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The Resource Ribozymes and siRNA protocols, edited by Mouldy Sioud

Ribozymes and siRNA protocols, edited by Mouldy Sioud

Ribozymes and siRNA protocols
Ribozymes and siRNA protocols
Statement of responsibility
edited by Mouldy Sioud
In this completely updated and expanded edition of a classic bench manual, hands-on experts take advantage of the latest advances in ribozyme, DNAzyme, hammerhead ribozymes and derivatives, and RNA interference technologies to describe in detail the exciting and successful methods now available for gene inactivation in vitro and in vivo. Their optimized techniques employ hairpin ribozymes, DNAzymes, hammerhead ribozymes and derivatives, group I intron ribozymes, RNase P ribozymes, and siRNAs, as well as general methods for RNA structure analysis, delivery of oligonucleotides, and gene therapy. Also provided are novel methods for identifying accessible cellular mRNA sites; group I intron and RNAse P ribozyme protocols for effective design, selection, and therapeutic applications; and the latest RNAi methods for sequence-specific gene silencing in a wide variety of organisms. Additional techniques cover the analysis of ribozyme structures and conformational transitions using nucleotide analog interference mapping and fluorescence resonance energy transfer, the use of ribozymes in clinical and gene therapy, and the use of ribozymes and DNAzymes in rodent models of human disease. Each proven protocol includes a background introduction outlining the principle behind the technique, step-by-step instructions, lists of equipment and reagents, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, Ribozymes and siRNA Protocols details for experienced and novice investigators alike the many exciting advances in our understanding of nucleic acid enzymes, as well as demonstrating how they may be used to analyze gene function and target validation, and to productively develop novel therapeutics for human diseases
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non fiction
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  • dictionaries
  • bibliography
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Methods in molecular biology
Series volume
v. 252
Ribozymes and siRNA protocols, edited by Mouldy Sioud
Ribozymes and siRNA protocols, edited by Mouldy Sioud
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Bibliography note
Includes bibliographical references and index
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online resource
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Ribozyme- and sirna-mediated mrna degradation: A general introduction / M. Sioud -- Combination of chemical and enzymatic rna synthesis / R.K. Gaur, A. Hanne and G. Krupp -- Determination of kinetic parameters for hammerhead and hairpin ribozymes / M.J. Fedor -- Real-time monitoring of rna and DNA reactions by fluorescence detection / K.K. Singh, A. Hanne and G. Krupp -- Quantification of ribozyme target rna using real-time pcr / D. Klein, C. Ricordi and R.L. Pastori -- Analysis of ribozyme structure and function by nucleotide analog interference mapping / S. Basu, C. Pazsint and G. Chowdhury -- Analysis of global conformational transitions in ribozymes / D.M. Lilley -- In vivo detection of ribozyme cleavage products and rna structure by use of terminal transferase-dependent pcr / H.H. Chen [and others] -- Identification of efficient cleavage sites in long-target rnas / W.H. Pan and G.A. Clawson -- Selection in vitro of allosteric ribozymes / A. Roth and R.R. Breaker -- Regulation of ribozyme cleavage activity by oligonucleotides / Y. Komatsu and E. Ohtsuka -- Tetracycline-regulated expression of hammerhead ribozymes in vivo / E.T. Bowden and A.T. Riegel -- Ribozyme expression systems / M. Sano and K. Taira -- Design and expression of chimeric u1/ribozyme transgenes / R. Abounader [and others] -- Design and validation of therapeutic hammerhead ribozymes for autosomal dominant diseases / J.J. Fritz [and others] -- Helicase-attached novel hybrid ribozymes / H. Kawasaki [and others] -- Functional gene discovery using hybrid ribozyme libraries / Y. Kato [and others] -- Maxizyme technology / M. Iyo, H. Kawasaki and K. Taira -- Target-site selection for the 10-23 dnazyme / M.J. Cairns and L.Q. Sun -- In vitro selected rna-cleaving DNA enzymes from combinatorial libraries / S. Chakraborti, B. Sriram and A.C. Banerjea -- Nucleic acid sequence analysis using dnazymes / M.J. Cairns and L.Q. Sun -- Crystallization of the hairpin ribozyme: Illustrative protocols / P.B. Rupert and A.R. Ferre-D'Amare -- An experimental method for selecting effective target sites and designing hairpin ribozymes / A. Barroso-delJesus [and others] -- Design and optimization of sequence-specific hairpin ribozymes / C. Romero-Lopez [and others] -- Design, targeting, and initial screening of strsv-derived hairpin ribozymes for optimum helix 1 length and catalytic efficiency in vitro / M.W. Richardson [and others] -- Optimization and application of the group i ribozyme trans-splicing reaction / C. Einvik [and others] -- Repair of myotonic dystrophy protein kinase (dmpk) transcripts by trans-splicing ribozymes / L.A. Phylactou -- General design and construction of rnase p ribozymes for gene-targeting applications / H. Zou [and others] -- In vitro selection of rnase p ribozymes that efficiently cleave a target mrna / K. Kim and F. Liu -- In vitro selection of external guide sequences for directing human rnase p to cleave a target mrna / S. Raj and F. Liu -- Rnase p-mediated inhibition of viral growth by exogenous administration of short oligonucleotide external guide sequence / W. Dunn and F. Liu -- Rnase p ribozyme as an antiviral agent against human cytomegalovirus / P. Trang and F. Liu -- Inhibition of gene expression by nucleic acid enzymes in rodent models of human disease / P.O. Iversen and M. Sioud -- Potential design rules and enzymatic synthesis of sirnas / M. Sioud and M. Leirdal -- Rna interference (rnai) with rnase iii-prepared sirnas / D. Yang, A. Goga and J.M. Bishop -- Rnai expression vectors in mammalian cells / M. Miyagishi and K. Taira -- Gene-array analysis of glioma cells after treatment with an anti-pkcalpha sirna: A general protocol / M. Leirdal and M. Sioud -- Rnai in living mice / H. Hasuwa and M. Okabe -- Construction and transfection of pcr products expressing sirnas or shrnas in mammalian cells / D. Castanotto and J.J. Rossi -- Systemic delivery of synthetic sirnas / M. Sioud and D.R. Sorensen -- Adenovirus-delivered sirna / C. Shen and S.N. Reske -- Rnai expression vectors in plant cells / H. Akashi, M. Miyagishi and K. Taira -- Delivery agents for oligonucleotides / O. Seksek and J. Bolard -- Selection of peptides for specific delivery of oligonucleotides into cancer cells / M. Shadidi and M. Sioud -- Clinical gene therapy research utilizing ribozymes: Application to the treatment of hiv/aids / F.K. Ngok [and others] -- Critical steps in the implementation of hematopoietic progenitor-cell gene therapy using ribozyme vectors: A laboratory protocol / M.P. Boyd [and others]
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2nd ed.
1 online resource (xv, 623 pages)
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