Current Protocols in Nucleic Acid Chemistry

Table of Contents

• Chapter 1 Synthesis of Modified Nucleosides
  • Introduction
  • Unit 1.1 Palladium‐Mediated C5 Substitution of Pyrimidine Nucleosides
  • Unit 1.2 Enzymatic Synthesis of M1G‐Deoxyribose
  • Unit 1.3 Synthesis of N2‐Substituted Deoxyguanosine Nucleosides from 2‐Fluoro‐6‐O‐(Trimethylsilylethyl)‐2′‐Deoxyinosine
  • Unit 1.4 Unnatural Nucleosides with Unusual Base Pairing Properties
  • Unit 1.5 Development of a Universal Nucleobase and Modified Nucleobases for Expanding the Genetic Code
  • Unit 1.6 Syntheses of Specifically 15N‐Labeled Adenosine and Guanosine
  • Unit 1.7 Synthesis of Protected 2′‐Deoxy‐2′‐fluoro‐β‐D‐arabinonucleosides
  • Unit 1.8 Synthesis, Characterization, and Application of Substituted Pyrazolopyrimidine Nucleosides
  • Unit 1.9 Synthesis of 1,5‐Anhydrohexitol Building Blocks for Oligonucleotide Synthesis
  • Unit 1.10 Synthesis and Properties of 7‐Substituted 7‐Deazapurine (Pyrrolo[2,3‐d]pyrimidine) 2′‐Deoxyribonucleosides
  • Unit 1.11 Reduction of Ribonucleosides to 2′‐Deoxyribonucleosides
  • Unit 1.12 Synthesis of Fluorinated Nucleosides
  • Unit 1.13 Synthesis of Ribonucleosides by Condensation Using Trimethylsilyl Triflate
  • Unit 1.14 Synthesis of 2′‐O‐β‐d‐Ribofuranosylnucleosides
  • Unit 1.15 Preparation of 2′‐Deoxy‐2′‐Methylseleno‐Modified Phosphoramidites and RNA
  • Unit 1.16 Palladium‐Catalyzed Cross‐Coupling Reactions in C6 Modifications of Purine Nucleosides
  • Unit 1.17 Nucleobase‐Caged Phosphoramidites for Oligonucleotide Synthesis
  • Unit 1.18 Synthesis of Altritol Nucleoside Phosphoramidites for Oligonucleotide Synthesis
  • Unit 1.19 Synthesis of a 4‐Selenothymidine Phosphoramidite and Incorporation into Oligonucleotides
  • Unit 1.20 Synthesis of 2′‐Cyclohexenylnucleosides and Corresponding CeNA Building Blocks
  • Unit 1.21 Synthesis of 5‐Formyl‐2′‐Deoxyuridine and Its Incorporation into Oligodeoxynucleotides
  • Unit 1.22 O6‐(Benzotriazol‐1‐yl)inosine Derivatives for C6 Modification of Purine Nucleosides
  • Unit 1.23 Synthesis of a 2‐Selenothymidine Phosphoramidite and Its Incorporation into Oligodeoxyribonucleotides
  • 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‐α‐d‐Allofuranose
  • Unit 1.25 Synthesis of the Tellurium‐Derivatized Phosphoramidites and Their Incorporation into DNA Oligonucleotides
  • Unit 1.26 Two‐Step, One‐Pot Synthesis of Inosine, Guanosine, and 2′‐Deoxyguanosine O6‐Ethers via Intermediate O6‐(Benzotriazol‐1‐yl) Derivatives
  • Unit 1.27 Aqueous‐Phase Sonogashira Alkynylation to Synthesize 5‐Substituted Pyrimidine and 8‐Substituted Purine Nucleosides
  • Unit 1.28 Solid‐Phase Chemical Synthesis of 5′‐Triphosphate DNA, RNA, and Chemically Modified Oligonucleotides
  • Unit 1.29 Synthesis of a North‐Methanocarba‐Thymidine (N‐MCT) Analog
  • Unit 1.30 Use of a Novel 5′‐Regioselective Phosphitylating Reagent for One‐Pot Synthesis of Nucleoside 5′‐Triphosphates from Unprotected Nucleosides
• Chapter 2 Protection of Nucleosides for Oligonucleotide Synthesis
  • Introduction
  • Unit 2.1 Nucleobase Protection of Deoxyribo‐ and Ribonucleosides
  • Unit 2.2 Protection of 2′‐Hydroxy Functions of Ribonucleosides
  • Unit 2.3 Protection of 5′‐Hydroxy Functions of Nucleosides
  • Unit 2.4 A Base‐Labile Protecting Group (Fluorenylmethoxycarbonyl) for the 5′‐Hydroxy Function of Nucleosides
  • Unit 2.5 2′‐Hydroxyl‐Protecting Groups that are Either Photochemically Labile or Sensitive to Fluoride Ions
  • Unit 2.6 Deoxyribo‐ and Ribonucleoside H‐Phosphonates
  • Unit 2.7 Deoxyribonucleoside Phosphoramidites
  • Unit 2.8 Regioselective 2′‐Silylation of Purine Ribonucleosides for Phosphoramidite RNA Synthesis
  • Unit 2.9 Preparation of 2′‐O‐[(Triisopropylsilyl)oxy]methyl‐protected Ribonucleosides
  • Unit 2.10 Preparation of 5′‐Silyl‐2′‐Orthoester Ribonucleosides for Use in Oligoribonucleotide Synthesis
  • Unit 2.11 Enzymatic Regioselective Levulinylation of 2′‐Deoxyribonucleosides and 2′‐O‐Methylribonucleosides
  • Unit 2.12 Nucleobase Protection with Allyloxycarbonyl
  • Unit 2.13 Universal 2‐(4‐Nitrophenyl)ethyl and 2‐(4‐Nitrophenyl)ethoxycarbonyl Protecting Groups for Nucleosides and Nucleotides
  • Unit 2.14 Chromophoric 5′‐O‐Silyl Protection of N‐Protected 2′‐ACE Ribonucleosides for Solid‐Phase RNA Synthesis
  • Unit 2.15 Chemical Synthesis of Oligoribonucleotides with 2′‐O‐(2‐Cyanoethoxymethyl)‐Protected Phosphoramidites
  • Unit 2.16 Recent Advances in the Chemical Synthesis of RNA
• Chapter 3 Synthesis of Unmodified Oligonucleotides
  • Introduction
  • Unit 3.1 Solid‐Phase Supports for Oligonucleotide Synthesis
  • Unit 3.2 Attachment of Nucleosides and Other Linkers to Solid‐Phase Supports for Oligonucleotide Synthesis
  • Unit 3.3 Synthetic Strategies and Parameters Involved in the Synthesis of Oligodeoxyribonucleotides According to the Phosphoramidite Method
  • Unit 3.4 Synthesis of Oligodeoxyribo‐ and Oligoribonucleotides According to the H‐Phosphonate Method
  • Unit 3.5 Strategies for Oligoribonucleotide Synthesis According to the Phosphoramidite Method
  • Unit 3.6 Oligoribonucleotides with 2′‐O‐(tert‐Butyldimethylsilyl) Groups
  • Unit 3.7 Synthesis of Oligoribonucleotides Using the 2‐Nitrobenzyloxymethyl Group for 2′‐Hydroxyl Protection
  • Unit 3.8 Chemical Synthesis of RNA Sequences with 2′‐O‐[(Triisopropylsilyl)oxy]methyl‐protected Ribonucleoside Phosphoramidites
  • Unit 3.9 3‐(N‐tert‐Butylcarboxamido)‐1‐propyl and 4‐Oxopentyl Groups for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis
  • Unit 3.10 DNA Synthesis Without Base Protection
  • Unit 3.11 The 4‐Methylthio‐1‐Butyl Group for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis
  • Unit 3.12 Nucleoside Phosphoramidites Containing Cleavable Linkers
  • Unit 3.13 Microwave‐Assisted Functionalization of Solid Supports for Rapid Loading of Nucleosides
  • Unit 3.14 Solution‐Phase Synthesis of Di‐ and Trinucleotides Using Polymer‐Supported Reagents
