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Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles


DNA nanotechnology offers unparalleled precision and programmability for the bottom-up organization of materials. This approach relies on pre-assembling a DNA scaffold, typically containing hundreds of different strands, and using it to position functional components. A particularly attractive strategy is to employ DNA nanostructures not as permanent scaffolds, but as transient, reusable templates to transfer essential information to other materials. To our knowledge, this approach, akin to top-down lithography, has not been examined. Here we report a molecular printing strategy that chemically transfers a discrete pattern of DNA strands from a three-dimensional DNA structure to a gold nanoparticle. We show that the particles inherit the DNA sequence configuration encoded in the parent template with high fidelity. This provides control over the number of DNA strands and their relative placement, directionality and sequence asymmetry. Importantly, the nanoparticles produced exhibit the site-specific addressability of DNA nanostructures, and are promising components for energy, information and biomedical applications.

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Figure 1: An overview of the template-guided pattern transfer.
Figure 2: Pattern transfer using a cubic scaffold.
Figure 3: Introduction of geometric diversity via the template.
Figure 4: Introduction of sequence asymmetry to the patterning.
Figure 5: Microscopy analysis of the patterned AuNP self-assembly.
Figure 6: Fluorescence investigation of asymmetric patterning.


  1. 1

    Mirkin, C. A., Letsinger, R. L., Mucic, R. C. & Storhoff, J. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607–609 (1996).

    CAS  Google Scholar 

  2. 2

    Alivisatos, A. P. et al. Organization of ‘nanocrystal molecules’ using DNA. Nature 382, 609–611 (1996).

    CAS  Google Scholar 

  3. 3

    Tan, S. J., Campolongo, M. J., Luo, D. & Cheng, W. Building plasmonic nanostructures with DNA. Nature Nanotechnol. 6, 268–276 (2011).

    CAS  Google Scholar 

  4. 4

    Barrow, S. J., Funston, A. M., Wei, X. & Mulvaney, P. DNA-directed self-assembly and optical properties of discrete 1D, 2D and 3D plasmonic structures. Nano Today 8, 138–167 (2013).

    CAS  Google Scholar 

  5. 5

    Elghanian, R., Storhoff, J. J., Mucic, R. C., Letsinger, R. L. & Mirkin, C. A. Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277, 1078–1081 (1997).

    CAS  Google Scholar 

  6. 6

    Park, S. Y. et al. DNA-programmable nanoparticle crystallization. Nature 451, 553–556 (2008).

    CAS  Google Scholar 

  7. 7

    Nykypanchuk, D., Maye, M. M., van der Lelie, D. & Gang, O. DNA-guided crystallization of colloidal nanoparticles. Nature 451, 549–552 (2008).

    CAS  Google Scholar 

  8. 8

    Maye, M. M., Kumara, M. T., Nykypanchuk, D., Sherman, W. B. & Gang, O. Switching binary states of nanoparticle superlattices and dimer clusters by DNA strands. Nature Nanotechnol. 5, 116–120 (2010).

    CAS  Google Scholar 

  9. 9

    Auyeung, E. et al. DNA-mediated nanoparticle crystallization into Wulff polyhedra. Nature 505, 73–77 (2014).

    Google Scholar 

  10. 10

    Macfarlane, R. J., O'Brien, M. N., Petrosko, S. H. & Mirkin, C. A. Nucleic acid-modified nanostructures as programmable atom equivalents: forging a new ‘Table of Elements’. Angew. Chem. Int. Ed. 52, 5688–5698 (2013).

    CAS  Google Scholar 

  11. 11

    Loweth, C. J., Caldwell, W. B., Peng, X., Alivisatos, A. P. & Schultz, P. G. DNA-based assembly of gold nanocrystals. Angew. Chem. Int. Ed. 38, 1808–1812 (1999).

