Main description:

Viruses and RNAi share an intricate relationship at many levels. RNAi is an important antiviral defense mechanism in plants and invertebrates, microRNAs - of viral or cellular origin - affect many aspects of virus biology, and replication of many, if not all, mammalian viruses can be suppressed by RNAi. Antiviral RNAi: Concepts, Methods, and Applications provides a collection of protocols for the analysis of viral small RNAs and natural antiviral RNAi responses as well as for the development and optimization of RNAi-based antiviral drugs. As RNAi is a central regulatory mechanism in the cell, the methods in this volume can also be applied out of the context of a virus infection. Divided into five convenient parts, this detailed volume reviews important basic concepts in the field of antiviral RNAi, provides experimental and bio-informatic tools for the analysis of small silencing RNAs, covers methods to biochemically dissect RNAi-based antiviral defense and viral counter-defense mechanisms, describes methods for the design, expression, and delivery of therapeutic antiviral siRNAs, and finally presents genome-wide RNAi approaches for the identification of factors involved in virus replication. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and accessible, Antiviral RNAi: Concepts, Methods, and Applications serves as an ideal guide for both novice and experienced researchers alike striving to dissect the role of RNAi in the viral life cycle or to further boost the development of novel therapeutics and experimental tools based on RNAi technology.

Contents:

Part I: General Introduction

1. Defense and counter-defense in the RNAi-based antiviral immune system in insects

Joel T. van Mierlo, Koen W.R. van Cleef, and Ronald P. van Rij

2. RNAi and cellular miRNAs in infections by mammalian viruses

Joost Haasnoot and Ben Berkhout

3. Viral miRNAs

Karlie Plaisance-Bonstaff, and Rolf Renne

4. Progress in RNAi-based antiviral therapeutics

Jiehua Zhou and John J. Rossi

5. Chemical modification of small interfering RNA

Jesper B. Bramsen and Jorgen Kjems

Part II: Viral small RNAs

6. Viral small RNA cloning and sequencing

Valerie Gausson and Maria-Carla Saleh

7. Visitor, an informatic pipeline for analysis of viral siRNA sequencing datasets

Christophe Antoniewski

8. Computational prediction of viral miRNAs

Adam Grundhoff

9. Detection of Viral microRNAs by Northern Blot Analysis

Lydia V. McClure, Yao-Tang Lin, and Christopher S. Sullivan

10. Detection of viral microRNA with S1 Nuclease Protection assay

Matthias John and Sebastien Pfeffer

11. Characterization of RISC associated adenoviral small RNAs

Ning Xu and Goeran Akusjarvi

Part III: RNAi-based antiviral defense

12. Identification of Viral Suppressors of RNAi by a Reporter Assay in Drosophila S2 Cell Culture

Koen W.R. van Cleef, Joel T van Mierlo, Marius van den Beek, and Ronald P. van Rij

13. Dicer assay in Drosophila S2 cell extract

Baojun Yang and Hongwei Li

14. Slicer activity in Drosophila melanogaster S2 extract

Arabinda Nayak and Raul Andino

15. Gel Mobility Shift Assays for RNA-binding viral RNAi suppressors

Tibor Csorba and Jozsef Burgyan

16. dsRNA uptake in adult Drosophila

Benjamin Obadia and Maria-Carla Saleh

Part IV: Antiviral RNAi therapy

17. Design of small interfering RNAs for antiviral applications

Diana Rothe, Erik J. Wade, and Jens Kurreck

18. RNAi inducing lentiviral vectors for anti-HIV-1 gene therapy

Ying Poi Liu, Jan-Tinus Westerink, Olivier ter Brake, and Ben Berkhout

19. Production of multicopy shRNA lentiviral vectors for antiviral therapy

Scot D. Henry, Quiwei Pan, and Luc J.W. van der Laan

20. Intranasal delivery of antiviral siRNA

Sailen Barik

21. Antibody mediated delivery of siRNAs for anti-HIV therapy

Sang-Soo Kim, Sandesh Subramanya, Dan Peer, Motomu Shimaoka, and Premlata Shankar

22. Aptamer-targeted RNAi for HIV-1 therapy

Jiehua Zhou and John J. Rossi

Part V: RNAi screens to study virus-host interactions

23. RNAi screening for host factors involved in viral infection using Drosophila cells

Sara Cherry

24. Genome-wide RNAi Screen for Viral Replication in Mammalian Cell Culture

Bhupesh K. Prusty, Alexander Karlas, Thomas F. Meyer, and Thomas Rudel

25. RNAi screening in mammalian cells to identify novel host cell molecules involved in the regulation of viral infections

Carolyn B. Coyne and Sara Cherry