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RNA Nanostructures

Design, Characterization, and Applications

  • Book
  • © 2023

Overview

Editors:
  1. Kirill A. Afonin

    1. Department of Chemistry, UNC Charlotte, Charlotte, USA

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2709)

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About this book

This volume details protocols for computer-assisted design and experimental characterization of RNA nanostructures. Chapters guide readers through RNA nanotechnology, design and characterization of RNA nanostructures, assessment of immunology of nanomaterials, biosensing and drug delivery, various biomedical applications, and delivery approaches for therapeutic RNA nanoparticles. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. 

  Authoritative and cutting-edge, RNA Nanostructures: Design, Characterization, and Applications aims to address essential topics and concerns in the growing field of RNA nanotechnology. 

Keywords

Table of contents (23 protocols)

  1. Front Matter

    Pages i-xiii
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  2. Computational Design and In Silico Studies of RNA Nanostructures

    1. Front Matter

      Pages 1-1
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    2. Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures

      • Valentina Abondano Perdomo, Taejin Kim
      Pages 3-29

    3. Computer-Assisted Design and Characterization of RNA Nanostructures

      • Christina J. Bayard, Yaroslava G. Yingling
      Pages 31-49

    4. Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology

      • Jian Wang, Congzhou M. Sha, Nikolay V. Dokholyan
      Pages 51-64

    5. Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MD

      • James Byrnes, Kriti Chopra, Lewis A. Rolband, Leyla Danai, Shirish Chodankar, Lin Yang et al.
      Pages 65-94

  3. Production and Storage of Functional RNA Nanostructures

    1. Front Matter

      Pages 95-95
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    2. Metalated Nucleic Acid Nanostructures

      • Douglas Zhang, Thomas Hermann
      Pages 97-103

    3. Bioconjugation of Functionalized Oligodeoxynucleotides with Fluorescence Reporters for Nanoparticle Assembly

      • Erwin Doe, Hannah L. Hayth, Emil F. Khisamutdinov
      Pages 105-115

    4. Light-Assisted Drying for the Thermal Stabilization of Nucleic Acid Nanoparticles and Other Biologics

      • Susan R. Trammell
      Pages 117-130

    5. Preparation of Nucleic Acid Aptamer Functionalized Silver/Gold Nanoparticle Conjugates Using Thiol-Substituted Oligonucleotides

      • Joshua D. Quarles, Allen T. Livingston, Ashley E. Wood, Timea Gerczei Fernandez
      Pages 131-147

  4. Characterization of RNA Nanostructures

    1. Front Matter

      Pages 149-149
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    2. Thermodynamic Characterization of Nucleic Acid Nanoparticles Hybridization by UV Melting

      • Megan Teter, Ross Brumett, Abigail Coffman, Emil F. Khisamutdinov
      Pages 151-161

    3. Structural Characterization of DNA-Templated Silver Nanoclusters by Energy Dispersive Spectroscopy

      • Damian Beasock, Kirill A. Afonin
      Pages 163-178

    4. Small Volume Microrheology to Evaluate Viscoelastic Properties of Nucleic Acid-Based Supra-Assemblies

      • Akhilesh Kumar Gupta, Joel Petersen, Elizabeth Skelly, Kirill A. Afonin, Alexey V. Krasnoslobodtsev
      Pages 179-189

    5. Characterization of RNA Nanoparticles and Their Dynamic Properties Using Atomic Force Microscopy

      • Alexander J. Lushnikov, Yelixza I. Avila, Kirill A. Afonin, Alexey V. Krasnoslobodtsev
      Pages 191-202

  5. Intracellular Delivery and Immunorecognition of RNA Nanostructures

    1. Front Matter

      Pages 203-203
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    2. Synthesis of Mesoporous Silica Nanoparticles for the Delivery of Nucleic Acid Nanostructures

      • Tamanna Binte Huq, Juan L. Vivero-Escoto
      Pages 205-210

    3. Assessment of Intracellular Compartmentalization of RNA Nanostructures

      • Yasmine Radwan, Kirill A. Afonin, M. Brittany Johnson
      Pages 211-228

    4. Discriminating Immunorecognition Pathways Activated by RNA Nanostructures

      • Leyla Danai, M. Brittany Johnson, Kirill A. Afonin
      Pages 229-240
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Editors and Affiliations

  • Department of Chemistry, UNC Charlotte, Charlotte, USA

    Kirill A. Afonin

Bibliographic Information

  • Book Title: RNA Nanostructures

  • Book Subtitle: Design, Characterization, and Applications

  • Editors: Kirill A. Afonin

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3417-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-3416-5Published: 13 August 2023

  • Softcover ISBN: 978-1-0716-3419-6Published: 14 August 2024

  • eBook ISBN: 978-1-0716-3417-2Published: 12 August 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 334

  • Number of Illustrations: 18 b/w illustrations, 69 illustrations in colour

  • Topics: Biotechnology, Materials Science, general

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