Direct Evidence for Tautomerization of the Uracil Moiety within the Pb²⁺/Uridine-5′-monophosphate Complex: A Combined Tandem Mass Spectrometry and IRMPD study

Abstract

The structure of the [Pb(UMP)-H](+) (UMP = uridine-5'-monophosphate) complex was studied in the gas phase by combining electrospray ionization (ESI), tandem mass spectrometry, and mid-infrared multiple photon dissociation (IRMPD) spectroscopy. The results obtained show that Pb(2+) ions interact not only with the deprotonated phosphate group but also with a carbonyl group of the nucleobase moiety by folding of the mononucleotide, resulting in macrochelates that are not likely to be present in solution. Comparison between the IRMPD and DFT-computed spectra suggests that the ESI-generated complex likely corresponds to a mixture of several structures, and establishes the enolic tautomers as the most abundant species for the [Pb(UMP)-H](+) ion, while the very weak IRMPD signal observed at ∼1763 cm(-1) points to a minor population of oxo forms. Our data also suggest that losing the nucleobase residue under CID conditions does not necessarily mean a lack of interaction between the metal and the nucleobase moiety, as commonly reported in the literature for large oligonucleotides.

Structure of protonated thymidine characterized by infrared multiple photon dissociation and quantum calculations

“…During the last decade, InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy has been established as a powerful approach for probing the structure of gaseous ions . In this context, this technique has been notably widely applied to study the structure of either bare or metal‐cationized DNA building blocks . Many studies were motivated by the probable relationship between the presence of rare enol tautomers of nucleobases within nucleic acid building blocks and point mutation developing during nucleic acid replication .…”

Amino Acid Oxidation: A Combined Study of Cysteine Oxo Forms by IRMPD Spectroscopy and Simulations

“…The inherent bonding and conformational features of cysteine in its (de)protonated, nitrosated, and metal‐tagged forms have been previously interrogated both in the free amino acid and in the residue embodied in the glutathione peptide by a joint computational and experimental infrared multiple photon dissociation (IRMPD) assay. IRMPD spectroscopy, coupled with ESI tandem mass spectrometry (MS/MS), is a pivotal tool to provide direct structural clues about gaseous (bio)molecular ions, including (de)protonation site, metal‐binding patterns, and local intramolecular interactions in both native and modified amino acids and peptides, DNA/RNA bases and nucleotides, cluster ions, and fragmentation products …”

“…[18] Recently,avariety of mass spectrometric studies have been able to identify the reactive intermediates formed by (interfacial) ozonolysis of deprotonated cysteineatthe air-liquid interface, [5,19] to probe the stability and fragmentation behavior of intact and modified sulfinyl radical ions, [20,21] and elucidate the intrinsic mechanism involved in the formationo fc ysteine oxo forms [cysSO x ] À (x = 1, 2, 3) and sulfenate radicala nions in the gas phase. [22] The unambiguous and detailed characterization of the structurala nd dynamic behavior of theset ransient intermediates in isolated environments, in which external interferences are absent,w ill help to reveali ntrinsic properties rele-vant to their biological activity.T he inherentb onding and conformationalf eatureso fc ysteine in its (de)protonated, [23,24] nitrosated, [25] and metal-tagged [26] forms have been previously interrogated both in the free amino acid and in the residue embodied in the glutathione peptide [27] by aj oint computational and experimental infrared multiple photon dissociation (IRMPD) assay.I RMPD spectroscopy,c oupled with ESI tandem mass spectrometry (MS/MS), is ap ivotalt ool to provide direct structural clues about gaseous (bio)molecular ions, [28][29][30][31][32][33] including (de)protonations ite, metal-binding patterns,a nd local intramolecular interactions in both native and modified amino acids and peptides, [34][35][36][37][38][39][40][41][42] DNA/RNA bases and nucleotides, [43][44][45] cluster ions, [46] and fragmentation products. [47] We now examine the intrinsic chemical properties and geometric features of the conjugate bases of cysteine sulfenic, sulfinic, and sulfonica cids, [cysSO x ] À (x = 1, 2, 3), by meanso fE SI/ MS-IRMPD spectroscopy in the highly informativem id-IR spectral range (750-1900 cm À1 )i nc ombination with ab initio...…”

On the Ag+–cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory

“…The gas phase structures of the 1:1 complexes between alkali metal cations-Cytosine, 23 Na + -Halo-Uraciles, 24 Pb 2+ -Uridine 5´-monophosphate, 25 Pb 2+ -cytidine 5-monophosphate and Pb 2+ -deoxycytidine 5-monophosphate, 26 Cisplatin-Adenine/Guanine, 27 Pb 2+ -deprotonated 2deoxyguanosine 5'-monophsphate, 28 and metal-mediated Hoogsteen-type base pairs 29 The gas phase structures of the 1:1 complexes between alkali metal cations-Cytosine, 23 Na + -Halo-Uraciles, 24 Pb 2+ -Uridine 5´-monophosphate, 25 Pb 2+ -cytidine 5-monophosphate and Pb 2+ -deoxycytidine 5-monophosphate, 26 Cisplatin-Adenine/Guanine, 27 Pb 2+ -deprotonated 2deoxyguanosine 5'-monophsphate, 28 and metal-mediated Hoogsteen-type base pairs 29 …”