Photofragmentation of 2‐Deoxy‐D‐Ribose Molecules in the Gas Phase

Abstract

We have measured the synchrotron-induced photofragmentation of isolated 2-deoxy-D-ribose molecules (C(5)H(10)O(4)) at four photon energies, namely, 23.0, 15.7, 14.6, and 13.8 eV. At all photon energies above the molecule's ionization threshold we observe the formation of a large variety of molecular cation fragments, including CH(3) (+), OH(+), H(3)O(+), C(2)H(3) (+), C(2)H(4) (+), CH(x)O(+) (x=1,2,3), C(2)H(x)O(+) (x=1-5), C(3)H(x)O(+) (x=3-5), C(2)H(4)O(2) (+), C(3)H(x)O(2) (+) (x=1,2,4-6), C(4)H(5)O(2) (+), C(4)H(x)O(3) (+) (x=6,7), C(5)H(7)O(3) (+), and C(5)H(8)O(3) (+). The formation of these fragments shows a strong propensity of the DNA sugar to dissociate upon absorption of vacuum ultraviolet photons. The yields of particular fragments at various excitation photon energies in the range between 10 and 28 eV are also measured and their appearance thresholds determined. At all photon energies, the most intense relative yield is recorded for the m/q=57 fragment (C(3)H(5)O(+)), whereas a general intensity decrease is observed for all other fragments- relative to the m/q=57 fragment-with decreasing excitation energy. Thus, bond cleavage depends on the photon energy deposited in the molecule. All fragments up to m/q=75 are observed at all photon energies above their respective threshold values. Most notably, several fragmentation products, for example, CH(3) (+), H(3)O(+), C(2)H(4) (+), CH(3)O(+), and C(2)H(5)O(+), involve significant bond rearrangements and nuclear motion during the dissociation time. Multibond fragmentation of the sugar moiety in the sugar-phosphate backbone of DNA results in complex strand lesions and, most likely, in subsequent reactions of the neutral or charged fragments with the surrounding DNA molecules.

Vacuum ultraviolet photoionization of carbohydrates and nucleotides

“…Similar difficulties are also shown in previous studies [8][9][10][11][12][13][14][15][16][17] on interactions between high energy particles and 2-deoxyribose, in which the molecular ion undergoes fragmentation and yields ions with various fragmentation pathways involving bond rearrangements, intramolecular proton or hydrogen transfer, and dehydration. While the exact fragmentation pathways remain somewhat ambiguous, suggested 8,9,12,[14][15][16][17] identities of fragment ions are nearly identical regardless of the ionization method, implying that upon removal of an electron, the molecular ion follows specific relaxation pathways that lead to bond dissociation. For example, dehydration of the 2deoxyribose molecular ion is observed from other reported ionization studies using VUV, 8,9,15 H + /He + , 13 and electron 17 sources, and is also observed for ribose in the current study.…”

“…[1][2][3][4][5][6][7][8][9] In particular, studies [10][11][12][13][14][15] strongly support the idea that radiation induced damage of DNA and RNA molecules can be accounted for by the fact that carbohydrates, which are constituents of the nucleic acid molecules, are highly susceptible to molecular fragmentation by high energy particles and radiation. The dominant carbohydrate ionization products are fragment ions only, [8][9][10][11][12][13][14][15][16][17] and intact molecular ions are rarely observed.…”

Resistance of Bacterial Endospores to Outer Space for Planetary Protection Purposes—Experiment PROTECT of the EXPOSE-E Mission

“…The DNA is the most sensitive target molecule in the cell at these wavelengths. Photons of this highly energetic UV range are likely to ionize DNA components, including the sugar-phosphate backbone of the DNA (Vall-Ilosera et al, 2008;Cadet and Douki, 2011). The latter reaction is expected to lead to the formation of DNA strand breaks (Horneck and Rabbow, 2007).…”

Fragmentation of deprotonated d-ribose and d-fructose in MALDI—Comparison with dissociative electron attachment

“…It is thus not surprising that the scientific community has invested considerable effort in trying to understand the structure and composition of the vast variety of polysaccharides and the role of the sugars in the multiplicity of biologically relevant molecules. Mass spectrometry of sugars has been conducted with a variety of ionization methods, including electrospray ionization [1,2], direct laser desorption and matrix assisted laser desorption ionization (MALDI) [3][4][5][6][7], fast atom bombardment (FAB) [8][9][10], chemical ionization [11], field desorption [12,13], liquid secondary ion mass spectrometry [14], infrared multiple-photon dissociation [15], one-photon dissociation [16] as well as low-energy ion induced dissociation [17,18]. A number of studies have also been conducted on the fragmentation pattern of cationized sugars after (c) Example for notation of cross-ring cleavage according to Domon and Costello [28].…”