Contents
1 Structure of Nucleosides 11.1 Introduction 1
1.2 Pyrimidine and Purine Bases 2
1.2.1
Pyrimidines 3
1.2.2 Purines 4
1.2.3 Nomenclature of
Pyrimidines and Purines 4
1.2.4 Abbreviations 4
1.3 Carbohydrate Moieties of Nucleosides 5
1.4 Bonding Between Carbohydrate Moiety and Heterocyclic Base 7
1.4.1
Purine Nucleosides 7
1.4.2 Pyrimidine Nucleosides 9
1.5 Size of the Oxide Ring in the Sugar 10
1.6 Configuration of the Glycoside (Anomeric) Center 12
1.7 Nomenclature and Abridged Formulas of Nucleosides 15
1.8 Minor Nucleosides 18
1.9 Pseudouridine 23
1.10 Nucleoside Antibiotics 26
1.10.1
Purine Nucleosides 26
1.10.2 Pyrimidine Nucleosides 30
1.11 Other Nucleosides 31
References 32
2 Properties of Nucleosides 33
2.1.1
General Concepts 33
2.1.2 Tautomerism 35
2.1.3 Reactions with
Electrophilic Reagents 39
2.1.4 Reactions with
Nucleophilic Reagents 44
2.1.5 Addition Reactions 47
2.1.6 Reactions
Involving Exocyclic Amino Groups 50
2.2 Reactions at the Carbohydrate Moiety 52
2.2.1
Substitution for Hydrogen Atoms in Hydroxyl Groups 52
2.2.2 Oxidation 56
2.3 Reactions Involving Heterocyclic Bases and the
Carbohydrate Moiety 58
2.4 Stability of N-Glycosidic Bonds 60
2.4.1 Effect of the
Heterocyclic Base Species 60
2.4.2 Effect of
Substituents in the Carbohydrate Moiety 62
2.4.3 Mechanism of
Hydrolysis of N-Glycosidic Bonds 63
2.5 Properties of Pseudouridine 66
References 70
4.2 Formation of Derivatives with Metals 98
4.3 Reactions at Heterocyclic Bases and Pentose 99
4.4 Some Properties of the Phosphate Group (General Concepts) 105
7.1 Conformation of Nucleosides and Nucleotides 304
7.1.1
Heterocyclic Bases 304
7.1.2 Ribose and Deoxyribose 305
7.1.3 Orientation of the Heterocyclic Bases Relative to the Sugar
307
7.2 Intermolecular Interactions Between the Heterocyclic Bases 312
7.2.1
Complementary Interactions 314
7.2.2 Stacking Interactions 317
7.3 Conformation of Single-Stranded
Oligonucleotides and Polynucleotides 319
7.4 Structure of Double- and Multiple-Stranded Polynucleotide Complexes
325
7.5 Complexes of Polynucleotides with Mono- and Oligonucleotides 331
References 334
8 Macromolecular Structure of DNA and RNA. 335
8.1.1 The Watson and Crick Model 335
8.1.2 Polymorphism of the Double Helix of DNA 337
8.1.3 Single-Crystal X-Ray Structures of DNA 341
8.1.4 Denaturation and Renaturation of DNA 343
8.1.5 Some Aspects of DNA Behavior in Solution 350
8.1.6 Supercoiling of DNA 351
8.1.7 Unusual DNA Structures 354
8.1.8 Interaction of Ligands with Double Helices of DNA 357
8.2.1 Secondary Structure of RNA.
Fresco-Alberts-Doty Model 363
8.2.2 Elements of Secondary Structure 366
8.2.3 Macromolecular Structure of Transfer RNAs 371
8.2.4 Three-Dimensional Structure of High-Molecular Weight RNAs
381
9 Chemical Properties of Polynucleotides. Modification of Nucleic Acids 389
9.2 Reactions of Heterocyclic Bases of Polynucleotides 391
9.2.1 General Concepts 391
9.2.2 Modification of Heterocycle Bases 398
