1 Structure of the Nucleic Acids.- I. Introduction.- II. Methods used to isolate DNA and to determine its properties. The principal types of DNA.- III. Methods used to isolate RNA and to determine its properties. The principal types of RNA.- IV. Structure of the polynucleotide chain.- V. Terminal groups of the polynucleotide chain.- VI. Structure of nucleoside components of nucleic acids.- 1. Major components of RNA.- 2. Minor components of RNA.- 3. Major components of DNA.- 4. Minor components of DNA.- VII. Nucleotide composition and the determination of identical nucleotide sequences in polynucleotides.- VIII. Sequence of nucleotides in the polynucleotide chain.- 1. Partial cleavage of polynucleotides.- 2. Principles of the unit method.- 3. Investigation of the primary structure of polynucleotides.- IX. Synthetic polynucleotides.- 1. Chemical methods of synthesis.- 2. Principles of enzymic synthesis of oligonucleotides and polynucleotides.- 2 Conformation of Nucleosides and Nucleosides.- I. Introduction.- II. Conformation of the components of nucleic acids.- 1. Conformation of heterocyclic rings.- 2. Conformation of carbohydrate residues.- 5. Mutual arrangement of the carbohydrate residues and heterocyclic rings.- 4. Intramolecular interactions.- 3 Electronic Structure and Reactivity of the Monomer Components of Nucleic acids.- I. Introduction.- II. Distribution of electron density in the heterocyclic bases of nucleic acids.- 1. Theoretical considerations.- 2. Experimental data and their comparison with calculated data.- III. Energetic characteristics of the bases of nucleic acids.- 1. Resonance energy.- 2. Energy of the highest filled and lowest empty orbitals.- IV. Tautomerism of the bases of nucleic acids.- 1. Theoretical considerations.- 2. Experimental data.- V. Ionization constants of the bases of nucleic acids.- 1. General considerations.- 2. Localization of the attachment and detachment of protons in nucleosides and nucleotides.- 3. Localization of charges in the ions of bases.- 4. Effect of different factors on the acid-base balance of the bases.- VI. General matters concerned with reactivity of the bases of nucleic acids.- 1. The use of quantum chemical calculations.- 2. The use of correlation equations.- 4 The Secondary Structure of Nucleic Acids.- I. Introduction.- II. General aspects of interaction between the bases of nucleic acids.- 1. Pairing of complementary bases.- III. Characteristics of interaction between the bases of nucleic acids and their derivatives in aqueous solutions.- 1. Association and self-association of bases, nucleosides, and nucleotides.- 2. Thermodynamic self-association constants of purine and pyrimidine derivatives.- 3. Concentration changes in optical properties of solutions of monomer components of nucleic acids.- 4. Concentration changes in NMR spectra of solutions of bases and nucleosides.- 5. Changes in the properties of bases when incorporated in oligonucleotides by comparison with monomers.- 6. Thermodynamic characteristics of interaction between bases and dinucleoside phosphates.- 7. Nature of the forces stabilizing associations of bases in aqueous solution.- IV. Investigation of the macrostructure of double-stranded DNA.- 1. The Watson and Crick hypothesis.- 2. Secondary and higher structures of circular DNAs.- V. Investigation of the secondary structure of double-stranded RNAs.- VI. Destruction of the macromolecular structure of double-helical molecules (denaturation).- 1. Factors influencing thermal denaturation.- 2. Special features of the denaturation of circular DNAs.- VII. Processes leading to restoration of the double-helical structure (renaturation).- 1. Factors influencing the renaturation process.- 2. Intramolecular interactions in DNA.- VIII. Single-stranded polynucleotides.- 1. The secondary structure of tRNA.- 2. The tertiary structure of tRNA.- 3. The secondary and tertiary structures of 5S RNA..- 5 Substitutions and Additions in the Heterocyclic Rings of the Bases of Nucleic Acids and their Derivatives.- I. Introduction.- II. Substitution and addition reactions at carbon atoms.- 1. Halogenation.- 2. Nitration.- 3. Hydroxymethylation, aminomethylation, and chloromethylation.- 4. Reactions with diazonium salts.- 5. Reactions with N-arylhydroxylamines and their derivatives.- 6. Isotopic exchange of hydrogen atoms.- 7. Addition reactions at the C5-C6 double bond of pyrimidine derivatives.- 8. Reduction.- 9. Reactions with nucleophilic reagents without rupture of the ring.- III. Substitutions and additions reaction at the nitrogen atoms.- 1. Interaction with alkylating agents.- 2. Interaction with reagents containing polarized C=C bonds.