Fraying and electron autodetachment dynamics of trapped gas phase oligonucleotides

Danell, Allison S.; Parks, Joel H.

doi:10.1016/s1044-0305(03)00578-6

Cited by 45 publications

(51 citation statements)

References 32 publications

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“…Apart from the sequencing applications of EPD, numerous questions remain about the electron photodetachment mechanism, and how it compares with electron detachment dissociation [3][4][5] and thermal electron detachment [10,11]. We will briefly summarize our current understanding of the photodetachment mechanism [8].…”

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confidence: 99%

Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores

Gabelica

Rosu

Pauw

et al. 2007

J. Am. Soc. Mass Spectrom.

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Double stranded DNA multiply charged anions coupled to chromophores were subjected to UV-Vis photoactivation in a quadrupole ion trap mass spectrometer. The chromophores included noncovalently bound minor groove binders (activated in the near UV), noncovalently bound intercalators (activated with visible light), and covalently linked fluorophores and quenchers (activated at their maximum absorption wavelength). We found that the activation of only chromophores having long fluorescence lifetimes did result in efficient electron photodetachment from the DNA complexes. In the case of ethidium-dsDNA complex excited at 500 nm, photodetachment is a multiphoton process. The MS 3 fragmentation of radicals produced by photodetachment at ϭ 260 nm (DNA excitation) and by photodetachment at Ͼ 300 nm (chromophore excitation) were compared. The radicals keep no memory of the way they were produced. A weakly bound noncovalent ligand (m-amsacrine) allowed probing experimentally that a fraction of the electronic internal energy was converted into vibrational internal energy. This fragmentation channel was used to demonstrate that excitation of the quencher DABSYL resulted in internal conversion, unlike the fluorophore 6-FAM. Altogether, photodetachment of the DNA complexes upon chromophore excitation can be interpreted by the following mechanism: (1) ligands with sufficiently long excited-state lifetime undergo resonant two-photon excitation to reach the level of the DNA excited states, then (2) the excited-state must be coupled to the DNA excited states for photodetachment to occur. Our experiments also pave the way towards photodissociation probes of biomolecule conformation in the gas-phase by Since then, some major advances must be mentioned in electron activation methods [3][4][5] and in infrared photodissociation [6].We recently started exploring the gas-phase reaction pathways of multiply charged DNA single strands and double strands upon UV irradiation around 260 nm [7,8]. To our surprise, we found out that, instead of fragmentation, electron detachment was the major reaction pathway with strands containing guanines. Electron photodetachment itself is not useful for DNA structure analysis, but subsequent collisional activation of the oligonucleotide radicals produced by electron photodetachment gives fragmentation into w, d, a· and z· ions with good sequence coverage [7]. This technique combining electron photodetachment and collision-induced dissociation was coined electron photodetachment dissociation (EPD). It has now been shown to apply to peptides and proteins as well [9].Apart from the sequencing applications of EPD, numerous questions remain about the electron photodetachment mechanism, and how it compares with electron detachment dissociation [3][4][5] and thermal electron detachment [10,11]. We will briefly summarize our current understanding of the photodetachment mechanism [8]. The electron binding energy in multiply charged DNA anions depends on the balance between electron binding energy of the different DNA...

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mentioning

confidence: 99%

Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores

Gabelica

Rosu

Pauw

et al. 2007

J. Am. Soc. Mass Spectrom.

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“…Although both bare P 3 O 9 3− and Co(NO 2 ) 6 3− have been reported previously, 44 these ions are not formed under identical conditions for successfully generating Fe(CN) 6 3− (H 2 O) n . We find that P 3 O 9 3− is only observed with six or more water molecules attached, and this ion undergoes charge separation to form HP 3 O 9 2− (H 2 O) 5 + OH − . This is the first report of a critical cluster size for small trianions, and these are the smallest trianions (highest charge density) that have been observed in the gas phase.…”

