1 Why Study Nucleotide and Nucleic Acid Structure?.- 2 Defining Terms for the Nucleic Acids.- 2.1 Bases, Nucleosides, Nucleotides, and Nucleic Acids-Nomenclature and Symbols.- 2.2 Atomic Numbering Scheme.- 2.3 Torsion Angles and Their Ranges.- 2.4 Definitions of Torsion Angles in Nucleotides.- 2.5 Sugar Pucker Modes: The Pseudorotation Cycle.- 2.6 syn/anti Orientation About the Glycosyl Bond.- 2.7 Orientation About the C4?-C5? Bond.- 2.8 Helical Parameters: Hydrogen Bonding Between Bases.- Summary.- 3 Methods: X-Ray Crystallography, Potential Energy Calculations, and Spectroscopy.- 3.1 Crystal Structure Analysis of Small Molecules.- 3.2 Potential Energy Calculations.- 3.3 Crystallography of Macromolecules.- 3.4 Fiber Structure Determination.- 3.5 Spectroscopic Methods.- Summary.- 4 Structures and Conformational Properties of Bases, Furanose Sugars, and Phosphate Groups.- 4.1 Geometry of Bases.- 4.2 Preferred Sugar Puckering Modes.- 4.3 Factors Affecting Furanose Puckering Modes.- 4.4 Bond Distances and Angles in Furanoses.- 4.5 syn/anti Conformation.- 4.6 The high anti (-sc) Conformation.- 4.7 Factors Affecting the syn/anti Conformation: The Exceptional Guanosine.- 4.8 The Orientation About the C4?-C5? Bond.- 4.9 Factors Influencing the Orientation about the C4?-C5? Bond.- 4.10 The Rigid Nucleotide.- 4.11 The Phosphate Mono- and Diester Groups and the Pyrophosphate Link: Bonding Characteristics and Geometry.- 4.12 Orientation About the C-O and P-O Ester Bonds.- 4.13 Correlated Rotations of Torsion Angles in Nucleotides and in Nucleic Acids.- 4.14 Helical or Not Helical-and if, What Sense?.- Summary.- 5 Physical Properties of Nucleotides: Charge Densities, pK Values, Spectra, and Tautomerism.- 5.1 Charge Densities.- 5.2 pK Values of Base, Sugar, and Phosphate Groups: Sites for Nucleophilic Attack.- 5.3 Tautomerism of Bases.- Summary.- 6 Forces Stabilizing Associations Between Bases: Hydrogen Bonding and Base Stacking.- 6.1 Characterization of Hydrogen Bonds.- 6.2 Patterns of Base-Base Hydrogen Bonding: The Symmetry of a Polynucleotide Complex.- 6.3 Detailed Geometries of Watson-Crick and Hoogsteen Base Pairs.- 6.4 The Stability and Formation of Base Pairs as Determined by Thermodynamic, Kinetic, and Quantum Chemical Methods: Electronic Complementarity.- 6.5 Patterns of Vertical Base-Base Interactions.- 6.6 Thermodynamic Description of Stacking Interactions.- 6.7 Forces Stabilizing Base Stacking: Hydrophobic Bonding and London Dispersion.- 6.8 Formation and Breakdown of Double-Helix Structure Show Cooperative Behavior.- 6.9 Base-Pair Tautomerism and Wobbling: Structural Aspects of Spontaneous Mutation and the Genetic Code.- Summary.- 7 Modified Nucleosides and Nucleotides; Nucleoside Di- and Triphosphates; Coenzymes and Antibiotics.- 7.1 Covalent Bonds Bridging Base and Sugar in Fixed Conformations: Calipers for Spectroscopic Methods.- 7.2 Cyclic Nucleotides.- 7.3 Nucleosides with Modified Sugars: Halogeno-, Arabino-, and ?-Nucleosides.- 7.4 Modified Bases: Alkylation of Amino Groups (Cytokinins) and of Ring Nitrogen, Thioketo Substitution, Dihydrouridine, Thymine Dimers, Azanucleosides.