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A Dna Origami Plasmonic Sensor With Environment-independent Read-ou

Ditulis Senin, 22 November 2021 Tulis Komentar Edit

Abstract

DNA origami is a promising technology for its reproducibility, flexibility, scalability and biocompatibility. Among the several potential applications, DNA origami has been proposed as a tool for drug delivery and as a contrast agent, since a conformational change upon specific target interaction may be used to release a drug or produce a physical signal, respectively. However, its conformation should be robust with respect to the properties of the medium in which either the recognition or the read-out take place, such as pressure, viscosity and any other unspecific interaction other than the desired target recognition. Here we report on the read-out robustness of a tetragonal DNA-origami/gold-nanoparticle hybrid structure able to change its configuration, which is transduced in a change of its plasmonic properties, upon interaction with a specific DNA target. We investigated its response when analyzed in three different media: aqueous solution, solid support and viscous gel. We show that, once a conformational variation is produced, it remains unaffected by the subsequent physical interactions with the environment.

References

  1. [1]

    Ghosh, S. K.; Pal, T. Interparticle coupling effect on the surface plasmon resonance of gold nanoparticles: From theory to applications. Chem Rev. 2007, 107, 4797–4862.

    CAS  Article  Google Scholar

  2. [2]

    Reinhard, B. M.; Siu, M.; Agarwal, H.; Alivisatos, A. P.; Liphardt, J. Calibration of dynamic molecular rulers based on plasmon coupling between gold nanoparticles. Nano Lett. 2005, 5, 2246–2252.

    CAS  Article  Google Scholar

  3. [3]

    Prodan, E.; Radloff, C.; Halas, N. J.; Nordlander, P. A hybridization model for the plasmon response of complex nanostructures. Science 2003, 302, 419–422.

    CAS  Article  Google Scholar

  4. [4]

    Hill, R. T.; Mock, J. J.; Hucknall, A.; Wolter, S. D.; Jokerst, N. M.; Smith, D. R.; Chilkoti, A. Plasmon ruler with angstrom length resolution. ACS Nano 2012, 6, 9237–9246.

    CAS  Article  Google Scholar

  5. [5]

    Zhang, J.; Fu, Y.; Chowdhury, M. H.; Lakowicz, J. R. Metal-enhanced single-molecule fluorescence on silver particle monomer and dimer: Coupling effect between metal particles. Nano Lett. 2007, 7, 2101–2107.

    CAS  Article  Google Scholar

  6. [6]

    Lim, D. K.; Jeon, K. S.; Kim, H. M.; Nam, J. M.; Suh, Y. D. Nanogap-engineerable Raman-active nanodumbbells for single-molecule detection. Nat Mater. 2010, 9, 60–67.

    CAS  Article  Google Scholar

  7. [7]

    Taminiau, T. H.; Stefani, F. D.; Segerink, F. B.; Van Hulst, N. F. Optical antennas direct single-molecule emission. Nat Photonics 2008, 2, 234- 237.

    CAS  Article  Google Scholar

  8. [8]

    Bek, A.; Jansen, R.; Ringler, M.; Mayilo, S.; Klar, T. A.; Feldmann, J. Fluorescence enhancement in hot spots of AFM-designed gold nanoparticle sandwiches. Nano Lett. 2008, 8, 485–490.

    CAS  Article  Google Scholar

  9. [9]

    Ding, B. Q.; Deng, Z. T.; Yan, H.; Cabrini, S.; Zuckermann, R. N.; Bokor, J. Gold nanoparticle self-similar chain structure organized by DNA origami. J Am Chem Soc. 2010, 132, 3248–3249.

    CAS  Article  Google Scholar

  10. [10]

    Zhou, C.; Duan, X. Y.; Liu, N. A plasmonic nanorod that walks on DNA origami. Nat Commun. 2015, 6, 8102.

    CAS  Article  Google Scholar

  11. [11]

    Kuzyk, A.; Schreiber, R.; Fan, Z. Y.; Pardatscher, G.; Roller, E. M.; Högele, A.; Simmel, F. C.; Govorov, A. O.; Liedl, T. DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 2012, 483, 311–314.