    CAS  Google Scholar 

  12. 12

    Aldaye, F. A. & Sleiman, H. F. Sequential self-assembly of a DNA hexagon as a template for the organization of gold nanoparticles. Angew. Chem. Int. Ed. 45, 2204–2209 (2006).

    CAS  Google Scholar 

  13. 13

    Aldaye, F. A. & Sleiman, H. F. Dynamic DNA templates for discrete gold nanoparticle assemblies: control of geometry, modularity, write/erase and structural switching. J. Am. Chem. Soc. 129, 4130–4131 (2007).

    CAS  Google Scholar 

  14. 14

    Li, H., Park, S. H., Reif, J. H., LaBean, T. H. & Yan, H. DNA-templated self-assembly of protein and nanoparticle linear arrays. J. Am. Chem. Soc. 126, 418–419 (2003).

    Google Scholar 

  15. 15

    Le, J. D. et al. DNA-templated self-assembly of metallic nanocomponent arrays on a surface. Nano Lett. 4, 2343–2347 (2004).

    CAS  Google Scholar 

  16. 16

    Zhang, J., Liu, Y., Ke, Y. & Yan, H. Periodic square-like gold nanoparticle arrays templated by self-assembled 2D DNA nanogrids on a surface. Nano Lett. 6, 248–251 (2006).

    CAS  Google Scholar 

  17. 17

    Sharma, J. et al. Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323, 112–116 (2009).

    CAS  PubMed Central  PubMed  Google Scholar 

  18. 18

    Chen, W. et al. Nanoparticle superstructures made by polymerase chain reaction: collective interactions of nanoparticles and a new principle for chiral materials. Nano Lett. 9, 2153–2159 (2009).

    CAS  Google Scholar 

  19. 19

    Mastroianni, A. J., Claridge, S. A. & Alivisatos, A. P. Pyramidal and chiral groupings of gold nanocrystals assembled using DNA scaffolds. J. Am. Chem. Soc. 131, 8455–8459 (2009).

    CAS  PubMed Central  PubMed  Google Scholar 

  20. 20

    Lau, K. L., Hamblin, G. D. & Sleiman, H. F. Gold nanoparticle 3D-DNA building blocks: high purity preparation and use for modular access to nanoparticle assemblies. Small 10, 660–666 (2014).

    CAS  Google Scholar 

  21. 21

    Ding, B. et al. Gold nanoparticle self-similar chain structure organized by DNA origami. J. Am. Chem. Soc. 132, 3248–3249 (2010).

    CAS  Google Scholar 

  22. 22

    Shen, X. et al. Rolling up gold nanoparticle-dressed DNA origami into three-dimensional plasmonic chiral nanostructures. J. Am. Chem. Soc. 134, 146–149 (2011).

    Google Scholar 

  23. 23

    Pal, S. et al. DNA directed self-assembly of anisotropic plasmonic nanostructures. J. Am. Chem. Soc. 133, 17606–17609 (2011).

    CAS  Google Scholar 

  24. 24

    Kuzyk, A. et al. DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483, 311–314 (2012).

    CAS  Google Scholar 

  25. 25

    Shen, X. et al. Three-dimensional plasmonic chiral tetramers assembled by DNA origami. Nano Lett. 13, 2128–2133 (2013).

    CAS  Google Scholar 

  26. 26

    Surwade, S. P. et al. Nanoscale growth and patterning of inorganic oxides using DNA nanostructure templates. J. Am. Chem. Soc. 135, 6778–6781 (2013).

    CAS  Google Scholar 

  27. 27

    Halverson, J. D. & Tkachenko, A. V. DNA-programmed mesoscopic architecture. Phys. Rev. E 87, 062310 (2013).

    Google Scholar 

  28. 28

    Kim, J.-W. & Deaton, R. Molecular self-assembly of multifunctional nanoparticle composites with arbitrary shapes and functions: challenges and strategies. Part. Part. Syst. Char. 30, 117–132 (2013).

