Skip to main content Accessibility help
Hostname: page-component-7d8f8d645b-r82c8 Total loading time: 0 Render date: 2023-05-28T14:36:47.980Z Has data issue: false Feature Flags: { "useRatesEcommerce": true } hasContentIssue false

14 - DNA nanotechnology organizing other materials

Published online by Cambridge University Press:  05 December 2015

Nadrian C. Seeman
New York University
Get access


The initial goals of structural DNA nanotechnology did not stop with the organization of nucleic acid molecules into interesting and attractive shapes, or into lattices. The very first paper in the field had the goal of organizing other molecules into 3D periodic arrays, with the hope that if they were well enough ordered those guest molecules would be susceptible to crystallographic diffraction analysis. Figure 14-1 illustrates this point, where the DNA scaffold is shown in magenta and the guest macromolecule is drawn in turquoise. This motivating goal has yet to be realized in practice, but efforts continue, nearly 35 years after its initial proposal: it is truly a holy grail of structural DNA nanotechnology.

Indeed, one of the earliest subsequent papers suggested that DNA could be used to organize the components of nanoelectronics. Figure 14-2 shows two branched junctions forming a metallic “synapse” from two molecular wires, and Figure 14-3 shows the proposed 3D organization of a 107 Å3 memory element. The structures of the 4-arm and 6-arm junctions illustrated there are not particularly realistic, but the notion that DNA could scaffold the spatial organization other species of molecules was reinforced by these suggestions. As we will see below, the organization of nanoelectronic components by DNA remains an attractive goal.

Control of polymer topology. One of the earliest attempts involving nucleic acids and heteromolecules entails the use of DNA to direct the topology of industrial polymers. The initial experiments in this program entailed hanging alternating pendent diamino and dicarboxyl groups off the 2′ position of RNA molecules (the atom furthest from the helix axis in A-form RNA) so as to direct their topology. Although novel topological species have not yet been produced by this approach, this system has been used to demonstrate the templated 2′, 2′ ligation of nucleic acids that produces a peptide bond. Likewise, it has been used to generate topological targets with connectivity parallel to the helix axis. The catenane produced by joining one amine with one carboxyl group is illustrated in Figure 14-4.

Metallic nanoparticles. The advent of metallic and semiconducting nanoparticles has spurred a lot of effort to organize them by DNA. Very early attempts to assemble nanoparticle clusters were performed by Alivisatos and his colleagues, as well as by Mirkin and his collaborators. These approaches fundamentally used DNA as “smart glue” to put DNA-coated nanoparticles together.

Publisher: Cambridge University Press
Print publication year: 2016

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)


