So, it is imperative to maintain high coupling efficiency throughout the synthesis. One of the main obstacles to this is the presence of moisture, which lowers coupling efficiency in two ways: Water reacts with the activated tetrazolide of the incoming monomer instead of the 5-hydroxyl of the support, thereby scavenging excess monomer and lowering the coupling efficiency. In the basic reaction cycle, a solid support, derivatized with the initial protected nucleoside, is contained in a reaction column. Reagents and solvents are pumped through the column to effect the addition of successive protected nucleotide monomers (phosphoramidites). Figure 1. Note: this article focuses exclusively on DNA synthesis (while similar, there are differences with the chemical synthesis of RNA). Figure 1. Summary of solid-phase oligonucleotide synthesis cycle. In step 1, Detritylation, the 5'-DMT protecting group is removed from the first, solid-support-linked nucleoside. (1994). Protocols for Oligonucleotide Conjugates, 26. Beaucage, S. L. and Caruthers, M. H. (1981). Tetrahedron Lett., 22, 1859. Eckstein, F. (1991). Oligonucleotides and Analogies. Letsinger, R. L. finnan, J. L., Heavner, G. After cleavage/deprotection, the resulting crude mixture contains the tritylaeted product oligonucleotide, the truncated failure sequences with free 5-hydroxyl ends, by-products of deprotection (benzamide, isobutyramide, acrylonitrile, and acetamide and silicates from hydrolysis of the glass support.
DNA Synthesis Beta-Cyanoethyl Phosphoramidite Chemistry The synthesis of DNA from Я-cyanoethyl phosphoramidite monomers is currently the industry standard. With this method, high coupling efficiencies are easily attained. The absence of side reactions also confers high biological activity of the synthetic oligonucleotide.
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