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RNA Nanostructures

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Eckart Bindewald

    1. Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Bruce A. Shapiro

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

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • 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
    Download chapter PDF

  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. Rolling Circle Transcription for the Self-Assembly of Multimeric RNAi Structures and Its Applications in Nanomedicine

    • Mihue Jang, Hyung Jun Ahn
    Pages 65-74

  6. Computational Prediction of the Immunomodulatory Potential of RNA Sequences

    • Gandharva Nagpal, Kumardeep Chaudhary, Sandeep Kumar Dhanda, Gajendra Pal Singh Raghava
    Pages 75-90

  7. Cotranscriptional Production of Chemically Modified RNA Nanoparticles

    • Maria L. Kireeva, Kirill A. Afonin, Bruce A. Shapiro, Mikhail Kashlev
    Pages 91-105

  8. 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

  9. 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

  10. Design and Crystallography of Self-Assembling RNA Nanostructures

    • Mark A. Boerneke, Thomas Hermann
    Pages 135-149

  11. 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

  12. Design and Preparation of Aptamer–siRNA Chimeras (AsiCs) for Targeted Cancer Therapy

    • Sven Kruspe, Paloma H. Giangrande
    Pages 175-186

  13. Cellular Delivery of siRNAs Using Bolaamphiphiles

    • Kshitij Gupta
    Pages 187-205

  14. Preparation and Optimization of Lipid-Like Nanoparticles for mRNA Delivery

    • Bin Li, Yizhou Dong
    Pages 207-217

  15. 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

  16. Synthesis of PLGA–Lipid Hybrid Nanoparticles for siRNA Delivery Using the Emulsion Method PLGA-PEG–Lipid Nanoparticles for siRNA Delivery

    • Lei Wang, Benjamin Griffel, Xiaoyang Xu
    Pages 231-240

  17. Oxime Ether Lipids as Transfection Agents: Assembly and Complexation with siRNA

    • Anu Puri, Serena Zampino, Mathias Viard, Bruce A. Shapiro
    Pages 241-253

  18. 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

  19. 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

  20. Construction and In Vivo Testing of Prokaryotic Riboregulators

    • Alexander A. Green
    Pages 285-302
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Keywords

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

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