Observation of a small oligonucleotide duplex by electrospray ionization mass spectrometry

Electrospray ionization (ESI) has been demonstrated to be a "soft" ionization technique, allowing accurate molecular weight determination for biopolymers due to gas-phase multiple charging. Recent results have demonstrated that noncovalent associations can be preserved upon transfer into the gas phase with ESI, providing a new approach to the determination of both structurally-specific and nonspecific noncovalent associations in solution. The mass spectrometric experimental conditions necessary to preserve such noncovalent associations, and the physical constraints upon such, have yet to be elucidated, although it is clear that gentle interface conditions minimizing internal excitation of noncovalent complexes are helpful. Base-paired oligonucleotide hybridization constitutes one of the most important and thoroughly studied noncovalent associations of biopolymers. Our initial attempts to observe duplex oligonucleotides resulted in detection of only the monomeric constituents. Since then, we have developed interface conditions that are more gentle and yet still provide sufficient molecular ion desolvation to preserve such associations using new instrumentation with a greatly extended m/z range. In this communication, we report the successful ionization of duplex oligonucleotides and the conditions necessary for detection by negative ion ESI-MS.