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Tetrabutylammonium fluoride will remove phenyl, trichloroethyl and cyanoethyl groups from nucleotides. In addition to the desired nucleotide products other results including chain cleavage, phosphofluoridates and cyanoethylated thymidine units may be obtained depending on the conditions used. Fluoride ion has been used to successfully exchange phenyl and trichloroethyl groups for methyl, ethyl and butyl groups in nucleotide triesters. This represents a rapid high yield route to a variety of phosphate esters. The synthesis of a novel nucleotide analogue in which two chains are bridged through their phosphates is described.

Fluoride ion promoted deprotection and transesterification in nucleotide triesters