Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

Online ISBN: 9780471142706

DOI: 10.1002/0471142700

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Current Protocols in Nucleic Acid Chemistry Supplements

2014:    Supplement 56    
2013:    Supplement 55     Supplement 54     Supplement 53     Supplement 52    
2012:    Supplement 51     Supplement 50     Supplement 49     Supplement 48    
2011:    Supplement 47     Supplement 46     Supplement 45     Supplement 44    
2010:    Supplement 43     Supplement 42     Supplement 41     Supplement 40    
2009:    Supplement 39     Supplement 38     Supplement 37     Supplement 36    
2008:    Supplement 35     Supplement 34     Supplement 33     Supplement 32    
2007:    Supplement 31     Supplement 30     Supplement 29     Supplement 28    
2006:    Supplement 27     Supplement 26     Supplement 25     Supplement 24    
2005:    Supplement 23     Supplement 22     Supplement 21     Supplement 20    
2004:    Supplement 19     Supplement 18     Supplement 17     Supplement 16    
2003:    Supplement 15     Supplement 14     Supplement 13     Supplement 12    
2002:    Supplement 11     Supplement 10     Supplement 9       Supplement 8      
2001:    Supplement 7       Supplement 6       Supplement 5       Supplement 4      
1999:    Supplement 3       Supplement 2       Supplement 1       Core publication      



 Supplement 56, March 2014

Unit 4.58 Synthesis of 8-Oxoguanosine Phosphoramidite and Its Incorporation into Oligoribonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 5.14 Synthesis of G-N2-(CH2)3-N2-G Trimethylene DNA Interstrand Cross-Links
         Abstract | Full Text:  HTML   PDF

Unit 7.10 Molecular Modeling of Nucleic Acid Structure: Setup and Analysis
         Abstract | Full Text:  HTML   PDF

Unit 9.6 In Vitro Selection Using Modified or Unnatural Nucleotides
         Abstract | Full Text:  HTML   PDF

Unit 14.10 Anti-HIV Nucleoside Phosphonate GS-9148 and Its Prodrug GS-9131: Scale Up of a 2’-F Modified Cyclic Nucleoside Phosphonate and Synthesis of Selected Amidate Prodrugs
         Abstract | Full Text:  HTML   PDF

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 Supplement 55, December 2013

Unit 4.57 Synthesis of Triazole-Nucleoside Phosphoramidites and Their Use in Solid-Phase Oligonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 5.13 Synthesis of Building Blocks and Oligonucleotides Containing {T}O4-Alkylene- O4{T} Interstrand Cross-Links
         Abstract | Full Text:  HTML   PDF

Unit 7.9 Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation
         Abstract | Full Text:  HTML   PDF

Unit 11.13 Characterization of Conformational Dynamics of Bistable RNA by Equilibrium and Non-Equilibrium NMR
         Abstract | Full Text:  HTML   PDF

Unit 13.13 Chemical Synthesis of Dinucleotide Cap Analogs
         Abstract | Full Text:  HTML   PDF

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 Supplement 54, October 2013

Unit 3.22 2′-Hydroxy Protection of Ribonucleosides as 2-Cyano-2,2-Dimethylethanimine-N-Oxymethyl Ethers in Solid-Phase Synthesis of RNA Sequences
         Abstract | Full Text:  HTML   PDF

Unit 5.12 DNA Interstrand Cross-Link Formation Using Furan as a Masked Reactive Aldehyde
         Abstract | Full Text:  HTML   PDF

Unit 7.5 Molecular Modeling of Nucleic Acid Structure
         Abstract | Full Text:  HTML   PDF

Unit 7.8 Molecular Modeling of Nucleic Acid Structure: Energy and Sampling
         Abstract | Full Text:  HTML   PDF

Unit 13.12 A Simple Chemical Synthesis of Sugar Nucleoside Diphosphates in Water
         Abstract | Full Text:  HTML   PDF

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 Supplement 53, June 2013

Unit 3.1 Solid-Phase Supports for Oligonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 4.56 Preparation of Oligodeoxyribonucleotides Containing the Pyrimidine(6–4)pyrimidone Photoproduct by Using a Dinucleotide Building Block
         Abstract | Full Text:  HTML   PDF

Unit 7.19 Quantitative Analyses of Nucleic Acid Stability Under the Molecular Crowding Condition Induced by Cosolutes
         Abstract | Full Text:  HTML   PDF

Unit 15.5 Synthesis of Phosphoramidate Prodrugs: ProTide Approach
         Abstract | Full Text:  HTML   PDF

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 Supplement 52, March 2013

Unit 1.30 Use of a Novel 5′-Regioselective Phosphitylating Reagent for One-Pot Synthesis of Nucleoside 5′-Triphosphates from Unprotected Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 3.2 Attachment of Nucleosides and Other Linkers to Solid-Phase Supports for Oligonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 4.54 Synthesis of Threose Nucleic Acid (TNA) Triphosphates and Oligonucleotides by Polymerase-Mediated Primer Extension
         Abstract | Full Text:  HTML   PDF

Unit 4.55 Non-Nucleoside Phosphoramidites of Xanthene Dyes (FAM, JOE, and TAMRA) for Oligonucleotide Labeling
         Abstract | Full Text:  HTML   PDF

Unit 14.9 Biotinylation of a Propargylated Cyclic (3′-5′) Diguanylic Acid and of Its Mono-6-Thioated Analog Under “Click” Conditions
         Abstract | Full Text:  HTML   PDF

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 Supplement 51, December 2012

Unit 1.29 Synthesis of a North-Methanocarba-Thymidine (N-MCT) Analogue
         Abstract | Full Text:  HTML   PDF

Unit 4.53 Synthesis of Oligodeoxynucleotides with 5′ Caps Binding RNA Targets
         Abstract | Full Text:  HTML   PDF

Unit 5.11 Synthesis of Building Blocks and Oligonucleotides with {T}N3-Alkylene-N3{T} Cross-Links
         Abstract | Full Text:  HTML   PDF

Unit 7.18 Nucleic Acid Structure Characterization by Small Angle X-Ray Scattering (SAXS)
         Abstract | Full Text:  HTML   PDF

Unit 8.8 Binding to the DNA Minor Groove by Heterocyclic Dications: From AT-Specific Monomers to GC Recognition with Dimers
         Abstract | Full Text:  HTML   PDF

Unit 13.11 Rapid and Efficient Synthesis of Nucleoside Polyphosphates and Their Conjugates Using Sulfonyl Imidazolium Salts
         Abstract | Full Text:  HTML   PDF

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 Supplement 50, September 2012

Unit 1.28 Solid-Phase Chemical Synthesis of 5′-Triphosphate DNA, RNA, and Chemically Modified Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 4.50 Preparation of Azido Containing Oligonucleotides Through Diazo Transfer Reaction
         Abstract | Full Text:  HTML   PDF

Unit 4.51 Synthesis of Threose Nucleic Acid (TNA) Phosphoramidite Monomers and Oligonucleotide Polymers
         Abstract | Full Text:  HTML   PDF

Unit 4.52 Convenient and Efficient Approach to the Permanent or Reversible Conjugation of RNA and DNA Sequences with Functional Groups
         Abstract | Full Text:  HTML   PDF

Unit 17.5 Sequence, Stability, and Structure of G-Quadruplexes and Their Interactions with Drugs
         Abstract | Full Text:  HTML   PDF

Unit 17.6 Crystallography of DNA and RNA G-Quadruplex Nucleic Acids and Their Ligand Complexes
         Abstract | Full Text:  HTML   PDF

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 Supplement 49, June 2012

Unit 1.26 Two-Step, One-Pot Synthesis of Inosine, Guanosine, and 2′-Deoxyguanosine O6-Ethers via Intermediate O6-(Benzotriazol-1-yl) Derivatives
         Abstract | Full Text:  HTML   PDF

Unit 1.27 Aqueous-Phase Sonogashira Alkynylation to Synthesize 5-Substituted Pyrimidine and 8-Substituted Purine Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 3.21 Safe Deprotection Strategy for the Tert-Butyldimethylsilyl (TBS) Group During RNA Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 7.17 Attachment of Nitroxide Spin Labels to Nucleic Acids for EPR
         Abstract | Full Text:  HTML   PDF

Unit 10.14 Purification of Synthetic Oligonucleotides via Catching by Polymerization
         Abstract | Full Text:  HTML   PDF

Unit 13.10 Gram-Scale Chemical Synthesis of 2′-Deoxynucleoside-5′-O-Triphosphates
         Abstract | Full Text:  HTML   PDF

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 Supplement 48, March 2012

Unit 4.48 Synthesis and Application of Highly Reactive Amino Linkers for Functional Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 4.49 Oligodeoxynucleotide Containing S-Functionalized 2′-Deoxy-6-Thioguanosine: Facile Tools for Base-Selective and Site-Specific Internal Modification of RNA
         Abstract | Full Text:  HTML   PDF

Unit 12.9 DNA Origami: Synthesis and Self-Assembly
         Abstract | Full Text:  HTML   PDF

Unit 14.8 One-Flask Synthesis of Cyclic Diguanosine Monophosphate (c-di-GMP)
         Abstract | Full Text:  HTML   PDF

Unit 16.4 Synthesis of Dumbbell-Shaped Cyclic RNAs for RNA Interference
         Abstract | Full Text:  HTML   PDF

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 Supplement 47, December 2011

Unit 1.25 Synthesis of the Tellurium-Derivatized Phosphoramidites and Their Incorporation into DNA Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 4.47 Preparation of DNA Containing 5-Hydroxymethyl-2′-Deoxycytidine Modification Through Phosphoramidites with TBDMS as 5-Hydroxymethyl Protecting Group
         Abstract | Full Text:  HTML   PDF

Unit 7.16 Liquid Chromatography-Mass Spectrometry Analysis of DNA Polymerase Reaction Products
         Abstract | Full Text:  HTML   PDF

Unit 8.7 ICON Probes: Synthesis and DNA Methylation Typing
         Abstract | Full Text:  HTML   PDF

Unit 14.7 Synthesis of Entecavir and Its Novel Class of Analogs
         Abstract | Full Text:  HTML   PDF

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 Supplement 46, September 2011

Unit 4.1 A Status Update of Modified Oligonucleotides for Chemotherapeutics Applications
         Abstract | Full Text:  HTML   PDF

Unit 4.45 Preparation of Photoresponsive DNA Tethering Ortho-Methylated Azobenzene as a Supra-Photoswitch
         Abstract | Full Text:  HTML   PDF

Unit 4.46 RNA Aptamers and Spiegelmers: Synthesis, Purification, and Post-Synthetic PEG Conjugation
         Abstract | Full Text:  HTML   PDF

Unit 7.15 Use of Chromophoric Ligands to Visually Screen Co-Crystals of Putative Protein-Nucleic Acid Complexes
         Abstract | Full Text:  HTML   PDF

Appendix 2A Common Buffers and Stock Solutions
         Abstract | Full Text:  HTML   PDF

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 Supplement 45, June 2011

Unit 3.20 RNA Synthesis by Reverse Direction Process: Phosphoramidites and High Purity RNAs and Introduction of Ligands, Chromophores, and Modifications at 3′-End
         Abstract | Full Text:  HTML   PDF

Unit 12.8 Recent Progress in DNA Origami Technology
         Abstract | Full Text:  HTML   PDF

Unit 17.3 Resolution of Quadruplex Polymorphism by Size-Exclusion Chromatography
         Abstract | Full Text:  HTML   PDF

