IR and UV spectroscopic signatures of DNA higher-order structures in the gas phase

Introduction
Electrospray mass spectrometry (ESI-MS) can be used to transfer large biomolecular complexes from the solution to the gas phase. However, a longstanding question is whether the gas-phase multiply-charged ions produced by ESI-MS keep a folded conformation in the absence of solvent. Nucleic acid secondary structures are determined by hydrogen bonding interactions between nucleic bases and by stacking interactions between neighboring base pairs. Here we will show that infrared (IR) and ultraviolet (UV) action spectroscopies provide useful and complementary information on the structure of nucleic acid ions in the gas phase.
Methods
IR spectroscopy experiments on DNA negative ions were carried out at the CLIO free electron laser (FEL) center (Orsay, France) using an Esquire 3000 (Bruker) mass spectrometer modified to inject the IR beam through the ring electrode. IRMPD spectra are recorded by monitoring the fragmentation of mass-selected parent ions as a function of the excitation wavenumber, in the range 1000-2000 cm-1. UV spectroscopy experiments were carried out using a tunable OPO laser (Continuum Lasers) with frequency doubling. The laser is interfaced with either a Finnigan LCQ ESI-QIT mass spectrometer or a Bruker Apex-Qe 9.4 T ESI-FTICR mass spectrometer. The UV action spectra were recorded by monitoring electron detachment as a function of the wavelength between 220 and 300 nm.
Preliminary results
First, DNA oligonucleotide ions forming G-quadruplex structures were studied in the gas phase using IR multiple-photon dissociation spectroscopy. Data interpretation on these large biomolecule ions is made using carefully chosen control experiments. The IR spectrum of the (dTG4T)4 quadruplex has been recorded, and compared to that of the single strand. Given the strand stoichiometry and the selective incorporation of three ammonium cations, there is little doubt about the quadruplex structure of [(dTG4T)4•(NH4+)3]5-. The major finding is a fingerprint of hydrogen bonding in the gas phase in the guanine C6=O6 stretching mode, that allows probing the conservation of G-quartets in the gas phase. Further experiments also demonstrate the conservation of G-quadruplex hydrogen bonds in the human telomeric sequence d(TTAGGG)4 [Gabelica et al., JACS, accepted]. Second, we also studied DNA duplexes and G-quadruplex ions in the gas phase by UV spectroscopy. We recorded the UV spectra of the (dTG4T)4 quadruplex, with and without ammonium ions. Molecular modeling [Rueda et al., JACS, 2006, p3608] and ion mobility spectrometry data [Gabelica et al., JACS, 2007, 895] showed that G-quadruplexes keep their hydrogen-bonded structure but become more floppy if inner cations are removed. We found that the UV spectra differ dramatically with and without inner cations, suggesting that UV spectroscopy is very sensitive to stacking interactions between neighboring G-quartets. We also used UV spectroscopy to probe the structure of 12-mer DNA duplexes, by comparing the duplex spectra to those obtained on single strands. Preliminary results show that stacking interactions may be preserved in duplexes containing GC base pairs, but not in duplexes containing AT base pairs. Altogether, these results show the complementarities between IR and UV spectroscopy to characterize DNA structures in the gas phase: IR data mainly give access to information on hydrogen bonding of bases, and UV spectroscopy provides information on stacking interactions.