Multiple valence electron detachment following Auger decay of inner-shell vacancies in gas-phase DNA

Li, Wen; Kavatsyuk, O.; Douma, Wessel; Wang, Xin; Hoekstra, Ronnie; Mayer, D. T.; Robinson, M. S.; Gühr, Markus; Lalande, Mathieu; Abdelmouleh, Marwa; Ryszka, Michał; Poully, Jean‐Christophe; Schlathölter, Thomas

doi:10.1039/d1sc02885e

Cited by 8 publications

(26 citation statements)

References 51 publications

(71 reference statements)

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“…More recent experiments have challenged this interpretation, as even in deprotonated gas-phase oligonucleotides, soft X-ray absorption predominantly produces B + and BH + fragments. 10 This finding suggests that B + fragments can originate from non-protonated sites and their formation then normally involves single H transfer, while BH + formation even requires double H transfer. To elucidate the underlying processes it is a straightforward strategy to measure the relative strength of single and double H-transfer processes in glycosidic bond-cleavage processes as a function of photon energy at all inner-shell absorption edges.…”

Section: Introductionmentioning

confidence: 99%

“…Therapeutic X-rays as well as fast ions used in radiotherapy efficiently induce inner shell excitations and ionizations, either directly in DNA or in surrounding water molecules. The resulting inner-shell vacancies are typically filled by Auger processes, leading to emission of energetic electrons which are of high 2 relevance for radiation damage [10]. Soft X-rays are an excellent to to create such inner-shell ionization and excitation proocesses.…”

Section: Introductionmentioning

confidence: 99%

“…As a consequence, in ref [11] the B + fragment was ascribed to originate from a protonated nucleobase and the BH + fragment would originate from a protonated nucleobase acting as an acceptor in a H transfer process. More recent experiments have challenged this interpretation, as even in deprotonated gas-phase oligonucleotides, soft X-ray absorption predominantly produces B + and BH + fragments [10]. This finding suggests that B + fragments can originate from non-protonated sites and their formation then normally involves single H transfer, while BH + formation even requires double H transfer.…”

Section: Introductionmentioning

confidence: 99%

“…The resulting inner-shell vacancies are typically filled by Auger processes, leading to emission of energetic electrons which are of high relevance for radiation damage. 10 Soft X-rays are an excellent tool to create such inner-shell ionization and excitation proocesses. In contrast to nucleobase ππ* or nπ* UV-excitation, resonant soft X-ray absorption in e.g.…”

Section: Introductionmentioning

confidence: 99%

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Intramolecular hydrogen transfer in DNA induced by site-selective resonant core excitation

Wang

Rathnachalam

Zamudio-Bayer

et al. 2022

Phys. Chem. Chem. Phys.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Intramolecular hydrogen transfer in DNA induced by site-selective resonant core excitation

Wang

Rathnachalam

Zamudio-Bayer

et al. 2022

Phys. Chem. Chem. Phys.

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“…Wen et al experimentally [73] demonstrated, by monitoring the positive fragmentation patterns produced by absorption of soft X-ray and infrared photons, that the fragmentation of oligonucleotide dTGGGGT is not a direct consequence of the initial K-shell vacancy but it is rather due to the multiple detachment of valence electrons following the relaxation of the K-shell vacancy. 1.…”

Section: Near-edge Soft X-ray Absorption Mass Spectrometrymentioning

confidence: 99%

Photon induced charge and structural dynamics in gas-phase DNA

Wang¹

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2 1.1. DNA 3 wound around each other in an antiparallel direction. Each DNA strand consists of a long chain of nucleotides -the basic building blocks of DNA primary structure. As it is shown in fig. 1.1, a nucleotide is made up of a phosphate group, a deoxyribose sugar molecule, and one of four nitrogenous bases: adenine (A), guanine (G), cytosine (C) and thymine (T), of which A and G are purines, while C and T are pyrimidines. The nucleotides are combined together forming a long chain through the covalent bonds between the phosphate of one nucleotide and the sugar molecule of the neighboring nucleotide. This phosphate-sugar backbone is located on the outside of the DNA helix. DNA double strands are held together by hydrogen bonds between the nucleobases which are placed perpendicular to the axis of the helix [4], and located on the inside of the helix. The base pairing is specific and the rule is that the hydrogen bonds only form between A and T, or between G and C, leading to the fact that double strands are complementary to each other. The base pairing rule also plays an important role in DNA duplication. The DNA can reproduce by opening up the two paired strands. Each strand can act as a template to reconstruct a new partner strand by following the base pairing rule. In the end, one double-strand can replicate into two identically new DNA molecules.In addition to the canonical helical structure of DNA, which is also called B-form DNA (B-DNA), it has been found that DNA can form various secondary structures, such as A-DNA and Z-DNA, which also belong to the DNA helix families [8], as well as triplexes [9] and Gquadruplexes (G4) [10]. It was demonstrated that DNA capable of forming those structures was conserved throughout evolution. These conformations are known to have critical functional roles in vivo. In this thesis, structural dynamics of G4 unfolding are investigated on the molecular level by near-infrared (NIR) and vacuum ultraviolet (VUV) photoabsorption experiments. G4 self-assemble in solution from G-rich DNA monomers and fascinate with their beautiful topology. More details of G4 are given in the following. 4 1.2. DNA biochemical properties 5 6 8 1.4. X-rays interactions with DNA 9 10 12 1.5. Thesis outline 13 14 1. Introduction

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Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides

Liu

O’Reilly

Schwob

et al. 2023

Chemistry A European J

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Understanding how charge and energy, as well as protons and hydrogen atoms, are transferred in molecular systems as a result of an electronic excitation is fundamental for understanding the interaction between ionizing radiation and biological matter on the molecular level. To localize the excitation at the atomic scale, it was chosen to target phosphorus atoms in the backbone of gas-phase oligonucleotide anions and cations, by means of resonant photoabsorption at the L-and K-edges. The ionic photoproducts of the excitation process were studied by a combination of mass spectrometry and X-ray spectroscopy. The combination of absorption site selectivity and photoproduct sensitivity allowed the identification of X-ray spectral signatures of specific processes. Moreover, charge and/or energy as well as H transfer from the backbone to nucleobases has been directly observed. Although the probability of one versus two H transfer following valence ionization depends on the nucleobase, ionization of sugar or phosphate groups at the carbon K-edge or the phosphorus L-edge mainly leads to single H transfer to protonated adenine. Moreover, our results indicate a surprising proton-transfer process to specifically form protonated guanine after excitation or ionization of P 2p electrons.

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Multiple valence electron detachment following Auger decay of inner-shell vacancies in gas-phase DNA

Abstract: We have studied soft X-ray photoabsorption in the doubly deprotonated gas-phase oligonucleotide [dTGGGGT-2H]^2-. The dominating decay mechanism of the X-ray induced inner shell vacancy was found to be Auger decay...

Cited by 8 publications

References 51 publications

Intramolecular hydrogen transfer in DNA induced by site-selective resonant core excitation

Intramolecular hydrogen transfer in DNA induced by site-selective resonant core excitation

Photon induced charge and structural dynamics in gas-phase DNA

Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides

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