Low energy secondary electron induced damage of condensed nucleotides

McKee, A. D.; Schaible, M. J.; Rosenberg, R. A.; Kundu, S.; Orlando, Thomas M.

doi:10.1063/1.5090491

Title: Low energy secondary electron induced damage of condensed nucleotides

Journal Article · Tue May 28 00:00:00 EDT 2019 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.5090491· OSTI ID:1559940

^[1]; Schaible, M. J. ^[1]; Rosenberg, R. A. ^[2]; Kundu, S. ^[1];

^[1]

Georgia Inst. of Technology, Atlanta, GA (United States)
Argonne National Lab. (ANL), Lemont, IL (United States)

Radiation damage and stimulated desorption of nucleotides 2'-deoxyadenosine 5'-monophosphate (dAMP), adenosine 5'-monophosphate (rAMP), 2'-deoxycytidine 5'-monophosphate (dCMP), and cytidine 5'-monophosphate (rCMP) deposited on Au have been measured using x-rays as both the probe and source of low energy secondary electrons. The fluence dependent behavior of the O-1s, C-1s, and N-1s photoelectron transitions was analyzed to obtain phosphate, sugar, and nucleobase damage cross sections. Although x-ray induced reactions in nucleotides involve both direct ionization and excitation, the observed bonding changes were likely dominated by the inelastic energy-loss channels associated with secondary electron capture and transient negative ion decay. Growth of the integrated peak area for the O-1s component at 531.3 eV, corresponding to cleavage of the C—O—P phosphodiester bond, yielded effective damage cross sections of about 23 Mb and 32 Mb (1 Mb = 10^–18 cm²) for AMP and CMP molecules, respectively. The cross sections for sugar damage, as determined from the decay of the C-1s component at 286.4 eV and the glycosidic carbon at 289.0 eV, were slightly lower (about 20 Mb) and statistically similar for the r- and d- forms of the nucleotides. Here, the C-1s component at 287.6 eV, corresponding to carbons in the nucleobase ring, showed a small initial increase and then decayed slowly, yielding a low damage cross section (~5 Mb). Although there is no statistical difference between the sugar forms, changing the nucleobase from adenine to cytidine has a slight effect on the damage cross section, possibly due to differing electron capture and transfer probabilities.

View Accepted Manuscript (DOE)

View Accepted Manuscript (Publisher)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-06CH11357; FG02-02ER15337

OSTI ID:: 1559940

Alternate ID(s):: OSTI ID: 1523698

Journal Information:: Journal of Chemical Physics, Vol. 150, Issue 20; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 9 works

Citation information provided by
Web of Science

References (61)

