The relative kinetic stabilities of different 16-mer oligonucleotide duplexes were investigated by source collision-induced dissociation (CID) in a heated capillary electrospray ion source. They were compared with the relative 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 the gas phase. This suggests that the electrospray process preserves the double-helix structure of DNA. A step by step opening of the double helix structure is proposed for the gas-phase dissociation, competing with the covalent bond cleavage of bases. We also draw attention to the fact that by source CID, it is the kinetic stability of the complexes that is probed. In particular, this implies that only complexes of the same size can be compared. Copyright © 2001 John Wiley & Sons, Ltd.