Progress in Nucleic Acid Research and Molecular Biology

by Moldave

• ISBN13: 9780125400718
• ISBN10: 0125400713
• Format: Hardcover
• Copyright: 2002-06-25
• Publisher: Elsevier Science

Summary

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.

Table of Contents

Some Articles Planned for Future Volumes	xi
DNA Modifications by Antitumor Platinum and Ruthenium Compounds: Their Recognition and Repair	1	(68)
Viktor Brabec
Introduction	2	(1)
Current State of Knowledge on DNA Interactions of ``Classical'' Antitumor Cisplatin and Its Clinically Ineffective trans Isomer	3	(22)
DNA Interactions of Cisplatin Analogs	25	(13)
Activation of trans Geometry	38	(4)
Polynuclear Platinum Antitumor Drugs	42	(7)
Antitumor Ruthenium Compounds	49	(5)
Concluding Remarks	54	(15)
References	54	(15)
AMP- and Stress-Activated Protein Kinases: Key Regulators of Glucose-Dependent Gene Transcription in Mammalian Cells?	69	(22)
Isabelle Leclerc
Gabriela da Silva Xavier
Guy A. Rutter
AMP-Activated Protein Kinase	70	(1)
SNF1 and Glucose Repression in Yeast	71	(1)
AMPK and Regulation of Gene Transcription in Mammals	71	(6)
Downstream Targets of AMPK and Gene Transcription	77	(1)
Mitogen- and Stress-Activated Protein Kinases	78	(4)
Conclusions	82	(9)
References	82	(9)
Molecular Basis of Fidelity of DNA Synthesis and Nucleotide Specificity of Retroviral Reverse Transcriptases	91	(58)
Luis Menendez-Arias
Introduction	92	(1)
The Role of Reverse Transcriptase in Retroviral Mutagenesis	93	(1)
Retroviral Reverse Transcriptases	94	(3)
Fidelity of Retroviral Reverse Transctiptases	97	(11)
Control of Fidelity at Initiation of Reverse Transcription	108	(1)
Fidelity of Strand Transfer: Implications for Retroviral Recombination	109	(1)
Contribution of Accessory Proteins to Fidelity of Reverse Transcription	110	(2)
Mutational Analysis of HIV-1 Reverse Transcriptase: The Effects of Mutations on Fidelity of DNA Synthesis	112	(17)
Biological Consequences of Increasing or Decreasing Fidelity	129	(2)
Conclusions and Future Perspectives	131	(18)
References	132	(17)
Muc4/Sialomucin Complex, the Intramembrane ErbB2 Ligand, in Cancer and Epithelia: To Protect and To Survive	149	(38)
Kermit L. Carraway
Aymee Perez
Nebila Idris
Scott Jepson
Maria Arango
Masanobu Komatsu
Bushra Haq
Shari A. Price-Schiavi
Jin Zhang
Coralie A. Carothers Carraway
Membrane Mucins	150	(3)
Muc4/SMC Structure and Functions	153	(7)
Muc4/SMC Contributions to Tumor Progression	160	(3)
Muc4/SMC in Simple Epithelia	163	(7)
Muc4/SMC in Glandular Secretory Epithelia	170	(7)
Muc4/SMC in Stratified Epithelia	177	(2)
Conclusions and Future Directions	179	(8)
References	180	(7)
Functions of Alphavirus Nonstructural Proteins in RNA Replication	187	(36)
Leevi Kaariainen
Tero Ahola
Introduction	187	(1)
Replication Cycle of Alphaviruses	188	(2)
Alphavirus-Like Superfamily	190	(2)
Replication of Alphavirus RNAs	192	(5)
Processing of Alphavirus Nonstructural Polyprotein P1234	197	(1)
nsP1: A Unique RNA-Capping Enzyme and Membrane Anchor	198	(6)
nsP2: A Multifunctional Enzyme and Regulatory Protein	204	(4)
nsP3: An Ancient Conserved Protein and Phosphoprotein	208	(2)
nsP4: A Catalytic RNA Polymerase Subunit	210	(1)
The Replication Complex	211	(12)
References	214	(9)