14.1 Seeman, N.C., Nucleic Acid Junctions and Lattices. J. Theor. Biol. 99, 237–247 (1982).CrossRefGoogle ScholarPubMed
14.2 Robinson, B.H., Seeman, N.C., The Design of a Biochip: A Self-Assembling Molecular-Scale Memory Device. Protein Eng. 1, 295–300 (1987).CrossRefGoogle ScholarPubMed
14.3 Rosenberg, J.M, Seeman, N.C., Day, R.O., Rich, A., RNA Double Helices Derived from Studies of Small Fragments. Biochem. Biophys. Res. Comm. 69, 979–987 (1976).Google Scholar
14.4 Zhu, L., Lukeman, P.S., Canary, J., Seeman, N.C., Nylon/DNA: Single-Stranded DNA with Covalently Stitched Nylon Lining. J. Am. Chem. Soc. 125, 10178–10179 (2003).CrossRefGoogle ScholarPubMed
14.5 Liu, Y., Sha, R., Wang, R., Ding, L., Canary, J.W., Seeman, N.C., 2′, 2′-Ligation Demonstrates the Thermal Dependence of DNA-Directed Positional Control. Tetrahedron 64, 9417–8422 (2008).CrossRefGoogle ScholarPubMed
14.6 Liu, Y., Kuzuya, A., Sha, R., Guillaume, J., Wang, R., Canary, J.W., Seeman, N.C., Coupling Across a DNA Helical Turn Yields a Hybrid DNA/Organic Catenane Doubly Tailed with Functional Termini. J. Am. Chem. Soc. 130, 10882–10883 (2008).CrossRefGoogle ScholarPubMed
14.7 Alivisatos, A.P., Johnsson, K.P., Peng, X.G., Wilson, T.E., Loweth, C.J., Bruchez, M.P., Schultz, P.G., Organization of “Nanocrystal Molecules” using DNA. Nature 382, 609–611 (1996).CrossRefGoogle Scholar
14.8 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).CrossRefGoogle ScholarPubMed
14.9 Xiao, S., Liu, F., Rosen, A., Hainfeld, J.F., Seeman, N.C., Musier-Forsyth, K.M., Kiehl, R.A., Self-Assembly of Nanoparticle Arrays by DNA Scaffolding. J. Nanoparticle Res. 4, 313–317 (2002).CrossRefGoogle Scholar
14.10 Pinto, Y.Y., Le, J.D., Seeman, N.C., Musier-Forsyth, K., Taton, T.A., Kiehl, R. A., Sequence-Encoded Self-Assembly of Multiple-Nanocomponent Arrays by 2D DNA Scaffolding. Nano Letters 5, 2399–2402 (2005).CrossRefGoogle ScholarPubMed
14.11 Zheng, J., Constantinou, P.E., Micheel, C., Alivisatos, A.P., Kiehl, R.A., Seeman, N.C., 2D Nanoparticle Arrays Show the Organizational Power of Robust DNA Motifs. Nano Letters 6, 1502–1504 (2006).CrossRefGoogle Scholar
14.12 Zanchet, D., Micheel, C.M., Parak, W.J., Gerion, D., Alivisatos, A.P., Electrophoretic Isolation of Discrete Nanocrystal/DNA Conjugates. Nano Letters 1, 32–35 (2001).CrossRefGoogle Scholar
14.13 Lau, K.L., Hamblin, G.D., Sleiman, H.F., Gold-Nanoparticle 3D Building Blocks: High Purity Preparation and Use for Modular Access to Nanoparticle Assemblies. Small 10, 660–666 (2014).CrossRefGoogle ScholarPubMed
14.14 Sharma, J., Chhabra, R., Cheng, A., Brownell, J., Liu, Y., Yan, H., Control of Self-Assembly of DNA Tubules Through Integration of Gold Nanoparticles. Science 323, 112–116 (2009).CrossRefGoogle ScholarPubMed
14.15 Deng, Z., Samanta, A., Nangreave, J., Yan, H., Liu, Y., Robust DNA-Functionalized Core/Shell Quantum Dots with Fluorescent Emission Spanning from UV-Vis to Near-IR and Compatible with DNA-Directed Self-Assembly. J. Am. Chem. Soc. 134, 17424–17427 (2012).CrossRefGoogle ScholarPubMed
14.16 Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., LaBean, T.H., DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires. Science 301, 1882–1884 (2003).CrossRefGoogle ScholarPubMed
14.17 Wang, D., Capehart, S.L., Pal, S., Liu, M., Zhang, L., Shuck, P.J., Liu, Y., Yan, H., Francis, M.B., Yoreo, J.J. De, et al., Hierchical Assembly of Plasmonic Nanostructures Using Virus Capsid Scaffolds on DNA Origami Templates. ACS Nano 8, 7896–7904 (2014).Google Scholar
14.18 Yang, H., Metera, K.L., Sleiman, H.F., DNA Modified with Metal Complexes: Applications in the Construction of Higher-Order Metal DNA-Nanostructures. Coord. Chem. Revs. 254, 2403–2415 (2010).CrossRefGoogle Scholar
14.19 Takezawa, Y., Shionoya, M., Metal-Mediated DNA Base Pairing: Alternatives to Hydrogen-Bonded Watson–Crick Base Pairs. Acc. Chem. Res. 45, 2066–2076 (2012).CrossRefGoogle ScholarPubMed
14.20 Douglas, S.M., Bachelet, I., Church, G.M., A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads. Science 335, 831–834 (2012).CrossRefGoogle ScholarPubMed
14.21 Curl, R.F., Smalley, R.E., Probing C60. Science 242, 1017–1022 (1988).CrossRefGoogle ScholarPubMed
14.22 Ajayan, P.M., Iijima, S., Smallest Carbon Nanotube. Nature 358, 23 (1992).CrossRefGoogle Scholar
14.23 Maune, H.T., Han, S.P., Barish, R.D., Bockrath, M., Goddard, W.A., Rothemund, P.W.K., Winfree, E., Self-Assembly of Carbon Nanotubes into Two-Dimensional Geometries Using DNA Origami Templates. Nature Nanotech. 5, 61–66 (2010).CrossRefGoogle ScholarPubMed
14.24 Park, S.Y., Lytton-Jean, A. K.-R., Lee, B., Weigand, S., Schatz, G.C., Mirkin, C.A., DNA-Programmable Nanoparticle Crystallization. Nature 451, 553–556 (2008).CrossRefGoogle ScholarPubMed
14.25 Nykypanchuk, D., Maye, M.M., Lelie, D. van der, Gang, O., DNA-Guided Crystallization of Colloidal Nanoparticles. Nature 451, 549–552 (2008).CrossRefGoogle ScholarPubMed
14.26 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 Nanotech. 5, 116–120 (2010).CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the or variations. ‘’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats