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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
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