  • Unit 3.15 DNA Synthesis Without Base Protection Using the Phosphoramidite Approach
  • Unit 3.16 A Universal and Recyclable Solid Support for Oligonucleotide Synthesis
  • Unit 3.17 Release of DNA Oligonucleotides and Their Conjugates from Controlled‐Pore Glass Under Thermolytic Conditions
  • Unit 3.18 Nonenzymatic Oligomerization of Activated Nucleotides on Hairpin Templates
  • Unit 3.19 Chemical Synthesis of RNA with Base‐Labile 2′‐O‐(Pivaloyloxymethyl)‐Protected Ribonucleoside Phosphoramidites
  • Unit 3.20 RNA Synthesis by Reverse Direction Process: Phosphoramidites and High Purity RNAs and Introduction of Ligands, Chromophores, and Modifications at 3′‐End
  • Unit 3.21 Safe Deprotection Strategy for the Tert‐Butyldimethylsilyl (TBS) Group During RNA Synthesis
• Chapter 4 Synthesis of Modified Oligonucleotides and Conjugates
  • Introduction
  • Unit 4.1 A Status Update of Modified Oligonucleotides for Chemotherapeutics Applications
  • Unit 4.2 Modification of the 5′ Terminus of Oligonucleotides for Attachment of Reporter and Conjugate Groups
  • Unit 4.3 Direct Attachment of Conjugate Groups to the 5′ Terminus of Oligodeoxyribonucleotides
  • Unit 4.4 Synthesis and Characterization of Chimeric 2‐5A‐DNA Oligonucleotides
  • Unit 4.5 Attachment of Reporter and Conjugate Groups to the 3′ Termini of Oligonucleotides
  • Unit 4.6 3′‐Modified Oligonucleotides and their Conjugates
  • Unit 4.7 Synthesis and Purification of Oligonucleotide N3′→P5′ Phosphoramidates and their Phosphodiester and Phosphorothioate Chimeras
  • Unit 4.8 Incorporation of Halogenoalkyl, 2‐Pyridyldithioalkyl, or Isothiocyanate Linkers into Ligands
  • Unit 4.9 Modification of the 5′ Terminus of Oligodeoxyribonucleotides for Conjugation with Ligands
  • Unit 4.10 Conjugation of 5′‐Functionalized Oligodeoxyribonucleotides with Properly Functionalized Ligands
  • Unit 4.11 Synthesis and Purification of Peptide Nucleic Acids
  • Unit 4.12 Locked Nucleic Acids: Synthesis and Characterization of LNA‐T Diol
  • Unit 4.13 Cellular Delivery of Locked Nucleic Acids (LNAs)
  • Unit 4.14 Solid‐Phase Synthesis of Branched Oligonucleotides
  • Unit 4.15 Solid‐Phase Synthesis of 2′‐Deoxy‐2′‐fluoro‐ β‐D‐Oligoarabinonucleotides (2′F‐ANA) and Their Phosphorothioate Derivatives
  • Unit 4.16 Chemistry of CpG DNA
  • Unit 4.17 Synthesis of Phosphorothioate Oligonucleotides with Stereodefined Phosphorothioate Linkages
  • Unit 4.18 Synthesis of Oligonucleotide Conjugates via Aqueous Diels‐Alder Cycloaddition
  • Unit 4.19 5′‐Iodination of Solid‐Phase‐Linked Oligodeoxyribonucleotides
  • Unit 4.20 Reversible Biotinylation of the 5′‐Terminus of Oligodeoxyribonucleotides and its Application in Affinity Purification
  • Unit 4.21 Uridine 2′‐Carbamates: Facile Tools for Oligonucleotide 2′‐Functionalization
  • Unit 4.22 Stepwise Solid‐Phase Synthesis of Nucleopeptides
  • Unit 4.23 Synthesis of Oligoribonucleotides Containing N6‐Alkyladenosine and 2‐Methylthio‐N6‐Alkyladenosine
