Ribozymes and siRNA protocols / edited by Mouldy Sioud.

Format:

Book

Contributor:

Sioud, Mouldy.

Series:

Methods in molecular biology (Clifton, N.J.) ; v. 252.

Methods in molecular biology ; v. 252

Language:

English

Subjects (All):

Catalytic RNA--Laboratory manuals.

Catalytic RNA.

Small interfering RNA--Laboratory manuals.

Small interfering RNA.

RNA, Catalytic.

Gene Expression Profiling.

Genetic Therapy.

RNA, Small Interfering.

Medical Subjects:

RNA, Catalytic.

Gene Expression Profiling.

Genetic Therapy.

RNA, Small Interfering.

Genre:

Laboratory manuals.

Handbooks and manuals.

Physical Description:

xv, 623 pages : illustrations ; 24 cm.

Edition:

Second edition.

Place of Publication:

Totowa, N.J. : Humana Press, [2004]

Contents:

1 Ribozyme- and siRNA-Mediated mRNA Degradation: A General Introduction / Mouldy Sioud 1

2 Combination of Chemical and Enzymatic RNA Synthesis / Rajesh K. Gaur, Andreas Hanne, Guido Krupp 9

3 Determination of Kinetic Parameters for Hammerhead and Hairpin Ribozymes / Martha J. Fedor 19

4 Real-Time Monitoring of RNA and DNA Reactions by Fluorescence Detection / Kumud K. Singh, Andreas Hanne, Guido Krupp 33

5 Quantification of Ribozyme Target RNA Using Real-Time PCR / Dagmar Klein, Camillo Ricordi, Ricardo L. Pastori 49

6 Analysis of Ribozyme Structure and Function by Nucleotide Analog Interference Mapping / Soumitra Basu, Catherine Pazsint, Gopeswar Chowdhury 57

7 Analysis of Global Conformational Transitions in Ribozymes / David M. J. Lilley 77

8 In Vivo Detection of Ribozyme Cleavage Products and RNA Structure by Use of Terminal Transferase-Dependent PCR / Hsiu-Hua Chen, Daniela Castanotto, Jeanne LeBon, John J. Rossi, Arthur D. Riggs 109

9 Identification of Efficient Cleavage Sites in Long-Target RNAs / Wei-Hua Pan, Gary A. Clawson 125

10 Selection In Vitro of Allosteric Ribozymes / Adam Roth, Ronald R. Breaker 145

11 Regulation of Ribozyme Cleavage Activity by Oligonucleotides / Yasuo Komatsu, Eiko Ohtsuka 165

12 Tetracycline-Regulated Expression of Hammerhead Ribozymes In Vivo / Emma T. Bowden, Anna T. Riegel 179

13 Ribozyme Expression Systems / Masayuki Sano, Kazunari Taira 195

14 Design and Expression of Chimeric U1/Ribozyme Transgenes / Roger Abounader, Robert Montgomery, Harry Dietz, John Laterra 209

15 Design and Validation of Therapeutic Hammerhead Ribozymes for Autosomal Dominant Diseases / Jason J. Fritz, Marina Gorbatyuk, Alfred S. Lewin, William W. Hauswirth 221

16 Helicase-Attached Novel Hybrid Ribozymes / Hiroaki Kawasaki, Masaki Warashina, Tomoko Kuwabara, Kazunari Taira 237

17 Functional Gene Discovery Using Hybrid Ribozyme Libraries / Yoshio Kato, Masaru Tsunemi, Makoto Miyagishi, Hiroaki Kawasaki, Kazunari Taira 245

18 Maxizyme Technology / Mayu Iyo, Hiroaki Kawasaki, Kazunari Taira 257

19 Target-Site Selection for the 10-23 DNAzyme / Murray J. Cairns, Lun-Quan Sun 267

20 In Vitro Selected RNA-Cleaving DNA Enzymes From Combinatorial Libraries / Samitabh Chakraborti, Bandi Sriram, Akhil C. Banerjea 279

21 Nucleic Acid Sequence Analysis Using DNAzymes / Murray J. Cairns, Lun-Quan Sun 291

22 Crystallization of the Hairpin Ribozyme: Illustrative Protocols / Peter B. Rupert, Adrian R. Ferre-D'Amare 303

23 An Experimental Method for Selecting Effective Target Sites and Designing Hairpin Ribozymes / Alicia Barroso-delJesus, Elena Puerta-Fernandez, Cristina Romero-Lopez, Alfredo Berzal-Herranz 313

