RNA Nanostructures: Methods and Protocols

ISBN-13: 9781493971374 / Angielski / Twarda / 2017 / 383 str.

Eckart Bindewald; Bruce A. Shapiro

Opis

This volume presents a collection of computational and experimental protocols pertaining to the creation, characterization, and utilization of RNA nanostructures.

Spis treści

Preface…
Table of Contents…
Contributing Authors…

 

 1.  1. A New Method to Predict Ion Effects in RNA Folding

Li-Zhen Sun and Shi-Jie Chen

2. Computational Generation of RNA Nanorings

Rishabh Sharan, Eckart Bindewald, Wojciech Kasprzak, and Bruce A. Shapiro         

3.      Protocols for Molecular Dynamics Simulations of RNA Nanostructures

Taejin Kim, Wojciech K. Kasprzak, and Bruce A. Shapiro

 4.      Rolling Circle Transcription for the Self-Assembly of Multimeric RNAi Structures and its Applications in Nanomedicine
Mihue Jang and Hyung Jun Ahn

 5. Computational Prediction of the Immunomodulatory Potential of RNA Sequences
Gandharva Nagpal, Kumardeep Chaudhary, Sandeep Kumar Dhanda, and Gajendra Pal Singh Raghava 

6. Co-Transcriptional Production of Chemically Modified RNA Nanoparticles

Maria L. Kireeva, Kirill A. Afonin, Bruce A. Shapiro, and Mikhail Kashlev 

7. Supported Fluid Lipid Bilayer as a Scaffold to Direct Assembly of RNA Nanostructures
Aleksandra P. Dabkowska, Agnes Michanek, Luc Jaeger, Arkadiusz Chworos, Tommy Nylandera and Emma Sparr 

8. Evaluation of Thermal Stability of RNA Nanoparticles by Temperature Gradient Gel Electrophoresis (TGGE) in Native Condition
Kheiria Benkato,  Ben O’Brien, My N. Bui, Daniel Jasinski,  Peixuan Guo, and Emil F. Khisamutdinov

9. Design and Crystallography of Self-Assembling RNA Nanostructures
Mark A. Boerneke and Thomas Hermann

10. X-Aptamer Selection and Validation
Ganesh L. Lokesh, Hongyu Wang, Curtis H. Lam, Varatharasa Thiviyanathan, Nancy Ward, David G. Gorenstein and David E. Volk

11. Design and Preparation of Aptamer-siRNA Chimeras (AsiCs) for Targeted Cancer Therapy

Sven Kruspe and Paloma H. Giangrande

12. Cellular Delivery of siRNAs using Bolaamphiphiles

Kshitij Gupta

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

Bin Li and Yizhou Dong 

14. Chitosan Nanoparticles for miRNA Delivery
Merve Denizli, Burcu Aslan, Lingegowda S. Mangala, Dahai Jiang, Cristian Rodriguez-Aguayo, Gabriel Lopez-Berestein, and Anil K. Sood

15. Synthesis of PLGA/Lipid Hybrid Nanoparticles for siRNA Delivery using the Emulsion Method PLGA-PEG/Lipid Nanoparticles for siRNA Delivery

Lei Wang, Benjamin Griffel, and Xiaoyang Xu 

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

Anu Puri, Serena Zampino, Mathias Viard, and Bruce A. Shapiro

17. Polycationic Probe-Guided Nanopore Single-Molecule Counter for Selective miRNA Detection

Kai Tian, Ruicheng Shi, and Li-Qun Gu 

18. Intracellular Re-Association 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, And Kirill A. Afonin 

19. Construction and In Vivo Testing of Prokaryotic Riboregulators

Alexander A. Green 

20. Preparation of a Conditional RNA Switch

Paul Zakrevsky, Lorena Parlea, Eckart Bindewald, Kirill A. Afonin, and Bruce A. Shapiro 

21. Rational Engineering of a Modular Group I Ribozyme to Control its Activity by Self-Dimerization

Takahiro Tanaka, Yoshiya Ikawa, and Shigeyoshi Matsumura 

22. CRISPR-Cas RNA Scaffolds for Transcriptional Programming in Yeast

Jesse G. Zalatan 

23. Using Planar Phi29 pRNA Three-Way Junction to Control Size and Shape of RNA Nanoparticles for Biodistribution Profiling in Mice

Farzin Haque, Congcong Xu, Daniel L. Jasinski, Hui Li, and Peixuan Guo

Blurb

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.