Sirna Design: Methods and Protocols

ISBN-13: 9781627031189 / Angielski / Twarda / 2012 / 392 str.

Debra J. Taxman

Opis

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 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.

Recenzje

From the reviews:

"This book edited by D.J. Taxman is a valuable collection of 20 chapters covering aspects from values for parameters used in tools for designing siRNAs to screening methods for evaluating the efficiency of the designed siRNA. ... Through style and scientific information the book is aimed at researchers in the RNAi field, but its accessible delivery of contents makes it a good starting point for younger researchers in this topic." (Irina Ioana Mohorianu, zbMATH, Vol. 1276, 2014)

Spis treści

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 Jørgen 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

            Pål Sætrom

 

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