  • Unit 4.24 Oligodeoxyribonucleotide Analogs Functionalized with Phosphonoacetate and Thiophosphonoacetate Diesters
  • Unit 4.25 Base‐Modified Oligodeoxyribonucleotides: Using Pyrrolo[2,3‐d]pyrimidines to Replace Purines
  • Unit 4.26 An Aminooxy‐Functionalized Non‐Nucleosidic Phosphoramidite for the Construction of Multiantennary Oligonucleotide Glycoconjugates on a Solid Support
  • Unit 4.27 Large‐Scale Preparation of Conjugated Oligonucleoside Phosphorothioates by the High‐Efficiency Liquid‐Phase (HELP) Method
  • Unit 4.28 Disulfide Conjugation of Peptides to Oligonucleotides and Their Analogs
  • Unit 4.29 Methoxyoxalamido Chemistry in the Synthesis of Tethered Phosphoramidites and Functionalized Oligonucleotides
  • Unit 4.30 Using Morpholinos to Control Gene Expression
  • Unit 4.31 Solid‐Phase Oligonucleotide Labeling with DOTA
  • Unit 4.32 Synthesis of Peptide‐Oligonucleotide Conjugates by Diels‐Alder Cycloaddition in Water
  • Unit 4.33 Synthesis of Alkyne‐ and Azide‐Modified Oligonucleotides and Their Cyclization by the CuAAC (Click) Reaction
  • Unit 4.34 DNA Oligonucleotides Containing Stereodefined Phosphorothioate Linkages in Selected Positions
  • Unit 4.35 Heat‐Activatable Primers for Hot‐Start PCR: Oligonucleotide Synthesis and Basic PCR Setup
  • Unit 4.36 Oligodeoxynucleotides Containing N1‐Methyl‐2′‐Deoxyadenosine and N6‐Methyl‐2′‐Deoxyadenosine
  • Unit 4.37 Nucleoside Modification with Boron Clusters and Their Metal Complexes
  • Unit 4.38 Carbohydrate‐Oligonucleotide Conjugates
  • Unit 4.39 Synthesis of 2′‐Deoxyoxanosine from 2′‐Deoxyguanosine, Conversion to Its Phosphoramidite, and Incorporation into Oxanine‐Containing Oligodeoxynucleotides
  • Unit 4.40 Synthesis of Glycerol Nucleic Acid (GNA) Phosphoramidite Monomers and Oligonucleotide Polymers
  • Unit 4.41 Synthesis of Peptide‐Oligonucleotide Conjugates Using a Heterobifunctional Crosslinker
  • Unit 4.42 Time‐Dependent Thermocontrol of the Hydrophilic and Lipophilic Properties of DNA Oligonucleotide Prodrugs
  • Unit 4.43 Preparation of C5‐Functionalized Locked Nucleic Acids (LNAs)
  • Unit 4.44 Synthesis of Stable Aminoacyl‐tRNA Analogs
  • Unit 4.45 Preparation of Photoresponsive DNA Tethering Ortho‐Methylated Azobenzene as a Supra‐Photoswitch
  • Unit 4.46 RNA Aptamers and Spiegelmers: Synthesis, Purification, and Post‐Synthetic PEG Conjugation
  • Unit 4.47 Preparation of DNA Containing 5‐Hydroxymethyl‐2′‐Deoxycytidine Modification Through Phosphoramidites with TBDMS as 5‐Hydroxymethyl Protecting Group
  • Unit 4.48 Synthesis and Application of Highly Reactive Amino Linkers for Functional Oligonucleotides
  • Unit 4.49 Oligodeoxynucleotide Containing S‐Functionalized 2′‐Deoxy‐6‐Thioguanosine: Facile Tools for Base‐Selective and Site‐Specific Internal Modification of RNA
  • Unit 4.50 Preparation of Azido Containing Oligonucleotides Through Diazo Transfer Reaction
  • Unit 4.51 Synthesis of Threose Nucleic Acid (TNA) Phosphoramidite Monomers and Oligonucleotide Polymers