Electron Attachment to Microhydrated Deoxycytidine Monophosphate Kočišek, Jaroslav; Sedmidubská, Barbora; Indrajith, Suvasthika The Journal of Physical Chemistry B, Vol. 122, Issue 20 https://doi.org/10.1021/acs.jpcb.8b03033	journal	April 2018
Understanding the Interaction between Low-Energy Electrons and DNA Nucleotides in Aqueous Solution McAllister, Maeve; Smyth, Maeve; Gu, Bin The Journal of Physical Chemistry Letters, Vol. 6, Issue 15 https://doi.org/10.1021/acs.jpclett.5b01011	journal	July 2015
The measurement of molecular fragments from DNA components using synchrotron radiation Fujii, K.; Akamatsu, K.; Yokoya, A. Surface Science, Vol. 528, Issue 1-3 https://doi.org/10.1016/s0039-6028(02)02640-7	journal	March 2003
X-ray induced damage in DNA monitored by X-ray photoelectron spectroscopy Ptasińska, Sylwia; Stypczyńska, Agnieszka; Nixon, Tony The Journal of Chemical Physics, Vol. 129, Issue 6 https://doi.org/10.1063/1.2961027	journal	August 2008
The relationship between interfacial bonding and radiation damage in adsorbed DNA Rosenberg, R. A.; Symonds, J. M.; Vijayalakshmi, K. Phys. Chem. Chem. Phys., Vol. 16, Issue 29 https://doi.org/10.1039/c4cp01649a	journal	January 2014
The interaction of a protein–DNA surface complex with low-energy electrons Solomun, T.; Skalický, T. Chemical Physics Letters, Vol. 453, Issue 1-3 https://doi.org/10.1016/j.cplett.2007.12.078	journal	February 2008
Secondary electron energy distributions for gold as excited by C K _α (277 eV) and Al K _α (1487 eV) x rays Henke, Burton L.; Smith, Jerel A.; Attwood, David T. Applied Physics Letters, Vol. 29, Issue 9 https://doi.org/10.1063/1.89176	journal	November 1976
Inelastic electron interaction (attachment/ionization) with deoxyribose Ptasińska, S.; Denifl, S.; Scheier, P. The Journal of Chemical Physics, Vol. 120, Issue 18 https://doi.org/10.1063/1.1690231	journal	May 2004
Mechanism and Site of Attack for Direct Damage to DNA by Low-Energy Electrons Pan, X.; Sanche, L. Physical Review Letters, Vol. 94, Issue 19 https://doi.org/10.1103/physrevlett.94.198104	journal	May 2005
Chemical Basis of DNA Sugar−Phosphate Cleavage by Low-Energy Electrons Zheng, Yi; Cloutier, Pierre; Hunting, Darel J. Journal of the American Chemical Society, Vol. 127, Issue 47 https://doi.org/10.1021/ja054129q	journal	November 2005
Spur energy distributions in liquid water using a generalized oscillator strength from inelastic X-ray scattering measurements Karamitros, Mathieu; Mozumder, Asokendu Radiation Physics and Chemistry, Vol. 141 https://doi.org/10.1016/j.radphyschem.2016.11.014	journal	December 2017
Damage Induced to DNA by Low-Energy (0−30 eV) Electrons under Vacuum and Atmospheric Conditions Brun, Émilie; Cloutier, Pierre; Sicard-Roselli, Cécile The Journal of Physical Chemistry B, Vol. 113, Issue 29 https://doi.org/10.1021/jp902540k	journal	July 2009
On the Effect of Low-Energy Electron Induced DNA Strand Break in Aqueous Solution: A Theoretical Study Indicating Guanine as a Weak Link in DNA Schyman, Patric; Laaksonen, Aatto Journal of the American Chemical Society, Vol. 130, Issue 37 https://doi.org/10.1021/ja805000g	journal	September 2008
Measurement of inelastic cross sections for low-energy electron scattering from DNA bases Michaud, Marc; Bazin, Marc; Sanche, Le´on International Journal of Radiation Biology, Vol. 88, Issue 1-2 https://doi.org/10.3109/09553002.2011.577505	journal	May 2011
Quantitative analysis of saccharides by X-ray photoelectron spectroscopy Stevens, Joanna S.; Schroeder, Sven L. M. Surface and Interface Analysis, Vol. 41, Issue 6 https://doi.org/10.1002/sia.3047	journal	June 2009
