Nucleic Acid–Protein Recognition

Nucleic Acid–Protein Recognition

1st Edition - January 1, 1977

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  • Editor: Henry Vogel
  • eBook ISBN: 9780323144537

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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.

Table of Contents

  • List of Participants


    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


    In Vitro DNA Replication Catalyzed by Six Purified T4 Bacteriophage Proteins


    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


    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


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


    A Summary of Experiments Done in Vivo

    Recent Experiments Done in Vitro

    Direct Binding Experiments with P32

    Discussion: A Molecular Model for Translational Repression


    Part II Chromatin Structure

    Histone Interactions and Chromatin Structure


    Histone Interactions

    Neutron Studies of Chromatin Structure

    Neutron Scatter Studies of Chromatin Subunits

    Neutron Diffraction of Chromatin



    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


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



    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



    In Vitro Approaches to the Study of Adenovirus Transcription


    Materials and Methods

    Results and Discussion



    Part IV Repressors

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


    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


    Similarities between Lac Repressor and Lambda Repressor


    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


    Part V Restriction Endonucleases

    DNA Site Recognition by the EcoRI Restriction Endonuclease and Modification Methylase


    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



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



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



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



    Part VI Recognition of tRNA (I)

    The Molecular Structure of Transfer RNA and Its Interaction with Synthetases

    Three-Dimensional Structure of Transfer RNA


    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


    The Modified Nucleosides in Transfer RNA


    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



    RNA Primers for the Reverse Transcriptases of RNA Tumor Viruses



    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



    Synthetase-tRNA Recognition



    Aminoacylation of the Ambivalent Su+7 Amber Suppressor tRNA


    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




    The Interactions of Elongation Factor Tu


    Prokaryotic Elongation Factors

    Eukaryotic Elongation Factors


    Part VIII Ribosomal Interactions

    Some Remarks on Recent Studies on the Assembly of Ribosomes


    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


    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


    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?


    Processing of the 17 S Precursor Ribosomal RNA



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






    Part IX RNA Replicases and Ribonucleases

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


    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



    Structure and Function of RNA Processing Signals


    Reactions of RNase III

    A Hypothesis to Explain RNase III Action

    Further Implications and Predictions of This Hypothesis


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




Product details

  • No. of pages: 614
  • Language: English
  • Copyright: © Academic Press 1977
  • Published: January 1, 1977
  • Imprint: Academic Press
  • eBook ISBN: 9780323144537

About the Editor

Henry Vogel

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