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Restriction Endonucleases

Aus der Reihe Nucleic Acids and Molecular Biology

195,99 €

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Beschreibung

Produktdetails

Einband

Taschenbuch

Erscheinungsdatum

21.09.2012

Herausgeber

Alfred Pingoud

Verlag

Springer Berlin

Seitenzahl

443

Maße (L/B/H)

23,5/15,5/2,6 cm

Gewicht

709 g

Auflage

Softcover reprint of the original 1st ed. 2004

Sprache

Englisch

ISBN

978-3-642-62324-0

Beschreibung

Produktdetails

Einband

Taschenbuch

Erscheinungsdatum

21.09.2012

Herausgeber

Alfred Pingoud

Verlag

Springer Berlin

Seitenzahl

443

Maße (L/B/H)

23,5/15,5/2,6 cm

Gewicht

709 g

Auflage

Softcover reprint of the original 1st ed. 2004

Sprache

Englisch

ISBN

978-3-642-62324-0

Herstelleradresse

Springer-Verlag GmbH
Tiergartenstr. 17
69121 Heidelberg
DE

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  • Produktbild: Restriction Endonucleases
  • Produktbild: Restriction Endonucleases
  • Survey and Summary A Nomenclature for Restriction Enzymes, DNA Methyltransferases, Homing Endonucleases and Their Genes.- 1 Introduction.- 2 General Rules.- 3 Details of Types and Subtypes.- 3.1 Types I, II, III and IV.- 3.2 Type I.- 3.3 Type II.- 3.4 Type IIP.- 3.5 Type IIA.- 3.6 Type IIB.- 3.7 Type IIC.- 3.8 Type IIE.- 3.9 Type IIF.- 3.10 Type IIG.- 3.11 Type IIH.- 3.12 Type IIM.- 3.13 Type IIS.- 3.14 Type IIT.- 3.15 Nicking Enzymes.- 3.16 Control Proteins.- 3.17 Type III.- 3.18 Type IV.- 3.19 Hypothetical Enzymes.- 3.20 Homing Endonucleases.- 3.21 Adherence to These Conventions and Updates.- References.- Restriction-Modification Systems as Minimal Forms of Life.- 1 Introduction.- 2 Genomics and Mobility of Restriction-Modification Systems.- 2.1 Genomics.- 2.2 Horizontal Gene Transfer Inferred from Evolutionary Analyses.- 2.3 Presence on Mobile Genetic Elements.- 2.4 Genomic Contexts and Genome Comparison.- 2.4.1 Insertion into an Operon-Like Gene Cluster.- 2.4.2 Insertion with Long Target Duplication.- 2.4.3 Substitution Adjacent to a Large Inversion.- 2.4.4 Apparent Transposition.- 2.4.5 Linkage of a Restriction-Modification Gene Complex with Another Restriction-Modification Gene Complex or a Cell Death-Related Gene.- 2.5 Defective Restriction-Modification Gene Complexes.- 3 Attack on the Host Genome and the Selfish Gene Hypothesis.- 3.1 Post-Segregational Host Cell Killing.- 3.2 Comparison with other Post-Segregational Cell Killing Systems.- 3.3 Selfish Gene Hypothesis.- 3.4 Genomics as Explained by the Selfish Gene Hypothesis.- 4 Gene Regulation in the Life Cycle of Restriction-Modification Systems.- 4.1 Gene Organization.- 4.2 Gene Regulation.- 4.2.1 Restriction Gene Downstream of Modification Gene.- 4.2.2 Restriction Gene Upstream of Modification Gene.- 4.2.3 Modification Enzyme as a Regulator.- 4.2.4 Regulatory Proteins.- 4.2.5 Type I Restriction-Modification Systems.- 4.3 Restriction-Modification Gene Complexes May Be Able to Multiply Themselves.- 5 Intra-Genomic Competition Involving Restriction-Modification Gene Complexes.- 5.1 Two Restriction-Modification Systems with the Same Recognition Sequence Can Block the Post-Segregational Killing Potential of Each Other.- 5.2 Solitary Methyltransferases Can Attenuate the Post-Segregational Killing Activity of Restriction-Modification Systems.- 5.3 Resident Restriction-Modification Systems Can Abort the Establishment of a Similar Incoming Restriction-Modification System.- 5.4 Suicidal Defense Against Restriction-Modification Gene Complexes.- 5.5 Defense Against Invaders by Restriction-Modification Systems.- 6 Genome Dynamics and Genome Co-Evolution with Restriction-Modification Gene Complexes.- 6.1 Some Restriction-Modification Gene Complexes and Restriction Sites Are Eliminated from the Genome.- 6.2 Mutagenesis and Anti-Mutagenesis.- 6.3 End Joining.- 6.4 Homologous Recombination by Bacteriophages.- 6.5 Cellular Homologous Recombination in Conflict and Collaboration with Restriction-Modification Gene Complexes.- 6.6 Selfish Genome Rearrangement Model.- 7 Towards Natural Classification of Restriction Enzymes.- 8 Application of the Behavior of Restriction-Modification Gene Complexes as Selfish Elements.- 9 A Hypothesis on the Attack by Restriction-Modification Gene Complexes on the Chromosomes.- 10 Conclusions.- References.- Molecular Phylogenetics of Restriction Endonucleases.- 1 Discovery and Classification of Restriction Enzymes.- 2 Genomic Context of R-M Systems.- 3 Historical Perspective of Comparative Analyses of Restriction Enzymes: Are They Products of Divergent or Convergent Evolution?.- 4 Crystallography of Type II REases: Exploration of the “Midnight Zone of Homology”.- 5 Homology Between Restriction Endonucleases and Other Enzymes Acting on Nucleic Acids.- 6 Non-Homologous Active Sites in Homologous Structures.- 7 Cladistic Analysis of the PD-(D/E)xK Superfamily.- 8 Identification of PD-(D/E)xK Domains in Other Nucleases and Prediction of Their Position on the Phylogenetic Tree.- 9 In the End, Convergence Wins: Sequence Analyses Reveal Type II Enzymes Unrelated to the PD-(D/E)XK Superfamily.- 10 Evolutionary Trajectories of Restriction Enzymes: Relationships to Other Polyphyletic Groups of Nucleases.- References.- Sliding or Hopping? How Restriction Enzymes Find Their Way on DNA.- 1 Introduction.- 2 Mechanisms of Facilitated Target Site Location by Proteins on DNA.- 2.1 Sliding.- 2.2 Hopping.- 2.3 Intersegment Transfer.- 3 Critical Factors Determining the Efficiency of Target Site Location by Sliding and Hopping Processes.- 4 Sliding or “Hopping” — A Survey of Experimental Data.- 4.1 Structures of Restriction Endonucleases.- 4.2 Accurate Scanning of the DNA for the Presence of Target Sites.- 4.3 Length Dependence of Linear Diffusion.- 4.4 Processivity of DNA Cleavage.- 4.5 DNA Cleavage by a Covalently Closed EcoRV Variant.- 4.6 Cleavage of Topological Connected Plasmid Molecules.- 5 Conclusions.- References.- The Type I and III Restriction Endonucleases: Structural Elements in Molecular Motors that Process DNA.- 1 Energy-Dependent DNA Processing.- 2 Motor Enzyme Architecture of the ATP-Dependent Restriction Endonucleases.- 2.1 Motor Enzyme Motifs in the Type I and III Restriction Endonucleases.- 2.1.1 Gross Organisation of the Type I HsdR Subunits.- 2.1.2 Gross Organisation of the Type III Res Subunits.- 2.1.3 Core Helicase Motifs in ATP Binding and Catalysis.- 2.1.4 The “Q-Tip Helix” — A New Helicase Motif?.- 2.1.5 The DNA Binding Motifs — Family-Specific Deviations.- 2.2 A Motor Enzyme Fold in the Type I and III Restriction Endonucleases.- 2.3 Macromolecular Assembly of the Type I and III Restriction Endonucleases.- 3 Future Directions.- 3.1 Coupling Chemical Energy to Mechanical Motion.- 3.2 Tools for Nanotechnology Rather Than Biotechnology?.- References.- The Integration of Recognition and Cleavage: X-Ray Structures of Pre-Transition State Complex, Post-Reactive Complex and the DNA-Free Endonuclease.- 1 Introduction.- 2 The Pre-Transition State Complex.- 2.1 General Features.- 2.2 DNA Numbering Scheme.- 2.3 Secondary Structure.- 2.4 The EcoRI Kink.- 2.5 Recognition Overview.- 2.6 Sequence-Specific Hydrogen Bonds.- 2.7 Sequence-Specific Interactions Via Bound Water.- 2.8 Sequence-Specific Van der Waals Interactions.- 2.9 Redundancy of Direct Sequence-Specific Interactions.- 2.10 Bound Solvent.- 2.11 “Buried” DNA Phosphate Groups.- 2.12 Solvent-Mediated Contacts to the DNA Bases Flanking the Recognition Site.- 2.13 DNA Minor Groove.- 2.14 Contrasting the 1.85 and 2.7 Å Pre-Transition State Complexes.