Fast atom bombardment combined with tandem mass spectrometry for the study of dinucleotides

Cerny, Ronald L.; Gross, Michael L.; Grotjahn, Lutz

doi:10.1016/0003-2697(86)90276-9

Cited by 91 publications

(36 citation statements)

References 18 publications

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“…Various mass spectrometric methods have been used to characterize metal ion biomolecular interaction at the molecular level, to determine the site of metal ion attachment to the biomolecular and its effect on altering the properties and reactivities of the biomolecule [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17]. ESI-MS was shown to be an excellent means for characterizing of oligonucleotides [18,19], and provide unambiguous identification of singly and multiplycharged ions of deprotonated, protonated, and metalated oligonucleotides.…”

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confidence: 99%

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confidence: 99%

“…The dissociation reactions of protonated molecular ions from 12 possible hetero-deoxyribonucleotides were previously studied using fast atom bombardment with tandem mass spectrometry [5,6]. It was proposed that dissociation reactions of positive ions are influenced by a tertiary structure in which the phosphate oxygens, stabilized by interactions with the 3Ј-terminus base.…”

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confidence: 99%

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Cleavage reactions of the complex ions derived from self-complementary deoxydinucleotides and alkali-metal ions using positive ion electrospray ionization with tandem mass spectrometry

Xiang

Abliz

Takayama

2004

J. Am. Soc. Mass Spectrom.

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The dissociation reactions of the adduct ions derived from the four self-complementary deoxydinucleotides, d(ApT), d(TpA), d(CpG), d(GpC), and alkali-metal ions were studied in detail by positive ion electrospray ionization multiple-stage mass spectrometry (ESI-MS n ). For the [M ϩ H] ϩ ions of the four deoxydinucleotides, elimination of 5Ј-terminus base or loss of both of 5Ј-terminus base and a deoxyribose were the major dissociation pathway. The ESI-MS n spectra showed that Li ϩ , Na ϩ , and Cs ϩ bind to deoxydinucleotides mainly by substituting the H ϩ of phosphate group, and these alkali-metal ions preferred to bind to pyrimidine bases rather than purine bases. For a given deoxydinucleotide, the dissociation pathway of T he interaction between organic compounds or biologically active molecules and alkali-metal cations in the gas phase has attracted much attention. Such interactions may relate to chemical and biological processes occurring in solution; for example, ion salvation, catalysis, transport through membranes, affinity of active compounds toward receptors, and antibiotic activity [1]. The alkali metal ions, especially Na ϩ and K ϩ , are of particular importance in the mechanism of action of some biomolecules. Alkali-metal ion affinities are a good basis for analysis and modeling of such interactions in complex systems. The affinities of alkali-metal ions with nucleobases have been investigated by both the kinetic method and threshold collision-induced dissociation mass spectrometry [2,3]. On the basis of the research work on the formation of gas-phase ion-molecule complexes, Fujii [4] concluded that the alkali-metal ion affinity generally followed the order of Li ϩ Ͼ Na ϩ Ͼ K ϩ .Various mass spectrometric methods have been used to characterize metal ion biomolecular interaction at the molecular level, to determine the site of metal ion attachment to the biomolecular and its effect on altering the properties and reactivities of the biomolecule [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17]. ESI-MS was shown to be an excellent means for characterizing of oligonucleotides [18,19], and provide unambiguous identification of singly and multiplycharged ions of deprotonated, protonated, and metalated oligonucleotides.Knowledge of the fundamental modes of metal ion binding to simple DNA and RNA compounds will greatly improve our understanding of how metal ions interact with nucleic acids of more complexity. Deoxydinucleotides are the smallest subunits in nucleic acids bearing sequence information of DNA.The dissociation reactions of protonated molecular ions from 12 possible hetero-deoxyribonucleotides were previously studied using fast atom bombardment with tandem mass spectrometry [5,6]. It was proposed

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confidence: 99%

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confidence: 99%

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Cleavage reactions of the complex ions derived from self-complementary deoxydinucleotides and alkali-metal ions using positive ion electrospray ionization with tandem mass spectrometry

Xiang

Abliz

Takayama

2004

J. Am. Soc. Mass Spectrom.

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“…For route (a) it has been proposed [30] that the loss of a base side group, in the present case (C Ϫ H) Ϫ , is assisted by the attack of a phosphate group on the deoxyribose ring. This can occur in two ways, either by a nucleophilic attack on the carbon atom that is bonded to the ring nitrogen (N1), in which case the (C Ϫ H) Ϫ fragment is expelled directly via an S N 2 mechanism, or Table 1.…”

