Table of Contents
Last Updated August, 1999
Copyright©
1999 John Wiley & Sons, Inc. All rights reserved.
Foreword
Preface
Contributors
1 Synthesis of Modified Nucleosides
2 Protection of Nucleosides for Oligonucleotide Synthesis
3 Synthesis of Unmodified Oligonucleotides
4 Synthesis of Modified Oligonucleotides and Conjugates
5 Methods for Cross-Linking Nucleic Acids
6 Chemical and Enzymatic Probes for Nucleic Acid Structure
7 Biophysical Analysis of Nucleic Acid Structure
8 Nucleic Acid Binding Molecules
9 Combinatorial Methods in Nucleic Acid Chemistry
10 Purification and Analysis of Synthetic Nucleic
Acids and Components
Appendices
Index
1 Sythesis of Modified Nucleosides
1.1 Palladium-Mediated C5 Substitution of Pyrimidine Nucleosides
1.2 Condensation by Enzymatic Coupling
1.3 Synthesis of N2 Substituted Deoxyguanosine Nucleosides
from 2-Fluoro-O6-(trimethylsilyethyl)-2'-deoxyinosine
2 Protection of Nucleosides for Oligonucleotide Synthesis
2.1 Nucleobase Protection of Deoxyribo- and Ribonucleosides
2.2 Protection of the 2'-Hydroxyl Functions of Ribonucleosides
2.3 Protection of the 5'-Hydroxyl Function of Nucleosides
2.4 A Base-Labile Protecting Group for the 5'-Hydroxy Function of Nucleosides
3 Synthesis of Unmodified Oligonucleotides
3.1 Solid-Phase Supports for Oligonucleotide Synthesis
3.2 Functionalization of Solid Supports for Automated Oligonucleotide
Synthesis
3.3 Synthetic Strategies and Parameters Involved in the Synthesis of
Oligodeoxyribonucleotides According to the Phosphoramidite Method
3.4 Synthetic Strategies and Parameters Involved in the Synthesis of
Oligodeoxyribo- and Oligoribonucleotides According to the H-Phosphonate
Method
3.5 Strategies Involved in the Synthesis of Oligoribonucleotides According
to the Phosphoramidite Method
4 Synthesis of Modified Oligonucleotides and Conjugates
4.1 A Brief History and Perspective of Modified Oligonuculeotides for Chemotherapeutic
Applications
4.2 Modification of the 5'-Terminus of Oligonucleotides for the Attachment
of Reporter and Conjugate Groups
4.3 Attachment of Conjugate Groups to the 5'-terminus of Oligodeoxyribonucleotides
5 Methods for Cross-Linking Nucleic Acids
5.1 Engineering Disulfide Cross-Links in RNA Using Thiol-Disulfide Interchange
Chemistry
5.2 Chemical and Enzymatic Methods for Preparing Circular Single-Stranded
DNAs
5.3 Engineering Specific Cross-Links in Nucleic Acids with Glycol Linkers
5.4 Engineering Disulfide Cross-Links in RNA Via Air Oxidation
6 Chemical and Enzymatic Probes for Nucleic Acid
Structure
6.1 Probing RNA Structure with Chemical Reagents and Enzymes
6.2 Probing Nucleic Acid Structure with Shape-Selective Rhodium and
Ruthenium Complexes
6.3 Probing RNA Structure by Lead Cleavage
6.4 Probing Nucleic Acid Structure with Nickel and Cobalt Based Reagents
6.5 Probing RNA Structure with Hydroxyl Radicals
7 Biophysical Analysis of Nucleic Acid Structure
7.1 Biophysical Analysis of Nucleic Acids
7.2 NMR Determination of Oligonucleotide Structure
7.3 Optical Methods
7.4 Calorimetric Methods
7.5 Computer Simulation of Nucleic Acids
8 Nucleic Acid Binding Molecules
8.1 Determination of Binding Mode: Intercalation
8.2 Protocols for Determination of Binding Thermodynamics
9 Combinatorial Methods in Nucleic Acid Chemistry
9.1 Basic Principles of In Vitro Selection Using Combinatorial Nucleic
Acid Libraries
9.2 Design, Synthesis, and Amplification of DNA Pools for In Vitro
Selection
9.3 In Vitro Selection of RNA Aptamers to a Protein Target by
Filter Immobilization
9.4 Selection for Catalytic Function with Nucleic Acids
10 Purification and Analysis of Synthetic Nucleic Acids
and Components
10.1 Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Analysis
of Oligonucleotides
10.2 Analysis of Oligonucleotides by Electrospray Ionization Mass Spectrometry
Appendices
1 Standard Nomenclature, Data, and Abbreviations
A Abbreviations
B Nucleic Acid Structural Characteristics
C Abbreviations and Symbols for
Polynucleotide Chain Conformation
D Nucleoside/Nucleotide Nomenclature
2 Stock Solutions and Laboratory Guidelines
A Commonly Used Reagents and Solutions
3 Commonly Used Techniques
A References to Molecular Biology
Techniques
B Preparation of Sequencing Gels
C Introduction to the Synthesis
and Purification of Oligonucleotides
D Thin-Layer Chromatography
E Introduction to the Synthesis
and Purification of Oligonucleotides
4 Useful Web Sites
Suppliers Appendix
Indexes
