Abstract
Programed molecular structures allow us to research and make use of physical, chemical, and biological effects at the nanoscale. They are an example of the “bottom-up” approach to nanotechnology, with structures forming through self-assembly. DNA is a particularly useful molecule for this purpose, and some of its advantages include parallel (as opposed to serial) assembly, naturally occurring “tools,” such as enzymes and proteins for making modifications and attachments, and structural dependence on base sequence. This allows us to develop one, two, and three dimensional structures that are interesting for their fundamental physical and chemical behavior, and for potential applications such as biosensors, medical diagnostics, molecular electronics, and efficient light-harvesting systems. We describe five techniques that allow one to assemble and image such structures: concentration measurement by ultraviolet absorption, titration gel electrophoresis, thermal annealing, fluorescence microscopy, and atomic force microscopy in fluids.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Pelesko, J. A. (2007) Self Assembly: The Science of Things That Put Themselves Together, Chapman & Hall/CRC.
Zheng, J. W., Lukeman, P. S., Sherman, W. B., Micheel, C., Alivisatos, A. P., Constantinou, P. E., and Seeman, N. C. (2008) Metallic Nanoparticles Used to Estimate the Structural Integrity of DNA Motifs, Biophys. J. 95, 3340–3348.
Green, S. J., Bath, J., and Turberfield, A. J. (2008) Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion, Phys. Rev. Lett. 101.
Dirks, R. M., Bois, J. S., Schaeffer, J. M., Winfree, E., and Pierce, N. A. (2007) Thermodynamic Analysis of Interacting Nucleic Acid Strands, SIAM Review 49, 65–88.
Seelig, G., Soloveichik, D., Zhang, D. Y., and Winfree, E. (2006) Enzyme-Free Nucleic Acid Logic Circuits, Science 314, 1585–1588.
Zhang, D. Y., Turberfield, A. J., Yurke, B., and Winfree, E. (2007) Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA, Science 318, 1121–1125.
Liu, H. P., Chen, Y., He, Y., Ribbe, A. E., and Mao, C. D. (2006) Approaching the Limit: Can One DNA Oligonucleotide Assemble into Large Nanostructures?, Angew. Chem.-Int. Edit. 45, 1942–1945.
Soloveichik, D., Cook, M., and Winfree, E. (2008) Combining Self-Healing and Proofreading in Self-Assembly, Natural Computing 7, 203–218.
Shih, W. M., Quispe, J. D., and Joyce, G. F. (2004) A 1.7-Kilobase Single-Stranded DNA That Folds into a Nanoscale Octahedron, Nature 427, 618–621.
Rothemund, P. W. K. (2006) Folding DNA to Create Nanoscale Shapes and Patterns, Nature 440, 297–302.
Tataurov, A. V., You, Y., and Owczarzy, R. (2008) Predicting Ultraviolet Spectrum of Single Stranded and Double Stranded Deoxyribonucleic Acids, Biophys. Chem. 133, 66–70.
Lu, M., Guo, Q., Marky, L. A., Seeman, N. C., and Kallenbach, N. R. (1992) Thermodynamics of DNA Branching, J. Mol. Biol. 223, 781–789.
Zhang, C., He, Y., Chen, Y., Ribbe, A. E., and Mao, C. D. (2007) Aligning One-Dimensional DNA Duplexes into Two-Dimensional Crystals, J. Am. Chem. Soc. 129, 14134-+.
He, Y., Chen, Y., Liu, H. P., Ribbe, A. E., and Mao, C. D. (2005) Self-Assembly of Hexagonal DNA Two-Dimensional (2d) Arrays, J. Am. Chem. Soc. 127, 12202–12203.
He, Y., Ye, T., Su, M., Zhang, C., Ribbe, A. E., Jiang, W., and Mao, C. D. (2008) Hierarchical Self-Assembly of DNA into Symmetric Supramolecular Polyhedra, Nature 452, 198–U141.
Breslauer, K. J., Frank, R., Blocker, H., and Marky, L. A. (1986) Predicting DNA Duplex Stability from the Base Sequence, Proc. Natl. Acad. Sci. U. S. A. 83, 3746–3750.
Sugimoto, N., Nakano, S., Yoneyama, M., and Honda, K. (1996) Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes, Nucleic Acids Research 24, 4501–4505.
SantaLucia, J., Allawi, H. T., and Seneviratne, A. (1996) Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability, Biochemistry 35, 3555–3562.
Jungmann, R., Liedl, T., Sobey, T. L., Shih, W., and Simmel, F. C. (2008) Isothermal Assembly of DNA Origami Structures Using Denaturing Agents, J. Am. Chem. Soc. 130, 10062–10063.
Doyle, P. S., Ladoux, B., and Viovy, J. L. (2000) Dynamics of a Tethered Polymer in Shear Flow, Phys. Rev. Lett. 84, 4769–4772.
Acknowledgments
The authors sincerely thank Helene Budjarek for her technical expertise and assistance, and Rob Fee and Ralf Jungmann for helpful discussions. The authors acknowledge financial support from the Center for Nanoscience (Ludwig-Maximilian-Universität, Germany), the International Doctorate Program NanoBioTechnology (Elite Network of Bavaria), and the Nanosystems Initiative Munich.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Sobey, T.L., Simmel, F.C. (2011). Protocols for Self-Assembly and Imaging of DNA Nanostructures. In: Zuccheri, G., Samorì, B. (eds) DNA Nanotechnology. Methods in Molecular Biology, vol 749. Humana Press. https://doi.org/10.1007/978-1-61779-142-0_2
Download citation
DOI: https://doi.org/10.1007/978-1-61779-142-0_2
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-141-3
Online ISBN: 978-1-61779-142-0
eBook Packages: Springer Protocols