24 Design and Optimization of Sequence-Specific Hairpin Ribozymes / Cristina Romero-Lopez, Alicia Barroso-delJesus, Elena Puerta-Fernandez, Alfredo Berzal-Herranz 327

25 Design, Targeting, and Initial Screening of sTRSV-Derived Hairpin Ribozymes for Optimum Helix 1 Length and Catalytic Efficiency In Vitro / Max W. Richardson, Linda Hostalek, Michelle Dobson, Jason Hu, Richard Shippy, Andrew Siwkowski, Jonathan D. Marmur, Kamel Khalili, Paul E. Klotman, Arnold Hampel, Jay Rappaport 339

26 Optimization and Application of the Group I Ribozyme Trans-Splicing Reaction / Christer Einvik, Tonje Fiskaa, Eirik W. Lundblad, Steinar Johansen 359

27 Repair of Myotonic Dystrophy Protein Kinase (DMPK) Transcripts by Trans-Splicing Ribozymes / Leonidas A. Phylactou 373

28 General Design and Construction of RNase P Ribozymes for Gene-Targeting Application / Hua Zou, Karen Chan, Phong Trang, Fenyong Liu 385

29 In Vitro Selection of RNase P Ribozymes That Efficiently Cleave a Target mRNA / Kihoon Kim, Fenyong Liu 399

30 In Vitro Selection of External Guide Sequences for Directing Human RNase P to Cleave a Target mRNA / Stephen Raj, Fenyong Liu 413

31 RNase P-Mediated Inhibition of Viral Growth by Exogenous Administration of Short Oligonucleotide External Guide Sequence / Walter Dunn, Fenyong Liu 425

32 RNase P Ribozyme As an Antiviral Agent Against Human Cytomegalovirus / Phong Trang, Fenyong Liu 437

33 Inhibition of Gene Expression by Nucleic Acid Enzymes in Rodent Models of Human Disease / Per Ole Iversen, Mouldy Sioud 451

34 Potential Design Rules and Enzymatic Synthesis of siRNAs / Mouldy Sioud, Marianne Leirdal 457

35 RNA Interference (RNAi) With RNase III-Prepared siRNAs / Dun Yang, Andrei Goga, J. Michael Bishop 471

36 RNAi Expression Vectors in Mammalian Cells / Makoto Miyagishi, Kazunari Taira 483

37 Gene-Array Analysis of Glioma Cells After Treatment With Anti-PKC-[alpha] siRNA / Marianne Leirdal, Mouldy Sioud 493

38 RNAi in Living Mice / Hidetoshi Hasuwa, Masaru Okabe 501

39 Construction and Transfection of PCR Products Expressing siRNAs or shRNAs in Mammalian Cells / Daniela Castanotto, John J. Rossi 509

40 Systemic Delivery of siRNAs / Mouldy Sioud, Dag R. Sorensen 515

41 Adenovirus-Delivered siRNA / Changxian Shen, Sven N. Reske 523

42 RNAi Expression Vectors in Plant Cells / Hideo Akashi, Makoto Miyagishi, Kazunari Taira 533

43 Delivery Agents for Oligonucleotides / Olivier Seksek, Jacques Bolard 545

44 Selection of Peptides for Specific Delivery of Oligonucleotides Into Cancer Cells / Mohsen Shadidi, Mouldy Sioud 569

45 Clinical Gene Therapy Research Utilizing Ribozymes: Application to the Treatment of HIV/AIDS / Frances K. Ngok, Ronald T. Mitsuyasu, Janet L. Macpherson, Maureen P. Boyd, Geoff P. Symonds, Rafael G. Amado 581

46 Critical Steps in the Implementation of Hematopoietic Progenitor-Cell Gene Therapy Using Ribozyme Vectors: A Laboratory Protocol / Maureen P. Boyd, Frances K. Ngok, Alison V. Todd, Geoff P. Symonds, Janet L. Macpherson, Rafael G. Amado 599.

Notes:

Includes bibliographical references and index.

ISBN:

1588292266

OCLC:

52766190