Journal
BIOPOLYMERS
Volume 91, Issue 4, Pages 256-264Publisher
WILEY
DOI: 10.1002/bip.21134
Keywords
nucleic acid structure; hydrogen exchange; mass spectrometry
Categories
Funding
- Petroleum Research Fund
- Thermo Electron (American Society for Mass Spectrometry)
- NSF [CHE-05-47699]
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Nucleic acid higher order structure is of intense interest in antisense and antigene strategies toward novel chemotherapeutic agents. Understanding how structural characteristics affect solution-phase properties is essential for a rational approach to nucleic acid-targeted drug design. The most dominant nucleic acid secondary structure is the hairpin, formed by intrastrand hydrogen bonding between complementary nucleobases. We have previously applied gas-phase hydrogen/deuterium exchange (HDX) with mass spectrometry detection to show that anionic DNA duplexes have lower HDX rates than their constituent monomers, indicating that hydrogen bonding can shield hydrogens from exchanging with the bath gas D2S. The same HDX assay is applied here to investigate nucleic acid hairpin structure. Variations in hairpin solution-phase stabilities are achieved by changing their loop size, stem length, and stem composition (ratio of G/C and A/T(U) base pairs in the stern). These differences can be carried into the gas phase because electrospray ionization is a gentle ionization method that is able to Preserve noncovalent interactions. Observed gas-phase HDX rates of these hairpins are consistent with their relative solution-phase stabilities as predicted by MFold, i.e., less stable nucleic acid hairpins exchange faster than more stable hairpins. To our knowledge, the presented experiments demonstrate for the first time that gas-phase HDX may be used to characterize nucleic acid higher order structure and the results suggest that the relative stabilities Of nucleic acid hairpins in the gaseous phase are correlated with those in solution. (C) 2009 Wiley Periodicals, Inc. Biopolymers 91: 256-264,2009.
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