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Antisense and ribozyme methodology / / Ian Gibson, editor
| Antisense and ribozyme methodology / / Ian Gibson, editor |
| Pubbl/distr/stampa | London, [England] : , : Chapman & Hall, , 1997 |
| Descrizione fisica | 1 online resource (96 p.) |
| Disciplina |
572.88
615.36 |
| Collana | Laboratory Companion Series |
| Soggetto topico |
Antisense nucleic acids
Catalytic RNA |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-281-84239-7
9786611842390 3-527-61253-X 3-527-61252-1 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Antisense and Ribozyme Methodology; Contents; CHAPTER 1. Antisense and Ribozyme Methodology; 1.1 The Potential; 1.2 Antisense Technology; 1.2.1 Problems; 1.2.2 Resistance to Nucleases; 1.2.3 Entry into Cells; 1.2.4 How Antisense Works; 1.2.5 Success; 1.3 Ribozymes; 1.3.1 What Are They?; 1.3.2 Problems; 1.3.3 Stable Ribozymes; 1.3.4 Designing Ribozymes; 1.4 Ribozymes or Antisense DNAs?; 1.5 The Choice Today!!; CHAPTER 2. Design and Synthesis of Antisense DNA Molecules; 2.1 Introduction; 2.2 Synthesis of Methylphosphonodiester-Phosphodiester Chimeric Oligodeoxynucleotides
2.2.1 Materials and Chemicals2.2.2 Solutions; 2.2.3 Maximizing Product Purity; 2.2.4 Deprotection of Chimeric Oligodeoxynucleotides; 2.2.5 Failed Sequences; 2.3 Primary Purification by Reversed-Phase, Solid-Phase Extraction on C18 SEP-PAK Cartridges; 2.3.1 Equipment; 2.3.2 Method; 2.3.3 Purification of the Oligodeoxynucleotide; 2.3.4 Further Purification; 2.4 Analysis and Purification by HPLC; 2.4.1 Analysis of Chimeric Oligodeoxynucleotides by HPLC; 2.4.2 Purification of Chimeric Oligodeoxynucleotides by HPLC; 2.4.3 Re-Use of Columns 2.5 Synthesis of Chimeric Oligodeoxynucleotides with Fluorescein Attached2.6 Summary; CHAPTER 3. The Design and Synthesis of Hammerhead Ribozymes; 3.1 Introduction; 3.2 The Design of Hammerhead Ribozymes; 3.3 Improving the Reactions; 3.3.1 Accessibility of the Target - Substrate Binding; 3.3.2 Finding the Target; 3.3.3 Theoretical Considerations; 3.3.4 Experimental Approaches; 3.3.5 Kinetic Studies; 3.4 Length of Arms; 3.4.1 Choosing Antisense Arms of Hammerhead Ribozymes; 3.4.2 Arms of Different Lengths; 3.5 Cleavage of the Target Motif; 3.6 Synthesis of Ribozymes 3.6.1 Chemical Synthesis of Short Hammerhead Ribozymes3.6.2 Enzymatic Transcription in Vitro; 3.7 Endogenous Expression of Ribozyme Genes; CHAPTER 4. Delivery of Ribozymes and Antisense DNA Molecules into Mammalian Cells; 4.1 Introduction; 4.2 Exogenous Application; 4.2.1 lntracytoplasmic Delivery of Antisense Oligodeoxynucleotides by Reversible Plasma Membrane Permeabilization with Streptolysin O; 4.3 Microinjection; 4.4 Other Methods Used in Nucleic Acid Transfection; 4.5 Electroporation; 4.5.1 Method; 4.5.2 Transfection: Optimization of Conditions 4.5.3 Mechanism of Uptake Following Electroporation4.5.4 Benefits and Drawbacks of Electrophoretic-Mediated Uptake; 4.6 Diethylaminoethyl-Dextran (DEAE- Dextran) and DNA Transfection; 4.6.1 Methods for Transfection of Adherent Cells; 4.6.2 Possible Alterations of the Above Protocol; 4.6.3 Transfection of Cells Growing in Suspension; 4.6.4 Transfection Optimization; 4.6.5 Distribution Mechanism of DEAE-Dextran Uptake and lntracellular; 4.6.6 Benefits and Drawbacks; 4.7 Calcium Phosphate Transfection; 4.7.1 Method; 4.7.2 Possible Alterations to Above Method; 4.7.3 Method Optimization 4.7.4 Calcium Phosphate-Mediated Uptake and lntracellular Distribution |
| Record Nr. | UNINA-9910144117903321 |
| London, [England] : , : Chapman & Hall, , 1997 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Antisense and ribozyme methodology / / Ian Gibson, editor
| Antisense and ribozyme methodology / / Ian Gibson, editor |
| Pubbl/distr/stampa | London, [England] : , : Chapman & Hall, , 1997 |
| Descrizione fisica | 1 online resource (96 p.) |
| Disciplina |
572.88
615.36 |
| Collana | Laboratory Companion Series |
| Soggetto topico |
Antisense nucleic acids
Catalytic RNA |
| ISBN |
1-281-84239-7
9786611842390 3-527-61253-X 3-527-61252-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Antisense and Ribozyme Methodology; Contents; CHAPTER 1. Antisense and Ribozyme Methodology; 1.1 The Potential; 1.2 Antisense Technology; 1.2.1 Problems; 1.2.2 Resistance to Nucleases; 1.2.3 Entry into Cells; 1.2.4 How Antisense Works; 1.2.5 Success; 1.3 Ribozymes; 1.3.1 What Are They?; 1.3.2 Problems; 1.3.3 Stable Ribozymes; 1.3.4 Designing Ribozymes; 1.4 Ribozymes or Antisense DNAs?; 1.5 The Choice Today!!; CHAPTER 2. Design and Synthesis of Antisense DNA Molecules; 2.1 Introduction; 2.2 Synthesis of Methylphosphonodiester-Phosphodiester Chimeric Oligodeoxynucleotides
2.2.1 Materials and Chemicals2.2.2 Solutions; 2.2.3 Maximizing Product Purity; 2.2.4 Deprotection of Chimeric Oligodeoxynucleotides; 2.2.5 Failed Sequences; 2.3 Primary Purification by Reversed-Phase, Solid-Phase Extraction on C18 SEP-PAK Cartridges; 2.3.1 Equipment; 2.3.2 Method; 2.3.3 Purification of the Oligodeoxynucleotide; 2.3.4 Further Purification; 2.4 Analysis and Purification by HPLC; 2.4.1 Analysis of Chimeric Oligodeoxynucleotides by HPLC; 2.4.2 Purification of Chimeric Oligodeoxynucleotides by HPLC; 2.4.3 Re-Use of Columns 2.5 Synthesis of Chimeric Oligodeoxynucleotides with Fluorescein Attached2.6 Summary; CHAPTER 3. The Design and Synthesis of Hammerhead Ribozymes; 3.1 Introduction; 3.2 The Design of Hammerhead Ribozymes; 3.3 Improving the Reactions; 3.3.1 Accessibility of the Target - Substrate Binding; 3.3.2 Finding the Target; 3.3.3 Theoretical Considerations; 3.3.4 Experimental Approaches; 3.3.5 Kinetic Studies; 3.4 Length of Arms; 3.4.1 Choosing Antisense Arms of Hammerhead Ribozymes; 3.4.2 Arms of Different Lengths; 3.5 Cleavage of the Target Motif; 3.6 Synthesis of Ribozymes 3.6.1 Chemical Synthesis of Short Hammerhead Ribozymes3.6.2 Enzymatic Transcription in Vitro; 3.7 Endogenous Expression of Ribozyme Genes; CHAPTER 4. Delivery of Ribozymes and Antisense DNA Molecules into Mammalian Cells; 4.1 Introduction; 4.2 Exogenous Application; 4.2.1 lntracytoplasmic Delivery of Antisense Oligodeoxynucleotides by Reversible Plasma Membrane Permeabilization with Streptolysin O; 4.3 Microinjection; 4.4 Other Methods Used in Nucleic Acid Transfection; 4.5 Electroporation; 4.5.1 Method; 4.5.2 Transfection: Optimization of Conditions 4.5.3 Mechanism of Uptake Following Electroporation4.5.4 Benefits and Drawbacks of Electrophoretic-Mediated Uptake; 4.6 Diethylaminoethyl-Dextran (DEAE- Dextran) and DNA Transfection; 4.6.1 Methods for Transfection of Adherent Cells; 4.6.2 Possible Alterations of the Above Protocol; 4.6.3 Transfection of Cells Growing in Suspension; 4.6.4 Transfection Optimization; 4.6.5 Distribution Mechanism of DEAE-Dextran Uptake and lntracellular; 4.6.6 Benefits and Drawbacks; 4.7 Calcium Phosphate Transfection; 4.7.1 Method; 4.7.2 Possible Alterations to Above Method; 4.7.3 Method Optimization 4.7.4 Calcium Phosphate-Mediated Uptake and lntracellular Distribution |
| Record Nr. | UNISA-996203927503316 |
| London, [England] : , : Chapman & Hall, , 1997 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Antisense and ribozyme methodology / / Ian Gibson, editor
| Antisense and ribozyme methodology / / Ian Gibson, editor |
| Pubbl/distr/stampa | London, [England] : , : Chapman & Hall, , 1997 |
| Descrizione fisica | 1 online resource (96 p.) |
| Disciplina |
572.88
615.36 |
| Collana | Laboratory Companion Series |
| Soggetto topico |
Antisense nucleic acids
Catalytic RNA |
| ISBN |
1-281-84239-7
9786611842390 3-527-61253-X 3-527-61252-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Antisense and Ribozyme Methodology; Contents; CHAPTER 1. Antisense and Ribozyme Methodology; 1.1 The Potential; 1.2 Antisense Technology; 1.2.1 Problems; 1.2.2 Resistance to Nucleases; 1.2.3 Entry into Cells; 1.2.4 How Antisense Works; 1.2.5 Success; 1.3 Ribozymes; 1.3.1 What Are They?; 1.3.2 Problems; 1.3.3 Stable Ribozymes; 1.3.4 Designing Ribozymes; 1.4 Ribozymes or Antisense DNAs?; 1.5 The Choice Today!!; CHAPTER 2. Design and Synthesis of Antisense DNA Molecules; 2.1 Introduction; 2.2 Synthesis of Methylphosphonodiester-Phosphodiester Chimeric Oligodeoxynucleotides