    CAS  Google Scholar 

  29. 29

    Zhang, T., Yang, Z. & Liu, D. DNA discrete modified gold nanoparticles. Nanoscale 3, 4015–4021 (2011).

    CAS  Google Scholar 

  30. 30

    Suzuki, K., Hosokawa, K. & Maeda, M. Controlling the number and positions of oligonucleotides on gold nanoparticle surfaces. J. Am. Chem. Soc. 131, 7518–7519 (2009).

    CAS  PubMed  Google Scholar 

  31. 31

    Zhang, T. et al. DNA bimodified gold nanoparticles. Langmuir 28, 1966–1970 (2011).

    PubMed  Google Scholar 

  32. 32

    Zhang, C., Ma, J., Yang, J., Liu, S. & Xu, J. Binding assistance triggering attachments of hairpin DNA onto gold nanoparticles. Anal. Chem. 85, 11973–11978 (2013).

    CAS  PubMed  Google Scholar 

  33. 33

    Wang, Y. et al. Colloids with valence and specific directional bonding. Nature 491, 51–55 (2012).

    CAS  PubMed  Google Scholar 

  34. 34

    Xu, X., Rosi, N. L., Wang, Y., Huo, F. & Mirkin, C. A. Asymmetric functionalization of gold nanoparticles with oligonucleotides. J. Am. Chem. Soc. 128, 9286–9287 (2006).

    CAS  PubMed Central  PubMed  Google Scholar 

  35. 35

    Maye, M. M., Nykypanchuk, D., Cuisinier, M., van der Lelie, D. & Gang, O. Stepwise surface encoding for high-throughput assembly of nanoclusters. Nature Mater. 8, 388–391 (2009).

    CAS  Google Scholar 

  36. 36

    Feng, L., Dreyfus, R., Sha, R., Seeman, N. C. & Chaikin, P. M. DNA patchy particles. Adv. Mater. 25, 2779–2783 (2013).

    CAS  PubMed  Google Scholar 

  37. 37

    Xing, H. et al. DNA-directed assembly of asymmetric nanoclusters using Janus nanoparticles. ACS Nano 6, 802–809 (2011).

    PubMed  Google Scholar 

  38. 38

    Kim, J.-W., Kim, J.-H. & Deaton, R. DNA-linked nanoparticle building blocks for programmable matter. Angew. Chem. Int. Ed. 50, 9185–9190 (2011).

    CAS  Google Scholar 

  39. 39

    Tan, L. H., Xing, H., Chen, H. & Lu, Y. Facile and efficient preparation of anisotropic DNA-functionalized gold nanoparticles and their regioselective assembly. J. Am. Chem. Soc. 135, 17675–17678 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  40. 40

    Carneiro, K. M. M., Aldaye, F. A. & Sleiman, H. F. Long-range assembly of DNA into nanofibers and highly ordered networks using a block copolymer approach. J. Am. Chem. Soc. 132, 679–685 (2010).

    CAS  Google Scholar 

  41. 41

    Edwardson, T. G. W., Carneiro, K. M. M., McLaughlin, C. K., Serpell, C. J. & Sleiman, H. F. Site-specific positioning of dendritic alkyl chains on DNA cages enables their geometry-dependent self-assembly. Nature Chem. 5, 868–875 (2013).

    CAS  Google Scholar 

  42. 42

    Hurst, S. J., Lytton-Jean, A. K. R. & Mirkin, C. A. Maximizing DNA loading on a range of gold nanoparticle sizes. Anal. Chem. 78, 8313–8318 (2006).

    CAS  PubMed Central  PubMed  Google Scholar 

  43. 43

    Li, Z., Jin, R., Mirkin, C. A. & Letsinger, R. L. Multiple thiol-anchor capped DNA-gold nanoparticle conjugates. Nucleic Acids Res. 30, 1558–1562 (2002).

