Skip to main content Accessibility help
×
×
Home

DNA origami devices for molecular-scale precision measurements

  • Carlos E. Castro (a1), Hendrik Dietz (a2) and Björn Högberg (a3)

Abstract

Structural DNA nanotechnology offers the capacity to construct ultraminiaturized devices with programmed nanoscale geometry, mechanical and dynamic properties, and site-specific molecular functionalities. These features and the possibility to position and orient molecules in user-defined ways may be exploited to create custom instruments for precision measurements of molecular-scale structure, dynamics, and interactions. Such devices may help constrain molecular motion along interesting reaction coordinates and may also exert forces to probe the mechanical properties or dynamics of molecules under study. Multiple ways of reading out device states may be used, including atomic force microscopy or transmission electron microscopy imaging, single-molecule or bulk fluorescence, or ionic conductivity as in nanopore systems. Early successes with custom scientific instruments based on DNA origami underline the tremendous potential to enable new approaches to making scientific discoveries in biological and synthetic materials systems.

Copyright

References

Hide All
1. Gothelf, K.V., MRS Bull. 42 (12), 897 (2017).
2. Derr, N.D., Goodman, B.S., Jungmann, R., Leschziner, A.E., Shih, W.M., Reck-Peterson, S.L., Science 338 (6107), 662 (2012).
3. Hariadi, R.F., Appukutty, A.J., Sivaramakrishnan, S., ACS Nano 10 (9), 8281 (2016).
4. Hariadi, R.F., Sommese, R.F., Sivaramakrishnan, S., Elife 4, e05472 (2015).
5. Angelin, A., Weigel, S., Garrecht, R., Meyer, R., Bauer, J., Kumar, R.K., Hirtz, M., Niemeyer, C.M., Angew. Chem. Int. Ed. Engl. 54 (52), 15813 (2015).
6. Pedersen, R.O., Loboa, E.G., LaBean, T.H., Biomacromolecules 14 (12), 4157 (2013).
7. Shaw, A., Lundin, V., Petrova, E., Fordos, F., Benson, E., Al-Amin, A., Herland, A., Blokzijl, A., Högberg, B., Teixeira, A.I., Nat. Methods 11 (8), 841 (2014).
8. Stein, I.H., Steinhauer, C., Tinnefeld, P., J. Am. Chem. Soc. 133 (12), 4193 (2011).
9. Vogele, K., List, J., Pardatscher, G., Holland, N.B., Simmel, F.C., Pirzer, T., ACS Nano 10 (12), 11377 (2016).
10. Acuna, G.P., Moller, F.M., Holzmeister, P., Beater, S., Lalkens, B., Tinnefeld, P., Science 338 (6106), 506 (2012).
11. Pan, K., Boulais, E., Yang, L., Bathe, M., Nucleic Acids Res. 42 (4), 2159 (2014).
12. Bell, N.A., Engst, C.R., Ablay, M., Divitini, G., Ducati, C., Liedl, T., Keyser, U.F., Nano Lett. 12 (1), 512 (2012).
13. Wei, R., Martin, T.G., Rant, U., Dietz, H., Angew. Chem. Int. Ed. Engl. 51 (20), 4864 (2012).
14. Langecker, M., Arnaut, V., Martin, T.G., List, J., Renner, S., Mayer, M., Dietz, H., Simmel, F.C., Science 338 (6109), 932 (2012).
15. Krishnan, S., Ziegler, D., Arnaut, V., Martin, T.G., Kapsner, K., Henneberg, K., Bausch, A.R., Dietz, H., Simmel, F.C., Nat. Commun. 7, 12787 (2016).
16. Gopfrich, K., Li, C.Y., Ricci, M., Bhamidimarri, S.P., Yoo, J., Gyenes, B., Ohmann, A., Winterhalter, M., Aksimentiev, A., Keyser, U.F., ACS Nano 10 (9), 8207 (2016).
17. Shrestha, P., Jonchhe, S., Emura, T., Hidaka, K., Endo, M., Sugiyama, H., Mao, H., Nat. Nanotechnol. 12 (6), 582 (2017).
