Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

Online ISBN: 9780471142706

DOI: 10.1002/0471142700

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  1. Foreword
  2. Preface
  3. Chapter 1 Synthesis of Modified Nucleosides
    1. Introduction
    2. Unit 1.1 Palladium-Mediated C5 Substitution of Pyrimidine Nucleosides
    3. Unit 1.2 Enzymatic Synthesis of M1G-Deoxyribose
    4. Unit 1.3 Synthesis of N2-Substituted Deoxyguanosine Nucleosides from 2-Fluoro-6-O-(Trimethylsilylethyl)-2¢-Deoxyinosine
    5. Unit 1.4 Unnatural Nucleosides with Unusual Base Pairing Properties
    6. Unit 1.5 Development of a Universal Nucleobase and Modified Nucleobases for Expanding the Genetic Code
    7. Unit 1.6 Syntheses of Specifically 15N-Labeled Adenosine and Guanosine
    8. Unit 1.7 Synthesis of Protected 2¢-Deoxy-2¢-fluoro-beta-d-arabinonucleosides
    9. Unit 1.8 Synthesis, Characterization, and Application of Substituted Pyrazolopyrimidine Nucleosides
    10. Unit 1.9 Synthesis of 1,5-Anhydrohexitol Building Blocks for Oligonucleotide Synthesis
    11. Unit 1.10 Synthesis and Properties of 7-Substituted 7-Deazapurine (Pyrrolo[2,3-d]pyrimidine) 2¢-Deoxyribonucleosides
    12. Unit 1.11 Reduction of Ribonucleosides to 2¢-Deoxyribonucleosides
    13. Unit 1.12 Synthesis of Fluorinated Nucleosides
    14. Unit 1.13 Synthesis of Ribonucleosides by Condensation Using Trimethylsilyl Triflate
    15. Unit 1.14 Synthesis of 2¢-O-beta-d-Ribofuranosylnucleosides
    16. Unit 1.15 Preparation of 2¢-Deoxy-2¢-Methylseleno-Modified Phosphoramidites and RNA
    17. Unit 1.16 Palladium-Catalyzed Cross-Coupling Reactions in C6 Modifications of Purine Nucleosides
    18. Unit 1.17 Nucleobase-Caged Phosphoramidites for Oligonucleotide Synthesis
    19. Unit 1.18 Synthesis of Altritol Nucleoside Phosphoramidites for Oligonucleotide Synthesis
    20. Unit 1.19 Synthesis of a 4-Selenothymidine Phosphoramidite and Incorporation into Oligonucleotides
    21. Unit 1.20 Synthesis of 2¢-Cyclohexenylnucleosides and Corresponding CeNA Building Blocks
    22. Unit 1.21 Synthesis of 5-Formyl-2¢-Deoxyuridine and Its Incorporation into Oligodeoxynucleotides
    23. Unit 1.22 O6-(Benzotriazol-1-yl)inosine Derivatives for C6 Modification of Purine Nucleosides
    24. Unit 1.23 Synthesis of a 2-Selenothymidine Phosphoramidite and Its Incorporation into Oligodeoxyribonucleotides
    25. Unit 1.24 Synthesis of 2¢,4¢-Bridged Nucleosides Using a New Orthogonally Protected Sugar Synthon: 5-O-(tert-Butyldiphenylsilyl)-4-C-Hydroxymethyl-1,2-O-Isopropylidene-3-O-Napthyl-alpha-d-Allofuranose
    26. Unit 1.25 Synthesis of the Tellurium-Derivatized Phosphoramidites and Their Incorporation into DNA Oligonucleotides
  4. Chapter 2 Protection of Nucleosides for Oligonucleotide Synthesis
    1. Introduction
    2. Unit 2.1 Nucleobase Protection of Deoxyribo- and Ribonucleosides
    3. Unit 2.2 Protection of 2′-Hydroxy Functions of Ribonucleosides
    4. Unit 2.3 Protection of 5¢-Hydroxy Functions of Nucleosides
    5. Unit 2.4 A Base-Labile Protecting Group (Fluorenylmethoxycarbonyl) for the 5′-Hydroxy Function of Nucleosides
    6. Unit 2.5 2¢-Hydroxyl-Protecting Groups that are Either Photochemically Labile or Sensitive to Fluoride Ions