2.2.1 Materials and Chemicals2.2.2 Solutions; 2.2.3 Maximizing Product Purity; 2.2.4 Deprotection of Chimeric Oligodeoxynucleotides; 2.2.5 Failed Sequences; 2.3 Primary Purification by Reversed-Phase, Solid-Phase Extraction on C18 SEP-PAK Cartridges; 2.3.1 Equipment; 2.3.2 Method; 2.3.3 Purification of the Oligodeoxynucleotide; 2.3.4 Further Purification; 2.4 Analysis and Purification by HPLC; 2.4.1 Analysis of Chimeric Oligodeoxynucleotides by HPLC; 2.4.2 Purification of Chimeric Oligodeoxynucleotides by HPLC; 2.4.3 Re-Use of Columns 2.5 Synthesis of Chimeric Oligodeoxynucleotides with Fluorescein Attached2.6 Summary; CHAPTER 3. The Design and Synthesis of Hammerhead Ribozymes; 3.1 Introduction; 3.2 The Design of Hammerhead Ribozymes; 3.3 Improving the Reactions; 3.3.1 Accessibility of the Target - Substrate Binding; 3.3.2 Finding the Target; 3.3.3 Theoretical Considerations; 3.3.4 Experimental Approaches; 3.3.5 Kinetic Studies; 3.4 Length of Arms; 3.4.1 Choosing Antisense Arms of Hammerhead Ribozymes; 3.4.2 Arms of Different Lengths; 3.5 Cleavage of the Target Motif; 3.6 Synthesis of Ribozymes 3.6.1 Chemical Synthesis of Short Hammerhead Ribozymes3.6.2 Enzymatic Transcription in Vitro; 3.7 Endogenous Expression of Ribozyme Genes; CHAPTER 4. Delivery of Ribozymes and Antisense DNA Molecules into Mammalian Cells; 4.1 Introduction; 4.2 Exogenous Application; 4.2.1 lntracytoplasmic Delivery of Antisense Oligodeoxynucleotides by Reversible Plasma Membrane Permeabilization with Streptolysin O; 4.3 Microinjection; 4.4 Other Methods Used in Nucleic Acid Transfection; 4.5 Electroporation; 4.5.1 Method; 4.5.2 Transfection: Optimization of Conditions 4.5.3 Mechanism of Uptake Following Electroporation4.5.4 Benefits and Drawbacks of Electrophoretic-Mediated Uptake; 4.6 Diethylaminoethyl-Dextran (DEAE- Dextran) and DNA Transfection; 4.6.1 Methods for Transfection of Adherent Cells; 4.6.2 Possible Alterations of the Above Protocol; 4.6.3 Transfection of Cells Growing in Suspension; 4.6.4 Transfection Optimization; 4.6.5 Distribution Mechanism of DEAE-Dextran Uptake and lntracellular; 4.6.6 Benefits and Drawbacks; 4.7 Calcium Phosphate Transfection; 4.7.1 Method; 4.7.2 Possible Alterations to Above Method; 4.7.3 Method Optimization 4.7.4 Calcium Phosphate-Mediated Uptake and lntracellular Distribution |
| Record Nr. | UNINA-9910830630503321 |
| London, [England] : , : Chapman & Hall, , 1997 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Ribozymes . Volume 1 : principles, methods, applications / / edited by Sabine Müller, Benoît Masquida, Wade Winkler
| Ribozymes . Volume 1 : principles, methods, applications / / edited by Sabine Müller, Benoît Masquida, Wade Winkler |
| Pubbl/distr/stampa | Weinheim, Germany : , : Wiley-VCH, , [2021] |
| Descrizione fisica | 1 online resource (1076 pages) |
| Disciplina | 572.88 |
| Soggetto topico |
Genetic regulation
Catalytic RNA |
| Soggetto genere / forma | Electronic books. |
| ISBN |
3-527-81455-8
3-527-81452-3 3-527-81453-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Table of Contents -- Title Page -- Title Page -- Copyright -- Preface -- Foreword -- References -- Volume 1 -- Part I: Nucleic Acid Catalysis: Principles, Strategies and Biological Function -- 1 The Chemical Principles of RNA Catalysis -- 1.1 RNA Catalysis -- 1.2 Rates of Chemical Reactions and Transition State Theory -- 1.3 Phosphoryl Transfer Reactions in the Ribozymes -- 1.4 Catalysis of Phosphoryl Transfer -- 1.5 General Acid-Base Catalysis in Nucleolytic Ribozymes -- 1.6 pKa Shifting of General Acids and Bases in Nucleolytic Ribozymes -- 1.7 Catalytic Roles of Metal Ions in Ribozymes -- 1.8 The Choice Between General Acid-Base Catalysis and the Use of Metal Ions -- 1.9 The Limitations to RNA Catalysis -- Acknowledgment -- References -- 2 Biological Roles of Self‐Cleaving Ribozymes -- 2.1 Introduction -- 2.2 Use of Self‐cleaving Ribozymes for Replication -- 2.3 Self‐cleaving Ribozymes as Part of Transposable Elements -- 2.4 Hammerhead Ribozymes with Suggested Roles in mRNA Biogenesis -- 2.5 The glmS Ribozyme Regulates Glucosamine‐6‐phosphate Levels in Bacteria -- 2.6 The Biological Roles of Many Ribozymes Are Unknown -- 2.7 Conclusion -- Acknowledgments -- References -- Part II: Naturally Occurring Ribozymes -- 3 Chemical Mechanisms of the Nucleolytic Ribozymes -- 3.1 The Nucleolytic Ribozymes -- 3.2 Some Nucleolytic Ribozymes Are Widespread -- 3.3 Secondary Structures of Nucleolytic Ribozymes - Junctions and Pseudoknots -- 3.4 Catalytic Players in the Nucleolytic Ribozymes -- 3.5 The Hairpin and VS Ribozymes: The G Plus A Mechanism -- 3.6 The Twister Ribozyme: A G Plus A Variant -- 3.7 The Hammerhead Ribozyme: A 2'‐Hydroxyl as a Catalytic Participant -- 3.8 The Hepatitis Delta Virus Ribozyme: A Direct Role for a Metal Ion -- 3.9 The Twister Sister (TS) Ribozyme: Another Metallo‐Ribozyme.
