Spatially multiplexed single-molecule translocations through a nanopore at controlled speeds
Source abstract
Abstract
In current nanopore-based label-free single-molecule sensing technologies, stochastic processes influence the selection of translocating molecule, translocation rate and translocation velocity. As a result, single-molecule translocations are challenging to control both spatially and temporally. Here we present a method using a glass nanopore mounted on a three-dimensional nanopositioner to spatially select molecules, deterministically tethered on a glass surface, for controlled translocations. By controlling the distance between the nanopore and glass surface, we can actively select the region of interest on the molecule and scan it a controlled number of times and at a controlled velocity. Decreasing the velocity and averaging thousands of consecutive readings of the same molecule increases the signal-to-noise ratio by two orders of magnitude compared with free translocations. We demonstrate the method's versatility by assessing DNA-protein complexes, DNA rulers and DNA gaps, achieving down to single-nucleotide gap detection.
Source: europepmc · Quality: candidate unverified · Source record ↗
Research context
OpenAlex topics: Nanopore and Nanochannel Transport Studies · Quantum-Dot Cellular Automata · Advanced biosensing and bioanalysis techniques
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (41)
Show source-provided references
1. Branton, D. et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146–1153 (2008).10.1038/nbt.1495 ↗
2. Schneider, G. F. & Dekker, C. DNA sequencing with nanopores. Nat. Biotechnol. 30, 326–328 (2012).10.1038/nbt.2181 ↗
3. Brinkerhoff, H., Kang, A. S. W., Liu, J., Aksimentiev, A. & Dekker, C. Multiple rereads of single proteins at single-amino acid resolution using nanopores. Science 374, 1509–1513 (2021).10.1126/science.abl4381 ↗
4. Manrao, E. A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349–353 (2012).10.1038/nbt.2171 ↗
5. Derrington, I. M. et al. Subangstrom single-molecule measurements of motor proteins using a nanopore. Nat. Biotechnol. 33, 1073–1075 (2015).10.1038/nbt.3357 ↗
6. Fragasso, A., Schmid, S. & Dekker, C. Comparing current noise in biological and solid-state nanopores. ACS Nano 14, 1338–1349 (2020).10.1021/acsnano.9b09353 ↗
7. Li, J. et al. Ion-beam sculpting at nanometre length scales. Nature 412, 166–169 (2001).10.1038/35084037 ↗
8. Storm, A., Chen, J., Ling, X., Zandbergen, H. & Dekker, C. Fabrication of solid-state nanopores with single-nanometre precision. Nat. Mater. 2, 537–540 (2003).10.1038/nmat941 ↗
9. Dekker, C. Solid-state nanopores. Nanoscience and Technology: A Collection of Reviews from Nature Journals 60–66 (2010).10.1142/9789814287005_0007 ↗
10. Garaj, S. et al. Graphene as a subnanometre trans-electrode membrane. Nature 467, 190–193 (2010).10.1038/nature09379 ↗
11. Xue, L. et al. Solid-state nanopore sensors. Nat. Rev. Mater. 5, 931–951 (2020).10.1038/s41578-020-0229-6 ↗
12. Yusko, E. C. et al. Real-time shape approximation and fingerprinting of single proteins using a nanopore. Nat. Nanotechnol. 12, 360–367 (2017).10.1038/nnano.2016.267 ↗
13. Lu, B., Albertorio, F., Hoogerheide, D. P. & Golovchenko, J. A. Origins and consequences of velocity fluctuations during DNA passage through a nanopore. Biophys. J. 101, 70–79 (2011).10.1016/j.bpj.2011.05.034 ↗
14. Plesa, C., Van Loo, N., Ketterer, P., Dietz, H. & Dekker, C. Velocity of DNA during translocation through a solid-state nanopore. Nano Lett. 15, 732–737 (2015).10.1021/nl504375c ↗
15. Rosenstein, J. K., Wanunu, M., Merchant, C. A., Drndic, M. & Shepard, K. L. Integrated nanopore sensing platform with sub-microsecond temporal resolution. Nat. Methods 9, 487–492 (2012).10.1038/nmeth.1932 ↗
16. Steinbock, L. J., Otto, O., Chimerel, C., Gornall, J. & Keyser, U. F. Detecting DNA folding with nanocapillaries. Nano Lett. 10, 2493–2497 (2010).10.1021/nl100997s ↗
