N3 Protonation Induces Base Rotation of 2′-Deoxyadenosine-5′-monophosphate and Adenosine-5′-monophosphate

Abstract

Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments combined with theoretical calculations are performed to investigate the stable gas-phase conformations of the protonated adenine mononucleotides, [pdAdo+H](+) and [pAdo+H](+). Conformations that are present in the experiments are elucidated via comparative analyses of the experimental IRMPD spectra and the B3LYP/6-311+G(d,p) IR spectra predicted for the conformers optimized at this level of theory. N3 protonation is preferred as it induces base rotation, which allows a strong hydrogen bond to be formed between the excess proton of adenine and the phosphate moiety. In contrast, both N1 and N7 protonation are predicted to be >35 kJ/mol less favorable than N3 protonation. Only N3 protonated conformers are present in the experiments in measurable abundance. Both the low-energy conformers computed and the experimental IRMPD spectra of [pdAdo+H](+) and [pAdo+H](+) indicate that the 2'-hydroxyl moiety does not significantly impact the structure of the most stable conformer or the IRMPD spectral profile of [pAdo+H](+) vs that of [pdAdo+H](+). However, the 2'-hydroxyl leads to a 3-fold enhancement in the IRMPD yield of [pAdo+H](+) in the fingerprint region. Comparison of present results to those reported in a previous IRMPD study of the analogous protonated adenine nucleosides allows the effects of the phosphate moiety on the gas-phase conformations to be elucidated.

The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry

“…The effect of adenosine residues on the yield of c and y fragments from CAD of gaseous RNA (M+nH) n+ ions observed here, and the lack of it when A is replaced by c 3 A or c 1,3 A but not c 1 A or c 7 A (Figures 3 and 4), implies adenine protonation at N3, in agreement with data from hydrogen/deuterium exchange (51) and a combined experimental and theoretical study of adenosine-5′-monophosphoric acid (M+H) + ions (52). The increased proton affinity of N3 over that of N1 and N7 in adenosine-5′-monophosphoric acid (M+H) + ions results from stabilization (by >35 kJ/mol) of a syn , C2′-endo conformation in which the protonated N3 forms an ionic hydrogen bond with a nonbridging oxygen of the uncharged monophosphoester moiety (N3H + ···O = P motif) (52). This is the very same motif that we hold responsible for facilitating nucleophilic attack of the 2′-OH group on the phosphorus in the course of phosphodiester backbone bond cleavage by CAD of (M+nH) n+ ions of RNA (Scheme 2), although we cannot exclude the possibility of ionic hydrogen bonding to a bridging instead of a non-bridging oxygen of the uncharged phosphodiester moiety.…”

Undervalued N3 Coordination Revealed in the Cisplatin Complex with 2′-Deoxyadenosine-5′-monophosphate by a Combined IRMPD and Theoretical Study

“…Interestingly, although it is commonly held that the N3 site of adenine is not favored for electrophilic attack on adenine 11 , there is ample recent evidence made by IRMPD action spectroscopy showing that the N3 position is in fact favored in the protonation and alkali metal cation attachment of both the free base and adenine 9 DNA and RNA nucleosides [59][60][61] and nucleotides. 39 Also UVPD 62 and IRMPD 63 spectroscopy of alkali metal cation-adenine complexes and their hydrated forms confirm that N3 binding is preferred in a bidentate fashion with the N9 position on the tautomer A7 and support the view that N3 attack has likely been unduly undervalued.…”

Mechanisms and energetics for N-glycosidic bond cleavage of protonated adenine nucleosides: N3 protonation induces base rotation and enhances N-glycosidic bond stability

“…This differs from that found for the protonated cytosine and guanine nucleosides, where N-glycosidic bond cleavage occurs via two different TSs, TS 1 and TS n (where TS n lies lower in energy than TS 1 ). 34,47,75 Our previous IRMPD study of [dAdo+H] + and [Ado+H] + determined that both N3 and N1 protonated conformers may coexist in the gas phase. This explains the very similar apparent thresholds observed for the two primary CID channels of [Ado+H] + .…”

“…34,[43][44][45][46][47][48] In particular, the IRMPD study of [dAdo+H] + and [Ado+H] + found that the presence of the sugar moieties alters the preferred site of protonation to N3 from that of the isolated adenine nucleobase, N1. Recently, we examined the gas-phase conformations and energetics of a series of protonated DNA and RNA nucleosides and nucleotides using IRMPD action spectroscopy and electronic structure calculations.…”