    7. Unit 2.6 Deoxyribo- and Ribonucleoside H-Phosphonates
    8. Unit 2.7 Deoxyribonucleoside Phosphoramidites
    9. Unit 2.8 Regioselective 2¢-Silylation of Purine Ribonucleosides for Phosphoramidite RNA Synthesis
    10. Unit 2.9 Preparation of 2¢-O-[(Triisopropylsilyl)oxy]methyl-protected Ribonucleosides
    11. Unit 2.10 Preparation of 5¢-Silyl-2¢-Orthoester Ribonucleosides for Use in Oligoribonucleotide Synthesis
    12. Unit 2.11 Enzymatic Regioselective Levulinylation of 2¢-Deoxyribonucleosides and 2¢-O-Methylribonucleosides
    13. Unit 2.12 Nucleobase Protection with Allyloxycarbonyl
    14. Unit 2.13 Universal 2-(4-Nitrophenyl)ethyl and 2-(4-Nitrophenyl)ethoxycarbonyl Protecting Groups for Nucleosides and Nucleotides
    15. Unit 2.14 Chromophoric 5¢-O-Silyl Protection of N-Protected 2¢-ACE Ribonucleosides for Solid-Phase RNA Synthesis
    16. Unit 2.15 Chemical Synthesis of Oligoribonucleotides with 2¢-O-(2-Cyanoethoxymethyl)-Protected Phosphoramidites
    17. Unit 2.16 Recent Advances in the Chemical Synthesis of RNA
  5. Chapter 3 Synthesis of Unmodified Oligonucleotides
    1. Introduction
    2. Unit 3.1 Solid-Phase Supports for Oligonucleotide Synthesis
    3. Unit 3.2 Attachment of Nucleosides to Solid-Phase Supports
    4. Unit 3.3 Synthetic Strategies and Parameters Involved in the Synthesis of Oligodeoxyribonucleotides According to the Phosphoramidite Method
    5. Unit 3.4 Synthesis of Oligodeoxyribo- and Oligoribonucleotides According to the H-Phosphonate Method
    6. Unit 3.5 Strategies for Oligoribonucleotide Synthesis According to the Phosphoramidite Method
    7. Unit 3.6 Oligoribonucleotides with 2¢-O-(tert-Butyldimethylsilyl) Groups
    8. Unit 3.7 Synthesis of Oligoribonucleotides Using the 2-Nitrobenzyloxymethyl Group for 2¢-Hydroxyl Protection
    9. Unit 3.8 Chemical Synthesis of RNA Sequences with 2¢-O-[(Triisopropylsilyl)oxy]methyl-protected Ribonucleoside Phosphoramidites
    10. Unit 3.9 3-(N-tert-Butylcarboxamido)-1-propyl and 4-Oxopentyl Groups for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis
    11. Unit 3.10 DNA Synthesis Without Base Protection
    12. Unit 3.11 The 4-Methylthio-1-Butyl Group for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis
    13. Unit 3.12 Nucleoside Phosphoramidites Containing Cleavable Linkers
    14. Unit 3.13 Microwave-Assisted Functionalization of Solid Supports for Rapid Loading of Nucleosides
    15. Unit 3.14 Solution-Phase Synthesis of Di- and Trinucleotides Using Polymer-Supported Reagents
    16. Unit 3.15 DNA Synthesis Without Base Protection Using the Phosphoramidite Approach
    17. Unit 3.16 A Universal and Recyclable Solid Support for Oligonucleotide Synthesis
    18. Unit 3.17 Release of DNA Oligonucleotides and Their Conjugates from Controlled-Pore Glass Under Thermolytic Conditions
    19. Unit 3.18 Nonenzymatic Oligomerization of Activated Nucleotides on Hairpin Templates
    20. Unit 3.19 Chemical Synthesis of RNA with Base-Labile 2¢-O-(Pivaloyloxymethyl)-Protected Ribonucleoside Phosphoramidites
    21. Unit 3.20 RNA Synthesis by Reverse Direction Process: Phosphoramidites and High Purity RNAs and Introduction of Ligands, Chromophores, and Modifications at 3′-End
  6. Chapter 4 Synthesis of Modified Oligonucleotides and Conjugates
    1. Introduction
    2. Introduction
    3. Introduction
    4. Introduction
    5. Unit 4.1 A Status Update of Modified Oligonucleotides for Chemotherapeutics Applications
    6. Unit 4.2 Modification of the 5¢ Terminus of Oligonucleotides for Attachment of Reporter and Conjugate Groups
    7. Unit 4.3 Direct Attachment of Conjugate Groups to the 5¢ Terminus of Oligodeoxyribonucleotides
    8. Unit 4.4 Synthesis and Characterization of Chimeric 2-5A-DNA Oligonucleotides
    9. Unit 4.5 Attachment of Reporter and Conjugate Groups to the 3¢ Termini of Oligonucleotides
    10. Unit 4.6 3¢-Modified Oligonucleotides and their Conjugates
    11. Unit 4.7 Synthesis and Purification of Oligonucleotide N3¢rarrP5¢ Phosphoramidates and their Phosphodiester and Phosphorothioate Chimeras
    12. Unit 4.8 Incorporation of Halogenoalkyl, 2-Pyridyldithioalkyl, or Isothiocyanate Linkers into Ligands
    13. Unit 4.9 Modification of the 5¢ Terminus of Oligodeoxyribonucleotides for Conjugation with Ligands
    14. Unit 4.10 Conjugation of 5¢-Functionalized Oligodeoxyribonucleotides with Properly Functionalized Ligands
    15. Unit 4.11 Synthesis and Purification of Peptide Nucleic Acids
    16. Unit 4.12 Locked Nucleic Acids: Synthesis and Characterization of LNA-T Diol
    17. Unit 4.13 Cellular Delivery of Locked Nucleic Acids (LNAs)
    18. Unit 4.14 Solid-Phase Synthesis of Branched Oligonucleotides
    19. Unit 4.15 Solid-Phase Synthesis of 2¢-Deoxy-2¢-fluoro- beta-d-Oligoarabinonucleotides (2¢F-ANA) and Their Phosphorothioate Derivatives
    20. Unit 4.16 Chemistry of CpG DNA
    21. Unit 4.17 Synthesis of Phosphorothioate Oligonucleotides with Stereodefined Phosphorothioate Linkages
    22. Unit 4.18 Synthesis of Oligonucleotide Conjugates via Aqueous Diels-Alder Cycloaddition
    23. Unit 4.19 5¢-Iodination of Solid-Phase-Linked Oligodeoxyribonucleotides
    24. Unit 4.20 Reversible Biotinylation of the 5¢-Terminus of Oligodeoxyribonucleotides and its Application in Affinity Purification
    25. Unit 4.21 Uridine 2¢-Carbamates: Facile Tools for Oligonucleotide 2¢-Functionalization
    26. Unit 4.22 Stepwise Solid-Phase Synthesis of Nucleopeptides
    27. Unit 4.23 Synthesis of Oligoribonucleotides Containing N6-Alkyladenosine and 2-Methylthio-N6-Alkyladenosine
    28. Unit 4.24 Oligodeoxyribonucleotide Analogs Functionalized with Phosphonoacetate and Thiophosphonoacetate Diesters
    29. Unit 4.25 Base-Modified Oligodeoxyribonucleotides: Using Pyrrolo[2,3-d]pyrimidines to Replace Purines
    30. Unit 4.26 An Aminooxy-Functionalized Non-Nucleosidic Phosphoramidite for the Construction of Multiantennary Oligonucleotide Glycoconjugates on a Solid Support
    31. Unit 4.27 Large-Scale Preparation of Conjugated Oligonucleoside Phosphorothioates by the High-Efficiency Liquid-Phase (HELP) Method
    32. Unit 4.28 Disulfide Conjugation of Peptides to Oligonucleotides and Their Analogs
    33. Unit 4.29 Methoxyoxalamido Chemistry in the Synthesis of Tethered Phosphoramidites and Functionalized Oligonucleotides
    34. Unit 4.30 Using Morpholinos to Control Gene Expression
    35. Unit 4.31 Solid-Phase Oligonucleotide Labeling with DOTA
    36. Unit 4.32 Synthesis of Peptide-Oligonucleotide Conjugates by Diels-Alder Cycloaddition in Water
    37. Unit 4.33 Synthesis of Alkyne- and Azide-Modified Oligonucleotides and Their Cyclization by the CuAAC (Click) Reaction
    38. Unit 4.34 DNA Oligonucleotides Containing Stereodefined Phosphorothioate Linkages in Selected Positions
    39. Unit 4.35 Heat-Activatable Primers for Hot-Start PCR: Oligonucleotide Synthesis and Basic PCR Setup
    40. Unit 4.36 Oligodeoxynucleotides Containing N1-Methyl-2¢-Deoxyadenosine and N6-Methyl-2¢-Deoxyadenosine
    41. Unit 4.37 Nucleoside Modification with Boron Clusters and Their Metal Complexes
    42. Unit 4.38 Carbohydrate-Oligonucleotide Conjugates
    43. Unit 4.39 Synthesis of 2¢-Deoxyoxanosine from 2¢-Deoxyguanosine, Conversion to Its Phosphoramidite, and Incorporation into Oxanine-Containing Oligodeoxynucleotides
    44. Unit 4.40 Synthesis of Glycerol Nucleic Acid (GNA) Phosphoramidite Monomers and Oligonucleotide Polymers
    45. Unit 4.41 Synthesis of Peptide-Oligonucleotide Conjugates Using a Heterobifunctional Crosslinker
    46. Unit 4.42 Time-Dependent Thermocontrol of the Hydrophilic and Lipophilic Properties of DNA Oligonucleotide Prodrugs
    47. Unit 4.43 Preparation of C5-Functionalized Locked Nucleic Acids (LNAs)
    48. Unit 4.44 Synthesis of Stable Aminoacyl-tRNA Analogs
    49. Unit 4.45 Preparation of Photoresponsive DNA Tethering Ortho-Methylated Azobenzene as a Supra-Photoswitch
    50. Unit 4.46 RNA Aptamers and Spiegelmers: Synthesis, Purification, and Post-Synthetic PEG Conjugation
    51. Unit 4.47 Preparation of DNA Containing 5-Hydroxymethyl-2¢-Deoxycytidine Modification Through Phosphoramidites with TBDMS as 5-Hydroxymethyl Protecting Group
    52. Unit 4.48 Synthesis and Application of Highly Reactive Amino Linkers for Functional Oligonucleotides
    53. Unit 4.49 Oligodeoxynucleotide Containing S-Functionalized 2′-Deoxy-6-Thioguanosine: Facile Tools for Base-Selective and Site-Specific Internal Modification of RNA
  7. Chapter 5 Methods for Cross-Linking Nucleic Acids
    1. Introduction
    2. Unit 5.1 Engineering Disulfide Cross-Links in RNA Using Thiol-Disulfide Interchange Chemistry
    3. Unit 5.2 Chemical and Enzymatic Methods for Preparing Circular Single-Stranded DNAs
    4. Unit 5.3 Engineering Specific Cross-Links in Nucleic Acids Using Glycol Linkers
    5. Unit 5.4 Engineering Disulfide Cross-Links in RNA Via Air Oxidation
    6. Unit 5.5 Use of Electrophilic Substitution to Form Site-Specific Cross-Links in DNA
    7. Unit 5.6 Synthesis of Endcap Dimethoxytrityl Phosphoramidites for Endcapped Oligonucleotides
    8. Unit 5.7 Engineering Terminal Disulfide Bonds Into DNA
    9. Unit 5.8 Preparation of DNA and RNA Fragments Containing Guanine N2-Thioalkyl Tethers
    10. Unit 5.9 Synthesis of Building Blocks and Oligonucleotides with {G}O6-Alkyl-O6{G} Cross-Links
    11. Unit 5.10 Syntheses of DNA Duplexes That Contain a N4C-Alkyl-N4C Interstrand Cross-Link
  8. Chapter 6 Chemical and Enzymatic Probes for Nucleic Acid Structure
    1. Introduction
    2. Unit 6.1 Probing RNA Structure with Chemical Reagents and Enzymes
    3. Unit 6.2 Probing Nucleic Acid Structure with Shape-Selective Rhodium and Ruthenium Complexes
    4. Unit 6.3 Probing RNA Structure by Lead Cleavage
    5. Unit 6.4 Probing Nucleic Acid Structure with Nickel- and Cobalt-Based Reagents
    6. Unit 6.5 Probing RNA Structures with Hydroxyl Radicals
    7. Unit 6.6 Chemical Reagents for Investigating the Major Groove of DNA
    8. Unit 6.7 Probing DNA Structure with Hydroxyl Radicals
    9. Unit 6.8 Probing RNA Structure and Metal-Binding Sites Using Terbium(III) Footprinting
    10. Unit 6.9 Probing RNA Structure and Function by Nucleotide Analog Interference Mapping
    11. Unit 6.10 Bisulfite Modification for Analysis of DNA Methylation
  9. Chapter 7 Biophysical Analysis of Nucleic Acids
    1. Introduction
    2. Unit 7.1 Biophysical Analysis of Nucleic Acids
    3. Unit 7.2 NMR Determination of Oligonucleotide Structure
    4. Unit 7.3 Optical Methods
    5. Unit 7.4 Calorimetry of Nucleic Acids
    6. Unit 7.5 Molecular Modeling of Nucleic Acid Structure
    7. Unit 7.6 Methods to Crystallize RNA
    8. Unit 7.7 Recent Advances in RNA Structure Determination by NMR
    9. Unit 7.8 Molecular Modeling of Nucleic Acid Structure: Energy and Sampling
    10. Unit 7.9 Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation
    11. Unit 7.10 Molecular Modeling of Nucleic Acid Structure: Setup and Analysis
    12. Unit 7.11 Characterization of DNA Structures by Circular Dichroism
    13. Unit 7.12 Biophysical Analysis of Triple-Helix Formation
    14. Unit 7.13 Diffraction Techniques in Structural Biology
    15. Unit 7.14 Determination of Nucleic Acid Hydration Using Osmotic Stress
    16. Unit 7.15 Use of Chromophoric Ligands to Visually Screen Co-Crystals of Putative Protein-Nucleic Acid Complexes
    17. Unit 7.16 Liquid Chromatography-Mass Spectrometry Analysis of DNA Polymerase Reaction Products
  10. Chapter 8 Nucleic Acid Binding Molecules
    1. Introduction
    2. Unit 8.1 Determination of Binding Mode: Intercalation
    3. Unit 8.2 Determination of Binding Thermodynamics
    4. Unit 8.3 A Competition Dialysis Assay for the Study of Structure-Selective Ligand Binding to Nucleic Acids
    5. Unit 8.4 Chemistry of Minor Groove Binder–Oligonucleotide Conjugates
    6. Unit 8.5 A Fluorescent Intercalator Displacement Assay for Establishing DNA Binding Selectivity and Affinity
    7. Unit 8.6 Synthesis of Dimeric 2-Amino-1,8-Naphthyridine and Related DNA-Binding Molecules
    8. Unit 8.7 ICON Probes: Synthesis and DNA Methylation Typing
  11. Chapter 9 Combinatorial Methods in Nucleic Acid Chemistry
    1. Introduction
    2. Unit 9.1 Theoretical Principles of In Vitro Selection Using Combinatorial Nucleic Acid Libraries
    3. Unit 9.2 Design, Synthesis, and Amplification of DNA Pools for In Vitro Selection
    4. Unit 9.3 In Vitro Selection of RNA Aptamers to a Protein Target by Filter Immobilization
    5. Unit 9.4 Selection for Catalytic Function with Nucleic Acids
    6. Unit 9.5 In Vitro Selection of RNA Aptamers to a Small Molecule Target
    7. Unit 9.6 In Vitro Selection Using Modified or Unnatural Nucleotides
    8. Unit 9.7 The Continuous Evolution In Vitro Technique
  12. Chapter 10 Purification and Analysis of Synthetic Nucleic Acids and Components
    1. Introduction
    2. Unit 10.1 Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of Oligonucleotides
