Oligonucleotide synthesis purification

This group, used for 5 -phosphate protection, has hydrophobicity similar to that of the dimethoxytrityl group and thus was expected to assist in reverse-phase HPLC purification of product from failure sequences in oligonucleotide synthesis. The group is cleaved with Bu4N F in DMSO at 70°. ... 

Warren, W. and Vella, G., Analysis and purification of synthetic oligonucleotides by high-performance liquid chromatography, in Oligonucleotide Synthesis Protocols, Agrawal, S., Ed., Humana Press, Totowa, NJ, 1993, 235. 

Nucleotides and nucleic acids are critical tools in the areas of gene expression, therapeutics, and diagnostics. However, there are certain challenges associated with their large-scale purification and subsequent characterization. While solid-state oligonucleotide synthesis is relatively simple and can be totally automated, intra- and intermolecular associations may occur involving shorter sequences that may hybridize with the desired full length... 

Solutions of that type are improbable. In exchange for a simplification mixture of the formose reaction, we must specify the presence of glycolaldehyde, glyceraldehyde, and borate minerals (and the absence of many potentially interfering substances, such as cyanide) and a route by which the protective borate will be removed so that the route to oligonucleotide formation remains open. Ribose is only one of the six components present in RNA. An extended number of steps involving the synthesis, purification, transportation, and highly specific... 

To probe for one-dimensional diffusion, we synthesized DNA/RNA chimeric oligonucleotides. Special precautions were taken to avoid ribonuclease contamination during synthesis, purification, and use of these chimeras. For example, all water was treated with diethylpyrocarbonate before exposure to the chimeras. Ribonucleotide 2 -hydroxyl groups were deprotected with 1 M tetrabutyl ammonium fluoride in dimethyl formamide (Aldrich Chemical Milwaukee, WI). Purified oligonucleotides were labeled on the 5 end with [y-32p]ATP (duPont Wilmington, DE) by T4 kinase (Promega Madison, WI), and desalted with a Nick gel filtration column (Pharmacia Uppsala, Sweden). 

Startg. N-protected nucleoside treated with 40% NH3 at 50° for 4 h deoxycytidine. Y 100%. The highly lipophilic, stable protective group survives the rigours of oligonucleotide synthesis. It is also an improvement on phthaloyl in that it serves as a purification handle, solubilizing otherwise insoluble oligonucleotides. F.e.s. A. Dik-shit et al.. Can. J. Chem. 66, 2989-94 (1988). 

Agrawal S, ladorola PL, Temsamani J et al (1996) Effect of G-rich sequences on the synthesis, purification, hybridization, cell uptake, and hemolytic activity of oligonucleotides. Bioorg Med Chem Lett 6 2219-2214... 

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