Note: Cover -- RNA -- Copyright -- Contents -- Preface -- Contributors -- 1 A Spectroscopist's View of RNA Conformation: RNA Structural Motifs -- 1.1 INTRODUCTION -- 1.2 THE DETERMINATION OF RNA STRUCTURES BY NMR -- 1.3 SOLUTION STRUCTURES AND CRYSTAL STRUCTURES COMPARED -- 1.4 LESSONS LEARNED ABOUT MOTIFS BY NMR -- 1.5 REFERENCES -- 2 Thermodynamics of RNA Secondary Structure Formation -- 2.1 INTRODUCTION -- 2.2 THERMODYNAMIC ANALYSIS OF RNA STRUCTURAL TRANSITIONS -- 2.3 THERMODYNAMICS OF RNA SECONDARY STRUCTURE MOTIFS -- 2.4 APPLICATIONS -- 2.5 FUTURE PERSPECTIVES -- 2.6 REFERENCES -- 3 RNA Structures Determined by X-ray Crystallography -- 3.1 INTRODUCTION -- 3.2 CRYSTALLIZATION OF RNA -- 3.3 HEAVY ATOM DERIVATIVES OF RNA CRYSTALS -- 3.4 DUPLEX STRUCTURES -- 3.5 TRANSFER RNA -- 3.6 THE HAMMERHEAD RIBOZYME -- 3.7 THE P4-P6 DOMAIN OF THE TETRAHYMENA GROUP I SELF-SPLICING INTRON -- 3.8 5S RIBOSOMAL RNA FRAGMENT -- 3.9 FUTURE DIRECTIONS -- 3.10 REFERENCES -- 4 RNA Conformational Dynamics -- 4.1 INTRODUCTION -- 4.2 THE FAST TIME SCALE: LOCAL INTERNAL DYNAMICS -- 4.3 BASE STACKING DYNAMICS -- 4.4 THE RATE OF BASE PAIRING -- 4.5 SECONDARY STRUCTURE FORMATION -- 4.6 TERTIARY STRUCTURE DYNAMICS -- 4.7 DYNAMICS OF CONFORMATIONAL SWITCHING -- 4.8 REFERENCES -- 5 Classical and Novel Chemical Tools for RNA Structure Probing -- 5.1 INTRODUCTION -- 5.2 VALIDATION OF RNA STRUCTURAL PROBING APPROACHES -- 5.3 PROBES, TARGETS, AND METHODOLOGY -- 5.4 APPROACHING ARCHITECTURAL FEATURES OF RNAs BY STRUCTURAL PROBING -- 5.5 PROBING RNAs IN COMPLEXES -- 5.6 OTHER APPLICATIONS OF NUCLEOTIDE MODIFICATIONS -- 5.7 PERSPECTIVES -- 5.8 REFERENCES -- 6 Chemical RNA Synthesis (Including RNA with Unusual Constituents) -- 6.1 INTRODUCTION -- 6.2 SYNTHETIC METHODS FOR OLIGONUCLEOTIDES -- 6.3 PROTECTING GROUPS -- 6.4 SYNTHESIS OF OLIGONUCLEOTIDE ANALOGUES -- 6.5 REFERENCES. , 7 The Phosphoryl Transfer Reactions in Pre-Messenger RNA Splicing -- 7.1 INTRODUCTION -- 7.2 THE ASSEMBLY OF THE ENZYME SUBSTRATE COMPLEX -- 7.3 THE FIRST PHOSPHORYL TRANSFER REACTION -- 7.4 THE SECOND PHOSPHORYL TRANSFER REACTION -- 7.5 SUMMARY -- 7.6 REFERENCES -- 8 RNA Editing -- 8.1 INTRODUCTION TO RNA EDITING -- 8.2 EDITING BY BASE MODIFICATION -- 8.3 INSERTION/DELETION EDITING -- 8.4 SUMMARY AND PERSPECTIVES -- 8.5 REFERENCES -- 9 Ribonuclease P -- 9.1 INTRODUCTION -- 9.2 STRUCTURE AND EVOLUTION OF THE RNA SUBUNIT -- 9.3 SUBSTRATE RECOGNITION AND CATALYTIC MECHANISM -- 9.4 THE ROLE OF THE PROTEIN SUBUNIT(S) -- 9.5 EVOLUTIONARY CONSIDERATIONS -- 9.6 ACKNOWLEDGMENTS -- 9.7 REFERENCES -- 10 Ribozyme Selection -- 10.1 THE HISTORY OF RIBOZYMES AND RIBOZYMES IN HISTORY -- 10.2 IN VITRO SELECTION OF RIBOZYMES -- 10.3 IDENTIFYING FUNCTIONAL