3.10 The Pistol Ribozyme: A Metal Ion as the General Acid -- 3.11 The glmS Ribozyme: Participation of a Coenzyme -- 3.12 A Classification of the Nucleolytic Ribozymes Based on Catalytic Mechanism -- Acknowledgments -- References -- Note -- 4 The glmS Ribozyme and Its Multifunctional Coenzyme Glucosamine‐6‐phosphate -- 4.1 Introduction -- 4.2 Ribozymes -- 4.3 Riboswitches -- 4.4 The glmS Riboswitch/Ribozyme -- 4.5 Biological Function of the glmS Ribozyme -- 4.6 glmS Ribozyme Structure and Function - Initial Biochemical Analyses -- 4.7 glmS Ribozyme Structure and Function - Initial Crystallographic Analysis -- 4.8 Metal Ion Usage by the glmS Ribozyme -- 4.9 In Vitro Selected glmS Catalyst Loses Coenzyme Dependence -- 4.10 Essential Coenzyme GlcN6P Functional Groups -- 4.11 Mechanism of glmS Ribozyme Self‐Cleavage -- 4.12 Potential for Antibiotic Development Affecting glmS Ribozyme/Riboswitch Function -- Acknowledgments -- References -- 5 The Lariat Capping Ribozyme -- 5.1 Introduction -- 5.2 Reactions Catalyzed by LCrz -- 5.3 The Structure of the LCrz Core -- 5.4 Communication Between LCrz and Flanking Elements -- 5.5 Reflections on the Evolutionary Aspect of LCrz -- 5.6 LCrz as a Research Tool -- 5.7 Conclusions and Unsolved Problems -- References -- 6 Self‐Splicing Group II Introns -- 6.1 Introduction -- 6.2 Milestones in the Characterization of Group II Introns -- 6.3 Evolutionary Conservation and Biological Role -- 6.4 Structural Architecture -- 6.5 Lessons and Tools from Group II Intron Research -- 6.6 Perspectives and Open Questions -- Acknowledgments -- References -- 7 The Spliceosome: an RNA-Protein Ribozyme Derived From Ancient Mobile Genetic Elements -- 7.1 Discovery of Introns and Splicing -- 7.2 snRNPs and the Spliceosome -- 7.3 The Spliceosomal Cycle -- 7.4 Chemistry of Splicing -- 7.5 Spliceosome Structural Analysis. 7.6 Spliceosome Structures -- 7.7 Insights from Spliceosome Disassembly -- 7.8 Conservation of Spliceosomal and Group II Active Sites -- 7.9 Summary and Perspectives -- References -- 8 The Ribosome and Protein Synthesis -- 8.1 Central Dogma of Molecular Biology -- 8.2 Structure of the E. coli Ribosome -- 8.3 Translation Cycle -- References -- 9 The RNase P Ribozyme -- 9.1 Introduction -- 9.2 Bacterial RNase P -- 9.3 Substrate Interaction -- 9.4 RNA‐based Metal Ion Catalysis -- 9.5 RNase P as an Antibiotic Target -- 9.6 Application of RNase P as a Tool in Gene Inactivation -- References -- 10 Ribozyme Discovery in Bacteria -- 10.1 Introduction -- 10.2 Protein Takeover -- 10.3 Ribozymes as Evolutionary Holdouts -- 10.4 The Role of Serendipity in Early Ribozyme Discoveries -- 10.5 Ribozymes Emerge from Structured Noncoding RNA Searches -- 10.6 Ribozymes Beget Ribozymes -- 10.7 Ribozyme Dispersal Driven by Association with Selfish Elements -- 10.8 Domesticated Ribozymes -- 10.9 New Ribozymes from Old -- 10.10 Will New ncRNAs Broaden the Scope of RNA Catalysis? -- Acknowledgments -- References -- 11 Small Self‐Cleaving Ribozymes in the Genomes of Vertebrates -- 11.1 The Family of Small Self‐Cleaving Ribozymes in Eukaryotic Genomes: From Retrotransposition to Domestication -- 11.2 The Widespread Case of the Hammerhead Ribozyme: From Bacteria to Vertebrate Genomes -- 11.3 Other Intronic HHRs in Amniotes: Small Catalytic RNAs in Search of a Function -- 11.4 The Family of the Hepatitis D Virus Ribozymes -- 11.5 Other Small Self‐Cleaving Ribozymes Hidden in the Genomes of Vertebrates? -- References -- Part III: Engineered Ribozymes -- 12 Phosphoryl Transfer Ribozymes -- 12.1 Introduction -- 12.2 Kinase Ribozymes -- 12.3 Glycosidic Bond Forming Ribozymes -- 12.4 Capping Ribozymes -- 12.5 Ligase Ribozymes -- 12.6 Polymerase Ribozymes -- 12.7 Summary. References -- 13 RNA Replication and the RNA Polymerase Ribozyme -- 13.1 Introduction -- 13.2 Nonenzymatic RNA Polymerization -- 13.3 Enzymatic RNA Polymerization -- 13.4 Essential Requirements for an RNA Replicator -- 13.5 The Class I Ligase and the First RNA Polymerase Ribozymes -- 13.6 Structural Insight into the Catalytic Core of the RNA Polymerase Ribozyme -- 13.7 Selection for Improved Polymerase Activity I -- 13.8 Selection for Improved Polymerase Activity II -- 13.9 Conclusion and Outlook -- References -- 14 Maintenance of Genetic Information in the First Ribocell -- 14.1 The Ribocell and the Stages of the RNA World -- 14.2 The Error Thresholds -- 14.3 Compartmentalization -- 14.4 Minimal Gene Content of the First Ribocell -- Acknowledgments -- References -- 15 Ribozyme‐Catalyzed RNA Recombination -- 15.1 Introduction -- 15.2 RNA Recombination Chemistry -- 15.3 Azoarcus Group I Intron -- 15.4 Crystal Structure -- 15.5 Mechanism -- 15.6 Model for Prebiotic Chemistry -- 15.7 Spontaneous Self‐assembly of Azoarcus RNA Fragments -- 15.8 Autocatalysis -- 15.9 Cooperative Self‐assembly -- 15.10 Game Theoretic Treatment -- 15.11 Significance of Game Theoretic Treatments -- 15.12 Other Recombinase Ribozymes -- 15.13 Conclusions -- References -- 16 Engineering of Hairpin Ribozymes for RNA Processing Reactions -- 16.1 Introduction -- 16.2 The Naturally Occurring Hairpin Ribozyme -- 16.3 Structural Variants of the Hairpin Ribozyme -- 16.4 Hairpin Ribozymes that are Regulated by External Effectors -- 16.5 Twin Ribozymes for RNA Repair and Recombination -- 16.6 Hairpin Ribozymes as RNA Recombinases -- 16.7 Self‐Splicing Hairpin Ribozymes -- 16.8 Closing Remarks -- References -- 17 Engineering of the Neurospora Varkud Satellite Ribozyme for Cleavage of Nonnatural Stem‐Loop Substrates -- 17.1 Introduction. 