Location of the Negative Charge(s) on the Backbone of Single-Stranded Deoxyribonucleic Acid in the Gas Phase

Multiply-deprotonated, single-strand products of mono and heteronucleotides, prepared in a nanospray external source coupled to an ion trap mass spectrometer, were studied under low-energy collision conditions. Fragmentations enabled the negative charge carried by the selected anions to be located. Comparison of multi-deprotonated 5′-dephosphorylated and 5′-phosphorylated nucleotides showed that the former led to competitive BH and B − losses via isomerization into ion–dipole complexes prior to dissociation, which contrasts with the 5′-phosphorylated nucleoside yielding the competitive HPO 3 and nucleobase eliminations. The proposed mechanisms are discussed according to: (i) the charge state of the precursor studied and (ii) the thermochemical gas-phase properties such as the relative acidities of neutrals, which formally constitute the ion–dipole. The formation of various fragment ions from doubly- and triply-deprotonated precursor ions enabled the negative charge to be located, specifically at the terminal phosphodiester groups of the single-strand oligonucleotides. The potential energy is, therefore, minimal for distant charged phosphorylated groups. These findings suggest that a specific conformation is favored in order to minimize coulomb repulsion during the desolvation process. This hypothesis is consistent with the assumed behavior of triply- and quadruply-deprotonated, mono-cationized oligonucleotides, which involves a specific location of the sodium cation, as previously shown.