siRNA design : methods and protocols

Author(s)

• Taxman, Debra J.

Bibliographic Information

siRNA design : methods and protocols

edited by Debra J. Taxman

（Methods in molecular biology / John M. Walker, series editor, 942）（Springer protocols）

Humana Press : Springer, c2013

Note

Includes bibliographical references and index

Description and Table of Contents

Description

The discovery of RNA interference (RNAi) as a methodology for gene silencing has revolutionized biological research, providing an invaluable avenue for therapeutics, and small interfering RNA (siRNA) is the most common strategy utilized for enacting RNAi. siRNA Design: Methods and Protocols offers expertly crafted guidelines and protocols for the selection of siRNA targeting sequences, for the strategic incorporation of chemical modifications, and for advantageous structural modifications to the classic siRNA design. Protocols are provided for using endogenous cellular machinery to produce siRNA from optimized precursor short hairpin RNA (shRNA) and artificial microRNA (amiRNA) molecules. Strategies are also described for specific applications such as immunostimulatory siRNA that may provide therapeutic benefit against viral infections in mammals, the simultaneous targeting of multiple siRNAs, and siRNA-mediated crop virus resistance. The design of RNAi for gene silencing in embryonic, invertebrate, and plant systems requires a variety of unique approaches, several of which are described towards the end of this volume. Written for the highly successful Methods in Molecular Biology (TM) series, this work contains the kind of detailed description and implementation advice that guarantees successful results. Authoritative and easy to use, siRNA Design: Methods and Protocols will provide researchers, educators, clinicians, and biotech specialists with a broad understanding of the issues in RNAi and how they can be overcome strategically through design.

Table of Contents

1. What Parameters to Consider and Which Software Tools to Use for Target Selection and Molecular Design of Small Interfering RNAs Olga Matveeva 2. Methods for Selecting Effective siRNA Target Sequences Using a Variety of Statistical and Analytical Techniques Shigeru Takasaki 3. Designing Functional siRNA with Reduced Off-Target Effects Yuki Naito and Kumiko Ui-Tei 4. Design and Screening of siRNAs Against Highly Structured RNA Targets Neda Nasheri, John Paul Pezacki, and Selena M. Sagan 5. Engineering Small Interfering RNAs by Strategic Chemical Modification Jesper B. Bramsen and Jorgen Kjems 6. The Design, Selection and Evaluation of Highly Specific and Functional siRNA Incorporating Unlocked Nucleobase Analogs Narendra Vaish and Pinky Agarwal 7. The Design, Preparation, and Evaluation of Asymmetric Small Interfering RNA for Specific Gene Silencing in Mammalian Cells Chanil Chang, Sun Woo Hong, Pooja Dua, Soyoun Kim, and Dong-ki Lee 8. Design of Nuclease-Resistant Fork-Like Small Interfering RNA (fsiRNA) Elena L. Chernolovskaya and Marina A. Zenkova 9. Designing Dual-Targeting siRNA Duplexes Having Two Active Strands that Combine siRNA and MicroRNA-Like Targeting Pal Saetrom 10. Strategies for Designing and Validating Immunostimulatory siRNAs Michael P. Gantier 11. Designing Efficient and Specific Endoribonuclease Prepared siRNAs (esiRNAs) Vineeth Surendranath, Mirko Theis, Bianca H. Habermann, and Frank Buchholz 12. Short Hairpin RNA-Mediated Gene Silencing Luke S. Lambeth and Craig A. Smith 13. Design of Lentivirally Expressed siRNAs Ying Poi Liu and Ben Berkhout 14. Bi-Functional Short Hairpin RNA (bi-shRNA): Design and Pathway to Clinical Application Donald D. Rao, Neil Senzer, Zhaohui Wang, Padmasini Kumar, Chris M. Jay, and John Nemunaitis 15. Design and Chemical Modification of Synthetic Short shRNAs as Potent RNAi Triggers Anne Dallas and Brian H. Johnston 16. Production and Application of Long dsRNA in Mammalian Cells Katerina Chalupnikova, Jana Nejepinska, and Petr Svoboda 17. Design of RNAi Reagents for Invertebrate Model Organisms and Human Disease Vectors Thomas Horn and Michael Boutros 18. Construction of shRNA Expression Plasmids for Silkworm Cell Lines Using Single-Stranded DNA and Bst DNA Polymerase Hiromitsu Tanaka 19. Designing Effective amiRNA and Multimeric amiRNA Against Plant Viruses Muhammad Fahim and Philip J. Larkin 20. Downregulation of Plant Genes with MiRNA Induced Gene Silencing Felipe Fenselau de Felippes

by "Nielsen BookData"

• NCID: BB10844564
• ISBN:
  • 9781627031189
• LCCN: 2012947406
• Country Code: us
• Title Language Code: eng
• Text Language Code: eng
• Place of Publication: New York
• Pages/Volumes: xiii, 392 p.
• Size: 27 cm
• Classification:
  • DC23 : 572.88
• Subject Headings:
  • LCSH : Small interfering RNA -- Laboratory manuals
  • LCSH : Gene therapy
• Parent Bibliography ID:
  • BA10794673
  • BA88873632