Secondary ion mass spectrometry: the scope and limitations in structural analysis of oligoribonucleotides

Applicability of secondary ion mass spectrometry (SIMS) for structural analysis of oligoribonucleotides was studied. For this purpose a number of oligoribonucleotides having various base sequences, chain lengths, and internucleotide linkages were prepared, and their positive ion SIMS spectra were recorded without derivatization. The soft ionization produced ions possessing relatively low internal energies which underwent little fragmentation, so that both pseudo-molecular and sequence (fragment) ions were observed, the former being more abundant than the latter. Nevertheless, sufficient information can be obtained to elucidate the structure of oligoribonucleotides. Thus SIMS can be used as a useful method for structural analysis of a wide variety of oligoribonucleotides.