The Unique Biochemistry of Methanogenesis	223	(62)
Uwe Deppenmeier
Introduction	224	(1)
Methanogens: A Unique Group of Microorganisms	225	(3)
Biochemistry of Methanogenesis	228	(12)
Mechanism of ATP Synthesis in Methanogenic Archaea	240	(2)
Energy-Conserving Systems in Methanosarcina Strains	242	(28)
Energy Conservation in Obligate Hydrogenotrophic Methanogens	270	(15)
References	274	(11)
A History of Poly A Sequences: From Formation to Factors to Fuction	285	(106)
Mary Edmonds
Introduction	287	(3)
From Polymerases to Poly A(+) mRNA	290	(1)
Sequences Required for Polyadenylation	291	(5)
The Biochemistry of Polyadenylation	296	(10)
Cleavage/Polyadenylation Proteins	306	(7)
The Core Components of Cleavage/Polyadenylation	313	(7)
Cloning, Sequencing, and Expressing the Core Proteins	320	(15)
Regulation of Polyadenylation	335	(16)
Polyadenylation in Yeast	351	(13)
Polyadenylation in E. coli	364	(11)
Polyadenylation in Vaccinia Virus	375	(16)
References	381	(10)
A Growing Family of Guanine Nucleotide Exchange Factors Is Responsible for Activation of Ras-Family GTPases	391	(54)
Lawrence A. Quilliam
John F. Rebhun
Ariel F. Castro
Introduction	392	(2)
Regulation of in Vivo Ras-GTP Levels by Inhibition of GTPase-Activating Proteins	394	(1)
Early Identification of Ras-Family GEFs	395	(3)
GEF Structure and the Nucleotide Exchange Reaction	398	(6)
Dominant Inhibitory Ras Proteins Target GEFs	404	(2)
Biological Assays for GEF Activity	406	(1)
Ras-Family GEFs	407	(20)
GEFs and Disease	427	(1)
Are There More GEFs in Our Future?	428	(17)
References	428	(17)
Practical Approaches to Long Oligonucleotide-Based DNA Microarray: Lessons from Herpesviruses	445	(48)
Edward K. Wagner
J. J. Garcia Ramirez
S. W. Stingley
S. A. Aguilar
L. Buehler
G. B. Devi-Rao
Peter Ghazal
A Rationale for Developing DNA Microarrays for Herpesviruses	446	(1)
Herpes Simplex and Cytomegaloviruses---Two Herpesviruses That Share Features of Productive Infection but Differ Markedly in Patterns of Latency and Reactivation	447	(4)
Design Criteria for Herpesvirus DNA Microarrays	451	(4)
The Construction and Validation of an Oligonucleotide-Based Hsv-1 DNA Microarray on Glass Slides	455	(17)
Exemplary Applications	472	(14)
Conclusions	486	(7)
References	487	(6)
Sphingosine Kinases: A Novel Family of Lipid Kinases	493	(20)
Hong Liu
Debyani Chakravarty
Michael Maceyka
Sheldon Milstien
Sarah Spiegel
Pleiotropic Functions of Sphingosine-1-Phosphate	494	(1)
Sphingosine Kinase and Sphingosine-1-Phosphate in Yeast and Plants	495	(2)
Cellular Functions of Sphingosine Kinase in Mammalian Cells	497	(1)
How Is Sphingosine Kinase Activated?	498	(2)
Cloning of Mammalian Sphingosine Kinases	500	(4)
Sphingosine Kinase Family	504	(1)
Five Conserved Domains of the SPHK Superfamily	505	(3)
Phylogenetic Analysis of Sphingosine Kinases	508	(1)
Concluding Remarks	508	(5)
References	509	(4)
Mechanisms of EF-Tu, a Pioneer GTPase	513	(40)
Ivo M. Krab
Andrea Parmeggiani
Introduction	514	(10)
Structure-Function Relationships	524	(5)
EF-Ts as a Steric Chaperone for EF-Tu Folding	529	(2)
EF-Tu as Target of Antibiotics	531	(7)
Specific Aspects of EF-Tu GTPase Activity	538	(4)
Conclusions and Perspectives	542	(11)
References	543	(10)
Index	553