Molecular Biology of Nucleases: 1st Edition (Hardback) book cover

Molecular Biology of Nucleases

1st Edition

By Nawin C. Mishra

CRC Press

296 pages

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Hardback: 9780849376580
pub: 1995-03-06
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Description

Nucleases occupy a central position in the biochemistry of DNA transactions and other metabolism of nucleic acids in all organisms. They have also proven useful in modern biological studies crucial for the development of recombinant DNA technology and reverse genetics. Nucleases assist in the identification and characterization of genes responsible for several diseases and their possible alleviation by gene therapy. Molecular Biology of Nucleases introduces the properties and biological roles of nucleases. It is the one comprehensive source for newcomers to the field.

Table of Contents

Introduction

Historical Perspectives

Protein, RNA and Other Molecules as Enzymes and as Nucleases

Nature of Enzymatic Reactions Catalyzed by Nucleases

Classification

Nature of Substrate

Mode of Attack

Site Specificity

Assay

Genetics of Nucleases and Biological Roles

Ribonuclease

General Ribonucleases

Microbial Nucleases

Mammalian Ribonucleases

Plant Ribonucleases

Evolution of Ribonucleases

Ribonuclease Involved in RNA-Processing

RNaseIII

RNaseP

RNaseE

RNaseM5

RNaseD

Eukaryotic RNA Splicing Enzymes

Ribonuclease H

E. coli RNaseH

Retroviral Reverse Transcriptase RNaseH

Yeast RNaseH

Other Eukaryotic RNaseH

Biological Function of RNaseH

Proofreading Activity of RNA Polymerase

Deoxyribonuclease

Classification of Enzymes

Deoxyribonucleases

Endonucleases

Exonuclease

Properties of Enzymes from Different Organisms

Bacterial Enzymes

Endonucleases

Restriction Endonucleases

Occurrence, Classification, and Their General Properties

Different Restriction Endonucleases and Their Properties

Type I Restriction Endonucleases

Purification and General Properties

Recognition Sequences and Nature of Substrate

Genetics

Cleavage Mechanism

Type II Restriction Endonucleases

Enzyme Purification and Assay

General Properties of the Enzymes

Reaction Conditions and the Enzyme Specificity

Nature of Substrate

Inhibition of Restriction Endonucleases

Restriction Endonuclease Genes

Type III Restriction Endonucleases

Evolutionary Significance and Biological Role

Damage Specific Nucleases

Classification and Assay

AP Endonucleases

Enzymes that Directly Attack Phosphodiester Linkages in the Damaged DNA Region

Assay

Properties of the Two Groups of Enzymes from Different Organisms

AP Endonucleases

AP Endonuclease Associated with Other Enzyme Activities

AP Endonucleases

Direct Acting Enzymes

Topoisomerases

Choreography and Topology of DNA

Enzyme Assay

Electron Microscopy

Sedimentation Methods

Agarose Gel Electrophoresis

Properties of Enzymes from Different Groups of Organisms

Prokaryotic Topoisomerases

Eukaryotic Topoisomerases

Mitochondrial Topoisomerases

Viral Topoisomerases

Genetics and Biological Role

Prokaryotic Topoisomerase Mutants

Eukaryotic Topoisomerase Mutants

Recombinases

General Description and Classification

General Recombinase

Site Specific Recombinase

Transpositional Recombinase

RNA Recombinase

Properties of Different Recombinases

General Recombinase

Site Specific Recombinase

Prokaryotic Site Specific Recombinase

Eukaryotic Site Specific Recombinase

Transpositional Recombinase

Control of Recombinases

RNA Recombinase

Sugar Non-Specific Nucleases

General Description, Classification, and Methods of Assay

Properties of Enzymes from Different Groups of Organisms

Microbial Nucleases

Animal Nucleases

Plant Nucleases

Non-Protein Nucleases

Ribozymes

RNaseP

Introns as Ribozymes

Group II Intron Ribozymes

Splicosomal SnRNA Ribozyme

Maturase

Hammerhead RNA as Ribozyme

Cis- and Transacting Ribozyme Endonuclease

Chemzymes

Chemicals and Metal Ligand Complexes as Nucleases

Peptides

Designer Nuclease

Molecules that Interact with Nucleases

Inhibitors

Proteins as Nuclease Inhibitors

RNA as Nuclease Inhibitors

Other Molecules that Act as Nuclease Inhibitors

Proteins that Interact with the Activity of Nuclease by Interacting with the Substrate (Nucleic Acids)

