Comparison between solution-phase stability and gas-phase kinetic stability of oligodeoxynucleotide duplexes

The relative kinetic stabilities of different 16-mer oligonucleotide duplex es were investigated by source collision-induced dissociation (CID) in a he ated capillary electrospray ion source. They were compared with the relativ e stabilities in solution obtained by thermal denaturation monitored by UV spectrophotometry. The results clearly show that both hydrogen bonding and base stacking interactions that are present in solution are maintained in t he gas phase. This suggests that the electrospray process preserves the dou ble-helix structure of DNA. A step by step opening of the double helix stru cture is proposed for the gas-phase dissociation, competing with the covale nt bond cleavage of bases. We also draw attention to the fact that by sourc e CID, it is the kinetic stability of the complexes that is probed. In part icular, this implies that only complexes of the same size can be compared. Copyright (C) 2001 John Wiley & Sons, Ltd.