A comprehensive evaluation of the kinetic method applied in the determination of the proton affinity of the nucleic acid molecules

Donna, Leonardo Di; Napoli, Anna; Sindona, Giovanni; Athanassopoulos, Constantinos M.

doi:10.1016/j.jasms.2004.04.027

Cited by 27 publications

(20 citation statements)

References 26 publications

(36 reference statements)

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“…The extensive fragmentation of the A 8 strand should be related to nucleobase thermo‐chemical data. Previous work has shown that adenosine nucleotides are less acidic than thymidine64 ones but adenosine is characterised by a higher gas‐phase basicity,70, 71 making adenine a good leaving group. The influence of DNA sequence on the covalent bond fragmentation from duplexes has been reported and explained by the contribution of weak base stacking 27.…”

Section: Resultsmentioning

confidence: 99%

“…However, such a hypothesis cannot be assumed here. Nevertheless, the relative values of gas‐phase basicity of nucleobase70, 71 relative to that of the amino acid66 should influence the zwitterionic forms of deprotonated complexes. With the assumption of zwitterionic form, we hypothesise a competition for proton addition and then a competition for ZW location between the basic adenine base and R or K side chain.…”

Section: Resultsmentioning

confidence: 99%

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Charge state effect on the zwitterion influence on stability of non‐covalent interaction of single‐stranded DNA with peptides

2007

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Negative ion ESI mass spectrometry was used to study the gas-phase stability and dissociation pathways of peptide-DNA complexes. We show that bradykinin and three modified peptides containing the basic residue arginine or lysine form stable interactions with single-stranded oligonucleotides. ESI-MS/MS of complexes of T(8) with PPGFSPFRR resulted in a major dissociation pathway through cleavage of the peptide covalent bond. The stability of the complex is due to electrostatic interaction between the negatively charged phosphate group and the basic side chain of the arginine and lysine residues as demonstrated by Vertes et al. and Woods et al. In fact, the present work establishes the role played by zwitterions on complex stabilisation. The presence of protons in nucleobase and/or amino acid contributes in reinforcing the strength of the salt bridge (SB) interaction. The zwitterionic form of the most basic of amino acid residues, arginine, is assumed to form a strong SB interaction to the negatively charged phosphate groups of DNA. This non-covalent complex is stable enough to withstand disruption of the non-covalent interaction and to first break the covalent bond. Moreover, the dependence of fragmentation patterns upon the complex charge state is explained by the fact that the net number of negative charges modulates the number of zwitterionic sites, which stabilise the complexes. Finally, the weak influence of the nucleobase is assumed by the existence of competition for proton addition between the nucleobase and the R/K side chain leading to a decrease in the stabilisation of the SB interaction.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Charge state effect on the zwitterion influence on stability of non‐covalent interaction of single‐stranded DNA with peptides

2007

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“…To date, mass spectral studies have been focused towards analysis and structural characterization of deoxyribonucleosides [2][3][4][5][6][7][8][9][10]. While thermochemical properties of individual nucleobases have been well studied experimentally in the gas phase, the studies on nucleosides are limited [11][12][13][14][15][16].Xia et al[11] performed extensive calculations on proton affinities (PAs) of nucleosides by the density functional approach. The PA of the four deoxyribonucleosides, i.e., 2=-deoxyadenosine (dA), 2=-deoxyguanosine (dG), 2=-deoxycytidine (dC), and 2=-deoxythymidine (dT) were reported to be in the order of dG Ͼ dC Ͼ dA Ͼ dT, and this order is similar to the PA order of the free bases (G Ͼ C Ͼ A Ͼ T).…”

mentioning

confidence: 99%

“…They concluded the protonation features of deoxyribonucleosides were less changed compared with the corresponding free bases. Donna et al [12] determined the PA of dA and demonstrated the effective use of the kinetic method for the thermochemical measurement of multifunctional molecules like nucleosides and nucleobases. Besides the wide array of proton affinity studies on deoxyribonucleosides [13][14][15][16], there have been no experimental or theoretical reports on the gas-phase acidities (⌬H acid ) of deoxyribonucleosides.…”

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confidence: 99%

Estimation of gas-phase acidities of deoxyribonucleosides: An experimental and theoretical study

