IR and UV spectroscopy of DNA ions stored in a quadrupole ion trap mass spectrometer

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. In solution, infrared (IR) and ultraviolet (UV) spectroscopies provide information on hydrogen bonding and stacking interactions in nucleic acids, respectively. Here we will show how IR and UV spectra of gas-phase ions can be recorded, and what can be learned on the structure of nucleic acids (double helices and quadruple helices) in the gas phase.

The IR spectroscopy experiments on DNA negative ions were carried out at the CLIO free electron laser (FEL) center using an electrospray quadrupole ion trap mass spectrometer (Esquire 3000, Bruker Daltonics, Germany) modified to inject the IR beam in the trap through the ring electrode. IRMPD spectra are recorded by monitoring the relative fragmentation efficiency of mass-selected parent ions as a function of the excitation wavenumber, in the range 1000-2000 cm-1. Data interpretation on these large biomolecule ions is made using carefully chosen control experiments. 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. The experiments demonstrate the conservation of G-quadruplex hydrogen bonds in the human telomeric sequence d(TTAGGG)4.

The UV spectroscopy experiments were carried out using a tunable OPO laser (Continuum Lasers, Santa Clara, CA, USA) with frequency doubling. The laser is interfaced with a Finnigan LCQ ESI-QIT mass spectrometer. The UV action spectra were recorded by monitoring electron detachment from DNA multiply charged anions as a function of the wavelength between 220 and 300 nm. Preliminary results suggest that stacking interactions are preserved in duplexes containing GC base pairs, and in G-quadruplexes containing inner cations.