- 7.5 The Chiral Phosphorus in Nucleoside Phosphorothioates.- 7.6 The Pyrophosphate Group in Nucleoside Di- and Triphosphates and in Nucleotide Coenzymes.- 7.7 Nucleoside Antibiotics: Puromycin as Example.- Summary.- 8 Metal Ion Binding to Nucleic Acids.- 8.1 Importance of Metal Ion Binding for Biological Properties of Nucleic Acids.- 8.2 Modes of Metal Ion Binding to Nucleotides and Preferred Coordination Sites.- 8.3 Platinum Coordination.- 8.4 Coordination of Metal Ions to Nucleoside Di- and Triphosphates: Nomenclature of Bidentate ?/? and of Tridentate ?/?/endo/exo Chelate Geometry.- Summary.- 9 Polymorphism of DNA versus Structural Conservatism of RNA: Classification of A-, B-, and Z-Type Double Helices.- 9.1 Polymorphism of Polynucleotide Double Helices.- 9.2 The Variety of Polynucleotide Helices with Right-Handed Screw Classified into Two Generically Different Families: A and B.- Summary.- 10 RNA Structure.- 10.1 A-RNA and A?-RNA Double Helices Are Similar.- 10.2 RNA Triple Helices Simultaneously Display Watson-Crick and Hoogsteen Base-Pairing.- 10.3 A Double Helix with Parallel Chains and Hoogsteen Base-Pairs Formed by Poly(U) and 2-Substituted Poly(A).- 10.4 Mini-Double Helices Formed by ApU and GpC.- 10.5 Turns and Bends in UpAH+.- Summary.- 11 DNA Structure.- 11.1 A-DNA, The Only Member of the A Family: Three Crystalline A-Type Oligonucleotides d(CCGG), d(GGTATACC), and d(GGCCGGCC).- 11.2 B-DNA Structures Exhibited by Polymeric DNA and by the Dodecanucleotide d(CGCGAATTCGCG): Introduction to B-Family Duplexes.- 11.3 Alternating B-DNA and the Tetranucleotide d(pATAT); d(TpA), Dinucleoside Phosphate Mimicking Double Helical Arrangement.- 11.4 The Conformationally Stiff Unique Poly(dA)?Poly(dT) Double Helix and Its Transformation into Triple Helix.- 11.5 C-DNA Double Helix Formed by Natural and Synthetic DNA.- 11.6 D-DNA Is Only Formed by Synthetic DNA with Alternating A, T-Sequence and by Phage T2 DNA.- 11.7 DNA-RNA Hybrids Restricted to RNA-Type Double-Helices: A and A. Polymers and r(GCG) d(TATACGC). The B-DNA Form of Poly(A)-Poly(dT)..- Summary.- 12 Left-Handed, Complementary Double Helices - A Heresy? The Z-DNA Family.- 12.1 Crystal Structures of Oligo(dG-dC) Display Left-Handed Double Helix.- 12.2 Extrapolation from Oligo- to Polynucleotides. The Z-DNA Family: Z-, ZI-, ZII, and Z?-DNA.- 12.3 Left-Handed Z-DNA Visualized in Fibers of Three Alternating Polydeoxynucleotides.- 12.4 Factors Stabilizing Z-DNA.- 12.5 Does Z-DNA Have a Biological Significance?.- Summary.- 13 Synthetic, Homopolymer Nucleic Acids Structures.- 13.1 Right-Handed, Base-Stacked Single Helix Revealed for Poly(C) and the O2?-Methylated Analog.- 13.2 Bases Turned in and out in Nine- and Twofold Single-Stranded Helices of Poly(A).- 13.3 A Double Helix with Parallel Strands for Poly(AH+)?Poly(AH+) Forms under Acidic Conditions. Helix, Loop, and Base-Pair Stacks in ApAH+pAH+ Dimer.- 13.4 The Deoxydinucleotide d(pTpT) Suggests Single-Stranded Poly(dT) Helix with Nonstacked Bases Turned out.- 13.5 The Antiparallel, A-RNA-Type Double Helices of Poly(U), Poly(s2U) and poly(X).- 13.6 Sticky Guanosine-Gel Structure of Guanosine and Guanylic Acid: Quadruple Helix Formed by Poly(G) and Poly(I).