- 3 The Post-Reactive Complex and the Cleavage Mechanism.- 3.1 EcoRI Endonuclease Crystal Packing.- 3.2 Catalytic Site.- 3.3 The Proposed Cleavage Mechanism.- 3.4 The Integration of EcoRI-Catalyzed DNA Cleavage with Substrate Recognition.- 3.5 Chimeric ß Sheets.- 4 Apo-Eco RI Endonuclease (The Protein in the Absence of DNA).- 4.1 Three Polypeptide Chains in the Asymmetric Unit.- 4.2 Disordered “Arm” Regions.- 4.3 Relation to Crystallographic Packing.- 4.4 Order—Disorder Transition Associated with DNA Binding.- 5 Summary and Conclusions.- References.- Structure and Function of EcoRV Endonuclease.- 1 Introduction.- 2 Structural Characteristics of EcoRV Endonuclease.- 2.1 DNA—Protein Interactions in Specific and Nonspecific Complexes.- 2.1.1 The Specific DNA Binding Mode.- 2.1.2 The Nonspecific DNA Binding Mode.- 2.2 The Structure of the Active Site.- 2.2.1 The Structure in the Absence of Divalent Cations.- 2.2.2 The Location of Bound Divalent Metal Ions.- 2.2.3 The Structure of the Enzyme Product Complex.- 3 Biochemical Characteristics of EcoRV Endonuclease and Structure—Function Relationships.- 3.1 Thermodynamics and Energetics of DNA Binding.- 3.1.1 Specific and Nonspecific Binding to DNA.- 3.1.2 The Energetics of Direct and Indirect Readout Interactions.- 3.2 Chemistry and Kinetics of DNA Cleavage.- 3.2.1 General Aspects of Phosphodiester Hydrolysis.- 3.2.2 Steady State and Rapid Reaction Kinetics.- 3.3 Mechanistic Hypotheses.- 3.3.1 The Role of the Conserved, Catalytic-Motif Residues.- 3.3.2 The Role of Metal Ions and the Need of Conformational Changes in Different Mechanisms.- 3.3.3 Catalytically Active and Inactive Conformational States.- 3.3.4 The Three Metal Ion Mechanism.- 4 Conclusions.- References.- Two of a Kind: BamHI and Bg1II.- 1 Introduction.- 2 BamHI Endonuclease.- 2.1 The Structure of Free BamHI.- 2.2 BamHI Nonspecific Complex.- 2.3 BamHI Specific Complex.- 2.4 The Pre-Reactive Complex of BamHI.- 2.5 The Structure of the BamHI Post-Reactive Complex.- 3 BglII Endonuclease.- 3.1 The Structure of Free BglII.- 3.2 The Structure of BglII Bound to its Cognate DNA Site.- Conclusions.- References.- Structure and Function of the Tetrameric Restriction Enzymes.- 1 Introduction.- 2 Structural Anatomy of the Tetrameric Restriction Enzymes.- 2.1 Monomer Structure.- 2.2 Dimer Arrangement.- 2.3 Tetramer Organization.- 3 Active Sites of the Tetrameric Restriction Enzymes.- 4 DNA Recognition by NgoMIV Restriction Endonuclease.- 5 Possible Model of DNA Recognition by Bse634I/Cfr10I Restriction Endonucleases.- 6 Functional Significance of the Tetrameric Architecture of Restriction Enzymes.- References.- Structure and Function of Type IIE Restriction Endonucleases — or: From a Plasmid that Restricts Phage Replication to a New Molecular DNA Recognition Mechanism.- 1 Introduction.- 2 The General Problem: Type IIE REases Need the Simultaneous Interaction with Two Copies of Their Recognition Sequence for Enzymatic Activity.- 3 Activation of Type IIE REases by Synthetic Oligonucleotide Duplexes.- 4 Activation of Type IIE REases by Cleavage Products and by Non-Cleavable Oligonucleotide Duplexes.- 5 The Enzymes’ Reaction Mechanism — General Aspects and Details.- 5.1 Cooperative Interaction with Two Recognition Sites.- 5.2 Stoichiometry of the Active Enzyme-Substrate Complexes.- 5.3 How Do Type IIE REases Communicate Between Remote DNA Recognition Sites in a DNA Molecule?.- 6 Sequence-Specific DNA Recognition by Type IIE REases.- 7 Domain Organization of Type IIE REases.- 8 Modular Architecture of NaeI and EcoRII and Its Functional Implications.- 9 Reaction Mechanism of Type IIE REases.- 10 Are NaeI and EcoRII Evolutionary Links Between REases, Topoisomerases and DNA Recombinases?.- 11 Does Nature Construct Proteins with New Functions by Shuffling Protein Domains?.