Note: Protein-Nucleic Acid Interactions -- Contents -- Chapter 1 Introduction -- 1.1 Overview -- 1.2 Fundamentals of DNA and RNA Structure -- 1.2.1 Stabilizing Forces -- 1.2.2 Chemical Differences between DNA and RNA -- 1.2.3 Canonical A- and B-form Helices -- 1.2.4 Deviation is the Norm -- 1.2.5 Bending and Supercoiling DNA -- 1.2.6 Folded RNA and Noncanonical DNA -- 1.3 Principles of Recognition -- 1.3.1 Forces that Contribute to Complex Formation -- 1.3.2 Site Recognition Overview -- 1.3.3 Recognizing Duplex DNA via Direct and Indirect Readout -- 1.3.4 Recognizing Single-stranded Nucleic Acids -- 1.3.5 Recognizing Folded RNAs -- 1.3.6 Recognizing Noncanonical DNA Structures -- 1.3.7 Conformational Rearrangements -- 1.4 Future Directions -- References -- Chapter 2 Role of Water and Effects of Small Ions in Site-specific Protein-DNA Interactions -- 2.1 Introduction -- 2.2 Affinity and Specificity -- 2.3 Macromolecular Hydration Influences ΔH°, ΔS° and ΔC°P -- 2.4 Water Release Attending Protein-DNA Association -- 2.5 Retained Water Molecules Contribute to Affinity and Specificity -- 2.6 Thermodynamic Effects of Retained Water -- 2.7 Overview of Small Ion Effects on Protein-DNA Interactions -- 2.8 Multiple Physical Phenomena Associated with Salt Dependence -- 2.9 Cation Release Favors Protein-DNA Association -- 2.10 Selective Effects of Anions on Protein-DNA Binding -- 2.11 Divalent Cation Binding at Active Sites Relieves Electrostatic Strain -- 2.12 Ion Effects and Cosolute Effects are Mechanistically Independent -- 2.13 Comparison with Nonspecific Binding: How Water and Ions Affect Specificity -- 2.14 Conclusions -- Acknowledgements -- References -- Chapter 3 Structural Basis for Sequence-specific DNA Recognition by Transcription Factors and their Complexes -- 3.1 Introduction -- 3.2 Transcriptional Regulators that Bind Core DNA Elements. , 3.2.1 Helix-turn-helix and Winged Helix-turn-helix -- 3.2.2 Basic Leucine-zipper and Basic Helix-loop-helix -- 3.2.3 Zinc-binding Domains that Bind as Monomeric Units -- 3.2.4 DNA Recognition by β-Ribbons -- 3.2.5 Immunoglobulin Fold -- 3.2.6 HMG Domain -- 3.3 Transcriptional Regulators that Bind as Dimers to two DNA Half Sites with Different Spacing and Polarity -- 3.3.1 Zn2Cys6 Binuclear Cluster -- 3.3.2 Nuclear Receptors -- 3.4 Transcription Regulatory Complexes that use a Combination of Different DNA-binding Motifs -- 3.4.1 Combinatorial DNA Interactions -- 3.4.2 ETS Family Ternary Complexes -- 3.4.3 NFAT/Fos-Jun/DNA Quaternary Complex -- 3.5 Conclusions -- References -- Chapter 4 Indirect Readout of DNA Sequence by Proteins -- 4.1 Introduction -- 4.1.1 DNA Sequence Recognition: A Historical Perspective -- 4.2 Indirect Readout -- 4.2.1 Direct vs. Indirect Readout -- 4.2.2 Language of Indirect Readout: DNA Geometry -- 4.2.3 Sequence-dependent Polymorphisms of B-DNA -- 4.2.3.1 Base Stacking -- 4.2.3.2 Hydrogen Bonding -- 4.2.3.3 Steric Repulsion -- 4.2.3.4 DNA Bending -- 4.2.4 Indirect Readout: A Universal Feature of Protein-DNA Interactions -- 4.3 DNA Sequence Recognition by CAP -- 4.3.1 Direct Readout by CAP -- 4.3.2 Indirect Readout by CAP -- 4.3.2.1 Conformation and Flexibility of the DNA Site for CAP -- 4.3.2.2 Indirect Readout at Positions 1-2 -- 4.3.2.3 Indirect Readout at Position 6 -- 4.3.2.4 Comparison with Other Protein-induced Positive Roll Deformations -- 4.3.3 DNA Bending vs. DNA Kinking - A Dynamic Duo? -- 4.4 Conclusions -- Acknowledgements -- References -- Chapter 5 Single-stranded Nucleic Acid (SSNA)-binding Proteins -- 5.1 Introduction -- 5.2 Basic Elements -- 5.2.1 Interaction Types -- 5.2.1.1 Salt Bridges and Electrostatics -- 5.2.1.2 Stacking Interactions -- 5.2.1.3 Steric Packing and van der Waals Interactions. , 5.2.1.4 Hydrogen Bonding -- 5.2.2 Folds, Evolution and Function -- 5.2.2.1 OB-fold -- 5.2.2.2 Sm-fold -- 5.2.2.3 RRM -- 5.2.2.4 KH -- 5.2.2.5 Others: Pumilio, TRAP and Whirly -- 5.3 Emergent Properties -- 5.3.1 Molecular Recognition: Specificity, Adaptability and Degeneracy -- 5.3.1.1 Specific yet Adaptable Recognition by Modular Puf Proteins -- 5.3.1.2 A "Hot-spot" for Recognition of Telomere DNA by Cdc13 -- 5.3.1.3 "Nucleotide Shuffling" and TEBP-α/β -- 5.3.1.4 Degeneracy in Splicing Branch Site Identification -- 5.3.2 Cooperativity -- 5.3.2.1 SSB and Multiple Cooperativity Modes -- 5.3.2.2 Anti-cooperativity and TEBP-α -- 5.3.2.3 Positive Heterotypic Cooperativity at Telomere Ends -- 5.3.3 Allostery -- 5.3.3.1 Small Molecule Effectors and SSNA-binding -- 5.3.3.2 Proteins as Allosteric Effectors for Binding and Release of SSNA -- 5.4 Conclusion and Perspective -- Acknowledgements -- References -- Chapter 6 DNA Junctions and their Interaction with Resolving Enzymes -- 6.1 The Four-way Junction in Genetic Recombination -- 6.2 Structure and Dynamics of DNA Junctions -- 6.2.1 Dynamics of the Four-way Junction -- 6.2.2 Metal Ions and the Electrostatics of the Four-way Junction -- 6.2.3 Branch Migration -- 6.2.4 Comparison with Four-way RNA Junctions -- 6.3 Proteins that Interact with DNA Junctions -- 6.4 Junction-resolving Enzymes -- 6.4.1 Occurrence of the Junction-resolving Enzymes -- 6.4.2 Phylogeny -- 6.4.3 Junction-resolving Enzymes are Dimeric -- 6.4.4 Structures of the Junction-resolving Enzymes -- 6.5 Molecular Recognition and Distortion of the Structure of DNA Junctions by Resolving Enzymes -- 6.5.1 Sequence Specificity of the Junction-resolving Enzymes -- 6.5.2 Structural Distortion of DNA Junctions by the Junction-resolving Enzymes -- 6.5.3 Coordination of the Resolution Process -- 6.6 T7 Endonuclease I -- 6.6.1 Biochemistry of Endonuclease I. , 6.6.2 Structure of Endonuclease I -- 6.6.3 The Active Site -- 6.6.4 Catalysis of Phosphodiester Bond Hydrolysis -- 6.6.5 Interaction between Endonuclease I and DNA Junctions -- 6.7 In Conclusion -- Acknowledgements -- References -- Chapter 7 RNA-protein Interactions in Ribonucleoprotein Particles and Ribonucleases -- 7.1 Introduction -- 7.2 Experimental Methods used to Determine RNA-protein Complex Structures -- 7.3 RNA-protein Interactions in Ribonucleoprotein Particles -- 7.3.1 Ribosome -- 7.3.2 RNAi Complexes -- 7.3.3 Signal Recognition Particle -- 7.3.4 s(no)RNPs -- 7.3.5 RNA Editing Complexes -- 7.4 RNA-protein