Nucleases: Molecular Biology and Applications

An authoritative study of a cornerstone of cutting–edge DNA technology
Nucleases are a class of enzymes that catalyze the hydrolysis of nucleic acids (DNA, RNA) in all organisms, including humans. In addition to their important biological role, nucleases have recently emerged as useful tools in laboratory studies, and have led to the development of such fields as recombinant DNA technology, molecular cloning, and genomics. Nawin Mishra’s Nucleases, the first comprehensive treatment of the subject, introduces the properties and biological roles of nucleases to newcomers in the field and provides the basis of their possible application to critical aspects of science, commerce, and industry.
Covering the structure and biochemical properties of nucleases, Mishra’s text further guides the reader to understand how these enzymes can be exploited to make new products for the diagnosis and treatment of disease. Molecular cloning, made possible by the evolving understanding and application of nucleases, may well lead to the identification and characterization of genes responsible for diseases and their possible alleviation by gene therapy and the development of designer drugs. Nucleases is a one–stop, authoritative resource for students of biology and researchers currently practicing in the field. Chapter topics include:RibonucleasesRestriction EndonucleasesTopoisomerasesSugar Non–Specific NucleasesMolecules That Interact with Nucleases
An ideal text and reference work for professionals and students in biochemistry, genetics, and molecular biology, Nucleases promises to be the field’s standard–bearer for years to come.

Spis treści:
Preface.
List of Nobel Prize Winners for Their Research Work with Nucleases.
About the Author.
1. Introduction.
I. Historical Perspectives.
II. Protein, RNA, DNA, and Other Molecules as Nucleases.
III. Natu re of Enzymatic Reactions Catalyzed by Nucleases.
IV. Classification.
A. Nature of Substrates.
B. Mode of Attack.
C. Site–Specificity and Structure–Selectivity.
V. Methods for the Study of Nucleases.
A. Methods for the Assay of the Enzymatic Activity.
B. Methods for the Study and Characterization of Nucleases.
VI. Genetics of Nucleases and Biological Roles.
VII. Applications of Nucleases.
2. Ribonuclease.
I. General Ribonucleases.
A. Microbial Ribonucleases.
1. RNaseT1.
2. RNaseT2.
B. Mammalian Ribonucleases.
1. Bovine Pancreatic Rnase.
2. RNaseA.
3. Human Pancreatic Ribonuclease (HPR).
4. Human Nonsecretory Ribonuclease (HNSR).
5. Human Major Basic Protein (MBP), Eosinophil Cationic Protein (ECP) and Eosinophil–Derived Neurotoxin (EDN).
6. Angiogenin.
7. Interferon–Induced Mammalian Ribonuclease.
8. Human RNase with a Possible Role in Tumor Suppression.
C. Plant Ribonucleases.
D. Evolution of Ribonucleases.
II. Ribonucleases Involved in RNA Processing (Trimming, Splicing, and Editing).
A. RNaseIII and RNaseIII–Like Enzymes.
B. RNaseP.
C. RNaseE.
D. RNaseM5.
E. RNaseD.
F. Eukaryotic RNA–Splicing Enzymes.
1. Yeast tRNA Splicing Endonuclease.
III. Ribonuclease H.
A. E. coli RNaseH.
B. Retroviral Reverse Transcriptase RNaseH.
C. Yeast RNaseH.
D. Human RNaseH.
E. Other Eukaryotic RNaseH.
F. Biological Function of RNaseH.
IV. Proofreading Activity of RNA Polymerase.
3. Deoxyribonuclease.
I. Classification of Enzymes.
A. Deoxyribonucleases.
B. Endonucleases
C. Exonuclease.
II. Properties of Enzymes from Different Organisms.
A. Bacterial Enzymes.
1. Exonuclease I.
2. Exonuclease II.
3. Exonuclease III.
4. Application of the Enzyme Exonuclease III.
5. Exonucleases IVA and IVB.
6. Exonuclease V (RecBCD Enzyme).
7. RecBCD (Exo V) from Other Organisms.
8. Exonuclease VI.
9 . Exonuclease VII.
