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