17.2 Simple Primary and Secondary Structure Changes Compatible with Substrate Cleavage by the VS Ribozyme -- 17.3 The Structural Context -- 17.4 Structure‐Guided Engineering Studies -- 17.5 Summary and Future Prospects for VS Ribozyme Engineering -- References -- 18 Chemical Modifications in Natural and Engineered Ribozymes -- 18.1 Introduction -- 18.2 Chemical Modifications to Study Natural Ribozymes -- 18.3 In Vitro Selection with Chemically Modified Nucleotides: Expanding the Scope of DNA and RNA Catalysis -- 18.4 Outlook -- References -- 19 Ribozymes for Regulation of Gene Expression -- 19.1 Introduction -- 19.2 Conditional Gene Expression Control by Riboswitches -- 19.3 Allosteric Ribozymes as Engineered Riboswitches -- 19.4 In Vitro Selection Methods -- 19.5 In Vivo Screening Methods -- 19.6 Rational Design of Allosteric Ribozymes -- 19.7 Applications of Aptazymes for Gene Regulation -- References -- 20 Development of Flexizyme Aminoacylation Ribozymes and Their Applications -- 20.1 Introduction -- 20.2 The First Ribozymes Catalyzing Acyl Transfer to RNAs -- 20.3 The ATRib Variant Family: Ribozymes Catalyzing tRNA Aminoacylation via Self‐Acylated Intermediates -- 20.4 Prototype Flexizymes: Ribozymes Catalyzing Direct tRNA Aminoacylation -- 20.5 Flexizymes: Versatile Ribozymes for the Preparation of Aminoacyl‐tRNAs -- 20.6 Application of Flexizymes to Genetic Code Reprogramming -- 20.7 Development of Orthogonal tRNA/Ribosome Pairs Using Mutant Flexizymes -- 20.8 In Vitro Selection of Bioactive Peptides Containing nPAAs Through RaPID Display -- 20.9 tRid: A Method for Selective Removal of tRNAs from an RNA Pool -- 20.10 Use of a Natural Small RNA Library Lacking tRNA for In Vitro Selection of a Folic Acid Aptamer: Small RNA Transcriptomic SELEX -- 20.11 Summary and Perspective -- Acknowledgments -- References. 21 In Vitro Selected (Deoxy)ribozymes that Catalyze Carbon-Carbon Bond Formation. |
| Record Nr. | UNINA-9910555257903321 |
| Weinheim, Germany : , : Wiley-VCH, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Ribozymes . Volume 1 : principles, methods, applications / / edited by Sabine Müller, Benoît Masquida, Wade Winkler
| Ribozymes . Volume 1 : principles, methods, applications / / edited by Sabine Müller, Benoît Masquida, Wade Winkler |
| Pubbl/distr/stampa | Weinheim, Germany : , : Wiley-VCH, , [2021] |
| Descrizione fisica | 1 online resource (1076 pages) |
| Disciplina | 572.88 |
| Soggetto topico |
Genetic regulation
Catalytic RNA |
| ISBN |
3-527-81455-8
3-527-81452-3 3-527-81453-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Table of Contents -- Title Page -- Title Page -- Copyright -- Preface -- Foreword -- References -- Volume 1 -- Part I: Nucleic Acid Catalysis: Principles, Strategies and Biological Function -- 1 The Chemical Principles of RNA Catalysis -- 1.1 RNA Catalysis -- 1.2 Rates of Chemical Reactions and Transition State Theory -- 1.3 Phosphoryl Transfer Reactions in the Ribozymes -- 1.4 Catalysis of Phosphoryl Transfer -- 1.5 General Acid-Base Catalysis in Nucleolytic Ribozymes -- 1.6 pKa Shifting of General Acids and Bases in Nucleolytic Ribozymes -- 1.7 Catalytic Roles of Metal Ions in Ribozymes -- 1.8 The Choice Between General Acid-Base Catalysis and the Use of Metal Ions -- 1.9 The Limitations to RNA Catalysis -- Acknowledgment -- References -- 2 Biological Roles of Self‐Cleaving Ribozymes -- 2.1 Introduction -- 2.2 Use of Self‐cleaving Ribozymes for Replication -- 2.3 Self‐cleaving Ribozymes as Part of Transposable Elements -- 2.4 Hammerhead Ribozymes with Suggested Roles in mRNA Biogenesis -- 2.5 The glmS Ribozyme Regulates Glucosamine‐6‐phosphate Levels in Bacteria -- 2.6 The Biological Roles of Many Ribozymes Are Unknown -- 2.7 Conclusion -- Acknowledgments -- References -- Part II: Naturally Occurring Ribozymes -- 3 Chemical Mechanisms of the Nucleolytic Ribozymes -- 3.1 The Nucleolytic Ribozymes -- 3.2 Some Nucleolytic Ribozymes Are Widespread -- 3.3 Secondary Structures of Nucleolytic Ribozymes - Junctions and Pseudoknots -- 3.4 Catalytic Players in the Nucleolytic Ribozymes -- 3.5 The Hairpin and VS Ribozymes: The G Plus A Mechanism -- 3.6 The Twister Ribozyme: A G Plus A Variant -- 3.7 The Hammerhead Ribozyme: A 2'‐Hydroxyl as a Catalytic Participant -- 3.8 The Hepatitis Delta Virus Ribozyme: A Direct Role for a Metal Ion -- 3.9 The Twister Sister (TS) Ribozyme: Another Metallo‐Ribozyme.
