siRNA Design: Methods and Protocols

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