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confidence: 75%

Role of Water in Stabilizing Ferricyanide Trianion and Ion-Induced Effects to the Hydrogen-Bonding Water Network at Long Distance

2015

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Structures and reactivities of gaseous Fe(CN)(6)(3-)(H(2)O)n were investigated using infrared photodissociation (IRPD) kinetics, spectroscopy, and computational chemistry in order to gain insights into how water stabilizes highly charged anions. Fe(CN)(6)(3-)(H(2)O)(8) is the smallest hydrated cluster produced by electrospray ionization, and blackbody infrared dissociation of this ion results in loss of an electron and formation of smaller dianion clusters. Fe(CN)(6)(3-)(H(2)O)(7) is produced by the higher activation conditions of IRPD, and this ion dissociates both by loss of an electron and by loss of a water molecule. Comparisons of IRPD spectra to those of computed low-energy structures for Fe(CN)(6)(3-)(H(2)O)(8) indicate that water molecules either form two hydrogen bonds to the trianion or form one hydrogen bond to the ion and one to another water molecule. Magic numbers are observed for Fe(CN)(6)(3-)(H(2)O)n for n between 58 and 60, and the IRPD spectrum of the n = 60 cluster shows stronger water molecule hydrogen-bonding than that of the n = 61 cluster, consistent with the significantly higher stability of the former. Remarkably, neither cluster has a band corresponding to a free O-H stretch, and this band is not observed for clusters until n ≥ 70, indicating that this trianion significantly affects the hydrogen-bonding network of water molecules well beyond the second and even third solvation shells. These results provide new insights into the role of water in stabilizing high-valency anions and how these ions can pattern the structure of water even at long distances.

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“…A few observations about the rates of charge loss illustrated in Figures 1 and 2 are in order: (1) The rates for -4 to -3 charge loss are higher than those for -3 to -2 charge loss; in general, it is found that rates for -n to -(n -1) charge loss are higher than those for -(n -1) to -(n -2) charge loss. (2) The activation energies for a given -n to -(n -1) charge loss vary little as the base composition of the oligonucleotide changes, but the preexponential A factors vary by several orders of magnitude.…”

Section: Introductionmentioning

confidence: 92%

Charge Loss in Gas-Phase Multiply Negatively Charged Oligonucleotides

et al. 2004

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In an attempt to shed light on the mechanism by which gaseous samples of negatively charged oligonucleotides undergo extremely slow (i.e., over 1-1000 s) charge loss, we have carried out molecular dynamics simulations on an oligonucleotide anion, T 5 3-, containing five thymine, deoxyribose, and phosphate units in which the first, third, and fifth phosphates are negatively charged. The study is aimed at determining the rate at which an electron is detached from such a trianion by way of an internal Coulomb repulsion induced event. In this process, the intrinsic 5.0-5.1 eV electron binding strength of each phosphate site is reduced by the repulsive Coulomb potentials of the other two negative sites. As geometrical fluctuations cause the distances among the three negative phosphate sites to change, this causes the Coulomb repulsion energies at these sites to fluctuate. Once the Coulomb potential at any phosphate site exceeds ca. 5 eV, the electron on that site is able to undergo autodetachment. Although such an electron must tunnel through a barrier to escape, it is shown that the tunneling rate is not the rate-limiting step in electron loss; instead, it is the rate at which geometrical fluctuations cause the Coulomb potentials to exceed 5 eV that determines the rate of electron loss. Because these rates are extremely slow, special techniques had to be introduced to allow results of dynamics simulations on more flexible models of T 5 3-to be extrapolated to predict the behavior of the actual T 5 3-.

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Fraying and electron autodetachment dynamics of trapped gas phase oligonucleotides

Cited by 45 publications

References 32 publications

Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores

Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores

Role of Water in Stabilizing Ferricyanide Trianion and Ion-Induced Effects to the Hydrogen-Bonding Water Network at Long Distance

Charge Loss in Gas-Phase Multiply Negatively Charged Oligonucleotides

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