- 12 Activation of Type IIE REases for Biotechnological Purposes and for Mapping Epigenetic DNA Modifications.- 13 Final Remark.- References.- Analysis of Type II Restriction Endonucleases That Interact with Two Recognition Sites.- 1 Introduction.- 2 Different Classes of Interactions.- 3 Information from cis Reactions.- 3.1 One-Site/Two-Site Assays.- 3.2 Determining Reaction Mechanism.- 3.3 The Effect of Supercoiling.- 3.4 Catenane Substrates.- 4 DNA Binding and Looping with Sites in cis.- 5 Information from trans Reactions.- 5.1 Kinetic Studies.- 5.2 Binding Studies.- 6 Conclusion.- References.- The Role of Water in the EcoRI—DNA Binding.- 1 Introduction.- 2 Thermodynamics.- 3 Experimental Applications.- 3.1 Equilibrium Competition.- 3.1.1 Osmotic Stress Dependence or Knonsp-sp.- 3.1.2 pH and Salt Dependence of Knonsp-sp.- 3.2 Dissociation Kinetics of EcoRI from Its Specific Site.- 3.2.1 Osmotic Dependence of kd.- 3.2.2 pH and Salt Dependence of kd.- 3.3 Removing Water from an EcoRI—Noncognate DNA Complex with Osmotic Stress.- 3.3.1 Competitive Equilibrium at High Osmotic Stress.- 3.3.2 Dissociation Kinetics of the EcoRI from Noncognate Sites.- 3.4 Other Applications of Osmotic Stress to Restriction Nucleases.- 3.5 Application of Hydrostatic Pressure to Restriction Nucleases.- 4 Summary.- References.- Role of Metal Ions in Promoting DNA Binding and Cleavage by Restriction Endonucleases.- 1 Introduction.- 2 Selection of Metal Cofactors to Promote Endonuclease Activity.- 3 Magnesium Analogs.- 4 Inhibitory Influence of Metal Cofactors.- 5 Illustrative Examples and General Guidelines for Metal-Promoted Endonuclease Activity.- 5.1 EcoRV and EcoRI.- 5.2 PvuII.- 5.3 BamHI.- 6 Other Restriction Endonucleases.- 7 Concluding Remarks.- References.- Restriction Endonudeases: Structure of the Conserved Catalytic Core and the Role of Metal Ions in DNA Cleavage.- 1 Introduction.- 2 Common Structural Attributes of Type II REases.- 3 A Common Catalytic Core with Key Catalytic Sidechains.- 4 Phylogenetic Analysis of REases.- 5 Possible Roles for Divalent Metal Ions.- 6 The One-Two-Three Metal Debate.- 7 Generalizations Regarding REase Catalysis.- 8 One-Metal Catalytic Mechanism: EcoRI, BglII.- 9 Two-Metal Catalytic Mechanisms.- 9.1 EcoRV.- 9.2 BamHI.- 9.3 Tn7 Transposase.- 9.4 T7 Endonuclease I.- 10 Three-Metal Catalytic Mechanism.- 11 “Hypothetical” Active Sites of REase Superfamily Members.- 11.1 MunI.- 11.2 BsoBI.- 11.3 NaeI.- 11.4 MutH.- 11.5 Holiday Junction Resolvases, Hjc.- 12 Prospects for the Future.- References.- Protein Engineering of Restriction Enzymes.- 1 Introduction.- 2 Modifying Contacts of Restriction Enzymes to Their Recognition Sequence.- 2.1 Site-Directed Mutagenesis.- 2.2 In Vivo Selection Systems.- 3 Lengthening of Recognition Sequences.- 4 Changing the Subunit Composition.- 5 Future Directions (In Vitro Evolution).- References.- Engineering and Applications of Chimeric Nucleases.- 1 Introduction.- 2 Engineering of Chimeric Nucleases.- 2.1 Functional Domains in FokI Restriction Endonuclease.- 2.2 Chimeric Nucleases.- 2.3 Zinc Finger Binding and Specificity.- 2.4 Mechanism of Cleavageby Zinc Finger Chimeric Nucleases (ZFN).- 3 Application of Chimeric Nucleases.- 3.1 Stimulation of Homologous Recombination Through Targeted Cleavage in Frog Oocytes Using ZFN: Recombinogenic Repair.- 3.2 Targeted Chromosomal Cleavage and Mutagenesis in Fruit Flies Using ZFN:Mutagenic Repair.- 3.3 Gene Targeting in Human Cells Using ZFN.- 4 Future Experiments.- 4.1 Targeted Chromosomal Cleavage and Mutagenesis of the CCR5 Gene in a Human Cell Line.- 4.2 Targeted Correction of a CFTR Genetic Defect in a Human Cell Line Using ZFN.- 5 Potential Limitations of the Chimeric Nuclease Technology.- 6 Future Outlook.- References.