    CAS  Article  Google Scholar

  12. [12]

    Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440, 297–302.

    CAS  Article  Google Scholar

  13. [13]

    Zanacchi, F. C.; Manzo, C.; Alvarez, A. S.; Derr, N. D.; Garcia-Parajo, M. F.; Lakadamyali, M. A DNA origami platform for quantifying protein copy number in super-resolution. Nat Methods 2017, 14, 789–792.

    CAS  Article  Google Scholar

  14. [14]

    Hudoba, M. W.; Luo, Y.; Zacharias, A.; Poirier, M. G.; Castro, C. E. Dynamic DNA origami device for measuring compressive depletion forces. ACS Nano 2017, 11, 6566–6573.

    CAS  Article  Google Scholar

  15. [15]

    Hong, F.; Zhang, F.; Liu, Y.; Yan, H. DNA origami: Scaffolds for creating higher order structures. Chem Rev. 2017, 11 7, 12584–12640.

    Google Scholar

  16. [16]

    Jiang, Q.; Song, C.; Nangreave, J.; Liu, X. W.; Lin, L.; Qiu, D. L.; Wang, Z. G.; Zou, G. Z.; Liang, X. J.; Yan, H. et al. DNA origami as a carrier for circumvention of drug resistance. J Am Chem Soc. 2012, 134, 13396- 13403.

    CAS  Article  Google Scholar

  17. [17]

    Hemmig, E. A.; Fitzgerald, C.; Maffeo, C.; Hecker, L.; Ochmann, S. E.; Aksimentiev, A.; Tinnefeld, P.; Keyser, U. F. Optical voltage sensing using DNA origami. Nano Lett. 2018, 18, 1962–1971.

    CAS  Article  Google Scholar

  18. [18]

    Marini, M.; Piantanida, L.; Musetti, R.; Bek, A.; Dong, M. D.; Besenbacher, F.; Lazzarino, M.; Firrao, G. A revertible, autonomous, self-assembled DNA-origami nanoactuator. Nano Lett. 2011, 11, 5449- 5454.

    CAS  Article  Google Scholar

  19. [19]

    Torelli, E.; Marini, M.; Palmano, S.; Piantanida, L.; Polano, C.; Scarpellini, A.; Lazzarino, M.; Firrao, G. A DNA origami nanorobot controlled by nucleic acid hybridization. Small 2014, 10, 2918–2926.

    CAS  Article  Google Scholar

  20. [20]

    Prinz, J.; Schreiber, B.; Olejko, L.; Oertel, J.; Rackwitz, J.; Keller, A.; Bald, I. DNA origami substrates for highly sensitive surface-enhanced Raman scattering. J Phys Chem Lett. 2013, 4, 4140–4145.

    CAS  Article  Google Scholar

  21. [21]

    Acuna, G. P.; Möller, F. M.; Holzmeister, P.; Beater, S.; Lalkens, B.; Tinnefeld, P. Fluorescence enhancement at docking sites of DNA-directed self-assembled nanoantennas. Science 2012, 338, 506–510.

    CAS  Article  Google Scholar

  22. [22]

    Piantanida, L.; Naumenko, D.; Lazzarino, M. Highly efficient gold nanoparticle dimer formation via DNA hybridization. RSC Adv. 2014, 4, 15281–15287.

    CAS  Article  Google Scholar

  23. [23]

    Sönnichsen, C.; Reinhard, B. M.; Liphardt, J.; Alivisatos, A. P. A molecular ruler based on plasmon coupling of single gold and silver nanoparticles. Nat Biotechnol. 2005, 23, 741–745.

    Article  Google Scholar

  24. [24]

    Kuzyk, A.; Urban, M. J.; Idili, A.; Ricci, F.; Liu, N. Selective control of reconfigurable chiral plasmonic metamolecules. Sci Adv. 2017, 3, e1602803.

    Article  Google Scholar

  25. [25]

    Zhou, C.; Xin, L.; Duan, X. Y.; Urban, M. J.; Liu, N. Dynamic plasmonic system that responds to thermal and aptamer-target regulations. Nano Lett. 2018, 18, 7395–7399.