- Summary.- 14 Hypotheses and Speculations: Side-by-Side Model, Kinky DNA, and ?Vertical? Double Helix.- 14.1 Side-by-Side Model-An Alternative?.- 14.2 Does DNA Fold by Kinking?.- 14.3 K- and ?-Kinked DNA: Breathing with the Speed of Sound.- 14.4 Bends in DNA at Junctions of A- and B-Type Helices.- 14.5 Vertical Double Helix for Polynucleotides in high-anti Conformation.- Summary.- 15 tRNA-A Treasury of Stereochemical Information.- 15.1 Primary and Secondary Structure of tRNA: The Cloverleaf.- 15.2 Folding of the Cloverleaf into Tertiary Structure: The L Shape.- 15.3 Stabilization of tRNA Secondary and Tertiary Structure by Horizontal and Vertical Base-Base Interactions.- 15.4 Change in Sugar Pucker, ? Turn, and Loop with Phosphate-Base Stacking: Structural Features of General Importance.- 15.5 Some Stereochemical Correlations Involving Torsion Angles X,? and ?,?.- 15.6 Metal and Polyamine Cation Binding to tRNA.- 15.7 Anticodon Preformed to Allow Rapid Recognition of Codon via Minihelix.- Summary.- 16 Intercalation.- 16.1 General Phenomena of Intercalation into DNA and RNA Double Helices.- 16.2 Stereochemistry of Intercalation into DNA- and RNA-Type Dinucleoside Phosphates.- 16.3 Improving the Model: The Daunomycin-d(CpGpTpApCpG) Complex.- 16.4 Model Building Studies Extended to A- and B-DNA.- 16.5 DNA Saturated with Platinum Drug Unwinds into a Ladder to Produce L-DNA.- 16.6 Actinomycin D: An Intercalator Specific for the GpC Sequence.- Summary.- 17 Water and Nucleic Acids.- 17.1 Experimental Evidence for Primary and Secondary Hydration Shells around DNA Double Helices.- 17.2 Different Hydration States Associated with A-, B-, and C-DNA.- 17.3 Solvent Accessibilities in A- and B-DNA.- 17.4 Theoretical Considerations.- 17.5 Hydration Schemes in Crystal Structures of A-DNA Tetramer and B-DNA Dodecamer Suggest Rationale for A? B Transition.- 17.6 Water Pentagons in Crystalline Dinucleoside Phosphate Intercalation Complex: The Generalized Concept of Circular Hydrogen Bonds and of Flip-Flop Dynamics.- Summary.- 18 Protein-Nucleic Acid Interaction.- 18.1 General Considerations about Protein-Nucleic Acid Interactions.- 18.2 Model Systems Involving Nucleic Acid and Protein Constituents.- 18.3 Model Systems Combining Nucleic Acids and Synthetic Polypeptides or Protamines.- 18.4 Nucleotides and Single-Stranded Nucleic Acids Adopt Extended Forms When Binding to Proteins.- 18.5 Nature of Protein-Nucleotide and Nucleic Acid Interaction and Recognition.- 18.6 Proteins Binding to DNA Double Helix and Single Strands.- 18.7 Prealbumin-DNA Interaction: A Hypothetical Model.- Summary.- 19 Higher Organization of DNA.- 19.1 DNA Condensed into ?-Form, Supercoils, Beads, Rods and Toroids.- 19.2 Lamellar Microcrystals Formed by Fragmented DNA.- 19.3 DNA in Cells in Organized in the Form of Chromosomes.- 19.4 Structure of the Nucleosome Core.- 19.5 Organization of Nucleosomes into 100 A and 300 A Fibers The Super-Superhelix or Solenoid.- 19.6 Organization of Chromatin in Chromosomes: A Glimpse at Transcription.- 19.7 Topological Problems in Circularly Closed, Supercoiled DNA.- Summary.- References.