Nuclease methods and protocols
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Bibliographic Information
Nuclease methods and protocols
(Methods in molecular biology / John M. Walker, series editor, v. 160)
Humana Press ,c2001
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Description and Table of Contents
Description
Nucleases, enzymes that restructure or degrade nucleic acid polymers, are vital to the control of every area of metabolism. They range from "housekeeping" enzymes with broad substrate ranges to extremely specific tools (1). Many types of nucleases are used in lab protocols, and their commercial and clinical uses are expanding. The purpose of Nuclease Methods and Protocols is to introduce the reader to some we- characterized protein nucleases, and the methods used to determine their activity, structure, interaction with other molecules, and physiological role. Each chapter begins with a mini-review on a specific nuclease or a nuclease-related theme. Although many chapters cover several topics, they were arbitrarily divided into five parts: Part I, "Characterizing Nuclease Activity," includes protocols and assays to determine general (processive, distributive) or specific mechanisms. Methods to assay nuclease products, identify cloned nucleases, and determine their physiological role are also included here. Part II, "Inhibitors and Activators of Nucleases," summarizes assays for measuring the effects of other proteins and small molecules. Many of these inhibitors have clinical relevance. Part III, "Relating Nuclease Structure and Function," provides an overview of methods to determine or model the 3-D structure of nucleases and their complexes with substrates and inhibitors. A 3-D structure can greatly aid the rational design of nucleases and inhibitors for specific purposes. Part IV, "Nucleases in the Clinic," summarizes assays and protocols suitable for use with t- sues and for nuclease based therapeutics.
Table of Contents
Part I. Characterizing Nuclease Activity
Processivity of DNA Repair Enzymes
R. Stephen Lloyd
Analysis by HPLC of Distributive Activities and the Synthetic (Back) Reaction of Pancreatic-Type Ribonucleases
M. Victoria Nogues and Claudi M. Cuchillo.
lre1p: A Kinase and Site-Specific Endoribonuclease
Tania N. Gonzalez and Peter Walter
Microtiter-Plate Assay and Related Assays for Nonspecific Endonucleases
Gregor Meiss, Oleg Gimadutdinow, Peter Friedhoff, and Alfred M. Pingoud
Quantitating mRNAs with Relative and Competitive RT-PCR, Ellen A. Prediger
Expressing Self-Incompatibility RNases (S-RNases) in Transgenic Plants
Brian Beecher and Bruce A. McClure
Molecular Cloning, Tissue Distribution, and Chromosomal Localization of the Human Homolog of the R2/Th/Stylar Ribonuclease Gene Family
Francesco Acquati, Cinzia Nucci, Marco G. Bianchi, Tatiana Gorletta, and Roberto Taramelli
Part II. Inhibitors and Activators of Nucleases
Ribonuclease Inhibitors
Brittan L. Pasloske
Producing Soluble Recombinant RNases and Assays to Measure Their Interaction with Interferon-g In Vitro
Catherine H. Schein
Assays for the Evaluation of HIV-1 Integrase Inhibitors
Zeger Debyser, Peter Cherepanov, Wim Pluymers, and Erik De Clercq
The Direction of Ribonucleases H by Antisense Oligodeoxynucleotides
Richard V. Giles and David M. Tidd
The 2-5A/RNase L Pathway and Inhibition by RNase L Inhibitor (RLI)
Catherine Bisbal, Tamim Salehzada, Michelle Silhol, Camille Martinand, Florence Le Roy, and Bernard Lebleu
Part III. Relating Nuclease Structure and Function
Crystallization and Crystal Structure Determination of Ribonuclease A-Ribonuclease Inhibitor Protein Complex
Bostjan Kobe
Methods for Studying the Interaction of Barnase with Its Inhibitor Barstar
GideonSchreiber
Assaying In Vitro Refolding of RNases by Mass Spectrometry
Gennaro Marino, Piero Pucci, and Margherita Ruoppolo
Dissecting Nucleases into Their Structural and Functional Domains: Mapping the RNA-Binding Surface of RNase III by NMR
Andres Ramos and Annalisa Pastore
Using Electrostatics to Define the Active Site of Serratia Endonuclease
Kurt L. Krause and Mitchell D. Miller
Homology Modeling and Simulations of Nuclease Structures
Kizhake V. Soman, Catherine H. Schein, Hongyao Zhu, and Werner Braun
Methods for Determining Activity and Specificity of DNA Binding and DNA Cleavage by Class II Restriction Endonucleases
Albert Jeltsch and Alfred M. Pingoud
Engineered Properties and Assays for Human DNase I Mutants
Clark Q. Pan, Dominick V. Sinicropi, and Robert A. Lazarus
Part IV. Nucleases in the Clinic
Assays for Human DNase I Activity in Biological Matrices
Dominick V. Sinicropi and Robert A. Lazarus
Evaluation of Retroviral Ribonuclease H Activity
Jennifer T. Miller, Jason W. Rausch, and Stuart F. J. Le Grice
Assays for Detection of RNase A Superfamily Ribonucleases
Helene F. Rosenberg and Joseph B. Domachowske
Assay for Antitumor and Lectin Activity in RNase Homologs
Kazuo Nitta
Isolation and Enzymatic Activity of Angiogenin
James F. Riordan and Robert Shapiro
Preparation and Preclinical Characterization of RNase-Based Immunofusion Proteins
Dianne L. Newton and Susanna M. Rybak
Part V. Assays Using Nucleases
Restriction Endonucleases and Their Uses
Raymond J. Williams
Isolation and Characterization of an Unknown Restriction Endonuclease
Raymond J. Williams
Gene Modification with Hapaxoterministic Restriction Enzymes: Easing the Way, Shelby L. Berger
Techniques to Measure Nucleic Acid-Protein Binding a
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