Nucleic Acids : Structures, Properties, and Functions,9780935702491

Nucleic Acids : Structures, Properties, and Functions

by ; ; ; ; ; ;
ISBN13: 9780935702491
ISBN10: 0935702490
Format: Hardcover
Pub. Date: 2000-02-01
Publisher(s): Univ Science Books
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Summary

Provides a detailed account of the structures and physical chemistry properties of nucleic acids, with an emphasis on the implications for biological function. The volume is organized to be of use to physical chemists, physical biochemists, and molecular biologists as well as students in those disciplines, requiring only a basic understanding of physical chemistry and molecular biology as prerequisites. Each chapter begins with a statement of the biological significance of each topic, followed by a presentation of the basic physical ideas and major results. Quantitative details are developed in special sections or appendices.

Table of Contents

Preface ix
Introduction
1(12)
Biological Roles of the Nucleic Acids
1(1)
Physical Chemistry and Nucleic Acid Function
2(1)
Outline of this Book
3(3)
Obtaining Nucleic Acids for Physical Chemical Study
6(1)
The Periodical Literature of Nucleic Acids
7(1)
Books and Monographs
8(2)
Computer Analysis of Sequences and Structures
10(3)
References
10(3)
Bases, Nucleosides, and Nucleotides
13(32)
Structures
13(9)
Electron Distributions
22(9)
Base Pairing and Base Stacking
31(14)
References
41(4)
Chemical and Enzymatic Methods
45(34)
Introduction
45(1)
Synthesis and Hydrolysis
46(6)
Determination of Sequence
52(6)
Determination of Secondary Structure
58(11)
Determination of Tertiary Structure
69(10)
References
72(7)
Nucleic Acid Structures from Diffraction Methods
79(32)
Introduction
79(1)
Diffraction Methods
80(7)
General Features of Duplex DNA and RNA Structure
87(6)
Detailed Structure and Sequence Dependence of Double-Stranded DNA
93(7)
Double-Helical RNA Duplex
100(1)
DNA Helices with Imperfect Base Pairing
101(1)
Local Mobility of Double Helical Nucleic Acids
102(1)
Transfer RNA
103(8)
References
108(3)
Structure and Dynamics by NMR
111(54)
Introduction to NMR Methods
112(10)
Systematic Assignment of Resonances
122(12)
Parameters for Structure Analysis
134(7)
Characterization of Structures
141(5)
Dynamic Analysis
146(4)
Examples of NMR Studies of Nucleic Acids
150(8)
Conclusions
158(7)
References
158(7)
Electronic and Vibrational Spectroscopy
165(58)
Electronic Absorption Spectra in the Ultraviolet
166(15)
Fluorescence and Phosphorescence
181(4)
Circular Dichroism
185(14)
Linear Dichroism
199(8)
Infrared Absorption and Raman Scattering
207(16)
References
217(6)
Theoretical Methods
223(36)
Theoretical Foundations
223(7)
Simulation Methods
230(9)
Theoretical Rationale for Conformational Preferences of Nucleic Acid Components
239(3)
Sequence-Dependent Effects within Helices
242(7)
Mismatches, Damaged DNA, and DNA-Drug Interactions
249(4)
Concluding Perspectives
253(6)
References
254(5)
Conformational Changes
259(76)
Single-Strand Stacking
261(10)
Double Helix Formation by Oligonucleotides without Loops
271(20)
Double Helix Formation by Oligonucleotides with Loops
291(11)
Double Helix Formation with Polynucleotides
302(5)
Environmental Effects on Helix Stability
307(3)
Triple Helixes
310(1)
G-Quartets
311(1)
Predicting Secondary Structure
312(3)
Predicting Three-Dimensional Structure
315(2)
Helix-Helix Transitions
317(18)
Appendix
317(4)
References
321(14)
Size and Shape of Nucleic Acids in Solution
335(108)
Characterization at the Macromolecular Level
336(1)
Models for Molecular Structure
337(4)
Frictional Coefficients for Model Shapes
341(4)
Electrophoresis
345(9)
Sedimentation Velocity
354(6)
Diffusion
360(4)
Sedimentation Equilibrium
364(4)
Viscosity
368(1)
Viscoelasticity
369(3)
Rotational Dynamics
372(9)
Scattering
381(9)
Dynamic Light Scattering
390(6)
Microscopy: Visualization of Single Molecules
396(11)
Bending and Twisting of DNA
407(36)
References
433(10)
Supercoiled DNA
443(32)
Introduction
443(1)
Topoisomerases and Gyrases
444(2)
Geometry and Topology of DNA Supercoiling
446(17)
Energetics of Twisting and Bending
463(3)
Stress-Induced Reactions
466(9)
References
470(5)
Interaction of Nucleic Acids and Water and Ions
475(61)
Hydration
476(12)
Polyelectrolyte Behavior
488(16)
Hydration in Ionic Solutions
504(3)
Specific Binding of Metal Ions and Polyamines
507(14)
Mixed Aqueous-Nonaqueous Solvents
521(15)
Appendix
522(6)
References
528(8)
Interaction and Reaction with Drugs
536(61)
Modes of Interaction: Intercalation and Groove Binding
536(1)
Theoretical Description of Binding Equilibria
537(10)
Experimental Studies of Binding Equilibria
547(18)
Solution Studies of the Structure of Drug-DNA Complexes
565(6)
Kinetics of Ligand Binding
571(4)
Natural Products that React Covalently with DNA
575(10)
Synthetic DNA Binding Agents
585(12)
References
591(6)
Protein-Nucleic Acid Interactions
597(128)
Biological Role of Protein-Nucleic Acid Interactions
598(3)
Elementary Energetics and Specificity of Interaction
601(14)
DNA Sequence Motifs
615(11)
Twisting and Bending of DNA Sequences in Protein Complexes
626(15)
Looping of DNA Sequences
641(4)
Structural Motifs in Sequence Specific DNA-Protein Interactions
645(32)
Motifs in RNA-Protein Interactions
677(6)
Structural Motifs in Enzymes that Act on Nucleic Acids
683(9)
Solution Characterizationof Binding Interactions
692(12)
Kinetics and the Search Mechanism
704(21)
References
711(14)
Higher Order Structure
725(50)
DNA Condensation in Vitro
725(24)
DNA Packaging in Bacteriophage and Bacteria
749(7)
DNA Packaging in Eukaryotes
756(19)
References
766(9)
Index 775

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