Zwitterionic i-motif structures are preserved in DNA negatively charged ions produced by electrospray mass spectrometry

Abstract

DNA cytosine-rich strands can fold into an intercalated motif (i-motif) structure. The i-motif is formed by mutually intercalated duplexes containing proton-mediated C–H⁺–C (cytosine–proton–cytosine) base pairs. Negatively charged ions of DNA i-motifs produced by electrospray mass spectrometry are therefore zwitterionic if the base pairing motif is preserved in the gas phase. Here we used IRMPD spectroscopy and ion mobility spectrometry to assess whether i-motif structures were preserved in the gas phase. We first investigated the IRMPD spectral signature of the tetramer [dC₆]₄, which can only be formed via C–H⁺–C base pairing, compared to the single strand dC₆. The IR signature of i-motif formation is an apparent broadening of the band at 1650 cm⁻¹. DFT calculations show this apparent broadening is actually due to blue-shifts of the NH₂ scissoring modes and red shifts of CO stretching modes. We then investigated the gas-phase conformations of the telomeric sequence d(CCCAAT)₃CCC, that can form an intramolecular i-motif, by performing IRMPD spectroscopy and ion mobility spectrometry as a function of the charge state. We show that the negative ions of the lowest charge states correspond to a preserved i-motif structure. This is the first demonstration of the native extraction of solution-phase zwitterionic nucleic acids using negative electrospray ionization.