Progress in Nucleic Acid Research and Molecular Biology
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Table of contents
- Cover
- Contentsv
- Some Articles Planned for Future Volumesxi
- Chapter 1. DNA Modifications by Antitumor Platinum and Ruthenium Compounds: Their Recognition and Re1
- I. Introduction2
- II. Current State of Knowledge on DNA Interactions of ClassicalŽ Antitumor Cisplatin and Its Clin3
- III. DNA Interactions of Cisplatin Analogs25
- IV. Activation of trans Geometry38
- V. Polynuclear Platinum Antitumor Drugs42
- VI. Antitumor Ruthenium Compounds49
- VII. Concluding Remarks54
- References54
- Chapter 2. AMP- and Stress-Activated Protein Kinases: Key Regulators of Glucose-Dependent Gene Trans69
- I. AMP-Activated Protein Kinase70
- II. SNF1 and Glucose Repression in Yeast71
- III. AMPK and Regulation of Gene Transcription in Mammals71
- IV. Downstream Targets of AMPK and Gene Transcription77
- V. Mitogen- and Stress-Activated Protein Kinases78
- VI. Conclusions82
- References82
- Chapter 3. Molecular Basis of Fidelity of DNA Synthesis and Nucleotide Specificity of Retroviral Rev91
- I. Introduction92
- II. The Role of Reverse Transcriptase in Retroviral Mutagenesis93
- III. Retroviral Reverse Transcriptases94
- IV. Fidelity of Retroviral Reverse Transcriptases97
- V. Control of Fidelity at Initiation of Reverse Transcription108
- VI. Fidelity of Strand Transfer: Implications for Retroviral Recombination109
- VII. Contribution of Accessory Proteins to Fidelity of Reverse Transcription110
- VIII. Mutational Analysis of HIV-1 Reverse Transcriptase: The Effects of Mutations on Fidelity of DN112
- IX. Biological Consequences of Increasing or Decreasing Fidelity129
- X. Conclusions and Future Perspectives131
- References132
- Chapter 4. Muc4/Sialomucin Complex, the Intramembrane ErbB2 Ligand, in Cancer and Epithelia: To Prot149
- I. Membrane Mucins150
- II. Muc4/SMC Structure and Functions153
- III. Muc4/SMC Contributions to Tumor Progression160
- IV. Muc4/SMC in Simple Epithelia163
- V. Muc4/SMC in Glandular Secretory Epithelia170
- VI. Muc4/SMC in Stratified Epithelia177
- VII. Conclusions and Future Directions179
- References180
- Chapter 5. Functions of Alphavirus Nonstructural Proteins in RNA Replication187
- I. Introduction187
- II. Replication Cycle of Alphaviruses188
- III. Alphavirus-Like Superfamily190
- IV. Replication of Alphavirus RNAs192
- V. Processing of Alphavirus Nonstructural Polyprotein P1234197
- VI. nsP1: A Unique RNA-Capping Enzyme and Membrane Anchor198
- VII. nsP2: A Multifunctional Enzyme and Regulatory Protein204
- VIII. nsP3: An Ancient Conserved Protein and Phosphoprotein208
- IX. nsP4: A Catalytic RNA Polymerase Subunit210
- X. The Replication Complex211
- References214
- Chapter 6. The Unique Biochemistry of Methanogenesis223
- I. Introduction224
- II. Methanogens: A Unique Group of Microorganisms225
- III. Biochemistry of Methanogenesis228
- IV. Mechanism of ATP Synthesis in Methanogenic Archaea240
- V. Energy-Conserving Systems in Methanosarcina Strains242
- VI. Energy Conservation in Obligate Hydrogenotrophic Methanogens270
- References274
- Chapter 7. A History of Poly A Sequences: From Formation to Factors to Function285
- I. Introduction287
- II. From Polymerases to Poly A(+) mRNA290
- III. Sequences Required for Polyadenylation291
- IV. The Biochemistry of Polyadenylation296
- V. Cleavage/Polyadenylation Proteins306
- VI. The Core Components of Cleavage/Polyadenylation313
- VII. Cloning, Sequencing, and Expressing the Core Proteins320
- VIII. Regulation of Polyadenylation335
- IX. Polyadenylation in Yeast351
- X. Polyadenylation in E. coli364
- XI. Polyadenylation in Vaccinia Virus375
- References381
- Chapter 8. A Growing Family of Guanine Nucleotide Exchange Factors Is Responsible for Activation of391
- I. Introduction392
- II. Regulation of in Vivo Ras-GTP Levels by Inhibition of GTPase-Activating Proteins394
- III. Early Identification of Ras-Family GEFs395
- IV. GEF Structure and the Nucleotide Exchange Reaction398
- V. Dominant Inhibitory Ras Proteins Target GEFs404
- VI. Biological Assays for GEF Activity406
- VII. Ras-Family GEFs407
- VIII. GEFs and Disease427
- IX. Are There More GEFs in Our Future?428
- References428
- Chapter 9. Practical Approaches to Long Oligonucleotide-Based DNA Microarray: Lessons from Herpesvir445
- I. A Rationale for Developing DNA Microarrays for Herpesviruses446
- II. Herpes Simplex and Cytomegaloviruses„Two Herpesviruses That Share Features of Productive Infec447
- III. Design Criteria for Herpesvirus DNA Microarrays451
- IV. The Construction and Validation of an Oligonucleotide-Based Hsv-1 DNA Microarray on Glass Slides455
- V. Exemplary Applications472
- VI. Conclusions486
- References487
- Chapter 10. Sphingosine Kinases: A Novel Family of Lipid Kinases493
- I. Pleiotropic Functions of Sphingosine-1-Phosphate494
- II. Sphingosine Kinase and Sphingosine-1-Phosphate in Yeast and Plants495
- III. Cellular Functions of Sphingosine Kinase in Mammalian Cells497
- IV. How Is Sphingosine Kinase Activated?498
- V. Cloning of Mammalian Sphingosine Kinases500
- VI. Sphingosine Kinase Family504
- VII. Five Conserved Domains of the SPHK Superfamily505
- VIII. Phylogenetic Analysis of Sphingosine Kinases508
- IX. Concluding Remarks508
- References509
- Chapter 11. Mechanisms of EF-Tu, a Pioneer GTPase513
- I. Introduction514
- II. Structure–Function Relationships524
- III. EF-Ts as a Steric Chaperone for EF-Tu Folding529
- IV. EF-Tu as Target of Antibiotics531
- V. Specific Aspects of EF-Tu GTPase Activity538
- VI. Conclusions and Perspectives542
- References543
- Index553
Progress in Nucleic Acid Research and Molecular Biology provides a forum for discussion of new discoveries, approaches, and ideas in molecular biology. It contains contributions from leaders in their fields and abundant references.
Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes.
Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes.