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  • © 2017

RNA Nanostructures

Methods and Protocols

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains keynotes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1632)

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Table of contents (23 protocols)

  1. Front Matter

    Pages i-xv
  2. A New Method to Predict Ion Effects in RNA Folding

    • Li-Zhen Sun, Shi-Jie Chen
    Pages 1-17
  3. Computational Generation of RNA Nanorings

    • Rishabh Sharan, Eckart Bindewald, Wojciech K. Kasprzak, Bruce A. Shapiro
    Pages 19-32
  4. Protocols for Molecular Dynamics Simulations of RNA Nanostructures

    • Taejin Kim, Wojciech K. Kasprzak, Bruce A. Shapiro
    Pages 33-64
  5. Computational Prediction of the Immunomodulatory Potential of RNA Sequences

    • Gandharva Nagpal, Kumardeep Chaudhary, Sandeep Kumar Dhanda, Gajendra Pal Singh Raghava
    Pages 75-90
  6. Cotranscriptional Production of Chemically Modified RNA Nanoparticles

    • Maria L. Kireeva, Kirill A. Afonin, Bruce A. Shapiro, Mikhail Kashlev
    Pages 91-105
  7. Supported Fluid Lipid Bilayer as a Scaffold to Direct Assembly of RNA Nanostructures

    • Aleksandra P. Dabkowska, Agnes Michanek, Luc Jaeger, Arkadiusz Chworos, Tommy Nylander, Emma Sparr
    Pages 107-122
  8. Evaluation of Thermal Stability of RNA Nanoparticles by Temperature Gradient Gel Electrophoresis (TGGE) in Native Condition

    • Kheiria Benkato, Benjamin O’Brien, My N. Bui, Daniel L. Jasinski, Peixuan Guo, Emil F. Khisamutdinov
    Pages 123-133
  9. Design and Crystallography of Self-Assembling RNA Nanostructures

    • Mark A. Boerneke, Thomas Hermann
    Pages 135-149
  10. X-Aptamer Selection and Validation

    • Ganesh L. Lokesh, Hongyu Wang, Curtis H. Lam, Varatharasa Thiviyanathan, Nancy Ward, David G. Gorenstein et al.
    Pages 151-174
  11. Chitosan Nanoparticles for miRNA Delivery

    • Merve Denizli, Burcu Aslan, Lingegowda S. Mangala, Dahai Jiang, Cristian Rodriguez-Aguayo, Gabriel Lopez-Berestein et al.
    Pages 219-230
  12. Oxime Ether Lipids as Transfection Agents: Assembly and Complexation with siRNA

    • Anu Puri, Serena Zampino, Mathias Viard, Bruce A. Shapiro
    Pages 241-253
  13. Polycationic Probe-Guided Nanopore Single-Molecule Counter for Selective miRNA Detection

    • Kai Tian, Ruicheng Shi, Amy Gu, Michael Pennella, Li-Qun Gu
    Pages 255-268
  14. Intracellular Reassociation of RNA–DNA Hybrids that Activates RNAi in HIV-Infected Cells

    • Angelica N. Martins, Weina Ke, Vaishnavi Jawahar, Morriah Striplin, Caryn Striplin, Eric O. Freed et al.
    Pages 269-283

About this book

This volume presents a collection of computational and experimental protocols pertaining to the creation, characterization, and utilization of RNA nanostructures. The chapters in this book cover topics such as ion effects in RNA folding; design and crystallography of self-assembling RNA nanostructures; x-aptamer selection and validation; RNAi in HIV-infected cells; and preparation of a conditional RNA switch. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.


Cutting-edge and thorough, RNA Nanostructures: Methods and Protocols is a valuable resource for the design and production of RNA nanostructures. Researchers and scientists sharing these detailed protocols is important for sustained progress in the field.

Editors and Affiliations

  • Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, USA

    Eckart Bindewald

  • RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, USA

    Bruce A. Shapiro

Bibliographic Information

  • Book Title: RNA Nanostructures

  • Book Subtitle: Methods and Protocols

  • Editors: Eckart Bindewald, Bruce A. Shapiro

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7138-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-7137-4Published: 21 July 2017

  • Softcover ISBN: 978-1-4939-8395-7Published: 12 May 2018

  • eBook ISBN: 978-1-4939-7138-1Published: 20 July 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XV, 383

  • Number of Illustrations: 20 b/w illustrations, 75 illustrations in colour

  • Topics: Human Genetics

Buy it now

Buying options

eBook USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access