10. Exonucleases Associated with DNA Polymerases.
11. Exonuclease VIII.
B. Endonucleases.
1. Bacterial Enzymes.
2. Mammalian Deoxyribonuclease.
4. Restriction Endonucleases.
I. Occurrence, Classification, and Their General Properties.
A. Different Restriction Endonucleases and Their Properties.
II. Type I Restriction Endonucleases.
A. Purification and General Properties.
B. Recognition Sequences and Nature of Substrate.
C. Different Kinds of Type II Restriction Endonucleases.
D. Genetics.
E. Cleavage Mechanism.
III. Type II Restriction Endonucleases.
A. Enzyme Purification and Assay.
B. General Properties of the Enzyme.
C. Crystal Structure of the Restriction Endonucleases.
D. Reaction Conditions and Enzyme Specificity.
E. Nature of Substrate.
1. Synthetic Oligonucleotides.
2. DNA with Base Analogs.
3. Methylated DNA.
4. Single–Stranded DNA.
5. DNA–RNA Hybrids as Substrate.
F. Inhibition of Restriction Endonucleases.
G. Restriction Endonuclease Genes.
IV. Type III Restriction Endonucleases.
V. Evolutionary Significance and Biological Role.
VI. Application of Restriction Nucleases.
VII. General Tips for Beginners or the First–Time Users of Restriction Enzymes.
5. Damage–Specific Nucleases.
I. Classification and Assay .
A. AP Endonucleases.
B. Enzymes that Directly Attack Phosphodiester Linkages in the Damaged DNA Region.
C. Assay.
II. Properties of Two Groups of Enzymes from Different Organisms.
A. AP Endonucleases.
1. AP Endonucleases Associated with DNA Glycosylase Activity.
2. M. luteus Enzyme.
3. E. coli Endonuclease III.
B. AP Endonuclease Associated with Other Enzyme Activities.
1. E. coli Exonuclease III AP–Endonuclease Activity.
C. AP Endonucleases.
1. E. coli AP Endonucleases.
2. Fungal Apurinic Endonuclease.
3. Drosophila AP Endonucleases.
4. Human AP Endonucleases.< br>5. Plant AP Endonuclease.
D. Direct–Acting Enzymes.
1. E. coli UV Endonuclease.
2. Human Excision Nuclease.
6. Topoisomerases.
I. Choreography and Topology of DNA.
II. Enzyme Assay.
A. Electron Microscopy.
B. Sedimentation Methods.
C. Agarose Gel Electrophoresis.
III. Properties of Enzymes from Different Groups of Organisms.
A. Prokaryotic Topoisomerases.
1. Prokaryotic Topoisomerase I.
2. Prokaryotic Topoisomerase II.
3. Properties of Gyrase.
4. Other Activities of Gyrase.
5. Prokaryotic Topoisomerase III.
B. Eukaryotic Topoisomerases.
1. Eukaryotic Topoisomerase I.
2. Eukaryotic Topoisomerase II.
C. Mitochondrial Topoisomerase.
D. Viral Topoisomerases.
IV. Genetics and Biological Role.
A. Prokaryotic Topoisomerase Mutants.
1. Topoisomerase I.
2. Topoisomerase II.
B. Eukaryotic Topoisomerase Mutants.
1. Topoisomerase I Mutants of Yeast.
2. Topoisomerase II Mutants of Yeast.
3. Topoisomerase Mutants of Higher Eukaryotes.
7. Recombinases.
I. General Description and Classification.
A. General Recombinase.
B. Site–Specific Recombinase.
1. Prokaryotic.
2. Eukaryotic.
C. Transpositional Recombinase.
D. RNA Recombinase.
II. Properties of Different Recombinases.
A. General Recombinase.
1. Initiase.
2. X–Solvase.
3. Correctase.
B. Site–Specific Recombinase.
C. Prokaryotic Site–Specific Recombinase.
1. Integrase.
2. Invertase.
3. Resolvase.
D. Eukaryotic Site–Specific Recombinase.
1. Eukaryotic Site–Specific Recombinase.
2. ′′Homing′′ Nuclease (Intron Coded Nuclease).
3. Viral Integrase.
E. Transpositional Recombinase.
1. Prokaryotic Transposases.
2. Eukaryotic Transposase.
3. Retrotransposable Elements and Retrotransposases.
F. Control of Recombinases.
G. RNA Recombinase.
8. Sugar–NonSpecific Nucleases.
I. General Description