3.10 The Pistol Ribozyme: A Metal Ion as the General Acid -- 3.11 The glmS Ribozyme: Participation of a Coenzyme -- 3.12 A Classification of the Nucleolytic Ribozymes Based on Catalytic Mechanism -- Acknowledgments -- References -- Note -- 4 The glmS Ribozyme and Its Multifunctional Coenzyme Glucosamine‐6‐phosphate -- 4.1 Introduction -- 4.2 Ribozymes -- 4.3 Riboswitches -- 4.4 The glmS Riboswitch/Ribozyme -- 4.5 Biological Function of the glmS Ribozyme -- 4.6 glmS Ribozyme Structure and Function - Initial Biochemical Analyses -- 4.7 glmS Ribozyme Structure and Function - Initial Crystallographic Analysis -- 4.8 Metal Ion Usage by the glmS Ribozyme -- 4.9 In Vitro Selected glmS Catalyst Loses Coenzyme Dependence -- 4.10 Essential Coenzyme GlcN6P Functional Groups -- 4.11 Mechanism of glmS Ribozyme Self‐Cleavage -- 4.12 Potential for Antibiotic Development Affecting glmS Ribozyme/Riboswitch Function -- Acknowledgments -- References -- 5 The Lariat Capping Ribozyme -- 5.1 Introduction -- 5.2 Reactions Catalyzed by LCrz -- 5.3 The Structure of the LCrz Core -- 5.4 Communication Between LCrz and Flanking Elements -- 5.5 Reflections on the Evolutionary Aspect of LCrz -- 5.6 LCrz as a Research Tool -- 5.7 Conclusions and Unsolved Problems -- References -- 6 Self‐Splicing Group II Introns -- 6.1 Introduction -- 6.2 Milestones in the Characterization of Group II Introns -- 6.3 Evolutionary Conservation and Biological Role -- 6.4 Structural Architecture -- 6.5 Lessons and Tools from Group II Intron Research -- 6.6 Perspectives and Open Questions -- Acknowledgments -- References -- 7 The Spliceosome: an RNA-Protein Ribozyme Derived From Ancient Mobile Genetic Elements -- 7.1 Discovery of Introns and Splicing -- 7.2 snRNPs and the Spliceosome -- 7.3 The Spliceosomal Cycle -- 7.4 Chemistry of Splicing -- 7.5 Spliceosome Structural Analysis. 7.6 Spliceosome Structures -- 7.7 Insights from Spliceosome Disassembly -- 7.8 Conservation of Spliceosomal and Group II Active Sites -- 7.9 Summary and Perspectives -- References -- 8 The Ribosome and Protein Synthesis -- 8.1 Central Dogma of Molecular Biology -- 8.2 Structure of the E. coli Ribosome -- 8.3 Translation Cycle -- References -- 9 The RNase P Ribozyme -- 9.1 Introduction -- 9.2 Bacterial RNase P -- 9.3 Substrate Interaction -- 9.4 RNA‐based Metal Ion Catalysis -- 9.5 RNase P as an Antibiotic Target -- 9.6 Application of RNase P as a Tool in Gene Inactivation -- References -- 10 Ribozyme Discovery in Bacteria -- 10.1 Introduction -- 10.2 Protein Takeover -- 10.3 Ribozymes as Evolutionary Holdouts -- 10.4 The Role of Serendipity in Early Ribozyme Discoveries -- 10.5 Ribozymes Emerge from Structured Noncoding RNA Searches -- 10.6 Ribozymes Beget Ribozymes -- 10.7 Ribozyme Dispersal Driven by Association with Selfish Elements -- 10.8 Domesticated Ribozymes -- 10.9 New Ribozymes from Old -- 10.10 Will New ncRNAs Broaden the Scope of RNA Catalysis? -- Acknowledgments -- References -- 11 Small Self‐Cleaving Ribozymes in the Genomes of Vertebrates -- 11.1 The Family of Small Self‐Cleaving Ribozymes in Eukaryotic Genomes: From Retrotransposition to Domestication -- 11.2 The Widespread Case of the Hammerhead Ribozyme: From Bacteria to Vertebrate Genomes -- 11.3 Other Intronic HHRs in Amniotes: Small Catalytic RNAs in Search of a Function -- 11.4 The Family of the Hepatitis D Virus Ribozymes -- 11.5 Other Small Self‐Cleaving Ribozymes Hidden in the Genomes of Vertebrates? -- References -- Part III: Engineered Ribozymes -- 12 Phosphoryl Transfer Ribozymes -- 12.1 Introduction -- 12.2 Kinase Ribozymes -- 12.3 Glycosidic Bond Forming Ribozymes -- 12.4 Capping Ribozymes -- 12.5 Ligase Ribozymes -- 12.6 Polymerase Ribozymes -- 12.7 Summary. References -- 13 RNA Replication and the RNA Polymerase Ribozyme -- 13.1 Introduction -- 13.2 Nonenzymatic RNA Polymerization -- 13.3 Enzymatic RNA Polymerization -- 13.4 Essential Requirements for an RNA Replicator -- 13.5 The Class I Ligase and the First RNA Polymerase Ribozymes -- 13.6 Structural Insight into the Catalytic Core of the RNA Polymerase Ribozyme -- 13.7 Selection for Improved Polymerase Activity I -- 13.8 Selection for Improved Polymerase Activity II -- 13.9 Conclusion and Outlook -- References -- 14 Maintenance of Genetic Information in the First Ribocell -- 14.1 The Ribocell and the Stages of the RNA World -- 14.2 The Error Thresholds -- 14.3 Compartmentalization -- 14.4 Minimal Gene Content of the First Ribocell -- Acknowledgments -- References -- 15 Ribozyme‐Catalyzed RNA Recombination -- 15.1 Introduction -- 15.2 RNA Recombination Chemistry -- 15.3 Azoarcus Group I Intron -- 15.4 Crystal Structure -- 15.5 Mechanism -- 15.6 Model for Prebiotic Chemistry -- 15.7 Spontaneous Self‐assembly of Azoarcus RNA Fragments -- 15.8 Autocatalysis -- 15.9 Cooperative Self‐assembly -- 15.10 Game Theoretic Treatment -- 15.11 Significance of Game Theoretic Treatments -- 15.12 Other Recombinase Ribozymes -- 15.13 Conclusions -- References -- 16 Engineering of Hairpin Ribozymes for RNA Processing Reactions -- 16.1 Introduction -- 16.2 The Naturally Occurring Hairpin Ribozyme -- 16.3 Structural Variants of the Hairpin Ribozyme -- 16.4 Hairpin Ribozymes that are Regulated by External Effectors -- 16.5 Twin Ribozymes for RNA Repair and Recombination -- 16.6 Hairpin Ribozymes as RNA Recombinases -- 16.7 Self‐Splicing Hairpin Ribozymes -- 16.8 Closing Remarks -- References -- 17 Engineering of the Neurospora Varkud Satellite Ribozyme for Cleavage of Nonnatural Stem‐Loop Substrates -- 17.1 Introduction. 