Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-745bb68f8f-grxwn Total loading time: 0 Render date: 2025-02-05T18:03:31.620Z Has data issue: false hasContentIssue false

2 - The design of DNA sequences for branched systems

Published online by Cambridge University Press:  05 December 2015

Nadrian C. Seeman
Nadrian C. Seeman
Affiliation:
New York University
Get access

Summary

Structural DNA nanotechnology rests on three pillars: (1) nucleic acid hybridization, (2) facile synthesis of designed DNA sequences, and (3) the ability to design branched DNA molecules. This chapter is primarily about the third topic, but before we get into it, we should briefly discuss the other two topics. The hybridization of DNA strands is taken for granted by virtually all investigators today, but this was not always so. When the first hybridization was done in 1956 by Rich and Davies (see Chapter 1), the result was treated with skepticism, typified by the comment, “You mean [the two strands hybridize] without an enzyme?”

The first approaches to DNA nanotechnology entailed sequence design that attempted to minimize sequence symmetry in every way possible. Such sequences are not readily obtained from natural sources, so the synthesis of DNA molecules of arbitrary sequence is a sine qua non for DNA nanotechnology; the field would not exist without the phosphoramidite-based synthesis methodology developed by Caruthers and his colleagues. Fortunately, DNA synthesis has existed for about as long as needed by DNA nanotechnology: synthesis within laboratories or centralized facilities has been around since the 1980s; today it is possible to order all the DNA components needed for DNA nanotechnology, so long as they are free of complex modifications, i.e., so-called “vanilla” DNA. In addition, the biotechnology enterprise has generated demand for many variants on the theme of DNA (e.g., biotinylated molecules), and these molecules are also readily synthesized or purchased.

The details of DNA base pairing. What about branched DNA? All of us know that A pairs with T and G pairs with C. That's how biology works. However, we are not talking about biology here. We are talking about making things out of DNA that do not form readily in biological systems. What problems arise in this case? What can go wrong, and why? Are there simple solutions to the issues that arise? To answer these questions we should examine the structure of DNA in more detail, and talk about the things DNA and its components can do, so as to be sure that we can get it to do what we want it to do.

When we talk about A pairing with T and G pairing with C, we are talking about hydrogen bonded interactions.

Type
Chapter
Information
Structural DNA Nanotechnology , pp. 11 - 27
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.)

