RNA Nanotechnology and Therapeutics

1. Front Matter

   Pages i-xi

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2. Overview of Methods in RNA Nanotechnology: Synthesis, Purification, and Characterization of RNA Nanoparticles

   • Farzin Haque, Peixuan Guo

   Pages 1-19

3. Multiple Approaches for the Investigation of Bacterial Small Regulatory RNAs Self-assembly

   • Christophe Lavelle, Florent Busi, Véronique Arluison

   Pages 21-42

4. Measuring the Elasticity of Ribonucleotide(s)-Containing DNA Molecules Using AFM

   • Kyung Duk Koh, Hsiang-Chih Chiu, Elisa Riedo, Francesca Storici

   Pages 43-57

5. Silver Nanoclusters for RNA Nanotechnology: Steps Towards Visualization and Tracking of RNA Nanoparticle Assemblies

   • Kirill A. Afonin, Danielle Schultz, Luc Jaeger, Elisabeth Gwinn, Bruce A. Shapiro

   Pages 59-66

6. Large Scale Purification of RNA Nanoparticles by Preparative Ultracentrifugation

   • Daniel L. Jasinski, Chad T. Schwartz, Farzin Haque, Peixuan Guo

   Pages 67-82

7. HPLC Purification of RNA Aptamers up to 59 Nucleotides with Single-Nucleotide Resolution

   • Zhen Huang, Chi-Yen Lin, William Jaremko, Li Niu

   Pages 83-93

8. Using RNA Nanoparticles with Thermostable Motifs and Fluorogenic Modules for Real-Time Detection of RNA Folding and Turnover In Prokaryotic and Eukaryotic Cells

   • Hui Zhang, Fengmei Pi, Dan Shu, Mario Vieweger, Peixuan Guo

   Pages 95-111

9. Fluorescence Labeling of Short RNA by Oxidation at the 3′-End

   • Chen Qiu, Wang-Yi Liu, Yong-Zhen Xu

   Pages 113-120

10. Methods and Assays for Specific Targeting and Delivery of RNA Nanoparticles to Cancer Metastases

    • Piotr Rychahou, Yi Shu, Farzin Haque, Jiyao Hu, Peixuan Guo, B. Mark Evers

    Pages 121-135

11. Functional Assays for Specific Targeting and Delivery of RNA Nanoparticles to Brain Tumor

    • Tae Jin Lee, Farzin Haque, Mario Vieweger, Ji Young Yoo, Balveen Kaur, Peixuan Guo et al.

    Pages 137-152

12. Aptamer-Mediated Nanoparticle Interactions: From Oligonucleotide–Protein Complexes to SELEX Screens

    • Laetitia Evadé, Eric Dausse, Said Taouji, Emilie Daguerre, Eric Chevet, Jean-Jacques Toulmé

    Pages 153-167

13. Methods for Assembling B-Cell Lymphoma Specific and Internalizing Aptamer–siRNA Nanoparticles Via the Sticky Bridge

    • Jiehua Zhou, John J. Rossi, Ka To Shum

    Pages 169-185

14. A High-Throughput Screening Assay for the Functional Delivery of Splice-Switching Oligonucleotides in Human Melanoma Cells

    • John M. Dean, Robert K. DeLong

    Pages 187-196

15. Design, Assembly, and Evaluation of RNA–Protein Nanostructures

    • Hirohisa Ohno, Eriko Osada, Hirohide Saito

    Pages 197-211

16. Mapping RNA Interactions to Proteins in Virions Using CLIP-Seq

    • Baochang Fan, Peng Ni, C. Cheng Kao

    Pages 213-224

17. Mapping Protein–RNA Interactions by RCAP, RNA-Cross-Linking and Peptide Fingerprinting

    • Robert C. Vaughan, C. Cheng Kao

    Pages 225-236

18. Back Matter

    Pages 237-239

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This volume contains a compilation of techniques and laboratory protocols directly related to RNA nano technology and its applications in nano biotechnology and nano medicine. The chapters in this book cover a wide range of research methods that can be easily comprehended and carried out in a step-by-step manner by graduate students and postdoctoral fellows from diverse scientific disciplines. Some of the covered topics include various biochemical, biophysical and bioinformatics approaches for analyzing RNA structures and properties; methods to analyze the multi-step assembly process of RNA nano architectures; purification of multifunctional RNA nanoparticles by ultracentrifugation and HPLC; real-time detection of RNA nano constructs in vivo; conjugation of imaging, targeting and therapeutic modules to RNA scaffold; and design and characterization of RNA-protein nanostructures. Written in the highly successful Methods of 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 key tips on troubles troubleshooting and avoiding known pitfalls.

Cutting-edge and practical, RNA Nanotechnology and Therapeutics: Methods and Protocols propels the field toward new heights by engaging researchers working in the diverse fields of physical, engineering, and life sciences.

• Nanobiotechnology
• Nanomedicine
• RNA assembly
• RNA folding
• RNA nanoarchitectures
• RNA-protein nanostructures
• ultracentrifugation

• Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, USA

  Peixuan Guo, Farzin Haque

Peixuan Guo, Ph. D. William Farish Endowed Chair in Nano biotechnology Professor of School of Pharmacy Director of Nano biotechnology Center University of Kentucky Director of NCI Cancer Nanotechnology Platform Partnership Program: RNA Nanotechnology for Cancer Therapy Mailing address College of Pharmacy University of Kentucky 565 Biopharm Complex 789 S. Limestone Street Lexington, KY 40536 Phone: (Office) (859)218-0128 (Cell Phone): (513)728-1411 peixuan.guo@uky.edu (future)

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