17.2 Simple Primary and Secondary Structure Changes Compatible with Substrate Cleavage by the VS Ribozyme -- 17.3 The Structural Context -- 17.4 Structure‐Guided Engineering Studies -- 17.5 Summary and Future Prospects for VS Ribozyme Engineering -- References -- 18 Chemical Modifications in Natural and Engineered Ribozymes -- 18.1 Introduction -- 18.2 Chemical Modifications to Study Natural Ribozymes -- 18.3 In Vitro Selection with Chemically Modified Nucleotides: Expanding the Scope of DNA and RNA Catalysis -- 18.4 Outlook -- References -- 19 Ribozymes for Regulation of Gene Expression -- 19.1 Introduction -- 19.2 Conditional Gene Expression Control by Riboswitches -- 19.3 Allosteric Ribozymes as Engineered Riboswitches -- 19.4 In Vitro Selection Methods -- 19.5 In Vivo Screening Methods -- 19.6 Rational Design of Allosteric Ribozymes -- 19.7 Applications of Aptazymes for Gene Regulation -- References -- 20 Development of Flexizyme Aminoacylation Ribozymes and Their Applications -- 20.1 Introduction -- 20.2 The First Ribozymes Catalyzing Acyl Transfer to RNAs -- 20.3 The ATRib Variant Family: Ribozymes Catalyzing tRNA Aminoacylation via Self‐Acylated Intermediates -- 20.4 Prototype Flexizymes: Ribozymes Catalyzing Direct tRNA Aminoacylation -- 20.5 Flexizymes: Versatile Ribozymes for the Preparation of Aminoacyl‐tRNAs -- 20.6 Application of Flexizymes to Genetic Code Reprogramming -- 20.7 Development of Orthogonal tRNA/Ribosome Pairs Using Mutant Flexizymes -- 20.8 In Vitro Selection of Bioactive Peptides Containing nPAAs Through RaPID Display -- 20.9 tRid: A Method for Selective Removal of tRNAs from an RNA Pool -- 20.10 Use of a Natural Small RNA Library Lacking tRNA for In Vitro Selection of a Folic Acid Aptamer: Small RNA Transcriptomic SELEX -- 20.11 Summary and Perspective -- Acknowledgments -- References. 21 In Vitro Selected (Deoxy)ribozymes that Catalyze Carbon-Carbon Bond Formation. |
| Record Nr. | UNINA-9910830997503321 |
| Weinheim, Germany : , : Wiley-VCH, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Structural and catalytic roles of metal ions in RNA / / edited by Astrid Sigel, Helmut Sigel, Roland K. O. Sigel
| Structural and catalytic roles of metal ions in RNA / / edited by Astrid Sigel, Helmut Sigel, Roland K. O. Sigel |
| Pubbl/distr/stampa | Berlin ; ; Munich ; ; Boston : , : De Gruyter, , 2011 |
| Descrizione fisica | 1 online resource (424 pages) : illustrations |
| Disciplina | 572.88 |
| Collana | Metal ions in life sciences |
| Soggetto topico | Catalytic RNA |
| Soggetto genere / forma | Electronic books. |
| ISBN | 3-11-043664-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Frontmatter -- Historical Development and Perspectives of the Series / Sigel, Astrid / Sigel, Helmut / Sigel, Roland K. O. -- Preface to Volume 9: Structural and Catalytic Roles of Metal Ions in RNA -- Contents -- Contributors to Volume 9 -- Titles of Volumes 1-44 in the Metal Ions in Biological Systems Series -- Contents of Volumes in the Metal Ions in Life Sciences Series -- 1 Metal Ion Binding to RNA / Auffinger, Pascal / Grover, Neena / Westhof, Eric -- 2 Methods to Detect and Characterize Metal Ion Binding Sites in RNA / Erat, Michèle C. / Sigel, Roland K. O. -- 3 Importance of Diffuse Metal Ion Binding to RNA / Tan, Zhi-Jie / Chen, Shi-Jie -- 4 RNA Quadruplexes / Halder, Kangkan / Hartig, Jörg S. -- 5 The Roles of Metal Ions in Regulation by Riboswitches / Ferré-D'Amaré, Adrian R. / Winkler, Wade C. -- 6 Metal Ions: Supporting Actors in the Playbook of Small Ribozymes / Johnson-Buck, Alexander E. / McDowell, Sarah E. / Walter, Nils G. -- 7 Multiple Roles of Metal Ions in Large Ribozymes / Donghi, Daniela / Schnabl, Joachim -- 8 The Spliceosome and Its Metal Ions / Butcher, Samuel E. -- 9 The Ribosome: A Molecular Machine Powered by RNA / Trappl, Krista / Polacek, Norbert -- 10 Metal Ion Requirements in Artificial Ribozymes that Catalyze Aminoacylation and Redox Reactions / Suga, Hiroaki / Futai, Kazuki / Jin, Koichiro -- 11 Metal Ion Binding and Function in Natural and Artificial Small RNA Enzymes from a Structural Perspective / Wedekind, Joseph E. -- 12 Binding of Kinetically Inert Metal Ions to RNA: The Case of Platinum(II) / Chapman, Erich G. / Hostetter, Alethia A. / Osborn, Maire F. / Miller, Amanda L. / DeRose, Victoria J. -- Subject Index |