Unit 17.4 Analysis of Multidimensional G-Quadruplex Melting Curves
         Abstract | Full Text:  HTML   PDF

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 Supplement 44, March 2011

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
         Abstract | Full Text:  HTML   PDF

Unit 4.43 Preparation of C5-Functionalized Locked Nucleic Acids (LNAs)
         Abstract | Full Text:  HTML   PDF

Unit 4.44 Synthesis of Stable Aminoacyl-tRNA Analogs
         Abstract | Full Text:  HTML   PDF

Unit 5.9 Synthesis of Building Blocks and Oligonucleotides with {G}O6-Alkyl- O6{G} Cross-Links
         Abstract | Full Text:  HTML   PDF

Unit 5.10 Syntheses of DNA Duplexes That Contain a N4C-Alklyl-N4C Interstrand Cross-Link
         Abstract | Full Text:  HTML   PDF

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 Supplement 43, December 2010

Unit 3.19 Chemical Synthesis of RNA with Base-Labile 2′-O(Pivaloyloxymethyl)-Protected Ribonucleoside Phosphoramadites
         Abstract | Full Text:  HTML   PDF

Unit 4.42 Time-Dependent Thermocontrol of the Hydrophile and Lipophilic Properties of DNA Oligonucleotide Prodrugs
         Abstract | Full Text:  HTML   PDF

Unit 7.14 Determination of Nucleic Acid Hydration Using Osmotic Stress
         Abstract | Full Text:  HTML   PDF

Unit 15.4 Synthesis of Peptidomimetic Conjugates of Cyclic Nucleoside Phosphates
         Abstract | Full Text:  HTML   PDF

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 Supplement 42, September 2010

Unit 1.23 Synthesis of a 2-Selenothymidine Phosphoramidite and Its Incorporation into Oligodeoxyribonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 4.40 Synthesis of Glycerol Nucleic Acid Phosphoramidite Monomers and Oligonucleotide Polymers
         Abstract | Full Text:  HTML   PDF

Unit 4.41 Synthesis of Peptide-Oligonucleotide Conjugates Using a Heterobifunctional Crosslinker
         Abstract | Full Text:  HTML   PDF

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 Supplement 41, June 2010

Unit 4.39 Synthesis of 2′-Deoxyoxanosine from 2′-Deoxyguanosine, Conversion to Its Phosphoramidite, and Incorporation into Oxanine-Containing Oligodeoxynucleotides
         Abstract | Full Text:  HTML   PDF

Unit 5.8 Preparation of DNA and RNA Fragments Containing Guanine N2-Thioalkyl Tethers
         Abstract | Full Text:  HTML   PDF

Unit 7.13 Diffraction Techniques in Structural Biology
         Abstract | Full Text:  HTML   PDF

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 Supplement 40, March 2010

Unit 9.3 In Vitro Selection of RNA Aptamers to a Protein Target by Filter Immobilization
         Abstract | Full Text:  HTML   PDF

Unit 9.5 In Vitro Selection of RNA Aptamers to a Small Molecule Target
         Abstract | Full Text:  HTML   PDF

Unit 9.7 The Continuous Evolution In Vitro Technique
         Abstract | Full Text:  HTML   PDF

Unit 17.2 Overview of Formation of G-Quadruplex Structures
         Abstract | Full Text:  HTML   PDF

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 Supplement 39, December 2009

Unit 3.18 Nonenzymatic Oligomerization of Activated Nucleotides on Hairpin Templates
         Abstract | Full Text:  HTML   PDF

Unit 4.38 Carbohydrate-Oligonucleotide Conjugates
         Abstract | Full Text:  HTML   PDF

Unit 9.2 Design, Synthesis, and Amplification of DNA Pools for In Vitro Selection
         Abstract | Full Text:  HTML   PDF

Unit 16.3 Chemical Modification of siRNA
         Abstract | Full Text:  HTML   PDF

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 Supplement 38, September 2009

Unit 2.16 Recent Advances in the Chemical Synthesis of RNA
         Abstract | Full Text:  HTML   PDF

Unit 4.35 Heat-Activatable Primers for Hot-Start PCR: Oligonucleotide Synthesis and Basic PCR Setup
         Abstract | Full Text:  HTML   PDF

Unit 4.36 Oligodeoxynucleotides Containing N1-Methyl-2′-Deoxyadenosine and N6-Methyl-2′-Deoxyadenosine
         Abstract | Full Text:  HTML   PDF

Unit 4.37 Nucleoside Modification with Boron Clusters and Their Metal Complexes
         Abstract | Full Text:  HTML   PDF

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 Supplement 37, June 2009

Unit 1.4 Unnatural Nucleosides with Unusual Base Pairing Properties
         Abstract | Full Text:  HTML   PDF

Unit 16.2 Preparation of Short Interfering RNA Containing the Modified Nucleosides 2-Thiouridine, Pseudouridine, or Dihydrouridine
         Abstract | Full Text:  HTML   PDF

Unit 17.1 UV Melting of G-Quadruplexes
         Abstract | Full Text:  HTML   PDF

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 Supplement 36, March 2009

Unit 1.22 O6-(Benzotriazol-1-yl)inosine Derivatives for C6 Modification of Purine Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 4.34 DNA Oligonucleotides Containing Stereodefined Phosphorothioate Linkages in Selected Positions
         Abstract | Full Text:  HTML   PDF

Unit 13.9 Solid-Supported Reagents for Synthesis of Nucleoside Monothiophosphates, Dithiodiphosphates, and Trithiotriphosphates
         Abstract | Full Text:  HTML   PDF

Unit 16.1 Overview of Gene Silencing by RNA Interference
         Abstract | Full Text:  HTML   PDF

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 Supplement 35, December 2008

Unit 1.21 Synthesis of 5-Formyl-2′-Deoxyruridine and Its Incorporation into Oligodeoxynucleotides
         Abstract | Full Text:  HTML   PDF

Unit 3.17 Release of DNA Oligonucleotides and Their Conjugates from Controlled-Pore Glass Under Thermolytic Conditions
         Abstract | Full Text:  HTML   PDF

Unit 4.33 Synthesis of Alkaline- and Azide-Modified Oligonucleotides and Their Cyclization by the CuAAC (Click) Reaction
         Abstract | Full Text:  HTML   PDF

Unit 10.2 Electrospray Ionization Mass Spectrometry of Oligonucleotides
         Abstract | Full Text:  HTML   PDF

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 Supplement 34, September 2008

Unit 2.15 Chemical Synthesis of Oligoribonucleotides with 2′-O-(2-Cyanoethoxymethyl)-Protected Phoshoramidites
         Abstract | Full Text:  HTML   PDF

Unit 11.12 RNA Intramolecular Dynamics by Single-Molecule
         Abstract | Full Text:  HTML   PDF

Unit 14.6 Synthesis of Fluoroneplanocin A
         Abstract | Full Text:  HTML   PDF

Appendix 3D Thin-Layer Chromatography
         Abstract | Full Text:  HTML   PDF

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 Supplement 33, June 2008

Unit 1.20 Synthesis of 2'-Cyclohexenylnucleosides and Corresponding CeNA Building Blocks
         Abstract | Full Text:  HTML   PDF

Unit 6.10 Bisulfite Modification for Analysis of DNA Methylation
         Abstract | Full Text:  HTML   PDF

Unit 10.1 Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 13.8 Solid-Supported Diphosphitylating and Triphosphitylating Reagents for Nucleoside Modification
         Abstract | Full Text:  HTML   PDF

Appendix 4A Useful Nucleic Acid Chemistry Web Sites
         Abstract | Full Text:  HTML   PDF

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  Supplement 32, March 2008

Unit 1.19 Synthesis of a 4-Selenothymidine Posphoramidite and Incorporation into Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 2.14 Chromophoric 5'- O -Silyl Protection of N -Protected 2'-ACE Ribonucleosides for Solid-Phase RNA Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 8.6 Synthesis of Dimeric 2-Amino-1,8-Naphthyridine and Related DNA-Binding Molecules
         Abstract | Full Text:  HTML   PDF

Unit 10.13 Detection of 2'- 5' Linkages in RNA by Anion Exchange
         Abstract | Full Text:  HTML   PDF

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  Supplement 31, January 2007

Unit 4.22 Stepwise Solid-Phase Synthesis of Nucleopeptides
         Abstract | Full Text:  HTML   PDF

Unit 4.32 Synthesis of Peptide-Oligonucleotide Conjugates by Diels-Alder Cycloaddition in Water
         Abstract | Full Text:  HTML   PDF

Unit 10.12 3,4-Diaminobenzophenone Matrix for Analysis of Oligonucleotides by MALDI-TOF Mass Spectrometry
         Abstract | Full Text:  HTML   PDF

Unit 13.7 Stereoselective Synthesis of Sugar Nucleotides Using Neighboring Group Participation
         Abstract | Full Text:  HTML   PDF

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  Supplement 30, September 2007

Unit 1.18 Synthesis of Altritol Nucleoside Phosphoramidites for Oligonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 2.13 Universal 2-(4-Nitrophenyl)ethyl and 2-(4-Nitrophenyl)ethoxycarbonyl Protecting Groups for Nucleosides and Nucleotides
         Abstract | Full Text:  HTML   PDF

Unit 3.16 A Universal and Recyclable Solid Support for Oligonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

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  Supplement 29, June 2007

Unit 1.17 Nucleobase-Caged Phosphoramidites for Oligonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 4.31 Solid-Phase Oligonucleotide Labeling with DOTA
         Abstract | Full Text:  HTML   PDF

Unit 7.12 Biophysical Analysis of Triple-Helix Formation
         Abstract | Full Text:  HTML   PDF

Unit 15.2 Synthesis of Cidofovir and ( S )-HPMPA Ether Lipid Prodrugs
         Abstract | Full Text:  HTML   PDF

Unit 15.3 Chemistry of bisSATE Mononucleotide Prodrugs
         Abstract | Full Text:  HTML   PDF

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  Supplement 28, March 2007

Unit 1.16 Palladium-Catalyzed Cross-Coupling Reactions in C6 Modifications of Purine Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 11.2 RNA Secondary Structure Prediction
         Abstract | Full Text:  HTML   PDF

Unit 14.5 Synthesis of 2′- and 3′-C-Methylribonucleosides
         Abstract | Full Text:  HTML   PDF

Appendix 1E A Convenient Stereochemical Notation for P -Chiral Nucleotide Analogs
         Abstract | Full Text:  HTML   PDF

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  Supplement 27, December 2006

Unit 1.13 Synthesis of Ribonucleosides by Condensation Using Trimethylsilyl Triflate
         Abstract | Full Text:  HTML   PDF

Unit 1.14 Synthesis of 2′- O -β- D -Ribofuranosylnucleosides
         Abstract | Full Text:  HTML   PDF

Unit 1.15 Preparation of 2′-Deoxy-2′-Methylseleno-Modified Phosphoramidites and RNA
         Abstract | Full Text:  HTML   PDF

Unit 4.30 Using Morpholinos to Control Gene Expression
         Abstract | Full Text:  HTML   PDF

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  Supplement 26, September 2006

Unit 3.14 Solution-Phase Synthesis of Di- and Trinucleotides Using Polymer-Supported Reagents
         Abstract | Full Text:  HTML   PDF

Unit 3.15 DNA Synthesis Without Base Protection Using the Phosphoramidite Approach
         Abstract | Full Text:  HTML   PDF

Unit 10.11 Mass Determination of Phosphoramidites
         Abstract | Full Text:  HTML   PDF

Unit 13.6 Chemical Phosphorylation of Deoxyribonucleosides and Thermolytic DNA Oligonucleotides
         Abstract | Full Text:  HTML   PDF

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  Supplement 25, June 2006

Unit 1.12 Synthesis of Fluorinated Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 4.29 Methoxyoxalamido Chemistry in the Synthesis of Tethered Phosphoramidites and Functionalized Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 14.4 Synthesis of Carbovir and Abacavir from a Carbocyclic Precursor
         Abstract | Full Text:  HTML   PDF

Unit 15.1 Synthesis of Amino Acid Phosphoramidate Monoesters via H -Phosphonate Intermediates
         Abstract | Full Text:  HTML   PDF

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  Supplement 24, March 2006

Unit 4.28 Disulfide Conjugation of Peptides to Oligonucleotides and Their Analogs
         Abstract | Full Text:  HTML   PDF

Unit 13.5 Synthesis of Methylenebis(phosphonate) Analogs of Dinucleotide Pyrophosphates
         Abstract | Full Text:  HTML   PDF

Unit 14.3 Synthesis of β- L -2′-Deoxythymidine ( L -dT)
         Abstract | Full Text:  HTML   PDF

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  Supplement 23, December 2005

Unit 2.12 Nucleobase Protection with Allyloxycarbonyl
         Abstract | Full Text:  HTML   PDF

Unit 3.12 Nucleoside Phosphoramidites Containing Cleavable Linkers
         Abstract | Full Text:  HTML   PDF

Unit 3.13 Microwave-Assisted Functionalization of Solid Supports for Rapid Loading of Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 10.10 Sequencing Oligonucleotides by Enrichment of Coupling Failures Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
         Abstract | Full Text:  HTML   PDF

Unit 13.4 Nucleoside-5′-Phosphoimidazolides: Reagents for Facile Synthesis of Dinucleoside Pyrophosphates
         Abstract | Full Text:  HTML   PDF

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  Supplement 22, September 2005

Unit 4.27 Large-Scale Preparation of Conjugated Oligonucleoside Phosphorothioates by the High-Efficiency Liquid-Phase (HELP) Method
         Abstract | Full Text:  HTML   PDF

Unit 12.7 Synthesis of Covalent Oligonucleotide-Streptavidin Conjugates and Their Application in DNA-Directed Immobilization (DDI) of Proteins
         Abstract | Full Text:  HTML   PDF

Unit 14.1 Synthesis of Acyclic Analogs of Adenosine
         Abstract | Full Text:  HTML   PDF

Unit 14.2 Synthesis of Acyclic Nucleoside Phosphonates
         Abstract | Full Text:  HTML   PDF

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  Supplement 21, June 2005

Unit 1.10 Synthesis and Properties of 7-Substituted 7-Deazapurine (Pyrrolo[2,3- d ]pyrimidine) 2′-Deoxyribonucleosides
         Abstract | Full Text:  HTML   PDF

Unit 1.11 Reduction of Ribonucleosides to 2′-Deoxyribonucleosides
         Abstract | Full Text:  HTML   PDF

Unit 2.11 Enzymatic Regioselective Levulinylation of 2′-Deoxyribonucleosides and 2′- O -Methylribonucleosides
         Abstract | Full Text:  HTML   PDF

Unit 4.26 An Aminooxy-Functionalized Non-Nucleosidic Phosphoramidite for the Construction of Multiantennary Oligonucleotide Glycoconjugates on a Solid Support
         Abstract | Full Text:  HTML   PDF

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  Supplement 20, March 2005

Unit 4.25 Base-Modified Oligodeoxyribonucleotides: Using Pyrrolo[2,3- d ]pyrimidines to Replace Purines
         Abstract | Full Text:  HTML   PDF

Unit 8.5 A Fluorescent Intercalator Displacement Assay for Establishing DNA Binding Selectivity and Affinity
         Abstract | Full Text:  HTML   PDF

Unit 12.5 DNA Microarray Preparation by Light-Controlled In Situ Synthesis
         Abstract | Full Text:  HTML   PDF

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  Supplement 19, December 2004

Unit 3.4 Synthesis of Oligodeoxyribo- and Oligoribonucleotides According to the H -Phosphonate Method
         Abstract | Full Text:  HTML   PDF

Unit 3.11 The 4-Methylthio-1-Butyl Group for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 11.11 Site-Specific Fluorescent Labeling of Large RNAs with Pyrene
         Abstract | Full Text:  HTML   PDF

Unit 12.6 Preparation of α-Oxo Semicarbazone Oligonucleotide Microarrays
         Abstract | Full Text:  HTML   PDF

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  Supplement 18, September 2004

Unit 3.10 DNA Synthesis Without Base Protection
         Abstract | Full Text:  HTML   PDF

Unit 4.24 Oligodeoxyribonucleotide Analogs Functionalized with Phosphonoacetate and Thiophosphonoacetate Diesters
         Abstract | Full Text:  HTML   PDF

Unit 12.4 Derivatization of Glass and Polypropylene Surfaces
         Abstract | Full Text:  HTML   PDF

Unit 13.3 Synthesis and Polymerase Incorporation of 5′-Amino-2′,5′-Dideoxy-5′- N -Triphosphate Nucleotides
         Abstract | Full Text:  HTML   PDF

Appendix 1A Selected Abbreviations Used in This Manual
         Abstract | Full Text:  HTML   PDF

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  Supplement 17, June 2004

Unit 4.23 Synthesis of Oligoribonucleotides Containing N 6 -Alkyladenosine and 2-Methylthio- N 6 -Alkyladenosine
         Abstract | Full Text:  HTML   PDF

Unit 6.9 Probing RNA Structure and Function by Nucleotide Analog Interference Mapping
         Abstract | Full Text:  HTML   PDF

Unit 12.3 Synthesis of 5′- O -Phosphoramidites with a Photolabile 3′- O -Protecting Group
         Abstract | Full Text:  HTML   PDF

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  Supplement 16, March 2004

Unit 2.10 Preparation of 5′-Silyl-2′-Orthoester Ribonucleosides for Use in Oligoribonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 4.22 Stepwise Solid-Phase Synthesis of Nucleopeptides
        Full Text:  HTML   PDF

Unit 13.2 Chemoenzymatic Preparation of Nucleoside Triphosphates
         Abstract | Full Text:  HTML   PDF

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  Supplement 15, December 2003

Unit 4.21 Uridine 2′-Carbamates: Facile Tools for Oligonucleotide 2′-Functionalization
         Abstract | Full Text:  HTML   PDF

Unit 13.1 Overview of the Synthesis of Nucleoside Phosphates and Polyphosphates
         Abstract | Full Text:  HTML   PDF

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  Supplement 14, September 2003

Unit 1.9 Synthesis of 1,5-Anhydrohexitol Building Blocks for Oligonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 4.17 Synthesis of Phosphorothioate Oligonucleotides with Stereodefined Phosphorothioate Linkages
         Abstract | Full Text:  HTML   PDF

Unit 4.18 Synthesis of Oligonucleotide Conjugates via Aqueous Diels-Alder Cycloaddition
         Abstract | Full Text:  HTML   PDF

Unit 4.19 5′-Iodination of Solid-Phase-Linked Oligodeoxyribonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 4.20 Reversible Biotinylation of the 5′-Terminus of Oligodeoxyribonucleotides and its Application in Affinity Purification
         Abstract | Full Text:  HTML   PDF

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  Supplement 13, June 2003

Unit 5.7 Engineering Terminal Disulfide Bonds Into DNA
         Abstract | Full Text:  HTML   PDF

Unit 6.8 Probing RNA Structure and Metal-Binding Sites Using Terbium( III) Footprinting
         Abstract | Full Text:  HTML   PDF

Unit 8.4 Chemistry of Minor Groove Binder–Oligonucleotide Conjugates
         Abstract | Full Text:  HTML   PDF

Unit 10.9 Capillary Electrophoresis of DNA
         Abstract | Full Text:  HTML   PDF

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  Supplement 12, March 2003

Unit 4.16 Chemistry of CpG DNA
         Abstract | Full Text:  HTML   PDF

Unit 5.6 Synthesis of Endcap Dimethoxytrityl Phosphoramidites for Endcapped Oligonucleotides
         Abstract | Full Text:  HTML   PDF

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  Supplement 11, December 2002

Unit 1.8 Synthesis, Characterization, and Application of Substituted Pyrazolopyrimidine Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 3.9 3-( N - tert -Butylcarboxamido)-1-propyl and 4-Oxopentyl Groups for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 7.11 Characterization of DNA Structures by Circular Dichroism
         Abstract | Full Text:  HTML   PDF

Unit 8.3 A Competition Dialysis Assay for the Study of Structure-Selective Ligand Binding to Nucleic Acids
         Abstract | Full Text:  HTML   PDF

Unit 11.10 Probing RNA Structural Dynamics and Function by Fluorescence Resonance Energy Transfer (FRET)
         Abstract | Full Text:  HTML   PDF

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  Supplement 10, September 2002

Unit 1.5 Development of a Universal Nucleobase and Modified Nucleobases for Expanding the Genetic Code
         Abstract | Full Text:  HTML   PDF

Unit 1.6 Syntheses of Specifically 15 N-Labeled Adenosine and Guanosine
         Abstract | Full Text:  HTML   PDF

Unit 1.7 Synthesis of Protected 2′-Deoxy-2′-fluoro-β- D -arabinonucleosides
         Abstract | Full Text:  HTML   PDF

Unit 4.15 Solid-Phase Synthesis of 2′-Deoxy-2′-fluoro-β- D -Oligoarabinonucleotides (2′F-ANA) and Their Phosphorothioate Derivatives
         Abstract | Full Text:  HTML   PDF

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  Supplement 9, June 2002

Unit 4.14 Solid-Phase Synthesis of Branched Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 11.8 Use of Fluorescence Spectroscopy to Elucidate RNA Folding Pathways
         Abstract | Full Text:  HTML   PDF

Unit 11.9 Use of Chemical Modification To Elucidate RNA Folding Pathways
         Abstract | Full Text:  HTML   PDF

Unit 12.1 Key Experimental Approaches in DNA Nanotechnology
         Abstract | Full Text:  HTML   PDF

Unit 12.2 Preparation of Gold Nanoparticle–DNA Conjugates
         Abstract | Full Text:  HTML   PDF

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  Supplement 8, March 2002

Unit 4.11 Synthesis and Purification of Peptide Nucleic Acids
         Abstract | Full Text:  HTML   PDF

Unit 4.12 Locked Nucleic Acids: Synthesis and Characterization of LNA-T Diol
         Abstract | Full Text:  HTML   PDF

Unit 4.13 Cellular Delivery of Locked Nucleic Acids (LNAs)
         Abstract | Full Text:  HTML   PDF

Unit 9.5 In Vitro Selection of RNA Aptamers to a Small Molecule Target
         Full Text:  HTML   PDF

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  Supplement 7, December 2001

Unit 2.9 Preparation of 2′- O -[(Triisopropylsilyl)oxy]methyl-protected Ribonucleosides
         Abstract | Full Text:  HTML   PDF

Unit 3.8 Chemical Synthesis of RNA Sequences with 2′- O -[(Triisopropylsilyl)oxy]methyl-protected Ribonucleoside Phosphoramidites
         Abstract | Full Text:  HTML   PDF

