| Preface | p. ix |
| Introduction | p. 1 |
| Biological Roles of the Nucleic Acids | p. 1 |
| Physical Chemistry and Nucleic Acid Function | p. 2 |
| Outline of this Book | p. 3 |
| Obtaining Nucleic Acids for Physical Chemical Study | p. 6 |
| The Periodical Literature of Nucleic Acids | p. 7 |
| Books and Monographs | p. 8 |
| Computer Analysis of Sequences and Structures | p. 10 |
| References | p. 10 |
| Bases, Nucleosides, and Nucleotides | p. 13 |
| Structures | p. 13 |
| Electron Distributions | p. 22 |
| Base Pairing and Base Stacking | p. 31 |
| References | p. 41 |
| Chemical and Enzymatic Methods | p. 45 |
| Introduction | p. 45 |
| Synthesis and Hydrolysis | p. 46 |
| Determination of Sequence | p. 52 |
| Determination of Secondary Structure | p. 58 |
| Determination of Tertiary Structure | p. 69 |
| References | p. 72 |
| Nucleic Acid Structures from Diffraction Methods | p. 79 |
| Introduction | p. 79 |
| Diffraction Methods | p. 80 |
| General Features of Duplex DNA and RNA Structure | p. 87 |
| Detailed Structure and Sequence Dependence of Double-Stranded DNA | p. 93 |
| Double-Helical RNA Duplex | p. 100 |
| DNA Helices with Imperfect Base Pairing | p. 101 |
| Local Mobility of Double Helical Nucleic Acids | p. 102 |
| Transfer RNA | p. 103 |
| References | p. 108 |
| Structure and Dynamics by NMR | p. 111 |
| Introduction to NMR Methods | p. 112 |
| Systematic Assignment of Resonances | p. 122 |
| Parameters for Structure Analysis | p. 134 |
| Characterization of Structures | p. 141 |
| Dynamic Analysis | p. 146 |
| Examples of NMR Studies of Nucleic Acids | p. 150 |
| Conclusions | p. 158 |
| References | p. 158 |
| Electronic and Vibrational Spectroscopy | p. 165 |
| Electronic Absorption Spectra in the Ultraviolet | p. 166 |
| Fluorescence and Phosphorescence | p. 181 |
| Circular Dichroism | p. 185 |
| Linear Dichroism | p. 199 |
| Infrared Absorption and Raman Scattering | p. 207 |
| References | p. 217 |
| Theoretical Methods | p. 223 |
| Theoretical Foundations | p. 223 |
| Simulation Methods | p. 230 |
| Theoretical Rationale for Conformational Preferences of Nucleic Acid Components | p. 239 |
| Sequence-Dependent Effects within Helices | p. 242 |
| Mismatches, Damaged DNA, and DNA-Drug Interactions | p. 249 |
| Concluding Perspectives | p. 253 |
| References | p. 254 |
| Conformational Changes | p. 259 |
| Single-Strand Stacking | p. 261 |
| Double Helix Formation by Oligonucleotides without Loops | p. 271 |
| Double Helix Formation by Oligonucleotides with Loops | p. 291 |
| Double Helix Formation with Polynucleotides | p. 302 |
| Environmental Effects on Helix Stability | p. 307 |
| Triple Helixes | p. 310 |
| G-Quartets | p. 311 |
| Predicting Secondary Structure | p. 312 |
| Predicting Three-Dimensional Structure | p. 315 |
| Helix-Helix Transitions | p. 317 |
| Appendix | p. 317 |
| References | p. 321 |
| Size and Shape of Nucleic Acids in Solution | p. 335 |
| Characterization at the Macromolecular Level | p. 336 |
| Models for Molecular Structure | p. 337 |
| Frictional Coefficients for Model Shapes | p. 341 |
| Electrophoresis | p. 345 |
| Sedimentation Velocity | p. 354 |
| Diffusion | p. 360 |
| Sedimentation Equilibrium | p. 364 |
| Viscosity | p. 368 |
| Viscoelasticity | p. 369 |
| Rotational Dynamics | p. 372 |
| Scattering | p. 381 |
| Dynamic Light Scattering | p. 390 |
| Microscopy: Visualization of Single Molecules | p. 396 |
| Bending and Twisting of DNA | p. 407 |
| References | p. 433 |
| Supercoiled DNA | p. 443 |
| Introduction | p. 443 |
| Topoisomerases and Gyrases | p. 444 |
| Geometry and Topology of DNA Supercoiling | p. 446 |
| Energetics of Twisting and Bending | p. 463 |
| Stress-Induced Reactions | p. 466 |
| References | p. 470 |
| Interaction of Nucleic Acids and Water and Ions | p. 475 |
| Hydration | p. 476 |
| Polyelectrolyte Behavior | p. 488 |
| Hydration in Ionic Solutions | p. 504 |
| Specific Binding of Metal Ions and Polyamines | p. 507 |
| Mixed Aqueous-Nonaqueous Solvents | p. 521 |
| Appendix | p. 522 |
| References | p. 528 |
| Interaction and Reaction with Drugs | p. 535 |
| Modes of Interaction: Intercalation and Groove Binding | p. 536 |
| Theoretical Description of Binding Equilibria | p. 537 |
| Experimental Studies of Binding Equilibria | p. 547 |
| Solution Studies of the Structure of Drug-DNA Complexes | p. 565 |
| Kinetics of Ligand Binding | p. 571 |
| Natural Products that React Covalently with DNA | p. 575 |
| Synthetic DNA Binding Agents | p. 585 |
| References | p. 591 |
| Protein-Nucleic Acid Interactions | p. 597 |
| Biological Role of Protein-Nucleic Acid Interactions | p. 598 |
| Elementary Energetics and Specificity of Interaction | p. 601 |
| DNA Sequence Motifs | p. 615 |
| Twisting and Bending of DNA Sequences in Protein Complexes | p. 626 |
| Looping of DNA Sequences | p. 641 |
| Structural Motifs in Sequence Specific DNA-Protein Interactions | p. 645 |
| Motifs in RNA-Protein Interactions | p. 677 |
| Structural Motifs in Enzymes that Act on Nucleic Acids | p. 683 |
| Solution Characterization of Binding Interactions | p. 692 |
| Kinetics and the Search Mechanism | p. 704 |
| References | p. 711 |
| Higher Order Structure | p. 725 |
| DNA Condensation in Vitro | p. 725 |
| DNA Packaging in Bacteriophage and Bacteria | p. 749 |
| DNA Packaging in Eukaryotes | p. 756 |
| References | p. 766 |
| Index | p. 775 |
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