  • Unit 4.52 Convenient and Efficient Approach to the Permanent or Reversible Conjugation of RNA and DNA Sequences with Functional Groups
  • Unit 4.53 Synthesis of Oligodeoxynucleotides with 5′‐Caps Binding RNA Targets
  • Unit 4.54 Synthesis of Threose Nucleic Acid (TNA) Triphosphates and Oligonucleotides by Polymerase‐Mediated Primer Extension
  • Unit 4.55 Non‐Nucleoside Phosphoramidites of Xanthene Dyes (FAM, JOE, and TAMRA) for Oligonucleotide Labeling
• Chapter 5 Methods for Cross‐Linking Nucleic Acids
  • Introduction
  • Unit 5.1 Engineering Disulfide Cross‐Links in RNA Using Thiol‐Disulfide Interchange Chemistry
  • Unit 5.2 Chemical and Enzymatic Methods for Preparing Circular Single‐Stranded DNAs
  • Unit 5.3 Engineering Specific Cross‐Links in Nucleic Acids Using Glycol Linkers
  • Unit 5.4 Engineering Disulfide Cross‐Links in RNA Via Air Oxidation
  • Unit 5.5 Use of Electrophilic Substitution to Form Site‐Specific Cross‐Links in DNA
  • Unit 5.6 Synthesis of Endcap Dimethoxytrityl Phosphoramidites for Endcapped Oligonucleotides
  • Unit 5.7 Engineering Terminal Disulfide Bonds Into DNA
  • Unit 5.8 Preparation of DNA and RNA Fragments Containing Guanine N2‐Thioalkyl Tethers
  • Unit 5.9 Synthesis of Building Blocks and Oligonucleotides with {G}O6‐Alkyl‐O6{G} Cross‐Links
  • Unit 5.10 Syntheses of DNA Duplexes That Contain a N4C‐Alkyl‐N4C Interstrand Cross‐Link
  • Unit 5.11 Synthesis of Building Blocks and Oligonucleotides with {T}N3‐Alkylene‐N3{T} Cross‐Links
• Chapter 6 Chemical and Enzymatic Probes for Nucleic Acid Structure
  • Introduction
  • Unit 6.1 Probing RNA Structure with Chemical Reagents and Enzymes
  • Unit 6.2 Probing Nucleic Acid Structure with Shape‐Selective Rhodium and Ruthenium Complexes
  • Unit 6.3 Probing RNA Structure by Lead Cleavage
  • Unit 6.4 Probing Nucleic Acid Structure with Nickel‐ and Cobalt‐Based Reagents
  • Unit 6.5 Probing RNA Structures with Hydroxyl Radicals
  • Unit 6.6 Chemical Reagents for Investigating the Major Groove of DNA
  • Unit 6.7 Probing DNA Structure with Hydroxyl Radicals
  • Unit 6.8 Probing RNA Structure and Metal‐Binding Sites Using Terbium(III) Footprinting
  • Unit 6.9 Probing RNA Structure and Function by Nucleotide Analog Interference Mapping
  • Unit 6.10 Bisulfite Modification for Analysis of DNA Methylation
• Chapter 7 Biophysical Analysis of Nucleic Acids
  • Introduction
  • Unit 7.1 Biophysical Analysis of Nucleic Acids
  • Unit 7.2 NMR Determination of Oligonucleotide Structure
  • Unit 7.3 Optical Methods
  • Unit 7.4 Calorimetry of Nucleic Acids
  • Unit 7.5 Molecular Modeling of Nucleic Acid Structure
  • Unit 7.6 Methods to Crystallize RNA
  • Unit 7.7 Recent Advances in RNA Structure Determination by NMR
  • Unit 7.8 Molecular Modeling of Nucleic Acid Structure: Energy and Sampling
  • Unit 7.9 Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation
  • Unit 7.10 Molecular Modeling of Nucleic Acid Structure: Setup and Analysis