    CAS  Article  Google Scholar

  26. [26]

    Schreiber, R.; Luong, N.; Fan, Z. Y.; Kuzyk, A.; Nickels, P. C.; Zhang, T.; Smith, D. M.; Yurke, B.; Kuang, W.; Govorov, A. O. et al. Chiral plasmonic DNA nanostructures with switchable circular dichroism. Nat Commun. 2013, 4, 2948.

  27. [27]

    Piantanida, L.; Naumenko, D.; Torelli, E.; Marini, M.; Bauer, D. M.; Fruk, L.; Firrao, G.; Lazzarino, M. Plasmon resonance tuning using DNA origami actuation. Chem Commun. 2015, 51, 4789–4792.

    CAS  Article  Google Scholar

  28. [28]

    Kim, D. N.; Kilchherr, F.; Dietz, H.; Bathe, M. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res. 2012, 40, 2862–2868.

    CAS  Article  Google Scholar

  29. [29]

    Castro, C. E.; Kilchherr, F.; Kim, D. N.; Shiao, E. L.; Wauer, T.; Wortmann, P.; Bathe, M.; Dietz, H. A primer to scaffolded DNA origami. Nat Methods 2011, 8, 221–229.

    CAS  Article  Google Scholar

  30. [30]

    Masciotti, V.; Naumenko, D.; Lazzarino, M.; Piantanida, L. Tuning gold nanoparticles plasmonic properties by DNA nanotechnology. In DNA Nanotechnology: Methods and Protocols. Zuccheri, G., Ed.; Springer: New York, N Y, 2018; pp 279–297.

    Chapter  Google Scholar

  31. [31]

    Dubochet, J.; Adrian, M.; Chang, J. J.; Homo, J. C.; Lepault, J.; McDowall, A. W.; Schultz, P. Cryo-electron microscopy of vitrified specimens. Quart Rev Biophys. 1988, 21, 129–228.

    CAS  Article  Google Scholar

  32. [32]

    Glaeser, R. M. Retrospective: Radiation damage and its associated "information limitations". J Struct Biol. 2008, 163, 271–276.

    CAS  Article  Google Scholar

  33. [33]

    Lei, D. S.; Marras, A. E.; Liu, J. F.; Huang, C. M.; Zhou, L. F.; Castro, C. E.; Su, H. J.; Ren, G. Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography. Nat Commun. 2018, 9, 592.

  34. [34]

    Zhang, L.; Lei, D. S.; Smith, J. M.; Zhang, M.; Tong, H. M.; Zhang, X.; Lu, Z. Y.; Liu, J. K.; Alivisatos, A. P.; Ren, G. Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography. Nat Commun. 2016, 7, 11083.

  35. [35]

    Amenitsch, H.; Rappolt, M.; Kriechbaum, M.; Mio, H.; Laggner, P.; Bernstorff, S. First performance assessment of the small-angle X-ray scattering beamline at ELETTRA. J Synchrotron Radiat. 1998, 5, 506- 508.

    CAS  Article  Google Scholar

  36. [36]

    Bernstorff, S.; Amenitsch, H.; Laggner, P. High-throughput asymmetric double-crystal monochromator of the SAXS beamline at ELETTRA. J Synchrotron Radiat. 1998, 5, 1215–1221.

    CAS  Article  Google Scholar

  37. [37]

    Forget, A.; Pique, R. A.; Ahmadi, V.; Lüdeke, S.; Shastri, V. P. Mechanically tailored agarose hydrogels through molecular alloying with β-sheet polysaccharides. Macromol Rapid Commun. 2015, 36, 196–203.

    CAS  Article  Google Scholar

  38. [38]

    Rüther, A.; Forget, A.; Roy, A.; Carballo, C.; Mießmer, F.; Dukor, R. K.; Nafie, L. A.; Johannessen, C.; Shastri, V. P.; Lüdeke, S. Unravelling a direct role for polysaccharide β-strands in the higher order structure of physical hydrogels. Angew Chem., Int Ed. 2017, 56, 4603–4607.