| Record Nr. | UNINA-9910460802603321 |
| Berlin ; ; Munich ; ; Boston : , : De Gruyter, , 2011 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Structural and catalytic roles of metal ions in RNA / / edited by Astrid Sigel, Helmut Sigel, Roland K. O. Sigel
| Structural and catalytic roles of metal ions in RNA / / edited by Astrid Sigel, Helmut Sigel, Roland K. O. Sigel |
| Pubbl/distr/stampa | Berlin ; ; Munich ; ; Boston : , : De Gruyter, , 2011 |
| Descrizione fisica | 1 online resource (424 pages) : illustrations |
| Disciplina | 572.88 |
| Collana | Metal ions in life sciences |
| Soggetto topico | Catalytic RNA |
| ISBN | 3-11-043664-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Frontmatter -- Historical Development and Perspectives of the Series / Sigel, Astrid / Sigel, Helmut / Sigel, Roland K. O. -- Preface to Volume 9: Structural and Catalytic Roles of Metal Ions in RNA -- Contents -- Contributors to Volume 9 -- Titles of Volumes 1-44 in the Metal Ions in Biological Systems Series -- Contents of Volumes in the Metal Ions in Life Sciences Series -- 1 Metal Ion Binding to RNA / Auffinger, Pascal / Grover, Neena / Westhof, Eric -- 2 Methods to Detect and Characterize Metal Ion Binding Sites in RNA / Erat, Michèle C. / Sigel, Roland K. O. -- 3 Importance of Diffuse Metal Ion Binding to RNA / Tan, Zhi-Jie / Chen, Shi-Jie -- 4 RNA Quadruplexes / Halder, Kangkan / Hartig, Jörg S. -- 5 The Roles of Metal Ions in Regulation by Riboswitches / Ferré-D'Amaré, Adrian R. / Winkler, Wade C. -- 6 Metal Ions: Supporting Actors in the Playbook of Small Ribozymes / Johnson-Buck, Alexander E. / McDowell, Sarah E. / Walter, Nils G. -- 7 Multiple Roles of Metal Ions in Large Ribozymes / Donghi, Daniela / Schnabl, Joachim -- 8 The Spliceosome and Its Metal Ions / Butcher, Samuel E. -- 9 The Ribosome: A Molecular Machine Powered by RNA / Trappl, Krista / Polacek, Norbert -- 10 Metal Ion Requirements in Artificial Ribozymes that Catalyze Aminoacylation and Redox Reactions / Suga, Hiroaki / Futai, Kazuki / Jin, Koichiro -- 11 Metal Ion Binding and Function in Natural and Artificial Small RNA Enzymes from a Structural Perspective / Wedekind, Joseph E. -- 12 Binding of Kinetically Inert Metal Ions to RNA: The Case of Platinum(II) / Chapman, Erich G. / Hostetter, Alethia A. / Osborn, Maire F. / Miller, Amanda L. / DeRose, Victoria J. -- Subject Index |
| Record Nr. | UNINA-9910797445803321 |
| Berlin ; ; Munich ; ; Boston : , : De Gruyter, , 2011 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Structural and catalytic roles of metal ions in RNA / / edited by Astrid Sigel, Helmut Sigel, Roland K. O. Sigel
| Structural and catalytic roles of metal ions in RNA / / edited by Astrid Sigel, Helmut Sigel, Roland K. O. Sigel |
| Pubbl/distr/stampa | Berlin ; ; Munich ; ; Boston : , : De Gruyter, , 2011 |
| Descrizione fisica | 1 online resource (424 pages) : illustrations |
| Disciplina | 572.88 |
| Collana | Metal ions in life sciences |
| Soggetto topico | Catalytic RNA |
| ISBN | 3-11-043664-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Frontmatter -- Historical Development and Perspectives of the Series / Sigel, Astrid / Sigel, Helmut / Sigel, Roland K. O. -- Preface to Volume 9: Structural and Catalytic Roles of Metal Ions in RNA -- Contents -- Contributors to Volume 9 -- Titles of Volumes 1-44 in the Metal Ions in Biological Systems Series -- Contents of Volumes in the Metal Ions in Life Sciences Series -- 1 Metal Ion Binding to RNA / Auffinger, Pascal / Grover, Neena / Westhof, Eric -- 2 Methods to Detect and Characterize Metal Ion Binding Sites in RNA / Erat, Michèle C. / Sigel, Roland K. O. -- 3 Importance of Diffuse Metal Ion Binding to RNA / Tan, Zhi-Jie / Chen, Shi-Jie -- 4 RNA Quadruplexes / Halder, Kangkan / Hartig, Jörg S. -- 5 The Roles of Metal Ions in Regulation by Riboswitches / Ferré-D'Amaré, Adrian R. / Winkler, Wade C. -- 6 Metal Ions: Supporting Actors in the Playbook of Small Ribozymes / Johnson-Buck, Alexander E. / McDowell, Sarah E. / Walter, Nils G. -- 7 Multiple Roles of Metal Ions in Large Ribozymes / Donghi, Daniela / Schnabl, Joachim -- 8 The Spliceosome and Its Metal Ions / Butcher, Samuel E. -- 9 The Ribosome: A Molecular Machine Powered by RNA / Trappl, Krista / Polacek, Norbert -- 10 Metal Ion Requirements in Artificial Ribozymes that Catalyze Aminoacylation and Redox Reactions / Suga, Hiroaki / Futai, Kazuki / Jin, Koichiro -- 11 Metal Ion Binding and Function in Natural and Artificial Small RNA Enzymes from a Structural Perspective / Wedekind, Joseph E. -- 12 Binding of Kinetically Inert Metal Ions to RNA: The Case of Platinum(II) / Chapman, Erich G. / Hostetter, Alethia A. / Osborn, Maire F. / Miller, Amanda L. / DeRose, Victoria J. -- Subject Index |
| Record Nr. | UNINA-9910824831503321 |
| Berlin ; ; Munich ; ; Boston : , : De Gruyter, , 2011 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
