Ribozyme Protocols / Edition 1

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Overview

A comprehensive collection of essential and easily reproducible techniques currently used by leading researchers to manipulate RNA molecules and to inactivate gene expression in vivo. The methods range from theoretical design to clinical application and include the synthesis and assay of ribozymes, as well as their use both in vitro and in vivo. Each method is presented by an expert with substantial hands-on experience and in far greater detail than is to be generally found in the research literature. The book will be indispensable not only to those workers new to the field, but also to experienced researchers who want to expand their range of expertise.

The book contains black-and-white illustrations.

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Editorial Reviews

Doody's Review Service
Reviewer: Karen Buchkovich, PhD (University of Illinois at Chicago College of Medicine)
Description: This is a collection of approximately 50 protocols on the design and use of ribozymes, the RNA molecules that break and/or form covalent bonds. The book includes protocols for the selection of ribozyme target sites, synthesis and production of ribozymes, analysis of ribozyme structure, optimization of ribozyme reaction parameters, delivery of ribozymes, and practical applications of ribozymes.
Purpose: The purpose is to provide a helpful compilation of ribozyme protocols that will be of use to researchers with limited or no experience with ribozymes. This collection of protocols is quite comprehensive, covering every imaginable aspect of ribozyme production and application. The contributors of the protocols are authorities in the field who have published original research papers on the topic.
Audience: This is a good introduction for those without background knowledge in the area.
Features: The protocols are presented in a clear, concise format that includes a brief introduction, list of required materials, a step-by-step methods section, notes, and references. The notes provide important theoretical information, alternative methodologies, and troubleshooting advice. Any scientist will tell you that the best laboratory protocols provide practical troubleshooting advice, as do most of the protocols in this book. The references included with the protocols are adequate, providing both recent, up-to-date references and older, seminal references. The overall organization and appearance of the book, including the index, illustrations, and type format, is practical and pleasing. The table of contents would be more helpful if subheadings were included to organize the 49 chapters. While the grouping of chapters according to subject is obvious after reading the preface, this organization was not apparent from the table of contents.
Assessment: This will be very useful for both novices and experts as a comprehensive collection of ribozyme protocols. I recommend its purchase to libraries supporting biomedical and agricultural research and to individual researchers interested in applying ribozyme technology.
Karen Buchkovich
This is a collection of approximately 50 protocols on the design and use of ribozymes, the RNA molecules that break and/or form covalent bonds. The book includes protocols for the selection of ribozyme target sites, synthesis and production of ribozymes, analysis of ribozyme structure, optimization of ribozyme reaction parameters, delivery of ribozymes, and practical applications of ribozymes. The purpose is to provide a helpful compilation of ribozyme protocols that will be of use to researchers with limited or no experience with ribozymes. This collection of protocols is quite comprehensive, covering every imaginable aspect of ribozyme production and application. The contributors of the protocols are authorities in the field who have published original research papers on the topic. This is a good introduction for those without background knowledge in the area. The protocols are presented in a clear, concise format that includes a brief introduction, list of required materials, a step-by-step methods section, notes, and references. The notes provide important theoretical information, alternative methodologies, and troubleshooting advice. Any scientist will tell you that the best laboratory protocols provide practical troubleshooting advice, as do most of the protocols in this book. The references included with the protocols are adequate, providing both recent, up-to-date references and older, seminal references. The overall organization and appearance of the book, including the index, illustrations, and type format, is practical and pleasing. The table of contents would be more helpful if subheadings were included to organize the 49 chapters. While the grouping of chaptersaccording to subject is obvious after reading the preface, this organization was not apparent from the table of contents. This will be very useful for both novices and experts as a comprehensive collection of ribozyme protocols. I recommend its purchase to libraries supporting biomedical and agricultural research and to individual researchers interested in applying ribozyme technology.
Booknews
A collection of 49 essential techniques currently in use by researchers manipulating RNA molecules and inactivating gene expression in vivo. The methods include theoretical design and clinical application from the synthesis and assay of ribozymes to their use both in vitro and in vivo. The protocols feature ribozyme design rules and production by transcription, explore the clinical potential of ribozymes, cover structure and determination methods, describe vectors and cassettes for in vivo expression, and detail computer programs which predict target RNA folding and select ribozyme cleavage sites. Annotation c. by Book News, Inc., Portland, Or.

3 Stars from Doody
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Product Details

  • ISBN-13: 9780896033894
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 5/8/1997
  • Series: Methods in Molecular Biology Series , #74
  • Edition description: 1997
  • Edition number: 1
  • Pages: 492
  • Product dimensions: 9.21 (w) x 6.14 (h) x 1.13 (d)

Table of Contents

Ribozymes: An Introduction
Helen A. James and Philip C. Turner

Computer-Aided Calculation of the Local Folding Potential of Target RNA and its Use for Ribozyme Design
Georg Sczakiel and Martin Tabler

Computational Approaches to the Identification of Ribozyme Target Sites
William James and Elizabeth Cowe

Computer Analysis of the Conservation and Uniqueness of Ribozyme-Targeted HIV Sequences
Mary Beth DeYoung and Arnold Hampel

Selection of Accessible Sites for Ribozymes on Large RNA Transcripts
Bruce L. Frank and John Goodchild

Selection of Efficient Ribozyme Cleavage Sites in Target RNAs
Andre Lieber, Mikkel Rohde, and Michael Strauss

Chemical Synthesis, Analysis, and Purification of Ribozymes
Ravi Vinayak

A Practical Method for the Production of RNA and Ribozymes
Francine E. Wincott and Nassim Usman

Preparation of Templates for Production of Ribozymes and Substrates
Rajesh K. Gaur and Guido Krupp

Enzymatic Synthesis and Characterization of Unmodified Ribozymes and Substrates
Guido Krupp

T7 Transcript Length Determination Using Enzymatic RNA Sequencing
Andrew Siwkowski

Chemical and Enzymatic Approaches to Construct Modified RNAs
Rajesh K. Gaur and Guido Krupp

Applications of Modified Transcripts
Rajesh K. Gaur, Frank Conrad, and Guido Krupp

Cloning Strategies for Catalytic Antisense RNAs
Martin Tabler and Mina Tsagris

PCR-Based Construction of Long Hammerhead Ribozymes
Martin Zillman and Gregory Robinson

Design and Production of Asymmetric Hammerhead Ribozymes
Martin Tabler and Georg Sczakiel

Minimized Hammerhead Ribozymes
Maxine J. McCall, Philip Hendry, and Trevor J. Lockett

Design of Hairpin Ribozymes for In Vitro and Cellular Applications
Qiao Yu and John M. Burke

Design of the Hairpin Ribozyme for Targeting Specific RNA Sequences
Arnold Hampel, Mary Beth DeYoung, Scott Galasinski, and Andrew Siwkowski

Design and Preparation of Sequence Specific RNase P Ribozymes
Denis Drainas and Guido Krupp

Theoretical Considerations in Measuring Reaction Parameters
Timothy S. McConnell

Experimental Approaches for Measuring Reaction Parameters
Timothy S. McConnell

Determination of Catalytic Parameters for Hairpin Ribozymes
Mary Beth DeYoung, Andrew Siwkowski, and Arnold Hampel

Characterizing Ribozyme Cleavage Reactions
Philip Hendry, Maxine J. McCall, and Trevor J. Lockett

Defining Optimum Reaction Conditions for Hammerhead Ribozymes
Philip Hendry, Maxine J. McCall, and Trevor J. Lockett

Using Fluorescence Resonance Energy Transfer to Investigate Hammerhead Ribozyme Kinetics
Thomas A. Perkins and John Goodchild

Design of Hybridizing Arms in Hammerhead Ribozymes
Philip Hendry, Maxine J. McCall, and Trevor J. Lockett

Optimization of Hammerhead Flanking Sequences Using Oligonucleotide Facilitators
John Goodchild

Enhancement of Ribozyme Function by RNA Binding Proteins
Nan Sook Lee, Edouard Bertrand, and John J. Rossi

Selection of Fast-Hybridizing Complementary RNA Species In Vitro
Ralf Kronenwett and Georg Sczakiel

In Vitro Selection of Hairpin Ribozymes
Bruno Sargueil and John M. Burke

The Detection of Hammerhead Ribozyme Cleavage by RT-PCR Methods
Rhonda Perriman

Detection of Ribozyme Cleavage Products Using Reverse Ligation Mediated PCR (RL-PCR)
Edouard Bertrand, Micheline Fromont-Racine, Raymond Pictet, and Thierry Grange

Quantitation of Ribozyme Target Abundance by QCPCR
Amber A. Beaudry and James A. McSwiggen

Trans-splicing Reactions by Ribozymes
Joshua T. Jones, Seong-Wook Lee, and Bruce A. Sull

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