Nucleic Acid–Protein Recognition

Nucleic Acid-Protein Recognition covers the proceedings of a symposium on ""Nucleic Acid-Protein Recognition"", held at Arden House, Harriman Campus of Columbia University on May 30-June 1, 1976. The symposium inaugurated the ""P & S Biomedical Sciences Symposia"" under the sponsorship of the College of Physicians and Surgeons of Columbia University. This book is organized into nine part encompassing 31 chapters. The opening parts describe the principles of DNA replication and the unique chromatin structure. These parts also examine the physical chemistry of the interactions of melting proteins with nucleic acids. The third part presents the different types of approaches that can be used to study the function of RNA polymerases and the development of a cell-free system that favors Pol II-catalyzed transcription from type 2 adenovirus DNA. Parts IV and V deal with the sequence determination of wild-type and mutant repressor and the restriction and modification of DNA endonucleases, while parts VI and VII focus of the recognition of tRNA. Part VIII discusses some significant studies on the assembly of ribosomes and the principles of ribosomal interactions. Lastly, Part IX considers the role of small RNA template in the reaction mechanism of RNA replicases and ribonucleases. This part also surveys the so-called RNase III cleavage of different types of RNA and the structure of nucleic acid-protein complexes.

List of Participants

Preface

Opening Address

An Overview of Protein-Nucleic Acid Interactions

Part I DNA Replication

RNA Priming of DNA Replication

Comparison of DNA and RNA Polymerases

RNA Priming of Phage Μ13 DNA Replication, a Rifampicin-Sensitive System

RNA Priming of Phage G4, a Rifampicin-Resistant System

Priming of Phage φΧ174, a Complex, Rifampicin-Resistant System

Other DNA Replicative Systems Dependent on RNA Priming

Summary and Conclusions

References

In Vitro DNA Replication Catalyzed by Six Purified T4 Bacteriophage Proteins

Introduction

Genetic Characterization of the T4 Bacteriophage Replication System

The General Structure of a Replication Fork

Fidelity Constraints on the Mechanism

Kinetic Constraints on the Mechanism

In Vitro Results with the Replication System

Future Directions

References

Molecular Approaches to the Interaction of Nucleic Acids with "Melting" Proteins

Nucleic Acid "Melting" Proteins—Definition and Occurrence

Approaches and Objectives of Melting Protein Studies

Types of Melting Protein Systems Considered

Formaldehyde as a Melting Protein Model

General Aspects of Overlap Binding and Cooperativity

Ribonuclease as a DNA Melting Protein

Gene 32-Protein-Nucleic Acid Interactions

Cooperativity, Control, and the Origins of Molecular Specificity

Physiological Function of Melting Proteins

References

Molecular Aspects of Gene 32 Expression in Escherichia coli Infected with the Bacteriophage T4

Introduction

A Summary of Experiments Done in Vivo

Recent Experiments Done in Vitro

Direct Binding Experiments with P32

Discussion: A Molecular Model for Translational Repression

References

Part II Chromatin Structure

Histone Interactions and Chromatin Structure

Introduction

Histone Interactions

Neutron Studies of Chromatin Structure

Neutron Scatter Studies of Chromatin Subunits

Neutron Diffraction of Chromatin

Discussion

References

The Linkage of Chromatin Subunits and the Role of Histone HI

Quantitative Features of the Chromatin Subunit

Location of Histone HI

Conserved Core Particle and Variable Linkage of Nucleosomes

References

The Structure of the Nucleosome: Evidence for an Arginine-Rich Histone Kernel

Text

References

Part III Transcription

Pro- and Eukaryotic RNA Polymerases

A ts Mutation Affecting the β' Subunit of Escherichia coli RNA Polymerase

RNA Polymerase Β (II) of Drosophila melanogaster

The Location of RNA Polymerase Β on Polytene Chromosomes

Conclusions

References

In Vitro Approaches to the Study of Adenovirus Transcription

Introduction

Materials and Methods

Results and Discussion

Conclusion

References

Part IV Repressors

A Code Controlling Specific Binding of Proteins to Double-Helical DNA and RNA

Introduction

Stereochemistry of Binding of Distamycin A and Its Analogs to DNA

Structure of Stereospecific Protein Sites

Properties of the Code That Controls Specific Protein-Nucleic Acid Interactions

Binding of Lac Repressor to the Lac Operator

Predictions for the Lambda Repressor and Ribosomal S8 Protein

References

Similarities between Lac Repressor and Lambda Repressor

Introduction

Large Amounts of Lac and Lambda Repressor Are Needed and Can Be Produced for Functional and Structural Analysis

Ν Terminus of Lac Repressor Binds Nonspecifically to the Backbone of DNA

The Ν Terminus of Lac Repressor Recognizes Lac Operator Specifically

Two Subunits of Lac Repressor Are Sufficient to Recognize Lac Operator

Inducer Is Bound to the Core of Lac Repressor; Induction Involves a Distortion of Residues 53 to 58

Ν Terminus of Lambda Repressor Recognizes Lambda Operator, and Lambda Repressor Core Recognizes Inducer

