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Photofragmentation of 2-deoxy-D-ribose molecules in the gas phase
KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
Ion Reaction Laboratory, Department of Nuclear Medicine and Radiobiology, University of Sherbrooke.
CNR-IMIP, Montelibretti.
CNR-INFM, Laboratorio Nazionale TASC.
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2008 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 9, no 7, 1020-1029 p.Article in journal (Refereed) Published
Abstract [en]

We have measured the synchrotron-induced photofragmentation of isolated 2-deoxy-D-ribose molecules (C5H10O4) 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 CH3+, OH+, H3O+, C2H3+, C2H4+, CHxO+ (x=1,2,3), C2HxO+ (x=1-5), C3HxO+ (x=3-5), C2H4O2+, C3HxO2+ (x=1,2,4-6), C4H5O2+, C4HxO3+ (x=6,7), C5H7O3+, and C5H8O3+. 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 (C3H5O+), 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, CH3+, H3O+, C2H4+, CH3O+, and C2H5O+, 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.

Place, publisher, year, edition, pages
2008. Vol. 9, no 7, 1020-1029 p.
Keyword [en]
cleavage reactions, DNA damage, gas-phase reactions, mass spectrometry, photolysis
National Category
Atom and Molecular Physics and Optics
Identifiers
URN: urn:nbn:se:kth:diva-8002DOI: 10.1002/cphc.200700635ISI: 000255845500010Scopus ID: 2-s2.0-43649083041OAI: oai:DiVA.org:kth-8002DiVA: diva2:13204
Note
QC 20100916Available from: 2008-02-20 Created: 2008-02-20 Last updated: 2010-09-16Bibliographically approved
In thesis
1. Synchrotron radiation studies of gas phase molecules: from hydrogen to DNA sugars
Open this publication in new window or tab >>Synchrotron radiation studies of gas phase molecules: from hydrogen to DNA sugars
2008 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

This thesis summarises experimental results on the molecular spectroscopy of gas phase molecules excited by synchrotron radiation in the VUV and soft X-ray regions. We have used three different detection techniques, photon induced fluorescence spectroscopy, photoionisation mass spectroscopy and near edge X-ray absorption fine structure spectroscopy to study molecular deuterium, hydrogen sulphide, ammonia, methanol, pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, and 2-deoxy-D-ribose, the last one also known as the DNA sugar. Out of this variety of techniques and molecules we have shown that: (1) high resolution dispersed fluorescence allows us to identify vibrational and rotational bands in molecular deuterium, as well as to estimate the predissociation probability of the same molecule [paper I]; (2) the main species fluorescing after core excitation of methane, ammonia [paper III], hydrogen sulphide [paper II], pyridine, pyrimidine and s-triazine is H Balmer α, followed by fluorescence from ionised species, molecular bands and Balmer β, γ , δ; (3) the Rydberg enhancement seen in fluorescence measurements of water [Melero et al. PRL 96 (2006) 063003], corroborated later in H2S [paper II], NH3 [paper III] and CH4 [paper III] and postulated as general behaviour for molecules formed by low-Z atoms, is also seen in larger organic cyclic molecules, e.g. azabenzenes; (4) when dissociative ionisation of pyridine, pyridazine, pyrimidine, pyrazine, s-triazine and 2-deoxy-D-ribose occurs, concerted bond rearrangement and nuclear motion takes place as opposed to stepwise dissociation [papers V and VI].

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. x, 56 p.
Series
Trita-FYS, ISSN 0280-316X ; 2008:1
Keyword
KTH thesis, synchrotron radiation, gas phase, bio molecules
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-4640 (URN)978-91-7178-852-8 (ISBN)
Public defence
2008-03-13, FA31, Albanova, Roslagstullabacken 21, Stockholm, 10:15
Opponent
Supervisors
Note
QC 20100916Available from: 2008-02-20 Created: 2008-02-20 Last updated: 2010-09-16Bibliographically approved

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Rachlew, Elisabeth

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