Stability of complementary and mismatched DNA duplexes: Comparison and contrast in gas versus solution phases

Abstract

We report herein a mass spectrometric study of a complete set of 9-mer DNA duplexes (5′-GGTTXTTGG-3′/3′-CCAAYAACC-5′, X/Y = G, C, A or T) with and without single internal mismatches. This work represents a first step toward establishing whether mass spectrometry can be used as a tool for examining both solution and gas phase stabilities of DNA duplexes, leading to an understanding of the intrinsic behavior of DNA. First, we have found that the relative ion abundances of the mismatched and matched electrosprayed duplexes correlate to solution phase behavior. That is, duplexes that are more stable in solution have higher relative ion abundances in the gas phase. This is consistent with previous MS results on complementary duplexes, and is advantageous in that relative solution stabilities can be thus obtained much more quickly than by using traditional melting temperature methods. Second, the gas phase stabilities of all the XY duplexes have been characterized, using collision-induced dissociation (CID) as a method to assess stability. Of the 16 XY duplexes we studied, four duplexes (GG, AC, TC and CC) exhibit enhanced gas phase stabilities, two (TA and AT) are unstable in the gas phase relative to in solution, and the remaining 10 (GC, CG, GT, AG, TG, TT, GA, CT, AA and CA) show a linear correlation between the gas and solution phase stabilities. This direct comparison between the gas phase and solution phase stabilities allows us insight into how solvation and the ESI process may affect DNA stability. The effects of base stacking and hydrogen bonding in the gas phase versus in solution are discussed. Our data indicate that in the gas phase, as in solution, duplex stability reflects both hydrogen bonding and base stacking interactions. However, unlike in solution, hydrogen bonding forces dominate in the gas phase.