    3. Unit 10.2 Electrospray Ionization Mass Spectrometry of Oligonucleotides
    4. Unit 10.3 Overview of Purification and Analysis of Synthetic Nucleic Acids
    5. Unit 10.4 Polyacrylamide Gel Electrophoresis (PAGE) of Synthetic Nucleic Acids
    6. Unit 10.5 Analysis and Purification of Synthetic Nucleic Acids Using HPLC
    7. Unit 10.6 Base Composition Analysis of Nucleosides Using HPLC
    8. Unit 10.7 Cartridge Methods for Oligonucleotide Purification
    9. Unit 10.8 Analysis of Oxidized DNA Fragments by Gel Electrophoresis
    10. Unit 10.9 Capillary Electrophoresis of DNA
    11. Unit 10.10 Sequencing Oligonucleotides by Enrichment of Coupling Failures Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
    12. Unit 10.11 Mass Determination of Phosphoramidites
    13. Unit 10.12 3,4-Diaminobenzophenone Matrix for Analysis of Oligonucleotides by MALDI-TOF Mass Spectrometry
    14. Unit 10.13 Detection of Aberrant 2¢-5¢ Linkages in RNA by Anion Exchange
  13. Chapter 11 RNA Folding Pathways
    1. Introduction
    2. Unit 11.1 RNA Folding Pathways
    3. Unit 11.2 RNA Secondary Structure Prediction
    4. Unit 11.3 Thermal Methods for the Analysis of RNA Folding Pathways
    5. Unit 11.4 Probing RNA Folding Pathways by RNA Fingerprinting
    6. Unit 11.5 Characterization of Tertiary Folding of RNA by Circular Dichroism and Urea
    7. Unit 11.6 Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays
    8. Unit 11.7 Rapid Magnesium Chelation as a Method to Study Real-Time Tertiary Unfolding of RNA
    9. Unit 11.8 Use of Fluorescence Spectroscopy to Elucidate RNA Folding Pathways
    10. Unit 11.9 Use of Chemical Modification To Elucidate RNA Folding Pathways
    11. Unit 11.10 Probing RNA Structural Dynamics and Function by Fluorescence Resonance Energy Transfer (FRET)
    12. Unit 11.11 Site-Specific Fluorescent Labeling of Large RNAs with Pyrene
    13. Unit 11.12 RNA Intramolecular Dynamics by Single-Molecule FRET
  14. Chapter 12 Nucleic Acid-Based Microarrays and Nanostructures
    1. Introduction
    2. Unit 12.1 Key Experimental Approaches in DNA Nanotechnology
    3. Unit 12.2 Preparation of Gold Nanoparticle–DNA Conjugates
    4. Unit 12.3 Synthesis of 5¢-O-Phosphoramidites with a Photolabile 3¢-O-Protecting Group
    5. Unit 12.4 Derivatization of Glass and Polypropylene Surfaces
    6. Unit 12.5 DNA Microarray Preparation by Light-Controlled In Situ Synthesis
    7. Unit 12.6 Preparation of alpha-Oxo Semicarbazone Oligonucleotide Microarrays
    8. Unit 12.7 Synthesis of Covalent Oligonucleotide-Streptavidin Conjugates and Their Application in DNA-Directed Immobilization (DDI) of Proteins
    9. Unit 12.8 Recent Progress in DNA Origami Technology
    10. Unit 12.9 DNA Origami: Synthesis and Self-Assembly
  15. Chapter 13 Nucleoside Phosphorylation and Related Modifications
    1. Introduction
    2. Unit 13.1 Overview of the Synthesis of Nucleoside Phosphates and Polyphosphates
    3. Unit 13.2 Chemoenzymatic Preparation of Nucleoside Triphosphates
    4. Unit 13.3 Synthesis and Polymerase Incorporation of 5¢-Amino-2¢,5¢-Dideoxy-5¢-N-Triphosphate Nucleotides
    5. Unit 13.4 Nucleoside-5¢-Phosphoimidazolides: Reagents for Facile Synthesis of Dinucleoside Pyrophosphates
