SiRNA design : methods and protocols / edited by Debra J. Taxman.

Contributor(s): Taxman, Debra J
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 942.Publisher: New York : Humana Press : Springer [distributor], ©2013Description: 1 online resource (xiii, 392 pages) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9781627031196; 1627031197Subject(s): Small interfering RNA | Investigative Techniques | RNA, Small Untranslated | RNA, Antisense | Publication Formats | Genetic Techniques | Epigenesis, Genetic | RNA | Publication Characteristics | Biology | Antisense Elements (Genetics) | Gene Expression Regulation | Analytical, Diagnostic and Therapeutic Techniques and Equipment | Biological Science Disciplines | Nucleic Acids, Nucleotides, and Nucleosides | RNA, Untranslated | Genetic Phenomena | Disciplines and Occupations | Chemicals and Drugs | Phenomena and Processes | Natural Science Disciplines | RNA, Small Interfering | Nucleic Acids | Genetics | Methods | Gene Targeting | Gene Silencing | Laboratory Manuals | Small interfering RNA | chemie | chemistry | biotechnologie | biotechnology | humane genetica | human genetics | Chemistry (General) | Chemie (algemeen)Genre/Form: Laboratory Manual. | Electronic books. Additional physical formats: Print version:: SiRNA design.DDC classification: 660.6 LOC classification: QP623.5.S63Online resources: Click here to access online
Contents:
What parameters to consider and which software tools to use for target selection and molecular design of small interfering RNAs / Olga Matveeva -- Methods for selecting effective siRNA target sequences using a variety of statistical and analytical techniques / Shigeru Takasaki -- Designing functional siRNA with reduced off-target effects / Yuki Naito and Kumiko Ui-Tei -- Design and screening of siRNAs against highly structured RNA targets / Neda Nasheri, John Paul Pezacki, and Selena M. Sagan -- Engineering small interfering RNAs by strategic chemical modification / Jesper B. Bramsen and Jørgen Kjems -- Design, selection, and evaluation of highly specific and functional siRNA incorporating unlocked nucleobase analogs / Narendra Vaish and Pinky Agarwal -- Design, preparation and evaluation of asymmetric small interfering RNA for specific gene silencing in mammalian cells / Chanil Chang [and others] -- Design of nuclease-resistant fork-like small interfering RNA (fsiRNA) / Elena L. Chernolovskaya and Marina A. Zenkova -- Designing dual-targeting siRNA duplexes having two active strands that combine siRNA and MicroRNA-like targeting / Pal Sætrom -- Strategies for designing and Validating immunostimulatory siRNAs / Michael P. Gantier -- Designing efficient and specific endoribonuclease-prepared siRNAs / Vineeth Surendranath [and others] -- Short hairpin RNA-mediated gene silencing / Luke S. Lambeth and Craig A. Smith -- Design of lentivirally expressed siRNAs / Ying Poi Liu and Ben Berkhout -- Bifunctional short hairpin RNA (bi-shRNA) : design and pathway to clinical application / Donald D. Rao [and others] -- Design and chemical modification of synthetic short shRNAs as potent RNAi triggers / Anne Dallas and Brian H. Johnston -- Production and application of long dsRNA in mammalian cells / Katerina Chalupnikova, Jana Nejepinska, and Petr Svoboda -- Design of RNAi reagents for invertebrate model organisms and human disease vectors / Thomas Horn and Michael Boutros -- Construction of shRNA expression plasmids for silkworm cell lines using single-stranded DNA and Bst DNA polymerase / Hiromitsu Tanaka -- Designing effective amiRNA and multimeric amiRNA against plant viruses / Muhammad Fahim and Philip J. Larkin -- Downregulation of plant genes with miRNA-induced gene silencing / Felipe Fenselau de Felippes.
Summary: 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.
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Includes bibliographical references and index.

What parameters to consider and which software tools to use for target selection and molecular design of small interfering RNAs / Olga Matveeva -- Methods for selecting effective siRNA target sequences using a variety of statistical and analytical techniques / Shigeru Takasaki -- Designing functional siRNA with reduced off-target effects / Yuki Naito and Kumiko Ui-Tei -- Design and screening of siRNAs against highly structured RNA targets / Neda Nasheri, John Paul Pezacki, and Selena M. Sagan -- Engineering small interfering RNAs by strategic chemical modification / Jesper B. Bramsen and Jørgen Kjems -- Design, selection, and evaluation of highly specific and functional siRNA incorporating unlocked nucleobase analogs / Narendra Vaish and Pinky Agarwal -- Design, preparation and evaluation of asymmetric small interfering RNA for specific gene silencing in mammalian cells / Chanil Chang [and others] -- Design of nuclease-resistant fork-like small interfering RNA (fsiRNA) / Elena L. Chernolovskaya and Marina A. Zenkova -- Designing dual-targeting siRNA duplexes having two active strands that combine siRNA and MicroRNA-like targeting / Pal Sætrom -- Strategies for designing and Validating immunostimulatory siRNAs / Michael P. Gantier -- Designing efficient and specific endoribonuclease-prepared siRNAs / Vineeth Surendranath [and others] -- Short hairpin RNA-mediated gene silencing / Luke S. Lambeth and Craig A. Smith -- Design of lentivirally expressed siRNAs / Ying Poi Liu and Ben Berkhout -- Bifunctional short hairpin RNA (bi-shRNA) : design and pathway to clinical application / Donald D. Rao [and others] -- Design and chemical modification of synthetic short shRNAs as potent RNAi triggers / Anne Dallas and Brian H. Johnston -- Production and application of long dsRNA in mammalian cells / Katerina Chalupnikova, Jana Nejepinska, and Petr Svoboda -- Design of RNAi reagents for invertebrate model organisms and human disease vectors / Thomas Horn and Michael Boutros -- Construction of shRNA expression plasmids for silkworm cell lines using single-stranded DNA and Bst DNA polymerase / Hiromitsu Tanaka -- Designing effective amiRNA and multimeric amiRNA against plant viruses / Muhammad Fahim and Philip J. Larkin -- Downregulation of plant genes with miRNA-induced gene silencing / Felipe Fenselau de Felippes.

Print version record.

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.

English.

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