References

2.1 Rich, A., The Era of RNA Awakening: Structural Biology of RNA in the Early Years. Quart. Revs. Biophys. 42, 117–137 (2009).CrossRefGoogle ScholarPubMed
2.2 Caruthers, M.H., Gene Synthesis Machines: DNA Chemistry and its Uses. Science 230, 281–285 (1985).CrossRefGoogle ScholarPubMed
2.3 Voet, D., Rich, A., The Crystal Structures of Purines, Pyrimidines and their Intermolecular Complexes. Prog. Nucl. Acid Res. Mol. Biol. 10, 183–265 (1970).Google ScholarPubMed
2.4 Judson, H.F., The Eighth Day of Creation, New York, Simon & Schuster, p. 114 (1979).Google Scholar
2.5 Cruikshank, D.W.J., A Detailed Refinement of the Crystal and Molecular Structure of Anthracene. Acta Cryst. 9, 915–923 (1956).Google Scholar
2.6 SantaLucia, J. Jr., A Unified View of Polymer, Dumbbell and Oligonucleotide DNA Nearest-Neighbor Thermodynamics. Proc. Nat. Acad. Sci. (USA) 95, 1460–1465 (1998).CrossRefGoogle ScholarPubMed
2.7 Brown, T., Hunter, W.N., Kneale, G., Kennard, O., Molecular Structure of the G•A Base Pair in DNA and its Implications for the Mechanism of Transversion. Proc. Nat. Acad. Sci. (USA) 83, 2402–2406 (1986).CrossRefGoogle ScholarPubMed
2.8 Patel, D.J., Kozlowski, S.A., Ikuta, S., Itakura, K., Deoxyguanosine-Deoxyadenine Pairing in the d (C-G-A-G-A-A-T-T-C-G-C-G) Duplex: Conformation and Dynamics at and adjacent to the dG-dA Mismatch Site. Biochem. 23, 3207–3217 (1984).Google Scholar
2.9 Felsenfeld, G., Davies, D.R., Rich, A., Formation of a Three-Stranded Polynucleotide Molecule. J. Am. Chem. Soc. 79, 2023–2024 (1957).CrossRefGoogle Scholar
2.10 Lam, E.Y.N., Beraldi, D., Tannahill, D., Balasubramanian, S., G-Quadruplex Structures are Stable and Detectable in Human Genomic DNA. Nature Comm. 4, article 1796 (2013).CrossRefGoogle ScholarPubMed
2.11 Kallenbach, N.R., Ma, R.-I., Seeman, N.C., An Immobile Nucleic Acid Junction Constructed from Oligonucleotides. Nature 305, 829–831 (1983).CrossRefGoogle Scholar
2.12 Seeman, N.C., Nucleic Acid Junctions and Lattices. J. Theor. Biol. 99, 237–247 (1982).CrossRefGoogle ScholarPubMed
2.13 Doyle, A.C., “The Sign of Four” (first published 1890). In The Complete Sherlock Holmes, New York, The Literary Guild, p. 118 (1936).Google Scholar
2.14 Lu, M., Guo, Q., Marky, L.A., Seeman, N.C., Kallenbach, N.R., Thermodynamics of DNA Chain Branching. J. Mol. Biol. 223, 781–789 (1992).CrossRefGoogle Scholar
2.15 Seeman, N.C., Kallenbach, N.R., Design of Immobile Nucleic Acid Junctions. Biophys. J. 44, 201–209 (1983).CrossRefGoogle ScholarPubMed
2.16 Hsieh, P., Panyutin, I.G., DNA Branch Migration. In Nucleic Acids and Molecular Biology, ed. Eckstein, F., Lilley, D.M.J., 9, pp. 42–65, Berlin, Springer-Verlag (1995).CrossRefGoogle Scholar
2.17 Wang, Y., Mueller, J.E., Kemper, B., Seeman, N.C., The Assembly and Characterization of 5-Arm and 6-Arm DNA Junctions. Biochem. 30, 5667–5674 (1991).CrossRefGoogle Scholar
2.18 Wang, X., Seeman, N.C., The Assembly and Characterization of 8-Arm and 12-Arm DNA Branched Junctions. J. Am. Chem. Soc. 129, 8169–8176 (2007).Google ScholarPubMed
2.19 Kallenbach, N.R., Ma, R.-I., Wand, A.J., Veeneman, G.H., Boom, J.H. van, Seeman, N.C., Fourth Rank Immobile Nucleic Acid Junctions. J. Biomol. Struct. Dyn. 1, 158–168 (1983).CrossRefGoogle ScholarPubMed
2.20 Mirkin, S.M., Lyamichev, V.L., Drushliak, K.N., Dobrynin, V.N., Filippov, S.A., Frank-Kamenetskii, M.D., DNA H Form Requires a Homopurine-Homopyrimidine Mirror Repeat. Nature 330, 495–497 (1987).CrossRefGoogle ScholarPubMed
2.21 Htun, H., Dahlberg, J.E., Topology and Formation of Triple-Stranded H-DNA. Science 243, 1571–1576 (1989).CrossRefGoogle ScholarPubMed
2.22 Haran, T.E., Crothers, D.M., Cooperativity in A-Tract Structure and Bending Properties of Composite TnAn Blocks. Biochem. 28, 2763–2767 (1989).Google ScholarPubMed
2.23 Hud, N.V., Plavec, J., A Unified Model for the Origin of DNA Sequence-Directed Curvature. Biopolymers 69, 144–159 (2003).CrossRefGoogle ScholarPubMed
2.24 Rich, A., Nordheim, A., Wang, A.H.-J., The Chemistry and Biology of Left-Handed Z-DNA. Ann. Rev. Biochem. 53, 791–846 (1984).CrossRefGoogle ScholarPubMed
2.25 Wang, H., Du, S.M., Seeman, N.C., Tight Single-Stranded DNA Knots. J. Biomol. Struct. Dyn. 10, 853–863 (1993).CrossRefGoogle ScholarPubMed
2.26 Du, S.M., Zhang, S., Seeman, N.C., DNA Junctions, Antijunctions and Mesojunctions. Biochem. 31, 10955–10963 (1992).CrossRefGoogle ScholarPubMed
2.27 Fu, T.-J., Seeman, N.C., DNA Double Crossover Structures. Biochem. 32, 3211–3220 (1993).CrossRefGoogle Scholar
2.28 He, Y., Tian, Y., Chen, Y., Deng, Z., Ribbe, A.E., Mao, C., Sequence Symmetry as a Tool for Designing DNA Nanostructures. Angew. Chem. Int. Ed. 44, 6694–6696 (2005),CrossRefGoogle ScholarPubMed
2.29 Rothemund, P.W.K., Scaffolded DNA Origami for Nanoscale Shapes and Patterns. Nature 440, 297–302 (2006).CrossRefGoogle Scholar

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] 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 @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ 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
×