  • Unit 7.11 Characterization of DNA Structures by Circular Dichroism
  • Unit 7.12 Biophysical Analysis of Triple‐Helix Formation
  • Unit 7.13 Diffraction Techniques in Structural Biology
  • Unit 7.14 Determination of Nucleic Acid Hydration Using Osmotic Stress
  • Unit 7.15 Use of Chromophoric Ligands to Visually Screen Co‐Crystals of Putative Protein‐Nucleic Acid Complexes
  • Unit 7.16 Liquid Chromatography‐Mass Spectrometry Analysis of DNA Polymerase Reaction Products
  • Unit 7.17 Attachment of Nitroxide Spin Labels to Nucleic Acids for EPR
  • Unit 7.18 Nucleic Acid Structure Characterization by Small Angle X‐Ray Scattering (SAXS)
• Chapter 8 Nucleic Acid Binding Molecules
  • Introduction
  • Unit 8.1 Determination of Binding Mode: Intercalation
  • Unit 8.2 Determination of Binding Thermodynamics
  • Unit 8.3 A Competition Dialysis Assay for the Study of Structure‐Selective Ligand Binding to Nucleic Acids
  • Unit 8.4 Chemistry of Minor Groove Binder–Oligonucleotide Conjugates
  • Unit 8.5 A Fluorescent Intercalator Displacement Assay for Establishing DNA Binding Selectivity and Affinity
  • Unit 8.6 Synthesis of Dimeric 2‐Amino‐1,8‐Naphthyridine and Related DNA‐Binding Molecules
  • Unit 8.7 ICON Probes: Synthesis and DNA Methylation Typing
  • Unit 8.8 Binding to the DNA Minor Groove by Heterocyclic Dications: From AT‐Specific Monomers to GC Recognition with Dimers
• Chapter 9 Combinatorial Methods in Nucleic Acid Chemistry
  • Introduction
  • Unit 9.1 Theoretical Principles of In Vitro Selection Using Combinatorial Nucleic Acid Libraries
  • Unit 9.2 Design, Synthesis, and Amplification of DNA Pools for In Vitro Selection
  • Unit 9.3 In Vitro Selection of RNA Aptamers to a Protein Target by Filter Immobilization
  • Unit 9.4 Selection for Catalytic Function with Nucleic Acids
  • Unit 9.5 In Vitro Selection of RNA Aptamers to a Small Molecule Target
  • Unit 9.6 In Vitro Selection Using Modified or Unnatural Nucleotides
  • Unit 9.7 The Continuous Evolution In Vitro Technique
• Chapter 10 Purification and Analysis of Synthetic Nucleic Acids and Components
  • Introduction
  • Unit 10.1 Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry of Oligonucleotides
  • Unit 10.2 Electrospray Ionization Mass Spectrometry of Oligonucleotides
  • Unit 10.3 Overview of Purification and Analysis of Synthetic Nucleic Acids
  • Unit 10.4 Polyacrylamide Gel Electrophoresis (PAGE) of Synthetic Nucleic Acids
  • Unit 10.5 Analysis and Purification of Synthetic Nucleic Acids Using HPLC
  • Unit 10.6 Base Composition Analysis of Nucleosides Using HPLC
  • Unit 10.7 Cartridge Methods for Oligonucleotide Purification
  • Unit 10.8 Analysis of Oxidized DNA Fragments by Gel Electrophoresis
  • Unit 10.9 Capillary Electrophoresis of DNA
  • Unit 10.10 Sequencing Oligonucleotides by Enrichment of Coupling Failures Using Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry
  • Unit 10.11 Mass Determination of Phosphoramidites
