Oligonucleotide Synthesis

Oligonucleotide Synthesis : Methods and Applications

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Description

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.
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Product details

  • Hardback | 436 pages
  • 154.9 x 231.1 x 27.9mm | 839.16g
  • Humana Press Inc.
  • Totowa, NJ, United States
  • English
  • 2005 ed.
  • 142 Illustrations, black and white; XVI, 436 p. 142 illus.
  • 1588292339
  • 9781588292339

Back cover copy

Nucleic acids chemistry has progressed rapidly in the last 10 years with the introduction of many new techniques and the development of many novel therapeutic entities. In Oligonucleotide Synthesis: Methods and Applications, laboratory experts describe in step-by-step detail the powerful new techniques they have developed for oligonucleotide synthesis and for the use of modified oligonucleotides in biotechnology. Among the protocol highlights are the synthesis of phosphorothioates via new sulfur transfer agents, the synthesis of LNA, peptide conjugation methods to improve cellular delivery and cell-specific targeting, triple helix formation, and a novel two-step process that yields a high purity DNA that is less costly. Novel applications include the use of molecular beacons to monitor the PCR amplification process, nuclease footprinting to study the sequence-selective binding of small molecules to DNA, nucleic acid libraries, optimization of RNA synthesis for siRNA applications, and the use of small interference RNA (siRNA) as an inhibitor of gene expression. The protocols follow the successful Methods in Molecular Biology(TM) series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and highly practical, Oligonucleotide Synthesis: Methods and Applications offers today's investigators not only insight into important new biotechnologies, but also a full range of the detailed protocols needed to work successfully in DNA synthesis and its applications today.
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Table of contents

Synthesis of DNA Using a New Two-Step Cycle
Douglas J. Dellinger, Jason R. Betley, Tadeusz K. Wyrzykiewicz, and Marvin H. Caruthers

RNA Synthesis Using 2'-O-(Tert-Butyldimethylsilyl) Protection
Brian S. Sproat

RNA Oligonucleotide Synthesis Via 5'-Silyl-2'-Orthoester Chemistry
Stephanie A. Hartsel, David E. Kitchen, Stephen A. Scaringe, and William S. Marshall

Dimethylthiarum Disulfide: New Sulfur Transfer Reagent in Phosphorothioates Oligonucleotide Synthesis
Zhiwei Wang, Quanlai Song, and Yogesh S. Sanghvi

Assay for Evaluating Ribonuclease H-Mediated Degradation of RNA-Antisense Oligonucleotide Duplexes
Annie Galarneau, Kyung-Lyum Min, Maria M. Mangos, and Masad J. Damha

Di- and Oligonucleotide Synthesis Using H-Phosphonate Chemistry
Jacek Stawinski and Roger Stromberg

Solid-Phase Synthesis of Circular Oligonucleotides
Enrique Pedroso, Nuria Escaja, Miriam Frieden, and Anna Grandas

Locked Nucleic Acid Synthesis
Henrik M. Pfundheller, Anders M. Sorensen, Christian Lomholt, Anders M. Johansen, Troels Koch, and Jesper Wengel

Synthesis of DNA Mimics Representing HypNA-pPNA Hetero-oligomers
Vladimir A. Efimov and Oksana G. Chakhmakhcheva

Base-Modified Oligonucleotides With Increased Duplex Stability: Pyrazolo[3,4-d]pyrimidines Replacing Purines
Frank Seela, Yang He, Junlin He, Georg Becher, Rita Kroschel, Matthias Zulauf, and Peter Leonard

Introduction of Hypermodified Nucleotides in RNA
Darrell R. Davis and Ashok C. Bajji

Chemical Methods for Peptide-Oligonucleotide Conjugate Synthesis
Dmitry A. Stetsenko and Michael J. Gait

Biotin-Labeled Oligonucleotides With Extraordinarily Long Tethering Arms
A. Michael Morocho, Valeri Karamyshev, Olga Shcherbinina, and Nikolai Polushin

Universal Labeling Chemistry for Nucleic Acid Detection on DNA Chips
Ali Laayoun,Eloy Bernal-Mendez, Isabelle Sothier, Mitsuharu Kotera, and Alain Troesch

Postsynthetic Functionalization of Triple Helix-Forming Oligonucleotides
Alexandre S. Boutorine, and Jian-Sheng Sun

Fluorescence-Based On-Line Detection as an Analytical Tool in RNA Electrophoresis
Ute Scheffer and Michael Gobel

Design and Optimization of Molecular Beacon Real-Time Polymerase Chain Reaction Assays
Jacqueline A. M. Vet and Salvatore A. E. Marras

High-Throughput Production of Optimized Primers (Fimers) for Whole-Genome Direct Sequencing
Nikolai Polushin, Andrei Malykh, A. Michael Morocho, Alexei Slesarev, and Sergei Kozyavkin

Nonenzymatic Template-Directed RNA Synthesis
Marcus Hey and Michael Gobel

DNAse I Footprinting of Small Molecule Binding Sites on DNA
Christian Bailly, Jerome Kluza, Christopher Martin, Thomas Ellis, and Michael J. Waring

Gene Targeting Using Peptide Nucleic Acid
Peter E. Nielsen

Nucleic Acid Library Construction Using Synthetic DNA Constructs
Hani S. Zaher and Peter J. Unrau

In Vitro Selection From Combinatorial Nucleic Acid Libraries
Andres Jaschke

In Vitro Selection Procedures for Identifying DNA and RNA Aptamers Targeted to Nucleic Acids and Proteins
Eric Dausse, Christian Cazenave, Bernard Rayner, and Jean-Jacques Toulme

Short Double-Stranded Ribonucleic Acid as Inhibitor of Gene Expression by the Interference Mechanism
Jean-Remi Bertrand, Andrei Maksimenko, and Claude Malvy

Index
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