Low-Energy Electron Transmission through Thin-Film Molecular and Biomolecular Solids Naaman, R.; Sanche, L. Chemical Reviews, Vol. 107, Issue 5 https://doi.org/10.1021/cr040200j	journal	May 2007
Dissociative electron attachment to hydrated single DNA strands Ptasińska, Sylwia; Sanche, Léon Physical Review E, Vol. 75, Issue 3 https://doi.org/10.1103/physreve.75.031915	journal	March 2007
Electron stopping power and inelastic mean free path in amino acids and protein over the energy range of 20–20,000 eV Tan, Zhenyu; Xia, Yueyuan; Zhao, Mingwen Radiation and Environmental Biophysics, Vol. 45, Issue 2 https://doi.org/10.1007/s00411-006-0049-0	journal	May 2006
Lack of proportionality of total electron yield and soft x-ray absorption coefficient Henneken, H.; Scholze, F.; Ulm, G. Journal of Applied Physics, Vol. 87, Issue 1 https://doi.org/10.1063/1.371854	journal	January 2000
Side-by-Side Comparison of DNA Damage Induced by Low-Energy Electrons and High-Energy Photons with Solid TpTpT Trinucleotide Park, Yeunsoo; Peoples, Anita R.; Madugundu, Guru S. The Journal of Physical Chemistry B, Vol. 117, Issue 35 https://doi.org/10.1021/jp405397m	journal	August 2013
Absolute cross section for low-energy-electron damage to condensed macromolecules: A case study of DNA Rezaee, Mohammad; Cloutier, Pierre; Bass, Andrew D. Physical Review E, Vol. 86, Issue 3 https://doi.org/10.1103/physreve.86.031913	journal	September 2012
Single, Double, and Multiple Double Strand Breaks Induced in DNA by 3−100 eV Electrons Huels, Michael A.; Boudaïffa, Badia; Cloutier, Pierre Journal of the American Chemical Society, Vol. 125, Issue 15 https://doi.org/10.1021/ja029527x	journal	April 2003
How Do Low-Energy (0.1−2 eV) Electrons Cause DNA-Strand Breaks? Simons, Jack Accounts of Chemical Research, Vol. 39, Issue 10 https://doi.org/10.1021/ar0680769	journal	October 2006
Resonant Formation of DNA Strand Breaks by Low-Energy (3 to 20 eV) Electrons Boudaïffa, B. Science, Vol. 287, Issue 5458 https://doi.org/10.1126/science.287.5458.1658	journal	March 2000
Halogen Anion Formation in 5-Halouracil Films: X Rays Compared to Subionization Electrons Klyachko, Dimitri V.; Huels, Michael A.; Sanche, Léon Radiation Research, Vol. 151, Issue 2 https://doi.org/10.2307/3579768	journal	February 1999
Resonant dissociation of DNA bases by subionization electrons Huels, Michael A.; Hahndorf, Ina; Illenberger, Eugen The Journal of Chemical Physics, Vol. 108, Issue 4 https://doi.org/10.1063/1.475503	journal	January 1998
On the mechanism of anion desorption from DNA induced by low energy electrons Ptasińska, Sylwia; Sanche, Léon The Journal of Chemical Physics, Vol. 125, Issue 14 https://doi.org/10.1063/1.2338320	journal	October 2006
Transport of secondary electrons through coatings of ion-irradiated metallic nanoparticles Haume, Kaspar; de Vera, Pablo; Verkhovtsev, Alexey The European Physical Journal D, Vol. 72, Issue 6 https://doi.org/10.1140/epjd/e2018-90050-x	journal	June 2018
Quantitative analysis of complex amino acids and RGD peptides by X-ray photoelectron spectroscopy (XPS): Quantitative XPS analysis of amino acids and RGD peptides Stevens, Joanna S.; de Luca, Alba C.; Pelendritis, Michalis Surface and Interface Analysis, Vol. 45, Issue 8 https://doi.org/10.1002/sia.5261	journal	April 2013
Unified Mechanism for the Generation of Isolated and Clustered DNA Damages by a Single Low Energy (5–10 eV) Electron Shao, Yu; Dong, Yanfang; Hunting, Darel The Journal of Physical Chemistry C, Vol. 121, Issue 4 https://doi.org/10.1021/acs.jpcc.6b12110	journal	January 2017
