Mark D. Matteucci

Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method.

Publisher Summary This chapter discusses the chemical synthesis of deoxy oligonucleotides by the phosphoramidite method. It discusses the synthesis methodology; detailed protocols for preparing the silica support, the phosphoramidite, and deoxy oligonucleotides; and the purification of synthetic deoxyribo nucleic acid (DNA). The phosphite triester approach to DNA synthesis using deoxynucleoside phosphoramidite as synthons has become the method of choice for the preparation of deoxy oligonucleotides. The general synthetic strategy involves adding mononucleotides sequentially to a deoxynucleoside, attached covalently to a silica-based insoluble polymeric support. Reagents, starting materials, and side products are then removed simply by filtration. At the conclusion of the synthesis, the deoxy oligonucleotide is chemically freed of blocking groups, hydrolyzed from the support, and purified to homogeneity by either polyacrylamide gel electrophoresis (PAGE) or high-performance liquid chromatography (HPLC). These preformed synthons are especially attractive for preparing DNA on automatic or semiautomatic DNA synthesizers, or for those who plan to manually synthesize a large number of deoxy oligonucleotides.