RNA and DNA editing : methods and protocols / edited by Ruslan Aphasizhev.

Contributor(s): Aphasizhev, Ruslan
Material type: TextTextSeries: Springer protocols (Series): ; Methods in molecular biology (Clifton, N.J.): v. 718.Publisher: New York : Humana, ©2011Description: 1 online resource (xiii, 275 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9781617790188; 1617790184Subject(s): RNA editing | DNA | Genetic transcription | Nucleotide sequence | RNA Editing | Base Sequence | DNA | Genetic transcription | Nucleotide sequence | RNA editing | Biology | Health & Biological Sciences | Genetics | enzymologie | enzymology | biomedische wetenschappen | biomedicine | humane genetica | human genetics | Medicine (General) | Geneeskunde (algemeen)Genre/Form: Electronic books. Additional physical formats: Print version:: RNA and DNA editing.DDC classification: 572.8/6 LOC classification: QH450.25Online resources: Click here to access online
Contents:
Three-dimensional reconstruction of trypanosoma brucei editosomes using single-particle electron microscopy / H.U. Goringer [and others] -- Icoda: RNAi-based inducible knock-in system in trypanosoma brucei / G.E. Ringpis, R.H. Lathrop and R. Aphasizhev -- Perturbing a-to-i RNA editing using genetics and homologous recombination / C.J. Staber [and others] -- Laser microdissection and pressure catapulting of single human motor neurons for RNA editing analysis / H. Sun [and others] -- Biochemical identification of A-to-I RNA editing sites by the inosine chemical erasing (ice) method / M. Sakurai and T. Suzuki -- Identifying mRNA editing deaminase targets by RNA-seq / B.R. Rosenberg, S. Dewell and F.N. Papavasiliou -- Mouse and other rodent models of C to U RNA editing / V. Blanc and N.O. Davidson -- In vivo analysis of RNA editing in plastids / S. Ruf and R. Bock -- Identifying specific trans-factors of RNA editing in plant mitochondria by multiplex single base extension typing / M. Takenaka -- Complementation of mutants in plant mitochondrial RNA editing by protoplast transfection / M. Takenaka and A. Zehrmann -- A high-throughput assay for DNA deaminases / M. Wang, C. Rada and M.S. Neuberger -- Biochemical fractionation and purification of high-molecular-mass apobec3g complexes / Y.L. Chiu -- Analysis of tRNA editing in native and synthetic substrates / J.L. Spears, K.W. Gaston and J.D. Alfonzo -- Post-transcriptional modification of RNAs by artificial box h/aca and box c/d rnps / C. Huang, J. Karijolich and Y.T. Yu -- Functional analysis of noncoding RNAs in trypanosomes: RNA walk, a novel approach to study RNA-RNA interactions between small RNA and its target / C. Wachtel and S. Michaeli -- A post-labeling approach for the characterization and quantification of RNA modifications based on site-directed cleavage by dnazymes / M. Meusburger, M. Hengesbach and M. Helm.
Summary: The recent expansion in diversity of RNA and DNA editing types has stimulated the development of many unique genetic, molecular, biochemical, and computational approaches to biological issues. In RNA and DNA Editing: Methods and Protocols, leading experts in the field introduce methods developed over the last few years to study editing substrates, mechanisms of specificity, and functions of RNA and DNA editing enzymes and complexes. Sections of the book are dedicated to state-of-the art techniques which enable investigation of uracil insertion/deletion RNA editing in mitochondrion of Trypanosoma brucei, adenosine to inosine RNA editing, cytidine to uracil RNA and DNA editing, as well as tRNA editing and RNA modifications. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA and DNA Editing: Methods and Protocols seeks to inspire the further development of these vital and powerful techniques.
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Includes bibliographical references and index.

Three-dimensional reconstruction of trypanosoma brucei editosomes using single-particle electron microscopy / H.U. Goringer [and others] -- Icoda: RNAi-based inducible knock-in system in trypanosoma brucei / G.E. Ringpis, R.H. Lathrop and R. Aphasizhev -- Perturbing a-to-i RNA editing using genetics and homologous recombination / C.J. Staber [and others] -- Laser microdissection and pressure catapulting of single human motor neurons for RNA editing analysis / H. Sun [and others] -- Biochemical identification of A-to-I RNA editing sites by the inosine chemical erasing (ice) method / M. Sakurai and T. Suzuki -- Identifying mRNA editing deaminase targets by RNA-seq / B.R. Rosenberg, S. Dewell and F.N. Papavasiliou -- Mouse and other rodent models of C to U RNA editing / V. Blanc and N.O. Davidson -- In vivo analysis of RNA editing in plastids / S. Ruf and R. Bock -- Identifying specific trans-factors of RNA editing in plant mitochondria by multiplex single base extension typing / M. Takenaka -- Complementation of mutants in plant mitochondrial RNA editing by protoplast transfection / M. Takenaka and A. Zehrmann -- A high-throughput assay for DNA deaminases / M. Wang, C. Rada and M.S. Neuberger -- Biochemical fractionation and purification of high-molecular-mass apobec3g complexes / Y.L. Chiu -- Analysis of tRNA editing in native and synthetic substrates / J.L. Spears, K.W. Gaston and J.D. Alfonzo -- Post-transcriptional modification of RNAs by artificial box h/aca and box c/d rnps / C. Huang, J. Karijolich and Y.T. Yu -- Functional analysis of noncoding RNAs in trypanosomes: RNA walk, a novel approach to study RNA-RNA interactions between small RNA and its target / C. Wachtel and S. Michaeli -- A post-labeling approach for the characterization and quantification of RNA modifications based on site-directed cleavage by dnazymes / M. Meusburger, M. Hengesbach and M. Helm.

Print version record.

The recent expansion in diversity of RNA and DNA editing types has stimulated the development of many unique genetic, molecular, biochemical, and computational approaches to biological issues. In RNA and DNA Editing: Methods and Protocols, leading experts in the field introduce methods developed over the last few years to study editing substrates, mechanisms of specificity, and functions of RNA and DNA editing enzymes and complexes. Sections of the book are dedicated to state-of-the art techniques which enable investigation of uracil insertion/deletion RNA editing in mitochondrion of Trypanosoma brucei, adenosine to inosine RNA editing, cytidine to uracil RNA and DNA editing, as well as tRNA editing and RNA modifications. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA and DNA Editing: Methods and Protocols seeks to inspire the further development of these vital and powerful techniques.

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