinghe, H. K. Selective probing of mRNA expression levels within a living cell. Appl. Phys. Lett. 95, 083117 (2009).10.1063/1.3213343 ↗
35. Cadinu, P. et al. Single molecule trapping and sensing using dual nanopores separated by a zeptoliter nanobridge. Nano Lett. 17, 6376–6384 (2017).10.1021/acs.nanolett.7b03196 ↗
36. Cadinu, P. et al. Double barrel nanopores as a new tool for controlling single-molecule transport. Nano Lett. 18, 2738–2745 (2018).10.1021/acs.nanolett.8b00860 ↗
37. Takahashi, Y. et al. Multifunctional nanoprobes for nanoscale chemical imaging and localized chemical delivery at surfaces and interfaces. Angew. Chem. Int. Ed. 50, 9638–9642 (2011).10.1002/anie.201102796 ↗
38. Ren, R. et al. Nanopore extended field-effect transistor for selective single-molecule biosensing. Nat. Commun. 8, 586 (2017).10.1038/s41467-017-00549-w ↗
39. McKelvey, K. et al. Fabrication, characterization, and functionalization of dual carbon electrodes as probes for scanning electrochemical microscopy (SECM). Anal. Chem. 85, 7519–7526 (2013).10.1021/ac401476z ↗
40. Freedman, K. J. et al. Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping. Nat. Commun. 7, 10217 (2016).10.1038/ncomms10217 ↗
41. Ramos, A., Morgan, H., Green, N. G. & Castellanos, A. The role of electrohydrodynamic forces in the dielectrophoretic manipulation and separation of particles. J. Electrostat. 47, 71–81 (1999).10.1016/S0304-3886(99)00031-5 ↗
42. Barik, A. et al. Graphene-edge dielectrophoretic tweezers for trapping of biomolecules. Nat. Commun. 8, 1867 (2017).10.1038/s41467-017-01635-9 ↗
43. Barik, A. et al. Ultralow-power electronic trapping of nanoparticles with sub-10 nm gold nanogap electrodes. Nano Lett. 16, 6317–6324 (2016).10.1021/acs.nanolett.6b02690 ↗
44. Shivalingam, A. et al. The interactions between a small molecule and G-quadruplexes are visualized by fluorescence lifetime imaging microscopy. Nat. Commun. 6, 8178 (2015).10.1038/ncomms9178 ↗
45. Gibbons, J. G., Branco, A. T., Yu, S. & Lemos, B. Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans. Nat. Commun. 5, 4850 (2014).10.1038/ncomms5850 ↗