Interactions in Ribonucleases -- 7.4.1 RNase E -- 7.4.2 RNase II -- 7.4.3 RNase III -- 7.4.4 Restrictocin -- 7.4.5 RNA Splicing Endonucleases -- 7.4.6 tRNase Z -- 7.5 Concluding Remarks -- Acknowledgements -- References -- Chapter 8 Bending and Compaction of DNA by Proteins -- 8.1 Introduction -- 8.2 Forces Controlling DNA Rigidity -- 8.2.1 DNA Elasticity and the Influence of DNA Sequence -- 8.2.2 Base Stacking Primarily Controls Helix Rigidity -- 8.2.3 Electrostatic Forces Modulate DNA Bending -- 8.3 Bending of DNA at High Resolution -- 8.3.1 Helix Parameters Controlling DNA Structure -- 8.3.1.1 Roll and Tilt -- 8.3.1.2 Twist -- 8.3.1.3 Propeller Twist, Slide, and Shift -- 8.3.1.4 Changes in DNA Groove Width -- 8.3.2 Influence of Exocyclic Groups on Base Stacking -- 8.3.3 Flexibility of Dinucleotide Steps -- 8.3.3.1 Pyrimidine-purine (Y-R) Steps -- 8.3.3.2 Purine-purine (R-R) or Pyrimidine-pyrimidine (Y-Y) Steps -- 8.3.3.3 Purine-pyrimidine (R-Y) Steps -- 8.4 Examples of DNA Bending Proteins -- 8.4.1 Histone Binding to DNA -- 8.4.2 Phage λ Xis Protein -- 8.4.3 Papillomavirus E2 Protein -- 8.4.4 Escherichia coli Fis Protein -- 8.4.4.1 Long-range DNA Condensation by Fis -- 8.4.5 Escherichia coli CAP Protein. , 8.4.6 Prokaryotic HU/IHF Protein Family -- 8.4.6.1 Single-DNA Molecule Analysis of HU/IHF Protein Binding -- 8.4.7 HMGB Protein Family -- 8.4.7.1 Single DNA Molecule Analyses of HMGB Protein Binding -- 8.4.7.2 DNA Binding by HMGB Shares Features with TBP -- 8.5 Concluding Remarks -- References -- Chapter 9 Mode of Action of Proteins with RNA Chaperone Activity -- 9.1 Introduction -- 9.1.1 RNA Folding -- 9.1.2 Proteins with RNA Chaperone Activity (RCA) -- 9.1.3 Measuring RCA -- 9.2 Mode of Action of Proteins with RCA -- 9.2.1 RNA Annealing Activity -- 9.2.1.1 Annealing of Protein-bound Guide RNAs with Target RNAs -- 9.2.2 Nucleic Acid Melting Activity -- 9.3 RNA Binding and Restructuring -- 9.3.1 Proteins with RCA Interact with RNA only Weakly -- 9.3.2 Proteins with Specific RNA-binding Affinity -- 9.3.3 Protein Structure and RNA Chaperone Activity -- Acknowledgements -- References -- Chapter 10 Structure and Function of DNA Topoisomerases -- 10.1 Introduction -- 10.2 Type IA Topoisomerases -- 10.2.1 Overview -- 10.2.2 Structures and Mechanism -- 10.2.3 Type IA Topoisomerase Paralogs -- 10.2.3.1 Topoisomerase III -- 10.2.3.2 Reverse Gyrase -- 10.3 Type IB Topoisomerases -- 10.3.1 Overview -- 10.3.2 General Architecture -- 10.3.3 DNA Recognition and Cleavage -- 10.3.4 Mechanism -- 10.4 Topoisomerase V - The Defining Member of the Type IC Topoisomerases? -- 10.5 Type IIA Topoisomerases -- 10.5.1 Overview -- 10.5.2 Structural Organization -- 10.5.2.1 ATPase Domain -- 10.5.2.2 DNA Breakage/Reunion Domain and the DNA Binding/Cleavage Core -- 10.5.3 Duplex DNA Transport Mechanism -- 10.5.3.1 Type IIA Topoisomerase Paralogs: Role of the C-terminal Domain in Modulating Duplex Transport -- 10.5.4 Physiological Specialization of Type IIA Topoisomerases -- 10.6 Type IIB Topoisomerases -- 10.6.1 Overview -- 10.6.2 Structure -- 10.6.3 Mechanism -- 10.7 Conclusions. , Acknowledgements.