DNA Sequences that Interact with Nucleases

Chi Like Elements in Eukaryotes

Other Inhibitor Molecules

Proteins that Interact with DNA or Nuclease to Orchestrate the Activity of Nucleases

Biological Function of Nucleases

Replication

Three Steps in DNA Replication

Role of Viral Nuclease in the Degradation of Host DNA

Involvement of Nuclease During the Separation of Daughter Helices at the End of Replication

Involvement of Nucleases in the Rolling Circle Mechanism of DNA Replication

Involvement of Nuclease in the Replication of Linear DNA

Involvement of Nuclease in the Replication of Chromosome in Eukaryotes

DNA Repair

Baseless Sites

Sites with Altered Base or Incorrect Base

Crosslinking and Other Damages

DNA Repair Mechanisms

Excision Repair

Bypass Repair Pathways

Recombinational Repair Pathway

Inducible and Error Prone Repair Pathway

Mismatch Repair

Mismatch Repair in Mammalian Cells

Incision of Damaged DNA Is a Complex Process Involving Several Proteins

Excision Repair Mutants of Neurospora

Excision Repair Mutants of Yeast

Excision Repair Mutants of Drosophila

Excision Repair Mutants of Mammalian Cells

Recombination

Different Kinds of Genetic Recombination

Recombination Mechanisms and Nucleases

Gene Conversion and Postmeiotic Segregation

In Vitro Recombination System

Fungal Recombination Nucleases

Mismatch Repairs During Recombination

Recombination Pathways

Recombinational Control of Gene Expression

Role of Recombinase in Mammalian Antibody Diversity, Allelic Exclusion , and Class Switch

T Cell Surface Receptor

Engineered Expression of Genes by Recombinase

DNA Transfection or Transformation

Mutation

DNA Supercoiling and Maintenance of Chromosome Structure

Transcription

RNA Processing

RNA Trimming

RNA Splicing

RNA Editing

Control of Translation

Viral Maturation and Encapsidation

Nuclease in Defense Mechanism

Nucleic Acid Salvage

Nucleases and Human Diseases

Involvement of Nucleases in Human Disease

Xeroderma Pigmentosum

Axatia Telangiectasia

Cockayne Syndrome

Cancer

Aging

Immunological Diseases

Other Human Diseases

Nucleases and Neurological Disorders

Reverse Genetics, Human Diseases, and Nucleases

Use of Nucleases in the Control of Human Diseases

Nucleases as Tools

Nature of "Transforming Principle" as DNA

Isolation of DNA and RNA

Nearest Neighborhood Analysis

Isolation of a Gene

Uniparental Transmission During Cytoplasmic Inheritance

Physical Map of DNA

Use of Nuclease in the Development of Recombinant DNA Technology and the Molecular Cloning of a Gene

Construction of an Artificial Chromosome

New Method for Mapping Eukaryotic Chromosomes

Chromosome Walking (Overlap Hybridization)

Role of Nucleases in Transposon Mobility

Use of Nuclease in the Physical Mapping of a Mutational Site

Biological Activity of a DNA Segment

Use of Nucleases in the Identification of the Function of a DNA Segment Via Transformation Experiments

Use of Nuclease in the Deletion Mapping of Biological Activity

Use of Nucleases in Identification of the Function of a DNA Segment via Marker Rescue Method

Organization of Eukaryotic Chromosomes

Distinction Between Active and Inactive Genes: The Relation Between Activity of a Gene and Nuclease Sensitive Site

DNA Footprinting

Construction of Mutants: Site Specific Mutation and Protein Engineering

Nucleases in Directed Mutagenesis

Nick Translation and Labeling of DNA with High Specificity Radioactivity

Role of Nucleases in PCR

Gene Knockout

RNase Protection Assay

Use of Nucleases in Forensic Science

Human Genome Project

Nucleases and Evolution

Ribozyme as Evidence for the Early World of RNA

Chemzyme, Ribozyme, and Proteinzyme

The Role of Recombinase in Evolution

Nucleases and Control of DNA Transactions and Their Roles in Evolution

Role of Nucleases in Directed Mutagenesis: Adaptive Mutation and SOS Response

Nucleases as Multifunctional Molecules

Possible Horizontal Transmission of Nuclease Gene and Intron

Conclusions

References

Index

Subject Categories

BISAC Subject Codes/Headings:
MED008000
MEDICAL / Biochemistry
SCI049000
SCIENCE / Life Sciences / Biology / Molecular Biology