    6. Unit 13.5 Synthesis of Methylenebis(phosphonate) Analogs of Dinucleotide Pyrophosphates
    7. Unit 13.6 Chemical Phosphorylation of Deoxyribonucleosides and Thermolytic DNA Oligonucleotides
    8. Unit 13.7 Stereoselective Synthesis of Sugar Nucleotides Using Neighboring Group Participation
    9. Unit 13.8 Solid-Supported Diphosphitylating and Triphosphitylating Reagents for Nucleoside Modification
    10. Unit 13.9 Solid-Supported Reagents for Synthesis of Nucleoside Monothiophosphates, Dithiodiphosphates, and Trithiotriphosphates
  16. Chapter 14 Biologically Active Nucleosides
    1. Introduction
    2. Unit 14.1 Synthesis of Acyclic Analogs of Adenosine
    3. Unit 14.2 Synthesis of Acyclic Nucleoside Phosphonates
    4. Unit 14.3 Synthesis of beta-l-2¢-Deoxythymidine (l-dT)
    5. Unit 14.4 Synthesis of Carbovir and Abacavir from a Carbocyclic Precursor
    6. Unit 14.5 Synthesis of 2¢- and 3¢-C-Methylribonucleosides
    7. Unit 14.6 Synthesis of Fluoroneplanocin A
    8. Unit 14.7 Synthesis of Entecavir and Its Novel Class of Analogs
    9. Unit 14.8 One-Flask Synthesis of Cyclic Diguanosine Monophosphate (c-di-GMP)
  17. Chapter 15 Nucleoside Prodrugs and Delivery Strategies
    1. Introduction
    2. Unit 15.1 Synthesis of Amino Acid Phosphoramidate Monoesters via H-Phosphonate Intermediates
    3. Unit 15.2 Synthesis of Cidofovir and (S)-HPMPA Ether Lipid Prodrugs
    4. Unit 15.3 Chemistry of bisSATE Mononucleotide Prodrugs
    5. Unit 15.4 Synthesis of Peptidomimetic Conjugates of Cyclic Nucleoside Phosphonates
  18. Chapter 16 RNA Silencing
    1. Introduction
    2. Unit 16.1 Overview of Gene Silencing by RNA Interference
    3. Unit 16.2 Preparation of Short Interfering RNA Containing the Modified Nucleosides 2-Thiouridine, Pseudouridine, or Dihydrouridine
    4. Unit 16.3 Chemical Modification of siRNA
    5. Unit 16.4 Synthesis of Dumbbell-Shaped Cyclic RNAs for RNA Interference
  19. Chapter 17 Quadruplex Formation
    1. Introduction
    2. Unit 17.1 UV Melting of G-Quadruplexes
    3. Unit 17.2 Overview of Formation of G-Quadruplex Structures
    4. Unit 17.3 Resolution of Quadruplex Polymorphism by Size-Exclusion Chromatography
    5. Unit 17.4 Analysis of Multidimensional G-Quadruplex Melting Curves
  20. Appendix 1 Standard Nomenclature, Data, and Abbreviations
    1. 1A Selected Abbreviations Used in This Manual
    2. 1B Characteristics of Nucleic Acids
    3. 1C IUPAC-IUB Joint Commission on Biochemical Nomenclature Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains
    4. 1D Nucleoside and Nucleotide Nomenclature
    5. 1E A Convenient Stereochemical Notation for P-Chiral Nucleotide Analogs
  21. Appendix 2 Laboratory Stock Solutions and Equipment
    1. 2A Common Buffers and Stock Solutions
  22. Appendix 3 Commonly Used Techniques
    1. 3A References to Commonly Used Techniques
    2. 3B Denaturing Polyacrylamide Gel Electrophoresis
    3. 3C Introduction to the Synthesis and Purification of Oligonucleotides
    4. 3D Thin-Layer Chromatography
    5. 3E Column Chromatography
  23. Appendix 4 Resources
    1. 4A Useful Nucleic Acid Chemistry Web Sites
  24. Suppliers
    1. Selected Suppliers of Reagents and Equipment

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