Section: Resultsmentioning

confidence: 96%

Structures, fragmentation, and protonation of trideoxynucleotide CCC mono- and dianions

Anichina

Feil

Uggerud

et al. 2008

J. Am. Soc. Mass Spectrom.

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“…Clearly, the trend in the dissociation E a s measured in the present work does not parallel the trend in PAs of either the nucleobases or the nucleosides, indicating that, if the base is protonated prior to cleavage of the glycosidic bond, additional factors influence the dissociation energetics. An alternative mechanism envisions the loss of the base initially in its deprotonated form (X Ϫ ), via a 1,2-elimination mechanism involving Habstraction at the C™2 of the deoxyribose by the neighbouring deprotonated phosphate group [4,8,10,23], followed by proton abstraction from the modified ODN. If the differences in the strengths of the Nglycosidic bond are similar to the differences in the nucleobase N™H bond energies [24], the energy barrier for the reaction should reflect differences in the ⌬H acid of the nucleobases.…”

Section: Dissociation Mechanism and The Influence Of Intramolecular Smentioning

confidence: 99%

Arrhenius activation parameters for the loss of neutral nucleobases from deprotonated oligonucleotide anions in the gas phase

Daneshfar

Klassen

2004

J. Am. Soc. Mass Spectrom.

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Arrhenius activation parameters (E a and A) for the loss of neutral nucleobase from a series of doubly deprotonated oligodexoynucleotide 10-mers of the type XT 9 , T 9 X, and T 5 XT 4 , where X ϭ A, C, and G, have been determined using the blackbody infrared radiative dissociation technique. At temperatures of 120 to 190°C, the anions dissociate exclusively by the loss of a neutral nucleobase (XH), followed by cleavage of the sugar 3Ј C™O bond leading to (a-XH) and w type ions or, in the case of the T 9 X 2Ϫ ions, the loss of H 2 O. The dissociation kinetics and energetics are sensitive to the nature and position of X. Over the temperature range investigated, the kinetics for the loss of AH and GH were similar, but ϳ100 times faster than for the loss of CH. For the loss of AH and GH, the values of E a are sensitive to the position of the base. The order of the E a s for the loss of XH from the 5Ј and 3Ј termini is: C Ͼ G Ͼ A; while for T 5 XT 4 the order is: C Ͼ A Ͼ G. The trends in the values of E a do not parallel the trend in deprotonation enthalpies or proton affinities of the nucleobases in the gas phase, indicating that the energetic differences do not simply reflect differences in their gas phase acidity or basicity. The pre-exponential factors (A) vary from 10 10 to 10 15 s Ϫ1 , depending on the nature and position of X. These results suggest that the reactivity of individual nucleobases is influenced by stabilizing intramolecular interactions. M ass spectrometry (MS), combined with soft ionization techniques such as electrospray (ES) and matrix assisted laser desorption/ ionization (MALDI), has become an indispensable tool for identifying the primary structure (sequence) of biopolymers: peptides, oligosaccharides, and oligonucleotides. The mass spectrometry-based sequencing approach typically involves isolating the biopolymer ion of interest in the gas phase, dissociating it to produce sequence specific fragment ions and accurately determining the mass of the ions. Sequence information is extracted from the mass differences of the sequential fragment ions of the same general structure. The MSbased sequencing approach has many attractive features, most notably its inherent speed and sensitivity and its ability to sequence biopolymers containing unnatural or unusual modifications. Despite its widespread use in the sequencing of biopolymers, fundamental questions regarding the gas phase dissociation mechanisms remain. Elucidating these mechanisms is of practical importance, since it will facilitate the rational development of MS-based techniques for sequencing. In addition, the dissociation of biomolecules in the gas phase reflects their intrinsic properties, which are of fundamental interest.For oligodeoxynucleotides (ODNs), sequence information can be obtained from the fragmentation behaviour of either the protonated or deprotonated gaseous ions and the dissociation behaviour of both forms has been extensively investigated [1][2][3][4][5][6][7][8][9][10]. The dissociation of deprotonated ODNs, the focus ...

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Fast atom bombardment combined with tandem mass spectrometry for the study of dinucleotides

Cited by 91 publications

References 18 publications

Cleavage reactions of the complex ions derived from self-complementary deoxydinucleotides and alkali-metal ions using positive ion electrospray ionization with tandem mass spectrometry

Cleavage reactions of the complex ions derived from self-complementary deoxydinucleotides and alkali-metal ions using positive ion electrospray ionization with tandem mass spectrometry

Structures, fragmentation, and protonation of trideoxynucleotide CCC mono- and dianions

Arrhenius activation parameters for the loss of neutral nucleobases from deprotonated oligonucleotide anions in the gas phase

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