Oligonucleotide Synthesis Methods and Applications

A collection of powerful new techniques for oligonucleotide synthesis and for the use of modified oligonucleotides in biotechnology. Among the protocol highlights are a novel two-step process that yields a high purity, less costly, DNA, the synthesis of phosphorothioates using new sulfur transfer agents, the synthesis of LNA, peptide conjugation methods to improve cellular delivery and cell-specific targeting, and triple helix formation. The applications include using molecular beacons to monitor the PCR amplification process, nuclease footprinting to study the sequence-selective binding of small molecules of DNA, nucleic acid libraries, and the use of small interference RNA (siRNA) as an inhibitor of gene expression.

Synthesis of DNA Using a New Two-Step Cycle.- RNA Synthesis Using 2?-O-(Tert-Butyldimethylsilyl) Protection.- RNA Oligonucleotide Synthesis Via 5?-Silyl-2?-Orthoester Chemistry.- Dimethylthiarum Disulfide.- Assay for Evaluating Ribonuclease H-Mediated Degradation of RNA-Antisense Oligonucleotide Duplexes.- Di- and Oligonucleotide Synthesis Using H-Phosphonate Chemistry.- Solid-Phase Synthesis of Circular Oligonucleotides.- Locked Nucleic Acid Synthesis.- Synthesis of DNA Mimics Representing HypNA-pPNA Hetero-Oligomers.- Base-Modified Oligonucleotides With Increased Duplex Stability.- of Hypermodified Nucleotides in RNA.- Chemical Methods for Peptide-Oligonucleotide Conjugate Synthesis.- Biotin-Labeled Oligonucleotides With Extraordinarily Long Tethering Arms.- Universal Labeling Chemistry for Nucleic Acid Detection on DNA Chips.- Postsynthetic Functionalization of Triple Helix-Forming Oligonucleotides.- Fluorescence-Based On-Line Detection as an Analytical Tool in RNA Electrophoresis.- Design and Optimization of Molecular Beacon Real-Time Polymerase Chain Reaction Assays.- High-Throughput Production of Optimized Primers (Fimers) for Whole-Genome Direct Sequencing.- Nonenzymatic Template-Directed RNA Synthesis.- DNase I Footprinting of Small Molecule Binding Sites on DNA.- Gene Targeting Using Peptide Nucleic Acid.- Nucleic Acid Library Construction Using Synthetic DNA Constructs.- In Vitro Selection From Combinatorial Nucleic Acid Libraries.- In Vitro Selection Procedures for Identifying DNA and RNA Aptamers Targeted to Nucleic Acids and Proteins.- Short Double-Stranded Ribonucleic Acid as Inhibitor of Gene Expression by the Interference Mechanism.