آنزیم‌های اصلاح‌کننده‌ی DNA و RNA ۲۰۰۹
DNA and RNA Modification Enzymes 2009

1. Cover

2. Title Page

3. Copyright Page

4. Dedication

5. Editor

6. Contributors

7. Contents

8. Preface

9. Acknowledgements

1. Nucleic Acids Are Not Boring Long Polymers of Only Four Types of Nucleotides: A Guided Tour

2. DNA Methyladon: From Bug to Beast

3. DNA Restriction-Modification Systems in Prokaryotes

4. Experimental Approaches to Study DNA Base Flipping

5. Molecular Modeling of Base Flipping in DNA

6. M-Hhal and M*EcoRI: Paradigms for Understanding the Conformational Mechanisms of DNA Methyltransferases

7. Mechanism and Evolution of DNA Recognition by DNA-(adenine N6)-Methyltransferases from the EcoDam Family

8. Structures and Activities of Mammalian DNA Methyl transferases

9. DNA Methylation and Human Diseases: An Overview

10. Expanding the Chemical Repertoire of DNA Methyltransferases by Cofactor Engineering

11. Studying Antibody MaturationUsing Techniques for Detecting Uracils in DNA

12. Enzymatic Formation of the Hypermodified DNA Base J (β-D-Glucopyranosyloxymethyluracil)

13. DNA Demethyladon

14. Demethylation of DNA and RNA by AlkB Proteins

15. The APOBEC1 Paradigm for Mammalian Cyddine Deaminases That Edit DNA and RNA

16. Mechanism of Action and Structural Aspects o f ADARS (A-to-I) and APOBEC-Related (C-to-U) Deaminases

17. Structure of RNA Editing Substrates and Their Recognition by RNA Base Deaminase

18. Biological Roles of ADARs

19. The Interplay between RNA and DNA Modifications: Back to the RNA World

20. Folate-Dependent Ihymidylate-Forming Enzymes: Parallels between DNA and RNA Metabolic Enzymes and Evolutionary Implications

21. Folds and Functions of Domains in RNA Modification Enzymes

22. Enzyme-RNA Substrate Recognition in RNA-Modifying Enzymes

23. Molecular Basis of tRNA Processing Reactions

24. RNA-Modifying Metalloenzymes

25. Pseudouridine Formation, the Most Common Transglycosylation in RNA

26. Enzymatic Formation of the 7-Deazaguanosine Hypermodified Nucleosides of tRNA

27. Biogenesis and Functions of Thio-Compounds in Transfer RNA: Comparison of Bacterial and Eukaryotic Ihiolation Machineries

28. Enzymatic Formation of 5-Aminomethyl-Uridine Derivatives in tRNA: Functional and Evolutionary Im plications

29. Deciphering the Complex Enzymatic Pathway for Biosynthesis of Wyosine Derivatives in Anticodon of tRNAphe

30. Multicomponent 2'-0-Ribose Methylation Machines: Evolving Box C /D RNP Structure and Function

31. Multicomponent Machines in RNA Modification: H/ACA Ribonucleoproteins

32. Spliceosomal snRNA Pseudouridylation

33. Transfer RNA Aminoacylation and Modified Nucleosides

34. Crystallographic Studies of Decoding by Modified Bases: Correlation of Structure and Function

35. Roles of the Ultra-Conserved Ribosomal RNA Methyltransferase KsgA in Ribosome Biogenesis

36. Antibiotic Resistance in Bacteria through Modification of Nucleosides in 16S Ribosomal RNA

37. Antibiotic Resistance in Bacteria Caused by M odified Nucleosides in 23S Ribosomal RNA

38. Function of Modified Nucleosides in RNA Stabilization

39. Roles of tRNA Modifications in tRNA Turnover

40. The “PACE'' Concept Pointed at New Key Proteins Involved in RNA Metabolism

41. Chemical Synthesis of DNA and RNA Containing Modified Nucleotides

51. Appendix 1: Chemical Structures, Classification of Modified Nucleosides in RNA and the MODOMICS Database Concerning the Corresponding RNA Modification Enzymes

52. Appendix 2: Databases of DNA Modifications

53. Appendix 3: RNA Modification Subsystems in the SEED Database

54. Appendix 4: List of Available Phosphoramidites of Modified Nucleotides for Chemical DNA/RNA Synthesis

55. Appendix 5: S-Adenosyl-L-Methionine and Analogs

56. Appendix 6: Web Links to Databases about RNA and DNA Modifications and Related Topics

57. Index