About the Book
New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical ther modynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the grad uate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases the availability of texts in active research areas should help stimulate the creation of new courses. CHARLES R. CANTOR New York Preface This monograph is based on a review on polynucleotide structures written for a book series in 1976.
Table of Contents:
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 Å and 300 Å 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.
