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Periodic Assembly of Nanospecies on Repetitive DNA Sequences Generated on Gold Nanoparticles by Rolling Circle Amplification

  • Weian Zhao
  • Michael A. Brook
  • Yingfu Li
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 474)

Summary

Periodical assembly of nanospecies is desirable for the construction of nanodevices. We provide a protocol for the preparation of a gold nanoparticle (AuNP)/DNA scaffold on which nanospecies can be assembled in a periodical manner. AuNP/DNA scaffold is prepared by growing long single-stranded DNA (ssDNA) molecules (typically hundreds of nanometers to a few microns in length) on AuNPs via rolling circle amplification (RCA). Since these long ssDNA molecules contain many repetitive sequence units, complementary DNA-attached nanospecies can be assembled through specific hybridization in a controllable and periodical manner.

Key Words

DNA DNA amplification enzymatic manipulation gold nanotechnology rolling circle amplification self-assembly. 

Notes

Acknowledgments

This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC); SENTINEL: Canadian Network for the Development and Use of Bioactive Paper; and the Canadian Institutes for Health Research (CIHR). We wish to thank Dr. Yan Gao for help with the AFM and Dr. Srinivas A. Kandadai for the helpful discussion. Y.L. holds a Canada Research Chair.

References

  1. 1.
    Katov NA. (2006) Nanoparticle Assemblies and Superstructures. CRC Press, Taylor and Francis, Boca Raton, FL.Google Scholar
  2. 2.
    Zhang J, Wang Z, Liu J, Chen S, Liu G. (2003) Self-Assembled Nanostructures. Kluwer Academic/Plenum, New York.Google Scholar
  3. 3.
    Seeman NC. (2003) DNA in a material world. Nature 429, 427–431.CrossRefGoogle Scholar
  4. 4.
    Rosi NL, Mirkin C. (2005) Nanostructures in biodiagnostics. Chem. Rev. 105, 1547–1562.CrossRefGoogle Scholar
  5. 5.
    Zhao W, Gao Y, Kandadai SA, Brook MA, Li Y. (2006) DNA polymerization on gold nanoparticles through rolling circle amplification: towards novel scaffolds for three-dimensional periodic nanoassemblies. Angew. Chem. Int. Ed. 45, 2409–2413.CrossRefGoogle Scholar
  6. 6.
    Fire A, Xu S. (1995) Rolling replication of short DNA circles. Proc. Natl. Acad. Sci. U. S. A. 92, 4641–4645.CrossRefGoogle Scholar
  7. 7.
    Liu D, Daubendiek SL, Zillman MA, Ryan K, Kool ET. (1996) Rolling circle DNA synthesis: small circular oligonucleotides as efficient templates for DNA polymerases. J. Am. Chem. Soc. 118, 1587–1594.CrossRefGoogle Scholar
  8. 8.
    Beyer S, Nickels P, Simmel FC. (2005) Periodic DNA nanotemplates synthesized by rolling circle amplification. Nano Lett. 5, 719–722.CrossRefGoogle Scholar
  9. 9.
    Deng Z, Tian Y, Lee S, Ribbe AE, Mao C. (2005) DNA-encoded self-assembly of gold nanoparticles into one-dimensional arrays. Angew. Chem. Int. Ed. 44, 3582–3585.CrossRefGoogle Scholar
  10. 10.
    Hill HD, Mirkin CA. (2006) The bio-barcode assay for the detection of protein and nucleic acid targets using DTT-induced ligand exchange. Nat. Protocol. 1, 324–336.CrossRefGoogle Scholar
  11. 11.
    Liu J, Lu Y. (2006) Preparation of aptamer-linked gold nanoparticle purple aggregates for colorimetric sensing of analytes. Nat. Protocol. 1, 246–252.CrossRefGoogle Scholar
  12. 12.
    Jin R, Wu G, Li Z, Mirkin CA, Schatz GC. (2003) What controls the melting properties of DNA-linked gold nanoparticle assemblies? J. Am. Chem. Soc. 125, 1643–1654.CrossRefGoogle Scholar
  13. 13.
    Billen LP, Li Y. (2004) Synthesis and characterization of topologically linked single-stranded DNA rings. Bioorg. Chem. 32, 582–598.CrossRefGoogle Scholar
  14. 14.
    Rickwood D, Hames BD. (1990) Gel Electrophoresis of Nucleic Acids: A Practical Approach. IRL Press, Oxford, NY.Google Scholar
  15. 15.
    Sambrook J, Russell DW. (2001) Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.Google Scholar
  16. 16.
    Kuhn H, Demidov VV, Frank-Kamenetskii MD. (2002) Rolling-circle amplification under topological constraints. Nucleic Acids Res. 30, 574–580.CrossRefGoogle Scholar
  17. 17.
    Lin C, Xie M, Chen J, Liu Y, Yan H. (2006) Rolling-circle amplification of a DNA nanojunction. Angew. Chem. Int. Ed. 45, 7537–7539.CrossRefGoogle Scholar
  18. 18.
    Zuker M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415.CrossRefGoogle Scholar
  19. 19.
    Li Z, Jin R, Mirkin CA, Letsinger RL. (2002) Multiple thiol-anchor capped DNA-gold nanoparticle conjugates. Nucleic Acids Res. 30, 1558–1562.CrossRefGoogle Scholar
  20. 20.
    Xu X, Rosi NL, Wang Y, Huo F, Mirkin CA. (2006) Asymmetric functionalization of gold nanoparticles with oligonucleotides. J. Am. Chem. Soc. 128, 9286–9287.CrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science + Business Media, LLC 2008

Authors and Affiliations

  • Weian Zhao
    • 1
  • Michael A. Brook
    • 1
  • Yingfu Li
    • 2
  1. 1.Department of ChemistryMcMaster UniversityHamiltonCanada
  2. 2.Departments of Chemistry and Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonCanada

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