17. Bell, N. A. W., Chen, K., Ghosal, S., Ricci, M. & Keyser, U. F. Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore. Nat. Commun. 8, 380 (2017).10.1038/s41467-017-00423-9 ↗
18. Steinbock, L. J., Bulushev, R. D., Krishnan, S., Raillon, C. & Radenovic, A. DNA translocation through low-noise glass nanopores. ACS Nano 7, 11255–11262 (2013).10.1021/nn405029j ↗
19. Aramesh, M. et al. Localized detection of ions and biomolecules with a force-controlled scanning nanopore microscope. Nat. Nanotechnol. 14, 791–798 (2019).10.1038/s41565-019-0493-z ↗
20. Yuan, Z., Liu, Y., Dai, M., Yi, X. & Wang, C. Controlling DNA translocation through solid-state nanopores. Nanoscale Res. Lett. 15, 80 (2020).10.1186/s11671-020-03308-x ↗
21. Rahman, M., Sampad, M. J. N., Hawkins, A. & Schmidt, H. Recent advances in integrated solid-state nanopore sensors. Lab Chip 21, 3030–3052 (2021).10.1039/D1LC00294E ↗
22. Hansma, P. K., Drake, B., Marti, O., Gould, S. A. & Prater, C. B. The scanning ion-conductance microscope. Science 243, 641–643 (1989).10.1126/science.2464851 ↗
23. Korchev, Y. E., Bashford, C. L., Milovanovic, M., Vodyanoy, I. & Lab, M. J. Scanning ion conductance microscopy of living cells. Biophys. J. 73, 653–658 (1997).10.1016/S0006-3495(97)78100-1 ↗
24. Novak, P. et al. Nanoscale live-cell imaging using hopping probe ion conductance microscopy. Nat. Methods 6, 279–281 (2009).10.1038/nmeth.1306 ↗
25. Leitao, S. M. et al. Time-resolved scanning ion conductance microscopy for three-dimensional tracking of nanoscale cell surface dynamics. ACS Nano 15, 17613–17622 (2021).10.1021/acsnano.1c05202 ↗
26. Navikas, V. et al. High-throughput nanocapillary filling enabled by microwave radiation for scanning ion conductance microscopy imaging. ACS Appl. Nano Mater. 3, 7829–7834 (2020).10.1021/acsanm.0c01345 ↗
27. Rief, M., Oesterhelt, F., Heymann, B. & Gaub, H. E. Single molecule force spectroscopy on polysaccharides by atomic force microscopy. Science 275, 1295–1297 (1997).10.1126/science.275.5304.1295 ↗
28. Chen, K. et al. Dynamics of driven polymer transport through a nanopore. Nat. Phys. 17, 1043–1049 (2021).10.1038/s41567-021-01268-2 ↗
29. Chen, K. et al. Digital data storage using DNA nanostructures and solid-state nanopores. Nano Lett. 19, 1210–1215 (2018).10.1021/acs.nanolett.8b04715 ↗
30. Tabatabaei, S. K. et al. DNA punch cards for storing data on native DNA sequences via enzymatic nicking. Nat. Commun. 11, 1742 (2020).10.1038/s41467-020-15588-z ↗
31. Clegg, R. M. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211, 353–388 (1992).10.1016/0076-6879(92)11020-J ↗
32. Lelek, M. et al. Single-molecule localization microscopy. Nat. Rev. Methods Primers 1, 39 (2021).10.1038/s43586-021-00038-x ↗
33. Jungmann, R. et al. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. 10, 4756–4761 (2010).10.1021/nl103427w ↗
34. Zhu, C. et al. Imaging with ion channels. Anal. Chem. 93, 5355–5359 (2021).10.1021/acs.analchem.1c00224 ↗
35. Radmacher, M., Cleveland, J. P., Fritz, M., Hansma, H. G. & Hansma, P. K. Mapping interaction forces with the atomic force microscope. Biophys. J. 66, 2159–2165 (1994).10.1016/S0006-3495(94)81011-2 ↗
36. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).10.1038/nmeth.2019 ↗
37. Nečas, D. & Klapetek, P. Gwyddion: an open-source software for SPM data analysis. Open Phys. 10, 181–188 (2012).10.2478/s11534-011-0096-2 ↗
38. Wang, H. & Hays, J. B. Simple and rapid preparation of gapped plasmid DNA for incorporation of oligomers containing specific DNA lesions. Mol. Biotechnol. 19, 133–140 (2001).10.1385/MB:19:2:133 ↗
39. Jozwiakowski, S. K. & Connolly, B. A. Plasmid-based lacZα assay for DNA polymerase fidelity: application to archaeal family-B DNA polymerase. Nucleic Acids Res. 37, e102 (2009).10.1093/nar/gkp494 ↗
40. Auburn, R. P. et al. Robotic spotting of cDNA and oligonucleotide microarrays. Trends Biotechnol. 23, 374–379 (2005).10.1016/j.tibtech.2005.04.002 ↗
41. Navikas, V. et al. Correlative 3D microscopy of single cells using super-resolution and scanning ion-conductance microscopy. Nat. Commun. 12, 4565 (2021).10.1038/s41467-021-24901-3 ↗