Sequence of the Ν Terminus of Lambda Repressor

How Lac and Lambda Repressors Recognize Their Operators

References

Part V Restriction Endonucleases

DNA Site Recognition by the EcoRI Restriction Endonuclease and Modification Methylase

Introduction

Genetics of EcoRI Restriction and Modification

Purification of the EcoRI Restriction Endonuclease and Methylase

Characterization of the EcoRI Restriction Endonuclease and Modification Methylase

Determination of the Substrate Sites for the EcoRI Endonuclease and Methylase

Specificity of Substrate Recognition

Conclusion

References

T4 Ligase Joins Flush-Ended DNA Duplexes Generated by Restriction Endonucleases

Text

References

Size of 5'-Terminal Fragments Cleaved from Poly(dG-dC) by EndoR·HhaI

Text

Reference

BamHI, HindIII, and EcoRI Restriction Endonuclease Cleavage Sites in the argECBH Region of the Escherichia coli Chromosome

Text

References

Part VI Recognition of tRNA (I)

The Molecular Structure of Transfer RNA and Its Interaction with Synthetases

Three-Dimensional Structure of Transfer RNA

References

Processing of tRNA Precursors in Escherichia coli

Monomeric tRNA Precursors Identified in an RNase Ρ Mutant

Multimeric tRNA Precursors Identified in the Mutant

Processing of Multimeric tRNA Precursors

Processing of Monomeric tRNA Precursors

Partial Purification of Processing Enzymes

Modes of Processing Reactions

The 3' Terminus of tRNA

Correlation between Processing of tRNA Precursors and Modification of Nucleosides

General Picture of Processing of tRNA Precursors in E. coli

Concluding Remarks

References

The Modified Nucleosides in Transfer RNA

Introduction

Chemical Nature of Modified Nucleosides in tRNA

Biosynthesis of Modified Nucleosides in tRNA

The Function of Modified Nucleosides in Transfer RNA

Modified Nucleosides as Tools in tRNA Research

Outlook

References

RNA Primers for the Reverse Transcriptases of RNA Tumor Viruses

Text

References

Part VII Recognition of tRNA (II)

Protein Recognition of Base Pairs in a Double Helix

Stacking Interactions Depend upon the Sequence of Purines and Pyrimidines

Intercalation Might Be Used to Discriminate Base Sequences in a Double Helix

Base Pair Recognition by Hydrogen Bonding

Two Hydrogen Bonds Are Better than One

Role of Ions in Recognition

Conclusions

References

Synthetase-tRNA Recognition

Text

References

Aminoacylation of the Ambivalent Su+7 Amber Suppressor tRNA

Introduction

A Further Test of Specificity

Origin, Purity and Heterogeneity of Su+7 tRNA

Evidence for Dual Specificity

The Kinetics of Tryptophanylation and Glutaminylation of Su+7 tRNA Are Very Similar

Does an Interaction between GRS and tRNATrp Preexist?

To What Extent Does Su+7 tRNA Accept Tryptophan in Vivo?

Implications of the Su+7 Mutation for the Selectivity of Aminoacylation

A Review of Su+3

Conclusions

Summary

References

The Interactions of Elongation Factor Tu

Introduction

Prokaryotic Elongation Factors

Eukaryotic Elongation Factors

References

Part VIII Ribosomal Interactions

Some Remarks on Recent Studies on the Assembly of Ribosomes

Introduction

In Vitro Reconstitution of 30 S Ribosomal Subunits

Requirements of the Isolated Ribosomal Components for Ribosome Assembly and Function

Role of 16 S RNA and r-Protein S12 in the Initiation of Natural mRNA

In Vitro Reconstitution of 50 S Ribosomal Subunits

Self-Assembly of Ribosomes

From Genes to Ribosomes

Concluding Remarks

References

Some Approaches for the Study of Ribosome-tRNA Interactions

Steps in Protein Synthesis

Ribosome Components Involved in tRNA Binding

Affinity Labeling Studies with Peptidyl-tRNA

Affinity Labeling with Aminoacyl-tRNA

Studies with Fluorescent tRNA Derivatives

References

RNARNA and Protein-RNA Interactions During the Initiation of Protein Synthesis

An mRNA-rRNA Complex

Secondary Structure of the Complex

Contribution of Initiation Factors and SI

mRNA Secondary Structure as a Negative Determinant in Initiation

Correlation of Complementarity with mRNA Binding?

References

Processing of the 17 S Precursor Ribosomal RNA

Text

References

Ribosomal Protein SI Alters the Ordered State of Synthetic and Natural Polynucleotides

Introduction

Results

Discussion

Summary

References

Part IX RNA Replicases and Ribonucleases

The Role of Template Structure in the Recognition Mechanism of Qß Replicase

Introduction

Recognition of MDV-1 RNA by Q0 Replicase

Localization of the MDV-1 (+) RNA Replicase Binding Site

Alterations in Nucleotide Sequence and Their Effect upon Replicase Binding

Requirements for Initiation of Synthesis

Discussions

References

Structure and Function of RNA Processing Signals

Introduction

Reactions of RNase III

A Hypothesis to Explain RNase III Action

Further Implications and Predictions of This Hypothesis

References

The Structure of Nucleic Acid-Protein Complexes as Evidenced by Dinucleotide Complexes with RNase-S

Text

References

Index

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