After cleavage of solid phase, deprotection of synthesized oligonucleotide is necessary to be carried out under mild conditions. In general, since amino group is protected by acyl group and cyano ethyl group is protecting group for hydroxy group of phosphoric acid, deprotections of them are carried out under basic conditions. And DMTr (dimethoxytrityl) is employed as a protecting group for 5'-OH of nucleotide so that acidic conditions are necessary for deprotecting process. Additionally, on the case of RNA synthesis, t-butyldimethylsilyl (TBDMS) group is used for hydroxy at 2'-position as protection. Deprotection for it is carried out using TBAF (tetrabutylammonium fluoride).

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