9.2.2.1 Reactions at Carbon Atoms 398
9.2.2.2 Reactions at Pyridine.Nitrogens 412
9.2.2.3 Reactions at Pyrrole Nitrogens and Exocyclic Amino Groups
417
9.3 Hydrolysis of N-Glycosidic Bonds 426
9.3.1 Direct Hydrolysis Methods 426
9.3.2 Indirect Hydrolysis Methods 427
9.4 Reactions of Carbohydrate Moieties, 428
9.4.1. Substitution for Hydrogen Atoms
in Hydroxyl Groups 428
9.4.2 Oxidation of 3’-Terminal cis-Glycol Group in RNA 433
9.5 Reactions of Nucleotide Phosphate Groups 434
9.5.1 Cleavage of Internucleotide
Linkages 435
9.5.2 Cleavage of the Sugar Phosphate Backbone with the Aid of
"Chemical Nucleases" 445
9.5.3 Reactions with Internucleotide Linkages Remaining Intact
448
9.6 Reactions of Terminal Phosphate Groups 449
9.7 Chemical Probing of Nucleic Acid Structure 455
9.7.1 Location of Modified Nucleotides
455
9.7.2 Systematic Chemical Probing of RNA Secondary and Tertiary
Structure 458
9.7.2.1 Transfer RNA 458
9.7.2.2 Ribosomal RNA 462
9.7.2.3 Searching for Unusual RNA Structures 463
9.7.3 Studying Conformational Changes in DNA 465
9.7.4 Evaluation of Four-stranded G4-DNA 468
10 Catalytic Activity of Nucleic Acids 471
10.1 RNA subunit of Ribonuclease P 471
10.2 Tetrahymena Ribozyme 474
10.3 Ribozymes Based on Self-Cleaving RNAs 483
References 489
11 Synthesis of Nucleic Acids 491
11.1 Introduction 491
11.2 Historical Background 493
11.3 General Principles of Chemoenzymatic Synthesis of Duplex DNAs 495
11.3.1 Implementation
of the Principle of Complementarity of Heterocyclic Bases in Nucleic Acids 495
11.3.2 Ways to Produce Duplex DNAs 498
11.3.3 Enzymatic Methods for Construction of Duplex DNAs 500
11.3.4 Chemical Methods for Assembling Duplex DNAs 501
11.4 Methods for Chemical Synthesis of Oligodeoxyribonucleotides 505
11.4.1 Nucleoside and Nucleotide
Components for Synthesis by the Phosphodiester and Phosphotriester Methods 506
11.4.1.1 Blocking of the Hydroxyl Groups of Pentose and Amino
Groups in Heterocyclic Bases 506
11.4.1.2 Protection of Phosphate Groups 509
11.4.1.3 Preparation of the Nucleoside and Nucleotide
Components 509
11.4.1.4 Mechanisms of Internucleotide Linkage Formation 512
11.4.2 Chemical Synthesis of Oligodeoxyribonucleotides in Solution
515
11.4.2.1 Phosphodiester Method 515
11.4.2.2 Phosphotriester Method 518
11.4.2.3 Phosphite triester Method 527
11.5 Solid-Phase Synthesis of Oligodeoxyribonucleotides and Its Automation 529
11.5.1 Basic Principle of Solid-Phase Synthesis 531
11.5.2 Polymer Supports and Immobilization of the First Monomer
Thereon 532
11.5.3 Phosphoramidite-Triester Method 534
11.5.4 Hydrophosphoryl Method 537
11.5.5 Phosphotriester Method 540
11.5.6 Automation of Synthesis 541
11.5.7 Multiple Simultaneous Synthesis on Polymer Segments 542
11.5.8 Separation and Purification of Synthetic
Oligonucleotides 545
11.6.1 Methods of Duplex DNA Construction 546
11.6.2 Synthesis of Genes and Their Functionally Important
Segments 546