Kumari

Devi

Prabhakar

et al. 2010

J. Am. Soc. Mass Spectrom.

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We determined the gas-phase acidities (⌬H acid ) of four deoxyribonucleosides, i.e., 2=-deoxyadenosine (dA), 2=-deoxyguanosine (dG), 2=-deoxycytidine (dC), and 2=-deoxythymidine (dT) by applying the extended kinetic method. The negatively charged proton-bound hetero-dimeric anions, [A Ϫ H Ϫ B]Ϫ of the deoxyribonucleosides (A) and reference compounds (B) were generated under electrospray ionization conditions. Collision-induced dissociation spectra ofϪ were recorded at four different collision energies using a triple quadrupole mass spectrometer. The abundance ratios of the individual monomeric product ions were used to determine the ⌬H acid of the deoxyribonucleosides. The obtained ⌬H acid value follows the order dA Ͼ dC Ͼ dT Ͼ dG. The ⌬G acid (298 K) values were determined by using ⌬G acid ϭ ⌬H acid -T⌬S acid where the ⌬H acid and ⌬S acid values were determined directly from the kinetic method plots. The ⌬H acid values were also predicted for the deoxyribonucleosides at the B3LYP/6-311ϩG**//B3LYP/6-311G** level of theory. The acidity trend obtained from the computational investigation shows good agreement with that obtained experimentally by the extended kinetic method. Theoretical calculations provided the most preferred deprotonation site as C5=-OH from sugar moiety in case of dA, and as ϪNH 2 (dC and dG) or ϪNH- . The determination of thermochemical properties of these molecules in the gas phase could be of importance for biological reasons because biological environment can be relatively nonpolar in nature. Moreover, the gasphase studies explore the reactivity of molecules and ions without solvent effects. To date, mass spectral studies have been focused towards analysis and structural characterization of deoxyribonucleosides [2][3][4][5][6][7][8][9][10]. While thermochemical properties of individual nucleobases have been well studied experimentally in the gas phase, the studies on nucleosides are limited [11][12][13][14][15][16].Xia et al.[11] performed extensive calculations on proton affinities (PAs) of nucleosides by the density functional approach. The PA of the four deoxyribonucleosides, i.e., 2=-deoxyadenosine (dA), 2=-deoxyguanosine (dG), 2=-deoxycytidine (dC), and 2=-deoxythymidine (dT) were reported to be in the order of dG Ͼ dC Ͼ dA Ͼ dT, and this order is similar to the PA order of the free bases (G Ͼ C Ͼ A Ͼ T). They concluded the protonation features of deoxyribonucleosides were less changed compared with the corresponding free bases. Donna et al. [12] determined the PA of dA and demonstrated the effective use of the kinetic method for the thermochemical measurement of multifunctional molecules like nucleosides and nucleobases. Besides the wide array of proton affinity studies on deoxyribonucleosides [13][14][15][16], there have been no experimental or theoretical reports on the gas-phase acidities (⌬H acid ) of deoxyribonucleosides. In this study, we report the first determination of ⌬H acid of dA, dG, dC, and dT through application of the extended kinetic method. We have also calculated the ...

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“…The kinetic method developed by Cooks et al 9. has been successfully applied to a wide range of systems for the determination of various thermochemical properties such as gas‐phase basicity and proton affinity,10–15 gas‐phase acidity (GA),2–8 metal ion affinity,16–19 electron affinity,20–22 ionization energy,23, 24 etc. The determination of the GA of an unknown compound by the kinetic method starts with the formation of proton‐bound dimeric anions, [A − H + B − ], where A − and B − (Eqn.…”

Section: The Kinetic Methodsmentioning

confidence: 99%

Estimation of gas‐phase acidities of a series of dicarboxylic acids by the kinetic method

Kumar¹,

Prabhakar²,

Nagaveni³

et al. 2005

Rapid Comm Mass Spectrometry

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The gas-phase acidities (GA) of a series of dicarboxylic acids were estimated by applying the extended kinetic method. Proton-bound heterodimeric anions [A] of a series of dicarboxylic acids (A) and reference compounds (B) were generated under electrospray ionization conditions, and the dissociation of these cluster ions was examined using a triple-quadrupole mass spectrometer. The mass-selected proton-bound heterodimeric anions were fragmented to yield individual monomer anions as the only product ions, and the abundance ratios of these anions were used to estimate the GA values of the dicarboxylic acids. The experiment was performed over a range of collision energies in order to more accurately determine GA values and to estimate the differences in the entropy of deprotonation of the dicarboxylic acids and the reference compounds. The trends in GA values obtained for the dicarboxylic acids could imply cyclization of the structures via intramolecular hydrogen bonding. The lower homologues show higher GA values than the higher homologues. À ions (X ¼ Cl, Br, I), we concluded that the gas-phase acidities (GAs) of the series of dicarboxylic acids studied lie between those of HI and HCl. However, the absolute GA values of dicarboxylic acids are not reported in the literature. Much of the recent research is focused on the determination of proton affinities of different compounds. In contrast, very limited data 2-8 are available on the estimation of GA values, and this is mainly due to the lack of a suitable reference scale and also problems encountered in the generation of proton-bound dimeric anions in the gas phase. In this work we have undertaken the estimation of the GA values of these compounds using negative ion ESI together with the kinetic method. We have also attempted to correlate the effect of chain length with the GA value of dicarboxylic acids. It is hoped that this study will be a useful addition to the gas-phase acidity scale.

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A comprehensive evaluation of the kinetic method applied in the determination of the proton affinity of the nucleic acid molecules

Cited by 27 publications

References 26 publications

Charge state effect on the zwitterion influence on stability of non‐covalent interaction of single‐stranded DNA with peptides

Charge state effect on the zwitterion influence on stability of non‐covalent interaction of single‐stranded DNA with peptides

Estimation of gas-phase acidities of deoxyribonucleosides: An experimental and theoretical study

Estimation of gas‐phase acidities of a series of dicarboxylic acids by the kinetic method

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