Activation energies for dissociation of double strand oligonucleotide anions: Evidence for Watson-Crick base pairing in vacuo

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)(2)(3-), (CCGG)(2)(3-), (AATTAAT)(2)(3-), (CCGGCCG)(2)(3-), A(7). T-7(3-), A(7). A(7)(3-), T-7. T-7(3-), and A(7). C-7(3-) were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 10(13) to 10(19) s(-1). Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a - base) and w ions. Four pieces of evidence are presented which indicate that Watson-Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A(7). T-7(3-), to the single strands is significantly higher than that for the related noncomplementary A(7). A(7)(3-) and T-7. T-7(3-) dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A(7). A(7)(3-) and A(7). C-7(3-) but not for A(7). T-7(3-) consistent with this process being shut down by WC hydrogen bonding, nl. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (-Delta H-d) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A(7). T-7(3-) duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent.