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Protocols for the In Silico Design of RNA Nanostructures

  • Protocol
Nanostructure Design

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 474))

Summary

Recent developments in the field of nanobiology have significantly expanded the possibilities for new modalities in the treatment of many diseases, including cancer. Ribonucleic acid (RNA) represents a relatively new molecular material for the development of these biologically oriented nanodevices. In addition, RNA nanobiology presents a relatively new approach for the development of RNA-based nanoparticles that can be used as crystallization substrates and scaffolds for RNA-based nanoarrays. Presented in this chapter are some methodological shaped-based protocols for the design of such RNA nanostructures. Included are descriptions and background materials describing protocols that use a database of three-dimensional RNA structure motifs; designed RNA secondary structure motifs; and a combination of the two approaches. An example is also given illustrating one of the protocols.

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Acknowledgments

We wish to thank Robert Hayes, Christine Viets, and Calvin Grunewald for their contributions to the development of our research tools. Computational support was provided in part by the National Cancer Institute's Advanced Biomedical Computing Center. This publication was supported by the Intramural Research Program of the National Institutes of Health, National Cancer Institute, Center for Cancer Research. This publication has been funded in whole or in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract N01-CO-12400. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, and mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. government.

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Authors and Affiliations

  1. Center for Cancer Research Nanobiology Program, SAIC-Frederick National Cancer Institute, Frederick, MD

    Bruce A. Shapiro & Yaroslava Yingling

  2. Basic Research Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD

    Eckart Bindewald & Wojciech Kasprzak

Authors
  1. Bruce A. Shapiro
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  2. Eckart Bindewald
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  3. Wojciech Kasprzak
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  4. Yaroslava Yingling
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Editor information

Editors and Affiliations

  1. Department of Molecular Biology, Tel Aviv University, Tel Aviv, Israel

    Ehud Gazit (Faculty of Life Science) (Faculty of Life Science)

  2. Center for Cancer Research Nanobiology Program, SAIC-Frederick National Cancer Institute, Frederick, MD

    Ruth Nussinov

  3. Department of Human Genetics Medical School, Tel Aviv University, Tel Aviv, Israel

    Ruth Nussinov

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

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Shapiro, B.A., Bindewald, E., Kasprzak, W., Yingling, Y. (2008). Protocols for the In Silico Design of RNA Nanostructures. In: Gazit, E., Nussinov, R. (eds) Nanostructure Design. Methods in Molecular Biology™, vol 474. Humana Press. https://doi.org/10.1007/978-1-59745-480-3_7

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  • DOI: https://doi.org/10.1007/978-1-59745-480-3_7

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-934115-35-0

  • Online ISBN: 978-1-59745-480-3

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