Unit 4.10 Conjugation of 5′-Functionalized Oligodeoxyribonucleotides with Properly Functionalized Ligands
         Abstract | Full Text:  HTML   PDF

Unit 6.7 Probing DNA Structure with Hydroxyl Radicals
         Abstract | Full Text:  HTML   PDF

Unit 9.6 In Vitro Selection Using Modified or Unnatural Nucleotides
         Abstract | Full Text:  HTML   PDF

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  Supplement 6, September 2001

Unit 2.8 Regioselective 2′-Silylation of Purine Ribonucleosides for Phosphoramidite RNA Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 5.5 Use of Electrophilic Substitution to Form Site-Specific Cross-Links in DNA
         Abstract | Full Text:  HTML   PDF

Unit 7.10 Molecular Modeling of Nucleic Acid Structure: Setup and Analysis
         Abstract | Full Text:  HTML   PDF

Unit 11.6 Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays
         Abstract | Full Text:  HTML   PDF

Unit 11.7 Rapid Magnesium Chelation as a Method to Study Real-Time Tertiary Unfolding of RNA
         Abstract | Full Text:  HTML   PDF

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  Supplement 5, July 2001

Unit 1.4 Unnatural Nucleosides with Unusual Base Pairing Properties
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Unit 4.8 Incorporation of Halogenoalkyl, 2-Pyridyldithioalkyl, or Isothiocyanate Linkers into Ligands
         Abstract | Full Text:  HTML   PDF

Unit 4.9 Modification of the 5′ Terminus of Oligodeoxyribonucleotides for Conjugation with Ligands
         Abstract | Full Text:  HTML   PDF

Unit 6.6 Chemical Reagents for Investigating the Major Groove of DNA
         Abstract | Full Text:  HTML   PDF

Unit 7.9 Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation
         Abstract | Full Text:  HTML   PDF

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  Supplement 4, April 2001

Unit 2.6 Deoxyribo- and Ribonucleoside H -Phosphonates
         Abstract | Full Text:  HTML   PDF

Unit 2.7 Deoxyribonucleoside Phosphoramidites
         Abstract | Full Text:  HTML   PDF

Unit 7.8 Molecular Modeling of Nucleic Acid Structure: Energy and Sampling
         Abstract | Full Text:  HTML   PDF

Unit 10.8 Analysis of Oxidized DNA Fragments by Gel Electrophoresis
         Abstract | Full Text:  HTML   PDF

Unit 11.5 Characterization of Tertiary Folding of RNA by Circular Dichroism and Urea
         Abstract | Full Text:  HTML   PDF

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  Supplement 3, December 2000

Unit 2.5 2′-Hydroxyl-Protecting Groups that are Either Photochemically Labile or Sensitive to Fluoride Ions
         Abstract | Full Text:  HTML   PDF

Unit 3.7 Synthesis of Oligoribonucleotides Using the 2-Nitrobenzyloxymethyl Group for 2′-Hydroxyl Protection
         Abstract | Full Text:  HTML   PDF

Unit 4.6 3′-Modified Oligonucleotides and their Conjugates
         Abstract | Full Text:  HTML   PDF

Unit 4.7 Synthesis and Purification of Oligonucleotide N3′→P5′ Phosphoramidates and their Phosphodiester and Phosphorothioate Chimeras
         Abstract | Full Text:  HTML   PDF

Appendix 3D Thin-Layer Chromatography
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Appendix 3E Column Chromatography
         Abstract | Full Text:  HTML   PDF

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  Supplement 2, October 2000

Unit 4.5 Attachment of Reporter and Conjugate Groups to the 3′ Termini of Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 7.7 Recent Advances in RNA Structure Determination by NMR
         Abstract | Full Text:  HTML   PDF

Unit 11.1 RNA Folding Pathways
         Abstract | Full Text:  HTML   PDF

Unit 11.2 RNA Secondary Structure Prediction
        Full Text:  HTML   PDF

Unit 11.3 Thermal Methods for the Analysis of RNA Folding Pathways
         Abstract | Full Text:  HTML   PDF

Unit 11.4 Probing RNA Folding Pathways by RNA Fingerprinting
         Abstract | Full Text:  HTML   PDF

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  Supplement 1, July 2000

Unit 3.6 Oligoribonucleotides with 2′- O -( tert -Butyldimethylsilyl) Groups
         Abstract | Full Text:  HTML   PDF

Unit 4.4 Synthesis and Characterization of Chimeric 2-5A-DNA Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 7.6 Methods to Crystallize RNA
         Abstract | Full Text:  HTML   PDF

Unit 10.3 Overview of Purification and Analysis of Synthetic Nucleic Acids
         Abstract | Full Text:  HTML   PDF

Unit 10.4 Polyacrylamide Gel Electrophoresis (PAGE) of Synthetic Nucleic Acids
         Abstract | Full Text:  HTML   PDF

Unit 10.5 Analysis and Purification of Synthetic Nucleic Acids Using HPLC
         Abstract | Full Text:  HTML   PDF

Unit 10.6 Base Composition Analysis of Nucleosides Using HPLC
         Abstract | Full Text:  HTML   PDF

Unit 10.7 Cartridge Methods for Oligonucleotide Purification
         Abstract | Full Text:  HTML   PDF

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  Core Publication, April 2000

Unit 1.1 Palladium-Mediated C5 Substitution of Pyrimidine Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 1.2 Enzymatic Synthesis of M 1 G-Deoxyribose
         Abstract | Full Text:  HTML   PDF

Unit 1.3 Synthesis of N2-Substituted Deoxyguanosine Nucleosides from 2-Fluoro-6- O -(Trimethylsilylethyl)-2′-Deoxyinosine
         Abstract | Full Text:  HTML   PDF