SEQUENCES AND STRUCTURES -- 10.4 IMPROVING AND CHANGING CATALYSIS -- 10.5 INVENTING CATALYSIS: THE ROAD TO THE RIBOSOME -- 10.6 ASSESSING THE BREADTH AND DEPTH OF SELECTED CATALYSTS:THE LIGASES -- 10.7 METALLORIBOZYMES -- 10.8 MODIFIED CATALYSTS -- 10.9 CONCLUSIONS -- 10.10 REFERENCES -- 11 Ribozyme Enzymology -- 11.1 INTRODUCTION -- 11.2 TYPES OF RNA CATALYSIS AND REACTION MECHANISMS -- 11.3 SECONDARY AND TERTIARY STRUCTURES OF RNA ENZYMES -- 11.4 THE ROLE OF METALS IN RNA CATALYSIS -- 11.5 KINETICS OF THE TETRAHYMENA AND HAMMERHEAD RIBOZYME REACTIONS -- 11.6 OTHER CATALYTIC RNAS -- 11.7 CONCLUSIONS -- ADDENDUM -- 11.8 REFERENCES -- 12 Viroids -- 12.1 INTRODUCTION -- 12.2 CLASSIFICATION OF VIROIDS -- 12.3 ISOLATION, PURIFICATION, AND SEQUENCING OF VIROIDS -- 12.4 DOMAIN MODEL FOR PSTV GROUP OF VIROIDS -- 12.5 SEQUENCE PATTERNS AND VARIATION IN VIROID SEQUENCES -- 12.6 REPLICATION OF VIROIDS -- 12.7 PROCESSING REACTION IN VITRO IN THREE VIROIDS VIA THE HAMMERHEAD SELF-CLEAVAGE REACTION. , 12.8 WHAT IS THE PROCESSING REACTION DURING ROLLING CIRCLE REPLICATION IN THE PSTV GROUP OF VIROIDS? -- 12.9 HOW DO VIROIDS EXERT THEIR PATHOGENIC EFFECTS? -- 12.10 REFERENCES -- 13 Structural Elements of Ribosomal RNA -- 13.1 INTRODUCTION -- 13.2 SECONDARY STRUCTURE ELEMENTS OF rRNAS -- 13.3 HIGH-RESOLUTION STRUCTURES -- 13.4 TERTIARY STRUCTURE OF rRNAS -- 13.5 CONFORMATIONAL SWITCHES IN rRNA -- 13.6 REFERENCES -- 14 Turnover of mRNA in Eukaryotic Cells -- 14.1 INTRODUCTION -- 14.2 ROLE OF DEADENYLATION IN THE DECAY OF EUKARYOTIC mRNAs -- 14.3 DEADENYLATION TRIGGERS DECAPPING AND 5' TO 3' DECAY -- 14.4 DEADENYLATION INDEPENDENT DECAPPING OF mRNAs -- 14.5 CONTROL OF mRNA DECAPPING -- 14.6 DEADENYLATION CAN ALSO LEAD TO 3' TO 5' DEGRADATION -- 14.7 ROLE OF ENDONUCLEOLYTIC CLEAVAGES IN THE DECAY OF EUKARYOTIC mRNAs -- 14.8 SUMMARY -- 14.9 REFERENCES -- 15 Applications of Ribonucleotide Analogues in RNA Biochemistry -- 15.1 INTRODUCTION -- 15.2 INCORPORATION OF ANALOGUES INTO OLIGORIBONUCLEOTIDES -- 15.3 PHOSPHOROTHIOATE INTERNUCLEOTIDIC LINKAGES -- 15.4 S-BRIDGING PHOSPHOROTHIOLATES -- 15.5 MODIFICATION OF THE NUCLEOBASES -- 15.6 RIBOSE MODIFICATION AT THE 2'-POSITION -- 15.7 FLUORESCENT LABELS FOR OLIGORIBONUCLEOTIDES -- 15.8 NUCLEIC ACID CROSS-LINKING -- 15.9 CONCLUSIONS -- 15.10 ACKNOWLEDGMENTS -- 15.11 REFERENCES -- 16 RNA in Biotechnology: Towards a Role for Ribozymes in Gene Therapy -- 16.1 INTRODUCTION -- 16.2 HAMMERHEAD RIBOZYMES AS TOOLS FOR THE SUPPRESSION OF GENE EXPRESSION -- 16.3 OTHER RIBOZYMES AS TOOLS FOR GENE THERAPY -- 16.4 FINAL REMARKS ON THE EXPRESSION SYSTEM -- ACKNOWLEDGMENTS -- 16.5 REFERENCES -- Appendix: Modified Nucleosides from RNA -- ACKNOWLEDGMENTS -- Subject Index.