DNA Dynamics and Single-Molecule Biology

1. Summary 3072 2. Introduction 3072 3. Recognition of DNA Sequences and Structures 3073 3.1. Classical View of Interactions 3074 3.2. Encounter Landscape 3074 3.3. Binding Landscape 3074 3.4. Significance of Distinguishing between the Landscapes 3074 3.5. Building to Physiological Complexity 3075 4. DNA Structure 3075 4.1. Forces on DNA 3075 4.2. Effects of Ionic Strength 3076 4.3. DNA Length Is Important 3076 4.4. Sequence Influences Structure 3076 4.5. Structural Perturbations at Protein−DNA Interfaces 3076 5. Single-Molecule Studies of Protein−DNA Interactions 3077 6. RNA Polymerase 3078 6.1. Encounter and Binding Landscapes of RNA Polymerase 3078 6.2. Limits to Experimentally Accessing Structure Space 3080 6.3. Target Sizes Inherently Restrict Sequence Space 3080 6.4. Beyond Promoter Binding 3080 7. Nucleosomes 3080 7.1. Nucleosomes Must Access Vast Regions of Sequence Space 3081 7.2. Sequence and Structure Preferences of Nucleosomes 3081 7.3. Visualizing Nucleosome Positioning with DNA Curtains 3081 7.4. Extrinsic Factors Can Affect Binding Landscapes 3082 8. Concluding Perspectives 3083 Author Information 3083 Corresponding Author 3083 Author Contributions 3083 Notes 3083 Biographies 3083 Acknowledgments 3084 References 3084