Electrospray mass spectrometry of phosphoramidites, a group of acid-labilecompounds

In contemporary solid-phase synthesis of oligonucleotides, phosphoramidites containing O-beta-cyanoethyl and N,N-diisopropyl groups are the most wides pread monomer units. The N,N-diisopropyl phosphoramidite group can be activ ated by mild acidic treatment and then it easily reacts with nucleophiles ( alcohols, water, etc.) to furnish the required phosphodiester Linkage effic iently and cleanly. Owing to these properties, these compounds cannot be in vestigated using classical electrospray ionization, Their mass spectometric analysis is further hampered by the fact that they are often transiently p rotected with acid-sensitive groups (4,4'-dimethoxytrityl, 3-monomethoxytri tyl or trityl), which give intense signals in the spectra, Nanoelectrospray measurements from non-aqueous solvents (e.g. acetonitrile, methanol, tetra hydrofuran) were carried out in order to eliminate the nucleophilic water, Different types of alkali metal salts were used to form adduct ions. Among these salts, lithium chloride was found to be the most suitable for the ana lysis of amidites, Fairly abundant [M + Li](+) and [M + Cl](-) ions are for med in the positive and negative ion mode, respectively. These ions represe nt the base peaks in most cases whereas the intensities of the peaks corres ponding to the protecting group are reduced by similar to 20%. This method is a powerful tool for the mass spectrometric identification of phosphorami dites, Copyright (C) 1999 John Wiley & Sons, Ltd.