FRET measurements of trapped oligonucleotide duplexes

Danell, Allison S.; Parks, Joel H.

doi:10.1016/s1387-3806(03)00253-7

Cited by 87 publications

(100 citation statements)

References 24 publications

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“…However, when the fluorophore 6-FAM is covalently attached to the DNA extremities by an alkyl linker, it is unable to provoke electron photodetachment. Danell and Parks [45] performed fluorescence counting experiments on BODIPY TMR-X and BODIPY TR-X upon 532-nm laser irradiation. Electron photodetachment was detected, and the authors subsequently found that this was due to a thermal autodetachment following internal energy input by the laser excitation.…”

Section: Mechanism Of Electron Photodetachment Following Chromophore mentioning

confidence: 99%

“…As FRET efficiency depends on the donor-acceptor distance (in 1/r 6 , FRET is commonly used to probe the conformation of biomolecules in solution, including nucleic acids [53]. Several groups developed specialized instrumentation to allow fluorescence measurements in trap mass spectrometers [54 -56], and probing gasphase ion conformation either by measuring changes in the donor fluorescence [45,57], or by measuring the acceptor fluorescence [58]. Here we propose using a fluorophore as the donor and a quencher as the acceptor, in a configuration known as a "molecular beacon" [59,60].…”

Section: Electronic-to-vibrational Energy Conversion: Towards Photodimentioning

confidence: 99%

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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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Section: Mechanism Of Electron Photodetachment Following Chromophore mentioning

confidence: 99%

Section: Electronic-to-vibrational Energy Conversion: Towards Photodimentioning

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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“…In gas-phase work, Parks and coworkers [7][8][9][10] and Zenobi and coworkers [11,12] investigated the fluorescence of trapped molecular ions commonly used as fluorescent molecular probes of biomolecules. Both groups attached fluorescent probes to peptide cations for the purposes of investigating gas-phase FRET [8,11].Chromophore and fluorophore labeling experiments both rely on energy transfer from the absorbing moiety to another part of the biomolecule, either via intramolecular vibrational energy transfer or via radiative or electronic interactions. To understand the initial absorption process and the efficiency of photoactivation, it is of interest to investigate the photophysics and chemical dynamics of the absorption, fluorescence, and dissociation processes in the fluorescent dye molecules themselves in the gas phase.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

“…Fluorophore labeling is also used in fluorescence resonant energy transfer (FRET) experiments, in which the acceptor/donor interactions of two attached fluorophores depend on the distances between them and therefore can provide conformational information [3][4][5][6]. In gas-phase work, Parks and coworkers [7][8][9][10] and Zenobi and coworkers [11,12] investigated the fluorescence of trapped molecular ions commonly used as fluorescent molecular probes of biomolecules. Both groups attached fluorescent probes to peptide cations for the purposes of investigating gas-phase FRET [8,11].…”

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Fluorescence and photodissociation of rhodamine 575 cations in a quadrupole ion trap

Sassin

Everhart

Dangi

et al. 2009

J. Am. Soc. Mass Spectrom.

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The fluorescence and photodissociation of rhodamine 575 cations confined to a quadrupole ion trap are observed during laser irradiation at 488 nm. The kinetics of photodissociation is measured by time-dependent mass spectra and time-dependent fluorescence. The rhodamine ion signal and fluorescence decay are studied as functions of buffer gas pressure, laser fluence, and irradiation time. The decay rates of the ions in the mass spectra agree with decay rates of the fluorescence. Some of the fragment ions also fluoresce and further dissociate. The photodissociation rate is found to depend on the incident laser fluence and buffer gas pressure. A s an alternative to collision-induced dissociation, surface-induced dissociation, infrared multiphoton dissociation, or direct UV/visible dissociation of biomolecular ions, there has been interest in labeling biomolecules with a chromophore tag to enhance photoactivation efficiency and selectivity. For example, Brodbelt and colleagues studied photodissociation mass spectra to sequence peptides labeled with both infrared absorbers [1] and UV chromophores [2]. Fluorophore labeling is also used in fluorescence resonant energy transfer (FRET) experiments, in which the acceptor/donor interactions of two attached fluorophores depend on the distances between them and therefore can provide conformational information [3][4][5][6]. In gas-phase work, Parks and coworkers [7][8][9][10] and Zenobi and coworkers [11,12] investigated the fluorescence of trapped molecular ions commonly used as fluorescent molecular probes of biomolecules. Both groups attached fluorescent probes to peptide cations for the purposes of investigating gas-phase FRET [8,11].Chromophore and fluorophore labeling experiments both rely on energy transfer from the absorbing moiety to another part of the biomolecule, either via intramolecular vibrational energy transfer or via radiative or electronic interactions. To understand the initial absorption process and the efficiency of photoactivation, it is of interest to investigate the photophysics and chemical dynamics of the absorption, fluorescence, and dissociation processes in the fluorescent dye molecules themselves in the gas phase. This work investigates the competition between fluorescence and photodissociation of rhodamine dye cations in a quadrupole ion trap. The ion trap is an ideal device for measuring chemical reactions that have slow reaction rates or processes that have long-lived intermediate states because of its ability to store a population of thermalized ions in the same location for extended periods of time. The photodepletion rate of the rhodamine cations is determined here by two independent methods: by directly observing the fluorescence photons and by recording the ion mass spectra. The resulting decays obtained by both methods are compared as a function of pressure, laser fluence, and irradiation time. The mechanism of rhodamine cation photodissociation at 488 nm is discussed.Several other groups have directly measured fluorescence from ions in...

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Resonance Energy Transfer Relates the Gas‐Phase Structure and Pharmacological Activity of Opioid Peptides

Kopysov

Boyarkin

2015

Angewandte Chemie

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Enkephalins are efficient pain-relief drugs that bind to transmembrane opioid receptors.One key structural parameter that governs the pharmacological activity of these opioid peptides and is typically determined from condensed-phase structures is the distance between the aromatic rings of their Tyr and Phe residues.W eu se resonance energy transfer,d etected by ac ombination of cold ion spectroscopya nd mass spectrometry,t oe stimate the Tyr-Phe spacing for enkephalins in the gas phase.I nc ontrast to the condensed-phase structures, these distances appear to differ substantially in enkephalins with different pharmacological efficiencies,suggesting that gasphase structures might be ab etter pharmacophoric metric for ligand peptides.

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FRET measurements of trapped oligonucleotide duplexes

Cited by 87 publications

References 24 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

Fluorescence and photodissociation of rhodamine 575 cations in a quadrupole ion trap

Resonance Energy Transfer Relates the Gas‐Phase Structure and Pharmacological Activity of Opioid Peptides

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