Li+, Na+, and K+ Binding to the DNA and RNA Nucleobases. Bond Energies and Attachment Sites from the Dissociation of Metal Ion-Bound Heterodimers

Cerda, Blas A.; Wesdemiotis, Chrys

doi:10.1021/ja9613421

Cited by 313 publications

(353 citation statements)

References 45 publications

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“…44 In this method, branching ratios are measured at different effective temperatures using bases that are structurally similar. The reference bases used in this study are not structurally similar.…”

Section: Reaction Entropymentioning

confidence: 99%

Binding Energies of Protonated Betaine Complexes: A Probe of Zwitterion Structure in the Gas Phase

1998

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The dissociation kinetics of proton-bound dimers of betaine with molecules of comparable gas-phase basicity were investigated using blackbody infrared radiative dissociation (BIRD). Threshold dissociation energies were obtained from these data using master equation modeling. For bases that have comparable or higher gas-phase basicity, the binding energy of the protonated base·betaine complex is ~1.4 eV. For molecules that are ~2 kcal/mol or more less basic, the dissociation energy of the complexes is ~1.2 eV. The higher binding energy of the former is attributed to an ion-zwitterion structure which has a much larger ion-dipole interaction. The lower binding energy for molecules that are ~2 kcal/mol or more less basic indicates that an ion-molecule structure is more favored. Semiempirical calculations at both the AM1 and PM3 levels indicate the most stable ion-molecule structure is one in which the base interacts with the charged quaternary ammonium end of betaine. These results indicate that the measurement of binding energies of neutral molecules to biological ions could provide a useful probe for the presence of zwitterions and salt bridges in the gas phase. From the BIRD data, the gas-phase basicity of betaine obtained from the kinetic method is found to be 239.2 ± 1.0 kcal/mol. This value is in excellent agreement with the value of 239.3 kcal/mol (298 K) from ab initio calculations at the MP2/6-31+g** level. The measured value is slightly higher than those reported previously. This difference is attributed to entropy effects. The lower ion internal energy and longer time frame of BIRD experiments should provide values closer to those at standard temperature.

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Section: Reaction Entropymentioning

confidence: 99%

Binding Energies of Protonated Betaine Complexes: A Probe of Zwitterion Structure in the Gas Phase

1998

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“…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.…”

mentioning

confidence: 99%

“…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 .…”

mentioning

confidence: 99%

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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“…These methods typically evaluate enthalpies of ion-molecule reactions or unimolecular dissociations of ionic adducts to derive gasphase thermodynamic properties such as bond energies and ion affinities. In some cases, the nature of the ion-molecule interaction could be further elucidated by determining the difference in the entropy changes for competing decomposition pathways [16,17]. To date, the vast majority of ion-molecule interaction studies performed by mass spectrometry focus on positive ion studies of cationic adduct species, especially protonated molecules [14] and alkali metal adducts [18 -21].…”

mentioning

confidence: 99%

Evaluation of the role of multiple hydrogen bonding in offering stability to negative ion adducts in electrospray mass spectrometry

Cai

Concha

Murray

et al. 2002

J. Am. Soc. Mass Spectrom.

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An experimental approach, electrospray mass spectrometry (ES-MS), and a theoretical approach employing computer modeling, have been used to characterize the interaction between small inorganic anions and neutral analyte molecules that form anionic adduct species in negative mode ES mass spectrometry. Certain anionic adducts of small saccharides (e.g., ␣-D-glucose, sucrose) have shown exceptional stability in ES mass spectra even when internal energies are raised at high "cone" voltages. Computer modeling studies reveal that multiple hydrogen bonding strengthens the interaction between these neutral molecules and the attaching anion. The equilibrium structures and stabilization energies of these anionic adducts have been evaluated by semi-empirical, ab initio, and density functional theory (DFT) methods. Chloride anion is found to be capable of forming "bridging" hydrogen bonds between monosaccharide rings of polysaccharides resulting in the stabilization of chloride adducts, thus reducing the tendency for the glycosidic bond to decompose. Moreover, the tendency for various hydroxyl hydrogens on saccharide molecules to dissociate in the form of HA ( [5][6][7][8], have been used to generate anionic adducts for ES-MS studies. The formation and decomposition of chloride adducts have been further investigated from a thermodynamic standpoint [9 -12]. However, the conditions that favor the formation and survival of anionic adducts have not been extensively defined and are not fully understood. Moreover, the interactions between neutral analyte molecules and the attaching small inorganic anions have not been fully characterized.Various mass spectrometry methods have been applied to probe the interactions between ions and neutral analyte molecules [13][14][15]. These methods typically evaluate enthalpies of ion-molecule reactions or unimolecular dissociations of ionic adducts to derive gasphase thermodynamic properties such as bond energies and ion affinities. In some cases, the nature of the ion-molecule interaction could be further elucidated by determining the difference in the entropy changes for competing decomposition pathways [16,17]. To date, the vast majority of ion-molecule interaction studies performed by mass spectrometry focus on positive ion studies of cationic adduct species, especially protonated molecules [14] and alkali metal adducts [18 -21]. Dication adduct species, such as alkaline earth metal [22] and transition metal [23] adducts of oligosaccharides have also been explored. Small inorganic anions attaching to neutral analyte molecules, on the other hand, have received far less research attention. However, a few studies employing anion attachment in negative ion ES-MS have appeared, such as reports on iodide attachment to acetone [24], chloride attachment to saccharides [1, 10 -12], and cyanide attachment (including covalent) to fullerenes [6,8]. In order to gain insight into the exact nature of the interactions between neutral analyte molecules and attaching small inorganic anions that are responsi...

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Li⁺, Na⁺, and K⁺ Binding to the DNA and RNA Nucleobases. Bond Energies and Attachment Sites from the Dissociation of Metal Ion-Bound Heterodimers

Cited by 313 publications

References 45 publications

Binding Energies of Protonated Betaine Complexes: A Probe of Zwitterion Structure in the Gas Phase

Binding Energies of Protonated Betaine Complexes: A Probe of Zwitterion Structure in the Gas Phase

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

Evaluation of the role of multiple hydrogen bonding in offering stability to negative ion adducts in electrospray mass spectrometry

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