    Article  Google Scholar

  39. [39]

    Mie, G. Beiträge zur Optik trüber Medien, speziell kolloidaler Metallösungen. Ann Phys. 1908, 330, 377–445.

    Article  Google Scholar

  40. [40]

    García De Abajo, F. J. Multiple scattering of radiation in clusters of dielectrics. Phys Rev B 1999, 60, 6086–6102.

    Article  Google Scholar

  41. [41]

    Myroshnychenko, V.; Rodríguez-Fernández, J.; Pastoriza-Santos, I.; Funston, A. M.; Novo, C.; Mulvaney, P.; Liz-Marzán, L. M.; García De Abajo, F. J. Modelling the optical response of gold nanoparticles. Chem Soc Rev. 2008, 37, 1792–1805.

    CAS  Article  Google Scholar

  42. [42]

    Walsh, A. S.; Yin, H. F.; Erben, C. M.; Wood, M. J. A.; Turberfield, A. J. DNA cage delivery to mammalian cells. ACS Nano 2011, 5, 5427–5432.

    CAS  Article  Google Scholar

  43. [43]

    Lee, H.; Lytton-Jean, A. K. R.; Chen, Y.; Love, K. T.; Park, A. I.; Karagiannis, E. D.; Sehgal, A.; Querbes, W.; Zurenko, C. S.; Jayaraman, M. et al. Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery. Nat Nanotechnol. 2012, 7, 389–393.

    CAS  Article  Google Scholar

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Acknowledgements

V. M. acknowledges financial support from MIUR (MIUR Giovani-Ambito "Salute dell'uomo"). Work at the Molecular Foundry, under the research project No. 3376, was supported by the Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. We acknowledge the Facility of Nanofabrication (FNF) of IOM for the support in sample preparation, Simone Dal Zilio and Silvio Greco for help in data analysis and stimulating discussions. We acknowledge Prof. Giuseppe Firrao for valuable comments and inspiring ideas, the NanoInnovation laboratory (Elettra Sincrotrone) for suggestion provided for AFM analysis and the BioLab (Elettra Sincrotrone) for the use of lab and instrumentation.

Author information

Author notes

  1. Luca Piantanida

    Present address: Present address: Micron School of Materials Science & Engineering, Boise State University, Boise, ID, 83725, USA

Affiliations

  1. CNR-IOM, AREA Science Park, Basovizza Trieste, I-34149, Italy

    Valentina Masciotti, Luca Piantanida, Denys Naumenko & Marco Lazzarino

  2. PhD Course in Nanotechnology, University of Trieste, Trieste, I-34127, Italy

    Valentina Masciotti

  3. Institute for Physics of Semiconductors, National Academy of Sciences of Ukraine, Kyiv, 03028, Ukraine

    Denys Naumenko

  4. Institute of Inorganic Chemistry, Graz University of Technology, Graz, A-8010, Austria

    Heinz Amenitsch

  5. Materials Research Laboratory, University of Nova Gorica, Nova Gorica, SI-5000, Slovenia

    Mattia Fanetti & Matjaž Valant

  6. Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China

    Matjaž Valant

  7. The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

    Dongsheng Lei & Gang Ren

  8. School of Physical Science and Technology, Electron Microscopy Center of LZU, Lanzhou University, Lanzhou, 730000, China

    Dongsheng Lei

Corresponding authors

Correspondence to Valentina Masciotti or Marco Lazzarino.

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Masciotti, V., Piantanida, L., Naumenko, D. et al. A DNA origami plasmonic sensor with environment-independent read-out. Nano Res. 12, 2900–2907 (2019). https://doi.org/10.1007/s12274-019-2535-0

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  • DOI : https://doi.org/10.1007/s12274-019-2535-0

Keywords

  • DNA origami
  • plasmonic sensor
  • molecular detection
  • gold nanoparticle

A Dna Origami Plasmonic Sensor With Environment-independent Read-ou

Source: https://link.springer.com/article/10.1007/s12274-019-2535-0

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