    CAS  PubMed Central  PubMed  Google Scholar 

  44. 44

    McLaughlin, C. K. et al. Three-dimensional organization of block copolymers on ‘DNA- minimal’ scaffolds. J. Am. Chem. Soc. 134, 4280–4286 (2012).

    CAS  Google Scholar 

  45. 45

    Serpell, C. J., Edwardson, T. G. W., Chidchob, P., Carneiro, K. M. M. & Sleiman, H. F. Precision polymers and 3D DNA nanostructures: emergent assemblies from new parameter space. J. Am. Chem. Soc. 136, 15767–15774 (2014).

    CAS  Google Scholar 

  46. 46

    Huo, F., Lytton-Jean, A. K. R. & Mirkin, C. A. Asymmetric functionalization of nanoparticles based on thermally addressable DNA interconnects. Adv. Mater. 18, 2304–2306 (2006).

    CAS  Google Scholar 

  47. 47

    Reineck, P. et al. Distance and wavelength dependent quenching of molecular fluorescence by Au@SiO2. Core–shell nanoparticles. ACS Nano 7, 6636–6648 (2013).

    CAS  Google Scholar 

  48. 48

    De, M., Ghosh, P. S. & Rotello, V. M. Applications of nanoparticles in biology. Adv. Mater. 20, 4225–4241 (2008).

    CAS  Google Scholar 

  49. 49

    Mao, C., LaBean, T. H., Reif, J. H. & Seeman, N. C. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000).

    CAS  Google Scholar 

  50. 50

    Rothemund, P. W. K., Papadakis, N. & Winfree, E. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2, e424 (2004).

    PubMed Central  PubMed  Google Scholar 

  51. 51

    Qian, L. & Winfree, E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 332, 1196–1201 (2011).

    CAS  PubMed Central  PubMed  Google Scholar 

  52. 52

    Nikitin, M. P., Shipunova, V. O., Deyev, S. M. & Nikitin, P. I. Biocomputing based on particle disassembly. Nature Nanotechnol. 9, 716–722 (2014).

    CAS  Google Scholar 

  53. 53

    Lee, J. H., Yigit, M. V., Mazumdar, D. & Lu, Y. Molecular diagnostic and drug delivery agents based on aptamer-nanomaterial conjugates. Adv. Drug Delivery Rev. 62, 592–605 (2010).

    CAS  Google Scholar 

  54. 54

    Mallikaratchy, P. R. et al. A multivalent DNA aptamer specific for the B-cell receptor on human lymphoma and leukemia. Nucleic Acids Res. 39, 2458–2469 (2011).

    CAS  Google Scholar 

  55. 55

    Rosi, N. L. et al. Oligonucleotide-modified gold nanoparticles for intracellular gene regulation. Science 312, 1027–1030 (2006).

    CAS  Google Scholar 

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The authors acknowledge the Natural Sciences and Engineering Research Council of Canada (NSERC), the Canada Foundation for Innovation, the Centre for Self-Assembled Chemical Structures and the Canada Research Chairs Program for financial support. T.G.W.E. thanks the Canadian Institutes of Health Research for a Drug Development Training Program scholarship. D.B. thanks the NSERC for a Bionano scholarship and C.J.S. thanks the NSERC for a Banting Postdoctoral Fellowship. H.F.S. is a Cottrell Scholar of the Research Corporation.

Author information




H.F.S. and T.G.W.E. designed the project. T.G.W.E. primarily contributed to the production of experimental results. K.L.L. carried out the synthesis of gold nanoparticles, TEM analysis, preparation of patterned AuNPs for the fluorescence studies and aided in data interpretation. D.B. carried out all the DLS experiments. C.J.S. synthesized the clip strands TC3-AB, PC4-AB and PC5-AB. All the authors have agreed to all the content of the manuscript.

Corresponding author

Correspondence to Hanadi F. Sleiman.

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The authors declare no competing financial interests.

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Edwardson, T., Lau, K., Bousmail, D. et al. Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles. Nature Chem 8, 162–170 (2016).

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