  • Unit 10.12 3,4‐Diaminobenzophenone Matrix for Analysis of Oligonucleotides by MALDI‐TOF Mass Spectrometry
  • Unit 10.13 Detection of Aberrant 2′‐5′ Linkages in RNA by Anion Exchange
  • Unit 10.14 Purification of Synthetic Oligonucleotides via Catching by Polymerization
• Chapter 11 RNA Folding Pathways
  • Introduction
  • Unit 11.1 RNA Folding Pathways
  • Unit 11.2 RNA Secondary Structure Prediction
  • Unit 11.3 Thermal Methods for the Analysis of RNA Folding Pathways
  • Unit 11.4 Probing RNA Folding Pathways by RNA Fingerprinting
  • Unit 11.5 Characterization of Tertiary Folding of RNA by Circular Dichroism and Urea
  • Unit 11.6 Time‐Resolved Hydroxyl Radical Footprinting of RNA with X‐Rays
  • Unit 11.7 Rapid Magnesium Chelation as a Method to Study Real‐Time Tertiary Unfolding of RNA
  • Unit 11.8 Use of Fluorescence Spectroscopy to Elucidate RNA Folding Pathways
  • Unit 11.9 Use of Chemical Modification To Elucidate RNA Folding Pathways
  • Unit 11.10 Probing RNA Structural Dynamics and Function by Fluorescence Resonance Energy Transfer (FRET)
  • Unit 11.11 Site‐Specific Fluorescent Labeling of Large RNAs with Pyrene
  • Unit 11.12 RNA Intramolecular Dynamics by Single‐Molecule FRET
• Chapter 12 Nucleic Acid‐Based Microarrays and Nanostructures
  • Introduction
  • Unit 12.1 Key Experimental Approaches in DNA Nanotechnology
  • Unit 12.2 Preparation of Gold Nanoparticle–DNA Conjugates
  • Unit 12.3 Synthesis of 5′‐O‐Phosphoramidites with a Photolabile 3′‐O‐Protecting Group
  • Unit 12.4 Derivatization of Glass and Polypropylene Surfaces
  • Unit 12.5 DNA Microarray Preparation by Light‐Controlled In Situ Synthesis
  • Unit 12.6 Preparation of α‐Oxo Semicarbazone Oligonucleotide Microarrays
  • Unit 12.7 Synthesis of Covalent Oligonucleotide‐Streptavidin Conjugates and Their Application in DNA‐Directed Immobilization (DDI) of Proteins
  • Unit 12.8 Recent Progress in DNA Origami Technology
  • Unit 12.9 DNA Origami: Synthesis and Self‐Assembly
• Chapter 13 Nucleoside Phosphorylation and Related Modifications
  • Introduction
  • Unit 13.1 Overview of the Synthesis of Nucleoside Phosphates and Polyphosphates
  • Unit 13.2 Chemoenzymatic Preparation of Nucleoside Triphosphates
  • Unit 13.3 Synthesis and Polymerase Incorporation of 5′‐Amino‐2′,5′‐Dideoxy‐5′‐N‐Triphosphate Nucleotides
  • Unit 13.4 Nucleoside‐5′‐Phosphoimidazolides: Reagents for Facile Synthesis of Dinucleoside Pyrophosphates
  • Unit 13.5 Synthesis of Methylenebis(phosphonate) Analogs of Dinucleotide Pyrophosphates
  • Unit 13.6 Chemical Phosphorylation of Deoxyribonucleosides and Thermolytic DNA Oligonucleotides
  • Unit 13.7 Stereoselective Synthesis of Sugar Nucleotides Using Neighboring Group Participation
  • Unit 13.8 Solid‐Supported Diphosphitylating and Triphosphitylating Reagents for Nucleoside Modification
  • Unit 13.9 Solid‐Supported Reagents for Synthesis of Nucleoside Monothiophosphates, Dithiodiphosphates, and Trithiotriphosphates