18. Liedl, T., Högberg, B., Tytell, J., Ingber, D.E., Shih, W.M., Nat. Nanotechnol. 5, 520 (2010), doi:10.1038/nnano.2010.107.
19. Kuzuya, A., Sakai, Y., Yamazaki, T., Xu, Y., Komiyama, M., Nat. Commun. 2, 449 (2011).
20. Funke, J.J., Ketterer, P., Lieleg, C., Schunter, S., Korber, P., Dietz, H., Sci. Adv. 2 (11), e1600974 (2016).
21. Le, J.V., Luo, Y., Darcy, M.A., Lucas, C.R., Goodwin, M.F., Poirier, M.G., Castro, C.E., ACS Nano 10 (7), 7073 (2016).
22. Funke, J.J., Ketterer, P., Lieleg, C., Korber, P., Dietz, H., Nano Lett. 16 (12), 7891 (2016).
23. Kilchherr, F., Wachauf, C., Pelz, B., Rief, M., Zacharias, M., Dietz, H., Science 353 (6304), aaf5508 (2016).
24. Hudoba, M.W., Luo, Y., Zacharias, A., Poirier, M.G., Castro, C.E., ACS Nano 11 (7), 6566 (2017).
25. Nickels, P.C., Wunsch, B., Holzmeister, P., Bae, W., Kneer, L.M., Grohmann, D., Tinnefeld, P., Liedl, T., Science 354 (6310), 305 (2016).
26. Iwaki, M., Wickham, S.F., Ikezaki, K., Yanagida, T., Shih, W.M., Nat. Commun. 7, 13715 (2016).
27. Martin, T.G., Bharat, T.A., Joerger, A.C., Bai, X.C., Praetorius, F., Fersht, A.R., Dietz, H., Scheres, S.H., Proc. Natl. Acad. Sci. U.S.A. 113 (47), E7456 (2016).
28. Suzuki, Y., Endo, M., Katsuda, Y., Ou, K., Hidaka, K., Sugiyama, H., J. Am. Chem. Soc. 136 (1), 211 (2014).
29. Sannohe, Y., Endo, M., Katsuda, Y., Hidaka, K., Sugiyama, H., J. Am. Chem. Soc. 132 (46), 16311 (2010).
30. Jungmann, R., Avendano, M.S., Dai, M., Woehrstein, J.B., Agasti, S.S., Feiger, Z., Rodal, A., Yin, P., Nat. Methods 13 (5), 439 (2016).
31. Dai, M., Jungmann, R., Yin, P., Nat. Nanotechnol. 11 (9), 798 (2016).
32. Reuss, M., Fördős, F., Blom, H., Öktem, O., Högberg, B., Brismar, H., New J. Phys. 19, 025013 (2017).
33. Schmied, J.J., Raab, M., Forthmann, C., Pibiri, E., Wunsch, B., Dammeyer, T., Tinnefeld, P., Nat. Protoc. 9 (6), 1367 (2014).
34. Pfitzner, E., Wachauf, C., Kilchherr, F., Pelz, B., Shih, W.M., Rief, M., Dietz, H., Angew. Chem. Int. Ed. Engl. 52 (30), 7766 (2013).
35. Maune, H.T., Han, S.P., Barish, R.D., Bockrath, M., Goddard, W.A. III, Rothemund, P.W., Winfree, E., Nat. Nanotechnol. 5 (1), 61 (2010).
36. Yang, Y., Wang, J., Shigematsu, H., Xu, W., Shih, W.M., Rothman, J.E., Lin, C., Nat. Chem. 8 (5), 476 (2016).
37. Gopinath, A., Miyazono, E., Faraon, A., Rothemund, P.W., Nature 535 (7612), 401 (2016).
38. Akbari, E., Mollica, M.Y., Lucas, C.R., Bushman, S.M., Patton, R.A., Shahhosseini, M., Song, J.W., Castro, C.E., Adv. Mater. 1703632 (2017), https://doi.org/10.1002/adma.201703632.
39. Modi, S., Swetha, M.G., Goswami, D., Gupta, G.D., Mayor, S., Krishnan, Y., Nat. Nanotechnol. 4 (5), 325 (2009).
40. Saha, S., Prakash, V., Halder, S., Chakraborty, K., Krishnan, Y., Nat. Nanotechnol. 10 (7), 645 (2015).
41. Chopra, A., Krishnan, S., Simmel, F.C., Nano Lett. 16 (10), 6683 (2016).
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

MRS Bulletin
  • ISSN: 0883-7694
  • EISSN: 1938-1425
  • URL: /core/journals/mrs-bulletin
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Metrics

Altmetric attention score

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed