Infrared Multiple Photon Dissociation Action Spectroscopy of Deprotonated RNA Mononucleotides: Gas-Phase Conformations and Energetics

Citations Over TimeTop 16% of 2013 papers

Abstract

The IRMPD action spectra of the deprotonated forms of the four common RNA mononucleotides, adenosine-5′-monophosphate (A5′p), guanosine-5′-monophosphate (G5′p), cytidine-5′-monophosphate (C5′p), and uridine-5′-monophosphate (U5′p), are measured to probe their gas-phase structures. The IRMPD action spectra of all four deprotonated RNA mononucleotides exhibit distinct IR signatures in the frequency region investigated, 570–1900 cm–1, that allows these deprotonated mononucleotides to be easily differentiated from one other. Comparison of the measured IRMPD action spectra to the linear IR spectra calculated at the B3LYP/6-31+G(d,p) level of theory finds that the most stable conformations of the deprotonated forms of A5′p, C5′p, and U5′p are accessed in the experiments, and these conformers adopt the C3′ endo conformation of the ribose moiety and the anti conformation of the nucleobase. In the case of deprotonated G5′p, the most stable conformer is also accessed in the experiments. However, the ground-state conformer differs from the other three deprotonated RNA mononucleotides in that it adopts the syn rather than anti conformation for the nucleobase. Present results are compared to results previously obtained for the deprotonated forms of the four common DNA mononucleotides to examine the fundamental conformational differences between these species, and thus elucidate the effects of the 2′-hydroxyl group on their structure, stability, and fragmentation behavior.

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