Direct experimental observation of the low ionization potentials of guanine in free oligonucleotides by using photoelectron spectroscopy

Yang, Xin; Wang, Xuebin; Vorpagel, Erich R.; Wang, Lai-Sheng

doi:10.1073/pnas.0405157101

Cited by 143 publications

(268 citation statements)

References 41 publications

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“…However, the stabilization of the labile hydrogens due to the hydrogen bonding actually appears to slow the reaction rate. This result coincides with other observations by Habibi-Goudarzi et al for the dissociation of the mononucleotide anions by°CID° [45],°Vrkic°and°O'Hair°for°the°reaction°with trimethylborate° [13],°and°Yang°et°al.°for°the°ionization energy° [46],°where°the°suspected°intramolecular°hydro-gen bonding capability of 5=-dGMP was cited as the reason for the substantially different dissociation pattern, reactivity, and ionization energy, respectively. Unlike the other 3=-phosphate mononucleotides, the Ϫsyn orientation of the guanine nucleobase enabled 3=-dGMP to exchange more than two hydrogens.…”

Section: =-Deoxy-guanosine Monophosphate Isomers (5=-dgmp and 3=-dgmp)supporting

confidence: 81%

Gas-phase hydrogen/deuterium exchange of 5′- and 3′-mononucleotides in a quadrupole ion trap: Exploring the role of conformation and system energy

Chipuk

Brodbelt

2007

J. Am. Soc. Mass Spectrom.

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Gas-phase hydrogen/deuterium (H/D) exchange reactions for deprotonated 2=-deoxy-5=-monophosphate and 2=-deoxy-3=-monophosphate nucleotides with D 2 O were performed in a quadrupole ion trap mass spectrometer. To augment these experiments, molecular modeling was also conducted to identify likely deprotonation sites and potential gas-phase conformations of the anions. A majority of the 5=-monophosphates exchanged extensively with several of the compounds completely incorporating deuterium in place of their labile hydrogen atoms. In contrast, most of the 3=-monophosphate isomers exchanged relatively few hydrogen atoms, even though the rate of the first two exchanges was greater than observed for the 5=-monophosphates. Mononucleotides that failed to incorporate more than two deuterium atoms under default reaction conditions were often found to exchange more extensively when reactions were performed under higher energy conditions. Integration of the experimental and theoretical results supports the use of a relay exchange mechanism and suggests that the exchange behavior depends highly on the identity and orientation of the nucleobase and the position and flexibility of the deprotonated phosphate moiety. These observations also highlight the importance of the distance between the various participating groups in addition to their gas-phase acidity and basicity. (J Am Soc Mass Spectrom 2007, 18, 724 -736)

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Section: =-Deoxy-guanosine Monophosphate Isomers (5=-dgmp and 3=-dgmp)supporting

confidence: 81%

Gas-phase hydrogen/deuterium exchange of 5′- and 3′-mononucleotides in a quadrupole ion trap: Exploring the role of conformation and system energy

Chipuk

Brodbelt

2007

J. Am. Soc. Mass Spectrom.

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“…2,3 PES can be a valuable technique to probe the electronic structure and stability of negatively charged biomolecules. 109 However, many gaseous biomolecules exist as a mixture of different isomers, which have different structures, but similar thermodynamic stability. The presence of close-lying multiple isomers posed a major challenge to the application of PES to biomolecules.…”

Section: Isomer-selective Photoelectron Spectroscopy Of Multiply-cmentioning

confidence: 99%

A multi-agent quantum Monte Carlo model for charge transport: Application to organic field-effect transistors

Bauer

Jäger

Jordan

et al. 2015

The Journal of Chemical Physics

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We have developed a multi-agent quantum Monte Carlo model to describe the spatial dynamics of multiple majority charge carriers during conduction of electric current in the channel of organic field-effect transistors. The charge carriers are treated by a neglect of diatomic differential overlap Hamiltonian using a lattice of hydrogen-like basis functions. The local ionization energy and local electron affinity defined previously map the bulk structure of the transistor channel to external potentials for the simulations of electron- and hole-conduction, respectively. The model is designed without a specific charge-transport mechanism like hopping- or band-transport in mind and does not arbitrarily localize charge. An electrode model allows dynamic injection and depletion of charge carriers according to source-drain voltage. The field-effect is modeled by using the source-gate voltage in a Metropolis-like acceptance criterion. Although the current cannot be calculated because the simulations have no time axis, using the number of Monte Carlo moves as pseudo-time gives results that resemble experimental I/V curves.

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“…The electron binding energy in multiply charged DNA anions depends on the balance between electron binding energy of the different DNA constituents (the phosphates, the sugars, and the bases) and the Coulombic repulsion between like charges [10 -12]. It has been shown that in a negatively charged environment, the electron binding energy of the nucleic bases can become lower than the electron binding energy of the phosphate groups, and that the highest occupied molecular orbital (HOMO) can be located on the bases [13][14][15]. Guanine is the base with the lowest ionization energy, followed by adenine, cytosine, and finally thymine.…”

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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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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Direct experimental observation of the low ionization potentials of guanine in free oligonucleotides by using photoelectron spectroscopy

Cited by 143 publications

References 41 publications

Gas-phase hydrogen/deuterium exchange of 5′- and 3′-mononucleotides in a quadrupole ion trap: Exploring the role of conformation and system energy

Gas-phase hydrogen/deuterium exchange of 5′- and 3′-mononucleotides in a quadrupole ion trap: Exploring the role of conformation and system energy

A multi-agent quantum Monte Carlo model for charge transport: Application to organic field-effect transistors

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

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