Low-energy electron diffraction and induced damage in hydrated DNA Orlando, Thomas M.; Oh, Doogie; Chen, Yanfeng The Journal of Chemical Physics, Vol. 128, Issue 19 https://doi.org/10.1063/1.2907722	journal	May 2008
Detection of energy-selected secondary electrons in coincidence with energy-loss events in thin carbon foils Pijper, Folbert J.; Kruit, Pieter Physical Review B, Vol. 44, Issue 17 https://doi.org/10.1103/physrevb.44.9192	journal	November 1991
Precursors of Solvated Electrons in Radiobiological Physics and Chemistry Alizadeh, Elahe; Sanche, Léon Chemical Reviews, Vol. 112, Issue 11 https://doi.org/10.1021/cr300063r	journal	June 2012
Damage to Model DNA Fragments from Very Low-Energy (<1 eV) Electrons Berdys, Joanna; Anusiewicz, Iwona; Skurski, Piotr Journal of the American Chemical Society, Vol. 126, Issue 20 https://doi.org/10.1021/ja049876m	journal	May 2004
Damage to amino acid–nucleotide pairs induced by 1 eV electrons Ptasińska, Sylwia; Li, Zejun; Mason, Nigel J. Physical Chemistry Chemical Physics, Vol. 12, Issue 32 https://doi.org/10.1039/b926267a	journal	January 2010
Probing low-energy electron induced DNA damage using single photon ionization mass spectrometry Chen, Yanfeng; Aleksandrov, Alexandr; Orlando, Thomas M. International Journal of Mass Spectrometry, Vol. 277, Issue 1-3 https://doi.org/10.1016/j.ijms.2008.07.003	journal	November 2008
Energy Thresholds of DNA Damage Induced by UV Radiation: An XPS Study Gomes, P. J.; Ferraria, A. M.; Botelho do Rego, A. M. The Journal of Physical Chemistry B, Vol. 119, Issue 17 https://doi.org/10.1021/acs.jpcb.5b01439	journal	April 2015
Low energy electron attachment to the nucleotide deoxycytidine monophosphate: direct evidence for the molecular mechanisms of electron-induced DNA strand breaks Kopyra, Janina Physical Chemistry Chemical Physics, Vol. 14, Issue 23 https://doi.org/10.1039/c2cp40847c	journal	January 2012
Low energy electron-driven damage in biomolecules Sanche, L. The European Physical Journal D, Vol. 35, Issue 2 https://doi.org/10.1140/epjd/e2005-00206-6	journal	August 2005
Adsorption of carbonyl compounds on clean and modified Cu(110) surfaces: A combined eels-ups study Prabhakaran, K.; Rao, C. N. R. Applied Surface Science, Vol. 44, Issue 3 https://doi.org/10.1016/0169-4332(90)90051-z	journal	May 1990
DNA Damage Induced by Low-Energy Electrons: Electron Transfer and Diffraction Zheng, Yi; Wagner, J. Richard; Sanche, Léon Physical Review Letters, Vol. 96, Issue 20 https://doi.org/10.1103/physrevlett.96.208101	journal	May 2006
Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep07391	journal	December 2014
Cleavage Enhancement of Specific Chemical Bonds in DNA by Cisplatin Radiosensitization Xiao, Fangxing; Luo, Xinglan; Fu, Xianzhi The Journal of Physical Chemistry B, Vol. 117, Issue 17 https://doi.org/10.1021/jp400852p	journal	April 2013
Mechanism for Damage to DNA by Low-Energy Electrons ^† Barrios, Robyn; Skurski, Piotr; Simons, Jack The Journal of Physical Chemistry B, Vol. 106, Issue 33 https://doi.org/10.1021/jp013861i	journal	August 2002
Thermal Stability and Reducibility of Oxygen-Containing Functional Groups on Multiwalled Carbon Nanotube Surfaces: A Quantitative High-Resolution XPS and TPD/TPR Study Kundu, Shankhamala; Wang, Yuemin; Xia, Wei The Journal of Physical Chemistry C, Vol. 112, Issue 43 https://doi.org/10.1021/jp804413a	journal	October 2008
Adenine adlayers on Cu(111): XPS and NEXAFS study Tsud, Nataliya; Bercha, Sofiia; Ševčíková, Klára The Journal of Chemical Physics, Vol. 143, Issue 17 https://doi.org/10.1063/1.4935055	journal	November 2015
