Antiviral RNAi

Here is a collection of protocols for the analysis of viral small RNAs and natural antiviral RNAi responses as well as for development and optimization of RNAi-based antiviral drugs. The methods here can also be applied outside the context of a virus infection.

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™ 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.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts Includes supplementary material: sn.pub/extras

Inhalt
Defense and counter-defense in the RNAi-based antiviral immune system in insects.- RNAi and cellular miRNAs in infections by mammalian viruses.- Viral miRNAs.- Progress in RNAi-based antiviral therapeutics.- Chemical modification of small interfering RNA.- Viral small RNA cloning and sequencing.- Visitor, an informatic pipeline for analysis of viral siRNA sequencing datasets.- Computational prediction of viral miRNAs.- Detection of Viral microRNAs by Northern Blot Analysis.- Detection of viral microRNA with S1 Nuclease Protection assay.- Characterization of RISC associated adenoviral small RNAs.- Identification of Viral Suppressors of RNAi by a Reporter Assay in Drosophila S2 Cell Culture.- Dicer assay in Drosophila S2 cell extract.- Slicer activity in Drosophila melanogaster S2 extract .- Gel Mobility Shift Assays for RNA-binding viral RNAi suppressors.- dsRNA uptake in adult Drosophila.- Design of small interfering RNAs for antiviral applications .- RNAi inducing lentiviral vectors for anti-HIV-1 gene therapy.- Production of multicopy shRNA lentiviral vectors for antiviral therapy.- Intranasal delivery of antiviral siRNA.- Antibody mediated delivery of siRNAs for anti-HIV therapy .- Aptamer-targeted RNAi for HIV-1 therapy.- RNAi screening for host factors involved in viral infection using Drosophila cells.- Genome-wide RNAi Screen for ViralReplication in Mammalian Cell Culture .- RNAi screening in mammalian cells to identify novel host cell molecules involved in the regulation of viral infections.