Protocols for Self-Assembly and Imaging of DNA Nanostructures

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 749)

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.

Key words

DNA Self-assembly Atomic force microscopy Fluorescence microscopy Nanostructures 

References

  1. 1.
    Pelesko, J. A. (2007) Self Assembly: The Science of Things That Put Themselves Together, Chapman & Hall/CRC.Google Scholar
  2. 2.
    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.Google Scholar
  3. 3.
    Green, S. J., Bath, J., and Turberfield, A. J. (2008) Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion, Phys. Rev. Lett. 101.Google Scholar
  4. 4.
    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.Google Scholar
  5. 5.
    Seelig, G., Soloveichik, D., Zhang, D. Y., and Winfree, E. (2006) Enzyme-Free Nucleic Acid Logic Circuits, Science 314, 1585–1588.Google Scholar
  6. 6.
    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.Google Scholar
  7. 7.
    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.Google Scholar
  8. 8.
    Soloveichik, D., Cook, M., and Winfree, E. (2008) Combining Self-Healing and Proofreading in Self-Assembly, Natural Computing 7, 203–218.Google Scholar
  9. 9.
    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.Google Scholar
  10. 10.
    Rothemund, P. W. K. (2006) Folding DNA to Create Nanoscale Shapes and Patterns, Nature 440, 297–302.Google Scholar
  11. 11.
    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.Google Scholar
  12. 12.
    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.Google Scholar
  13. 13.
    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-+.Google Scholar
  14. 14.
    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.Google Scholar
  15. 15.
    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.Google Scholar
  16. 16.
    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.Google Scholar
  17. 17.
    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.Google Scholar
  18. 18.
    SantaLucia, J., Allawi, H. T., and Seneviratne, A. (1996) Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability, Biochemistry 35, 3555–3562.Google Scholar
  19. 19.
    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.Google Scholar
  20. 20.
    Doyle, P. S., Ladoux, B., and Viovy, J. L. (2000) Dynamics of a Tethered Polymer in Shear Flow, Phys. Rev. Lett. 84, 4769–4772.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Physik DepartmentTechnische Universität MünchenMunichGermany

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