- 3. Interaction with reagents containing C=N bonds.- 4. Interaction with reagents containing C=O groups.- 5. Oxidation by peroxides.- 6 Reactions of Exocyclic Substituents of the Bases of Nucleic Acids and their Derivatives.- I. Introduction.- II. Substitution reactions at the nitrogen atom of an exocyclic amino group.- 1. N-Acylation.- 2. Reaction with aldehydes.- 3. Reaction with nitrous acid.- 4. Other substitutions in the amino group.- III. Substitutions at exocyclic oxygen and sulphur atoms.- 1. O-alkylation and the formation of cyclonucleosides..- 2. S-alkylation of thiopyrimidine derivatives.- 3. Oxidation of thiopyrimidine derivatives.- 7 Reactions Involving the Cleavage or Regrouping of Heterocyclic Rings of the Bases of Nucleic acids and their Derivatives.- I. Introduction.- II. Reactions of cleavage and rearrangement of the rings by the action of nucleophilic agents.- 1. Cleavage of the imidazole ring in purine derivatives.- 2. Cleavage of the pyrimidine ring in purine derivatives.- 3. Rearrangement of 1-N-alkyladenine derivatives into 6-exo-N-alkyl compounds.- 4. Opening and rearrangement of the ring in pyrimidine derivatives.- III. Cleavage by the action of hydrazine.- IV. Cleavage by the action of hydroxylamine.- V. Cleavage of rings by the action of potassium permanganate and osmium tetroxide.- VI. Cleavage by the action of peroxide derivatives.- 8 Hydrolysis of N-Glycosidic Bonds in Nucleosides, Nucleotides and their Derivatives.- I. Introduction.- II. Hydrolysis of N-glycosidic bonds catalyzed by acids.- 1. Effect of structural factors on the kinetics of hydrolysis of pyrimidine derivatives.- 2. Effect of structural factors on the kinetics of hydrolysis of purine derivatives.- 3. Acid hydrolysis of N-glycoside bonds in poly-nucleotides.- III. Hydrolysis of N-glycosidic bonds in pyrimidine deoxyribonucleosides, not catalyzed by acids or bases.- IV. Hydrolysis of N-glycosidic bonds in an alkaline medium.- V. Other reactions leading to cleavage of glycosidic bonds.- 9 Reactions of the Carbohydrate Residues of Nucleic Acids.- I. Introduction.- II. Acylation of hydroxyl groups of carbohydrate residues.- 1. Acylation.- 2. Aminoacylation.- 3. Preparation of esters with inorganic acids.- III. Alkylation of the hydroxyl groups of carbohydrate residues.- 1. Reaction with diazomethane.- 2. Reaction with alkyl halides.- 3. Reaction with triarylchloromethanes.- IV. Reactions of hydroxyl groups of carbohydrate residues with vinyl esters.- V. Reactions of hydroxyl groups of carbohydrate residues with carbonyl compounds and with their derivatives.- VI. Oxidation of carbohydrate residues.- 1. Oxidation of an isolated hydroxyl group.- 2. Oxidation of the cis-glycol group in ribo-derivatives.- 10 Cleavage of Phosphoester Bonds and some other Reactions of Phophate Groups of Nucleic Acids and their Derivatives.- I. Introduction.- II. Reactions with cleavage of P-O bonds.- 1. Hydrolysis of phosphomonoester bonds in ribonucleotides and degradation of RNA to nucleosides.- 2. Hydrolysis of phosphoester bonds in ribonucleoside cyclic phosphates.- 3. Hydrolysis of phosphodiester bonds in polynucleotides.- III. Reactions with rupture of C-O bonds.- 1. Cleavage of phosphoester bonds after removal of the heterocyclic bases.- 2. Cleavage of phosphoester bonds in terminal components of polynucleotides.- 3. Some other reactions of nucleic acids leading to the rupture of phosphodiester bonds.- IV. Reactions leading to the formation of phosphoester bonds.- 1. Alkylation at the phosphate group.- 2. Reactions of terminal phosphate groups in polynucleotides.- 11 Some Reactions of Minor Components of Nucleic Acids.- I. Introduction.- II. Reactions of 6-exo-N-isopentenyladenosine and its derivatives.- III. Reactions of pseudouridine and its derivatives.- IV. Reactions of 5-hydroxymethylpyrimidine derivatives.- 12 Photochemistry of the Nucleic Acids and their Components.- I Introduction.- II The basic concepts and laws of photochemistry.- III Absorption spectra of nucleic acids and their components.- IV Excited states of nucleic acids and their components.- 1 Characteristics of excited states.- 2. Electronic structure of bases of the nucleic acids in excited states.- V. Photochemical conversions of nucleic acids and their components.- 1. Photochemical reactions of pyrimidine derivatives.- 2. Photochemical reactions of purine derivatives.- VI. Photosensitized reactions.- VII. The photodynamic effect.- VIII. The action of visible light in the presence of iron ions.- IX. Photochemical reactions induced by excitation of a reagent.- X. Effect of chelating agents on photodimerization.- Index for Parts A and B.
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