Phosphoramidite
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Nucleoside phosphoramidites are used to synthesise short nucleic acid chains. The chemical process allows several modifications, such as linker arms or using alternative nucleotides, such as LNA or morpholino or 2' group modified (OMe, NH2, F) or abasic, non-canon bases (xanthine, hypoxanthine, tricyclic bases, etc) or bases with a fluorescent group, linker arm to attach a fluorescent group (aminoallyl) or biotin attached and so forth. There are a variety of alternative chemical methods to do so, in fact Pubmed list nearly a thousand articles that modify this method [1]. The prices depend on the company and the quantity required and are around 0.17$-0.30$ a base for DNA, while higher prices for RNA 3.50-4.50$/base (technology is not that efficient) and other variants (IDT [2], invitrogen [3]). The name nucleoside phosphoramidite comes from the phosphite group that has an NH2 instead of an OH group. The "phosphate" group in normal nucleic acids is pentavalent, while here it is trivalent. The structure of amidophosphoric acid is present in pubchem [4]. The efficiency of the chemical synthesis is about 98% per base (see capping step). This is ideal for short oligos, but when 100 or more bases are made the method is not that good and enzymatic ligation is used.
- Further information: oligonucleotide synthesis
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[edit] References
Verma S, Eckstein F.1998 Modified oligonucleotides: synthesis and strategy for users. Annu Rev Biochem.67:99-134.
Brown T, Brown DJS. 1991. In Oligonucleotides and Analogues. A Practical Approach, ed. F Eckstein, pp. 1– 24. Oxford: IRL