Unit 2.1 Nucleobase Protection of Deoxyribo- and Ribonucleosides
         Abstract | Full Text:  HTML   PDF

Unit 2.2 Protection of 2′-Hydroxy Functions of Ribonucleosides
         Abstract | Full Text:  HTML   PDF

Unit 2.3 Protection of 5′-Hydroxy Functions of Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 2.4 A Base-Labile Protecting Group (Fluorenylmethoxycarbonyl) for the 5′-Hydroxy Function of Nucleosides
         Abstract | Full Text:  HTML   PDF

Unit 3.1 Solid-Phase Supports for Oligonucleotide Synthesis
         Abstract | Full Text:  HTML   PDF

Unit 3.2 Attachment of Nucleosides to Solid-Phase Supports
         Abstract | Full Text:  HTML   PDF

Unit 3.3 Synthetic Strategies and Parameters Involved in the Synthesis of Oligodeoxyribonucleotides According to the Phosphoramidite Method
         Abstract | Full Text:  HTML   PDF

Unit 3.4 Synthetic Strategies and Parameters Involved in the Synthesis of Oligodeoxyribo- and Oligoribonucleotides According to the H -Phosphonate Method
        Full Text:  HTML   PDF

Unit 3.5 Strategies for Oligoribonucleotide Synthesis According to the Phosphoramidite Method
         Abstract | Full Text:  HTML   PDF

Unit 4.1 A Brief History, Status, and Perspective of Modified Oligonucleotides for Chemotherapeutic Applications
         Abstract | Full Text:  HTML   PDF

Unit 4.2 Modification of the 5′ Terminus of Oligonucleotides for Attachment of Reporter and Conjugate Groups
         Abstract | Full Text:  HTML   PDF

Unit 4.3 Direct Attachment of Conjugate Groups to the 5′ Terminus of Oligodeoxyribonucleotides
         Abstract | Full Text:  HTML   PDF

Unit 5.1 Engineering Disulfide Cross-Links in RNA Using Thiol-Disulfide Interchange Chemistry
         Abstract | Full Text:  HTML   PDF

Unit 5.2 Chemical and Enzymatic Methods for Preparing Circular Single-Stranded DNA s
         Abstract | Full Text:  HTML   PDF

Unit 5.3 Engineering Specific Cross-Links in Nucleic Acids Using Glycol Linkers
         Abstract | Full Text:  HTML   PDF

Unit 5.4 Engineering Disulfide Cross-Links in RNA Via Air Oxidation
         Abstract | Full Text:  HTML   PDF

Unit 6.1 Probing RNA Structure with Chemical Reagents and Enzymes
         Abstract | Full Text:  HTML   PDF

Unit 6.2 Probing Nucleic Acid Structure with Shape-Selective Rhodium and Ruthenium Complexes
         Abstract | Full Text:  HTML   PDF

Unit 6.3 Probing RNA Structure by Lead Cleavage
         Abstract | Full Text:  HTML   PDF

Unit 6.4 Probing Nucleic Acid Structure with Nickel- and Cobalt-Based Reagents
         Abstract | Full Text:  HTML   PDF

Unit 6.5 Probing RNA Structures with Hydroxyl Radicals
         Abstract | Full Text:  HTML   PDF

Unit 7.1 Biophysical Analysis of Nucleic Acids
         Abstract | Full Text:  HTML   PDF

Unit 7.2 NMR Determination of Oligonucleotide Structure
         Abstract | Full Text:  HTML   PDF

Unit 7.3 Optical Methods
         Abstract | Full Text:  HTML   PDF

Unit 7.4 Calorimetry of Nucleic Acids
         Abstract | Full Text:  HTML   PDF

Unit 7.5 Molecular Modeling of Nucleic Acid Structure
         Abstract | Full Text:  HTML   PDF

Unit 8.1 Determination of Binding Mode: Intercalation
         Abstract | Full Text:  HTML   PDF

Unit 8.2 Determination of Binding Thermodynamics
         Abstract | Full Text:  HTML   PDF

Unit 9.1 Theoretical Principles of In Vitro Selection Using Combinatorial Nucleic Acid Libraries
         Abstract | Full Text:  HTML   PDF

Unit 9.2 Design, Synthesis, and Amplification of DNA Pools for In Vitro Selection
         Full Text:  HTML   PDF

Unit 9.3 In Vitro Selection of RNA Aptamers to a Protein Target by Filter Immobilization
         Full Text:  HTML   PDF

Unit 9.4 Selection for Catalytic Function with Nucleic Acids
         Abstract | Full Text:  HTML   PDF

Unit 10.1 Analysis of Oligonucleotides by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
         Full Text:  HTML   PDF

Unit 10.2 Analysis of Oligonucleotides by Electrospray Ionization Mass Spectrometry
         Full Text:  HTML   PDF

Appendix 1A Selected Abbreviations Used in This Manual
        Full Text:  HTML   PDF

Appendix 1B Characteristics of Nucleic Acids
         Abstract | Full Text:  HTML   PDF

Appendix 1C IUPAC-IUB Joint Commission on Biochemical Nomenclature Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains
         Abstract | Full Text:  HTML   PDF

Appendix 1D Nucleoside and Nucleotide Nomenclature
         Abstract | Full Text:  HTML   PDF

Appendix 2A Common Buffers and Stock Solutions
         Abstract | Full Text:  HTML   PDF

Appendix 3A References to Commonly Used Techniques
         Abstract | Full Text:  HTML   PDF

Appendix 3B Denaturing Polyacrylamide Gel Electrophoresis
         Abstract | Full Text:  HTML   PDF

Appendix 3C Introduction to the Synthesis and Purification of Oligonucleotides
         Abstract | Full Text:  HTML   PDF

Appendix 4A Useful Nucleic Acid Chemistry Web Sites
         Full Text:  HTML   PDF

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