Location of the Na+ cation in negative ions of DNA evidenced by using MS2 experiments in ion trap mass spectrometry

Favre, Amélie; Gonnet, Florence; Tabet, Jean‐Claude

doi:10.1016/s1387-3806(99)00049-4

Cited by 21 publications

(22 citation statements)

References 24 publications

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“…The approximate location of the Ba ϩ2 ion should correspond to the portion of the original sequence common to both these fragments (i.e., the pTpTp motif), as illustrated in Scheme 2. The fact that the metal resides near the middle of the sequence is consistent with results reported for series of sodium-adducted ODNs [24].…”

Section: Fragmentation Of Low Charge State Precursorssupporting

confidence: 89%

“…These fragments include the M-B species (Figure 2b inset) as well as a number of metallated w and a-B ions, which are marked with asterisks to distinguish them from non-metallated w and a-B species. The combined array of both metallated and non-metallated sequence ions indicates that the Ba ϩ2 complex produced the same overall sequence coverage as the free ODN (Figure 2a), which is consistent with previous dissociation studies conducted with ODN/ metal complexes [23,24]. In addition, the distribution of charge among the sequence ions suggests that one negative charge was localized near each end of the sequence, as described above for the free ODN.…”

Section: Fragmentation Of Low Charge State Precursorssupporting

confidence: 88%

“…Several previous studies have focused on the interactions of the anticancer therapeutic cisplatin or its derivatives with DNA [16 -22]. Relatively few studies have addressed binary interactions of nucleic acids and metal cations [23][24][25][26][27]. Most of these studies have focused primarily on complexes with the smaller alkali and alkaline earth metals (e.g., Na ϩ , Mg ϩ2 ), although a few complexes with transition metals [25,26] or f-block elements [23,25] have also been investigated.…”

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confidence: 99%

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Charge state-dependent fragmentation of oligonucleotide/metal complexes

Keller

Brodbelt

2005

J. Am. Soc. Mass Spectrom.

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Collision-activated dissociation (CAD) has been employed to assess the gas-phase fragmentation behavior of a series of 1:1 oligodeoxynucleotide (ODN):metal complexes over a range of charge states, using several ten-residue ODNs and a wide array of alkali, alkaline earth, and transition metals. For parent species in low to intermediate charge states, complexation with Ca ϩ2 , Sr ϩ2 , or Ba ϩ2 altered the relative intensity of M-B species, promoting loss of cytosine over loss of guanine. The relative intensities of sequence ions were largely unaffected. This behavior was most prevalent for isomeric sequences with complementary residues at the 5=-and 3=-termini, suggesting that metal complexation may change the gas-phase conformation and/or conformational dynamics for some sequences. In higher charge states, some ODN/ Ba ϩ2 complexes produced abundant fragment ions corresponding to metallated a n Ϫm species, which are not commonly observed in CAD mass spectra for deprotonated ODNs. The formation of these ions was most favored for complexes between Ba ϩ2 and ODN sequences with a thymine residue at Position 6. Literature precedent exists for the formation of a n Ϫm ions from sequences in which covalent modification generates one or more neutral sites along the phosphate backbone. ODN/metal adducts in high charge states possess only a few acidic protons, and the juxtaposition of these neutral phosphate groups near thymine residues and the bound Ba ϩ2 ion may direct formation of the metallated a n Ϫm species. and function of DNA and RNA. Mono-and divalent cations are thought to induce bending in DNA duplexes [1,2], and are also known to stabilize triplex [3,4], and quadruplex [5,6] structures. Metal cations are also required for the proper folding and function of many forms of RNA, including most ribozymes [7,8]. The interactions of DNA with several natural products [9] and synthetic drugs and drug candidates [10,11] are known to be metal-mediated.Mass spectrometry (MS) is well-established as a useful tool for the structural characterization and sequencing of nucleic acids [12][13][14], and has also been employed to characterize a number of nucleic acid/metal ion interactions [15]. Several previous studies have focused on the interactions of the anticancer therapeutic cisplatin or its derivatives with DNA [16 -22]. Relatively few studies have addressed binary interactions of nucleic acids and metal cations [23][24][25][26][27]. Most of these studies have focused primarily on complexes with the smaller alkali and alkaline earth metals (e.g., Na ϩ , Mg ϩ2 ), although a few complexes with transition metals [25,26] or f-block elements [23,25] have also been investigated. The fragmentation behavior of these complexes has been characterized using parent species in relatively low charge states (often Ϫ2), but intermediate and high charge state precursors have not been studied. A more complete characterization of the entire charge state envelope produced by electrospray ionization would not only enhance our theoretical underst...

