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Unexpected linear ion trap collision-induced dissociation and Fourier transform ion cyclotron resonance infrared multi-photon dissociation fragmentation of a hydrated C-glycoside of 5-fluorouridine formed by the action of the pseudouridine synthases RluA and TruB.

ABSTRACT: As part of the investigation of the pseudouridine synthases, 5-fluorouridine in RNA was employed as a mechanistic probe. The hydrated, rearranged product of 5-fluorouridine was isolated as part of a dinucleotide and found to undergo unusual fragmentation during mass spectrometry, with the facile loss of HNCO from the product pyrimidine ring favored over phosphodiester bond rupture. Although the loss of HNCO from uridine and pseudouridine is well established, the pericyclic process leading to their fragmentation cannot operate with the saturated pyrimidine ring in the product of 5-fluorouridine. Based on the MS(n) results and calculations reported here, a new mechanism relying on the peculiar disposition of the functional groups of the product pyrimidine ring is proposed to account for the unusually facile fragmentation.

SUBMITTER: Miracco EJ

PROVIDER: S-EPMC5728650 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature

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Unexpected linear ion trap collision-induced dissociation and Fourier transform ion cyclotron resonance infrared multi-photon dissociation fragmentation of a hydrated C-glycoside of 5-fluorouridine formed by the action of the pseudouridine synthases RluA and TruB.

Miracco Edward J EJ Bogdanov Bogdan B Mueller Eugene G EG

Rapid communications in mass spectrometry : RCM 20110901 18

As part of the investigation of the pseudouridine synthases, 5-fluorouridine in RNA was employed as a mechanistic probe. The hydrated, rearranged product of 5-fluorouridine was isolated as part of a dinucleotide and found to undergo unusual fragmentation during mass spectrometry, with the facile loss of HNCO from the product pyrimidine ring favored over phosphodiester bond rupture. Although the loss of HNCO from uridine and pseudouridine is well established, the pericyclic process leading to the ...[more]

PMID: 23657957

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Project description:Hydrated divalent magnesium and calcium clusters are used as nanocalorimeters to measure the internal energy deposited into size-selected clusters upon capture of a thermally generated electron. The infrared radiation emitted from the cell and vacuum chamber surfaces as well as from the heated cathode results in some activation of these clusters, but this activation is minimal. No measurable excitation due to inelastic collisions occurs with the low-energy electrons used under these conditions. Two different dissociation pathways are observed for the divalent clusters that capture an electron: loss of water molecules (Pathway I) and loss of an H atom and water molecules (Pathway II). For Ca(H(2)O)(n)(2+), Pathway I occurs exclusively for n >or= 30 whereas Pathway II occurs exclusively for n <or= 22 with a sharp transition in the branching ratio for these two processes that occurs for n approximately 24. The number of water molecules lost by both pathways increases with increasing cluster size reaching a broad maximum between n = 23 and 32, and then decreases for larger clusters. From the number of water molecules that are lost from the reduced cluster, the average and maximum possible internal energy is determined to be approximately 4.4 and 5.2 eV, respectively, for Ca(H(2)O)(30)(2+). This value is approximately the same as the calculated ionization energies of M(H(2)O)(n)(+), M = Mg and Ca, for large n indicating that the vast majority of the recombination energy is partitioned into internal modes of the ion and that the dissociation of these ions is statistical. For smaller clusters, estimates of the dissociation energies for the loss of H and of water molecules are obtained from theory. For Mg(H(2)O)(n)(2+), n = 4-6, the average internal energy deposition is estimated to be 4.2-4.6 eV. The maximum possible energy deposited into the n = 5 cluster is <7.1 eV, which is significantly less than the calculated recombination energy for this cluster. There does not appear to be a significant trend in the internal energy deposition with cluster size whereas the recombination energy is calculated to increase significantly for clusters with fewer than 10 water molecules. These, and other results, indicate that the dissociation of these smaller clusters is nonergodic.

Dataset Information

Unexpected linear ion trap collision-induced dissociation and Fourier transform ion cyclotron resonance infrared multi-photon dissociation fragmentation of a hydrated C-glycoside of 5-fluorouridine formed by the action of the pseudouridine synthases RluA and TruB.

Publications

Unexpected linear ion trap collision-induced dissociation and Fourier transform ion cyclotron resonance infrared multi-photon dissociation fragmentation of a hydrated C-glycoside of 5-fluorouridine formed by the action of the pseudouridine synthases RluA and TruB.

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