siRNA Design

Methods and Protocols

Editors:

ISBN: 978-1-62703-118-9 (Print) 978-1-62703-119-6 (Online)

Table of contents (20 protocols)

  1. Front Matter

    Pages i-xiii

  2. No Access

    Book Protocol

    Pages 1-16

    What Parameters to Consider and Which Software Tools to Use for Target Selection and Molecular Design of Small Interfering RNAs

  3. No Access

    Book Protocol

    Pages 17-55

    Methods for Selecting Effective siRNA Target Sequences Using a Variety of Statistical and Analytical Techniques

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    Book Protocol

    Pages 57-68

    Designing Functional siRNA with Reduced Off-Target Effects

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    Book Protocol

    Pages 69-86

    Design and Screening of siRNAs Against Highly Structured RNA Targets

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    Book Protocol

    Pages 87-109

    Engineering Small Interfering RNAs by Strategic Chemical Modification

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    Book Protocol

    Pages 111-134

    The Design, Selection, and Evaluation of Highly Specific and Functional siRNA Incorporating Unlocked Nucleobase Analogs

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    Book Protocol

    Pages 135-152

    The Design, Preparation, and Evaluation of Asymmetric Small Interfering RNA for Specific Gene Silencing in Mammalian Cells

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    Book Protocol

    Pages 153-168

    Design of Nuclease-Resistant Fork-Like Small Interfering RNA (fsiRNA)

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    Book Protocol

    Pages 169-177

    Designing Dual-Targeting siRNA Duplexes Having Two Active Strands that Combine siRNA and MicroRNA-Like Targeting

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    Pages 179-191

    Strategies for Designing and Validating Immunostimulatory siRNAs

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    Pages 193-204

    Designing Efficient and Specific Endoribonuclease-Prepared siRNAs

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    Pages 205-232

    Short Hairpin RNA-Mediated Gene Silencing

  14. Book Protocol

    Pages 233-257

    Design of Lentivirally Expressed siRNAs

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    Pages 259-278

    Bifunctional Short Hairpin RNA (bi-shRNA): Design and Pathway to Clinical Application

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    Pages 279-290

    Design and Chemical Modification of Synthetic Short shRNAs as Potent RNAi Triggers

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    Book Protocol

    Pages 291-314

    Production and Application of Long dsRNA in Mammalian Cells

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    Book Protocol

    Pages 315-346

    Design of RNAi Reagents for Invertebrate Model Organisms and Human Disease Vectors

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    Book Protocol

    Pages 347-355

    Construction of shRNA Expression Plasmids for Silkworm Cell Lines Using Single-Stranded DNA and Bst DNA Polymerase

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    Book Protocol

    Pages 357-377

    Designing Effective amiRNA and Multimeric amiRNA Against Plant Viruses

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    Book Protocol

    Pages 379-387

    Downregulation of Plant Genes with miRNA-Induced Gene Silencing

  22. Back Matter

    Pages 389-392