Sodium stabilization of dinucleotide multiplexes in the gas phase

Abstract

The aggregation and conformations of sodiated dinucleotides were studied in the gas phase. MALDI was used to generate [M − (n − 1)H + nNa]⁺ ions, yielding single-strand ions having n = 1–3, duplex ions with n = 1–7 and triplex ions with n = 3–10. Collision cross-sections of each sodiated complex were measured in helium using ion mobility based methods and compared to calculated cross-sections of theoretical structures generated by molecular mechanics/dynamics calculations. Three distinct single-strand conformers were observed: one with the nucleobases stacked, one with the planes oriented perpendicular to each other and one with the bases coplanar to each other. One conformer is observed for all of the duplexes except dTG·dTG, dGT·dGT and dTT·dTT (in which two conformers are observed depending on whether the guanine or thymine bases stack). For low values of n, the Na⁺ ions cluster around the two deprotonated phosphates. However, as n increases, the Na⁺ ions become more dispersed along the duplex. One conformer is also observed for all of the triplexes. For n = 3–6, three Na⁺ ions and the three phosphates form a quasi-planar ring with the additional Na⁺ ions resting above, below and in the middle of the ring. Cytosine and thymine also coordinate to the Na⁺ ions but adenine and guanine prefer to stack and do not coordinate to the Na⁺ ions in the ring. The addition of the seventh to tenth Na⁺ ions breaks the sodium-phosphate ring and the Na⁺ ions become scattered around the triplex. Differences between experimental and theoretical cross-sections (averaged over the lowest 5 kcal mol⁻¹ structures) of each sodiated complex fell between 1–2%.