  • Unit 13.10 Gram‐Scale Chemical Synthesis of 2′‐Deoxynucleoside‐5′‐O‐Triphosphates
  • Unit 13.11 Rapid and Efficient Synthesis of Nucleoside Polyphosphates and Their Conjugates Using Sulfonyl Imidazolium Salts
• Chapter 14 Biologically Active Nucleosides
  • Introduction
  • Unit 14.1 Synthesis of Acyclic Analogs of Adenosine
  • Unit 14.2 Synthesis of Acyclic Nucleoside Phosphonates
  • Unit 14.3 Synthesis of β‐L‐2′‐Deoxythymidine (L‐dT)
  • Unit 14.4 Synthesis of Carbovir and Abacavir from a Carbocyclic Precursor
  • Unit 14.5 Synthesis of 2′‐ and 3′‐C‐Methylribonucleosides
  • Unit 14.6 Synthesis of Fluoroneplanocin A
  • Unit 14.7 Synthesis of Entecavir and Its Novel Class of Analogs
  • Unit 14.8 One‐Flask Synthesis of Cyclic Diguanosine Monophosphate (c‐di‐GMP)
  • Unit 14.9 Biotinylation of a Propargylated Cyclic (3′‐5′) Diguanylic Acid and of Its Mono‐6‐Thioated Analog Under “Click” Conditions
• Chapter 15 Nucleoside Prodrugs and Delivery Strategies
  • Introduction
  • Unit 15.1 Synthesis of Amino Acid Phosphoramidate Monoesters via H‐Phosphonate Intermediates
  • Unit 15.2 Synthesis of Cidofovir and (S)‐HPMPA Ether Lipid Prodrugs
  • Unit 15.3 Chemistry of bisSATE Mononucleotide Prodrugs
  • Unit 15.4 Synthesis of Peptidomimetic Conjugates of Cyclic Nucleoside Phosphonates
• Chapter 16 RNA Silencing
  • Introduction
  • Unit 16.1 Overview of Gene Silencing by RNA Interference
  • Unit 16.2 Preparation of Short Interfering RNA Containing the Modified Nucleosides 2‐Thiouridine, Pseudouridine, or Dihydrouridine
  • Unit 16.3 Chemical Modification of siRNA
  • Unit 16.4 Synthesis of Dumbbell‐Shaped Cyclic RNAs for RNA Interference
• Chapter 17 Quadruplex Formation
  • Introduction
  • Unit 17.1 UV Melting of G‐Quadruplexes
  • Unit 17.2 Overview of Formation of G‐Quadruplex Structures
  • Unit 17.3 Resolution of Quadruplex Polymorphism by Size‐Exclusion Chromatography
  • Unit 17.4 Analysis of Multidimensional G‐Quadruplex Melting Curves
  • Unit 17.5 Sequence, Stability, and Structure of G‐Quadruplexes and Their Interactions with Drugs
  • Unit 17.6 Crystallography of DNA and RNA G‐Quadruplex Nucleic Acids and Their Ligand Complexes
• Appendix 1 Standard Nomenclature, Data, and Abbreviations
  • Appendix 1B Characteristics of Nucleic Acids
  • Appendix 1C IUPAC‐IUB Joint Commission on Biochemical Nomenclature Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains
  • Appendix 1D Nucleoside and Nucleotide Nomenclature
  • Appendix 1E A Convenient Stereochemical Notation for P‐Chiral Nucleotide Analogs
• Appendix 2 Laboratory Stock Solutions and Equipment
  • Appendix 2A Common Buffers and Stock Solutions
• Appendix 3 Commonly Used Techniques
  • Appendix 3B Denaturing Polyacrylamide Gel Electrophoresis
  • Appendix 3C Introduction to the Synthesis and Purification of Oligonucleotides
  • Appendix 3D Thin‐Layer Chromatography
  • Appendix 3E Column Chromatography

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