Hydration of DNA base cations in the gas phase

Kim, Nam Joon; Kim, Yung Sam; Jeong, Gawoon; Ahn, Tae Kyu; Kim, Seong Keun

doi:10.1016/s1387-3806(02)00547-x

Cited by 37 publications

(39 citation statements)

References 19 publications

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“…) n with n up to 10 and 6, respectively [10]. The insert in Figure 2 compares the signals for thymine + and protonated thymine (TH + ) recorded in dry and hydrated expansion conditions (before and after opening the valve to the heated water reservoir, respectively).…”

Section: Mpi Of Nanohydrated Thyminementioning

confidence: 99%

“…a e-mail: s.p.eden@open.ac.uk means of UV irradiation [9,10]. Here we investigate the stabilities of nanohydrated thymine radical cations based on metastable dissociation measurements and ab initio calculations.…”

Section: Introductionmentioning

confidence: 99%

“…In addition to proton, hydrogen and hydride transfers that have been observed [12,13] or predicted [14] in DNA building blocks, diverse fragmentation and evaporation processes can occur. While the decrease in ionization energy of thymine with nanohydration has been experimentally and theoretically studied by several groups [15,16], scarce reports can be found on the structure and decay processes of thymine-water cluster ions [10]. This paper investigates the metastable evaporation of one water molecule from UV multiphoton ionized thymine-water clusters by mass spectrometry.…”

Section: Introductionmentioning

confidence: 99%

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Stabilities of nanohydrated thymine radical cations: insights from multiphoton ionization experiments and ab initio calculations

et al. 2017

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Abstract. Multi-photon ionization experiments have been carried out on thymine-water clusters in the gas phase. Metastable H2O loss from T + (H2O)n was observed at n ≥ 3 only. Ab initio quantum-chemical calculations of a large range of optimized T + (H2O)n conformers have been performed up to n = 4, enabling binding energies of water to be derived. These decrease smoothly with n, consistent with the general trend of increasing metastable H2O loss in the experimental data. The lowest-energy conformers of T + (H2O)3 and T + (H2O)4 feature intermolecular bonding via charge-dipole interactions, in contrast with the purely hydrogen-bonded neutrals. We found no evidence for a closed hydration shell at n = 4, also contrasting with studies of neutral clusters.

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Section: Mpi Of Nanohydrated Thyminementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Stabilities of nanohydrated thymine radical cations: insights from multiphoton ionization experiments and ab initio calculations

et al. 2017

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“…The effect of hydration of the DNA bases is very local and only a limited number of water molecules contribute to it significantly [1,2]. Many studies on the gas-phase interactions of neutral and anionic forms of nucleic acid bases [3][4][5][6][7][8][9][10][11][12][13] [19] of hydrated adenine and thymine cations. Much less attention has been paid to the hydration of protonated DNA components, although these forms are of considerable interest in view of their potential formation in radiation-induced damage of DNA and RNA, and interaction with a water environment.…”

mentioning

confidence: 99%

“…Many studies on the gas-phase interactions of neutral and anionic forms of nucleic acid bases [3][4][5][6][7][8][9][10][11][12][13] and nucleosides [14] with water molecules have been performed theoretically. A few experimental studies have been carried out on hydration enthalpies [15], IR spectra [13], UV spectra [16], hydration dynamics [17] of DNA bases, ionization potentials [18], and metastable decay [19] of hydrated adenine and thymine cations. Much less attention has been paid to the hydration of protonated DNA components, although these forms are of considerable interest in view of their potential formation in radiation-induced damage of DNA and RNA, and interaction with a water environment.…”

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confidence: 99%

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Wincel

2009

J. Am. Soc. Mass Spectrom.

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Thermochemical data, ⌬H o n , ⌬S o n , and ⌬G o n , for the hydration of protonated nucleic acid bases and protonated nucleosides have been experimentally studied by equilibrium measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion-beam reaction chamber. For protonated nucleobases the hydration enthalpies were found to be similar for all studied systems and varied between 12.4 -13.1 kcal/mol for the first and 11.2-11.5 kcal/mol for the second water molecule. While for protonated nucleosides the water binding enthalpies (11.7-13.3 kcal/mol) are very close to those for protonated nucleobases, the entropy values are "more negative." The structural and energetic aspects of hydrated ions are discussed in conjunction with the available theoretical data. (J Am Soc Mass Spectrom 2009, 20, 1900 -1905) © 2009 American Society for Mass Spectrometry N ucleic acid bases are amongst the primary building blocks of DNA and RNA, and water is generally considered to be their integral part. Hydration of nucleobases is crucially important for the structure, stability, and biologic functions of DNA [1,2]. Interaction between the DNA constituents and water molecules is important for a better understanding of the mechanistic role of water molecules in conformational transitions and mechanisms of DNA's bioactivity. The effect of hydration of the DNA bases is very local and only a limited number of water molecules contribute to it significantly [1,2]. Many studies on the gas-phase interactions of neutral and anionic forms of nucleic acid bases [3][4][5][6][7][8][9][10][11][12][13] [19] of hydrated adenine and thymine cations. Much less attention has been paid to the hydration of protonated DNA components, although these forms are of considerable interest in view of their potential formation in radiation-induced damage of DNA and RNA, and interaction with a water environment. To our best knowledge, the stabilities of protonated adenine tautomers and their complexes with water molecules [20] have only been investigated computationally, while there have been some experimental and theoretical studies on the hydration of protonated and deprotonated forms of the four mononucleotides (dAMP, dCMP, dGMP, and dTMP) [21]. More recently, the possible tautomeric forms of the monohydrated protonated uracil have been examined in the gas phase by using IR multiple-photon dissociation spectroscopy (IR-MPD) in combination with computational study [22].In this paper, we present the first experimental results on the energetics of hydration of protonated nucleic acid bases, NABs (uracil, Ura; thymine, Thy; adenine, Ade; and hypoxanthine, Hyp), and protonated nucleosides, NSDs (uridine, Urd; thymidine, Thd; adenosine, Ado; and inosine, Ino). These results were obtained from high-pressure mass spectrometry equilibria measurements in the gas phase. Previously, we measured the energetics of hydration of protonated and deprotonated amino acids [23][24][25]. ExperimentalAll experiments were performed on a high-pressure (HP...

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Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase

et al. 2015

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Collisions between O(3+) ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum-chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non-negligible amount of the radical cation monomer is observed. New fragment-ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization.

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Hydration of DNA base cations in the gas phase

Cited by 37 publications

References 19 publications

Stabilities of nanohydrated thymine radical cations: insights from multiphoton ionization experiments and ab initio calculations

Stabilities of nanohydrated thymine radical cations: insights from multiphoton ionization experiments and ab initio calculations

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase

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