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Section: Fragmentation Of Low Charge State Precursorssupporting

confidence: 89%

Section: Fragmentation Of Low Charge State Precursorssupporting

confidence: 88%

mentioning

confidence: 99%

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Charge state-dependent fragmentation of oligonucleotide/metal complexes

Keller

Brodbelt

2005

J. Am. Soc. Mass Spectrom.

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“…ESI-MS has been used for studies of noncovalent oligonucleotide complexes, including detection of complex structures of oligonucleotides in the gas phase, such as DNA hairpins, duplexes, triplexes, and quadruplexes [12][13][14][15][16][17]. Besides extensive studies of interactions between various DNA and drugs and proteins, the interactions of metals with nucleobases and oligonucleotides have been investigated [17][18][19][20][21]. Since 2002, noncovalent triplex DNA complexes have been studied by mass spectrometry, although all of them focused on the pyrimidine motif [13][14][15].…”

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confidence: 99%

“…To the best of our knowledge, this is the first investigation on the interactions between the purine motif and bivalent-cation metals using ESI-MS. ESI-MS can obtain binding stoichiometries for small amounts of analytes to DNA. Furthermore, specificity, binding affinity, and binding site of metal cation can be determined by ESI-MS and tandem mass spectrometry [18,20,21].…”

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confidence: 99%

Evaluation of effects of bivalent cations on the formation of purine-rich triple-helix DNA by ESI-FT-MS

Wan

Cui

Song

et al. 2009

J. Am. Soc. Mass Spectrom.

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The GGA triplet repeats are widely dispersed throughout eukaryotic genomes. (GGA)n or (GGT)n oligonucleotides can interact with double-stranded DNA containing (GGA:CCT)n to form triple-stranded DNA. The effects of 8 divalent metal ions (3 alkaline-earth metals and 5 transition metals) on formation of these purine-rich triple-helix DNA were investigated by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-MS). In the absence of metal ions, no triplex but single-strand, duplex, and purine homodimer ions were observed in mass spectra. The triple-helix DNA complexes were observed only in the presence of certain divalent ions. The effects of different divalent cations on the formation of purine-rich triplexes were compared. Transition-metal ions, especially Co 2ϩ and Ni 2ϩ , significantly boost the formation of triple-helix DNA, whereas alkaline-earth metal ions have no positive effects on triplex formation. In addition, Ba 2ϩ is notably beneficial to the formation of homodimer instead of triplex. (J Am Soc Mass

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Generation of gas‐phase sodiated arenes such as [(Na₃(C₆H₄)⁺] from benzene dicarboxylate salts

Attygalle

Chan

Axe³

et al. 2009

J. Mass Spectrom.

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Upon collision-induced activation, gaseous sodium adducts generated by electrospray ionization of disodium salts of 1,2- 1,3-, and 1,4-benzene dicarboxylic acids (m/z 233) undergo an unprecedented expulsion of CO(2) by a rearrangement process to produce an ion of m/z 189 in which all three sodium atoms are retained. When isolated in a collision cell of a tandem-in-space mass spectrometer, and subjected to collision-induced dissociation (CID), only the m/z 189 ions derived from the meta and para isomers underwent a further CO(2) loss to produce a peak at m/z 145 for a sodiated arene of formula (Na(3)C(6)H(4))(+). This previously unreported m/z 145 ion, which is useful to differentiate meta and para benzene dicarboxylates from their ortho isomer, is in fact the sodium adduct of phenelenedisodium. Moreover, the m/z 189 ion from all three isomers readily expelled a sodium radical to produce a peak at m/z 166 for a radical cation [(*C(6)H(4)CO(2)Na(2))(+)], which then eliminated CO(2) to produce a peak at m/z 122 for the distonic cation (*C(6)H(4)Na(2))(+).

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Location of the Na+ cation in negative ions of DNA evidenced by using MS2 experiments in ion trap mass spectrometry

Cited by 21 publications

References 24 publications

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Evaluation of effects of bivalent cations on the formation of purine-rich triple-helix DNA by ESI-FT-MS

Generation of gas‐phase sodiated arenes such as [(Na₃(C₆H₄)⁺] from benzene dicarboxylate salts

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Location of the Na+ cation in negative ions of DNA evidenced by using MS2 experiments in ion trap mass spectrometry

Cited by 21 publications

References 24 publications

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Evaluation of effects of bivalent cations on the formation of purine-rich triple-helix DNA by ESI-FT-MS

Generation of gas‐phase sodiated arenes such as [(Na3(C6H4)+] from benzene dicarboxylate salts

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Generation of gas‐phase sodiated arenes such as [(Na₃(C₆H₄)⁺] from benzene dicarboxylate salts