Biomolecular Damage Induced by Ionizing Radiation: The Direct and Indirect Effects of Low-Energy Electrons on DNA Alizadeh, Elahe; Orlando, Thomas M.; Sanche, Léon Annual Review of Physical Chemistry, Vol. 66, Issue 1 https://doi.org/10.1146/annurev-physchem-040513-103605	journal	April 2015
Low-Energy Electron-Induced DNA Damage: Effect of Base Sequence in Oligonucleotide Trimers Li, Zejun; Cloutier, Pierre; Sanche, Léon Journal of the American Chemical Society, Vol. 132, Issue 15 https://doi.org/10.1021/ja9099505	journal	April 2010
Low-energy (0-10 eV) electron transmission spectra of multilayer tryptophan films Leclerc, G.; Goulet, T.; Cloutier, P. The Journal of Physical Chemistry, Vol. 91, Issue 19 https://doi.org/10.1021/j100303a020	journal	September 1987
Soft X-ray and Low Energy Electron-Induced Damage to DNA under N ₂ and O ₂ Atmospheres Alizadeh, Elahe; Cloutier, Pierre; Hunting, Darel The Journal of Physical Chemistry B, Vol. 115, Issue 15 https://doi.org/10.1021/jp200947g	journal	April 2011
Bringing Electrons and Microarray Technology Together Solomun, T.; Sturm, H. The Journal of Physical Chemistry B, Vol. 111, Issue 36 https://doi.org/10.1021/jp075338v	journal	September 2007
Low‐Energy Electron‐Induced Strand Breaks in Telomere‐Derived DNA Sequences—Influence of DNA Sequence and Topology Rackwitz, Jenny; Bald, Ilko Chemistry – A European Journal, Vol. 24, Issue 18 https://doi.org/10.1002/chem.201705889	journal	February 2018
Image Contrast in Energy-Filtered BSE Images at Ultra-Low Accelerating Voltages Hashimoto, Yoichiro; Muto, Atsushi; Woods, Eric Microscopy Today, Vol. 24, Issue 3 https://doi.org/10.1017/s1551929516000390	journal	April 2016
Electron-Stimulated Desorption of H ^- from Condensed-Phase Deoxyribose Analogues: Dissociative Electron Attachment versus Resonance Decay into Dipolar Dissociation Antic, D.; Parenteau, L.; Sanche, L. The Journal of Physical Chemistry B, Vol. 104, Issue 19 https://doi.org/10.1021/jp000206m	journal	May 2000
Interaction of Self-Assembled Monolayers of DNA with Electrons: HREELS and XPS Studies Vilar, Manuel Rei; Botelho do Rego, Ana M.; Ferraria, Ana M. The Journal of Physical Chemistry B, Vol. 112, Issue 23 https://doi.org/10.1021/jp8008207	journal	June 2008
DNA Damage Induced by Low-Energy Electrons: Conversion of Thymine to 5,6-Dihydrothymine in the Oligonucleotide Trimer TpTpT Park, Yeunsoo; Li, Zejun; Cloutier, Pierre Radiation Research, Vol. 175, Issue 2 https://doi.org/10.1667/rr2381.1	journal	February 2011
Damage of DNA by Low Energy Electrons (< 3 eV) Bald, Ilko; Illenberger, Eugen; Kopyra, Janina Journal of Physics: Conference Series, Vol. 373 https://doi.org/10.1088/1742-6596/373/1/012008	journal	July 2012
Electronic Structure of Genomic DNA: A Photoemission and X-ray Absorption Study Kummer, Kurt; Vyalikh, Denis V.; Gavrila, Gianina The Journal of Physical Chemistry B, Vol. 114, Issue 29 https://doi.org/10.1021/jp1013237	journal	July 2010
Low-Energy Electron Transmission Through Thin-Film Molecular and Biomolecular Solids Naaman, R.; Sanche, L. ChemInform, Vol. 38, Issue 31 https://doi.org/10.1002/chin.200731257	journal	July 2007
How Do Low-Energy (0.1—2 eV) Electrons Cause DNA-Strand Breaks? Simons, Jack ChemInform, Vol. 38, Issue 1 https://doi.org/10.1002/chin.200701262	journal	January 2007
Transport of secondary electrons through coatings of ion-irradiated metallic nanoparticles Haume, Kaspar; de Vera, Pablo; Verkhovtsev, Alexey arXiv https://doi.org/10.48550/arxiv.1801.06894	text	January 2018

Cited By (2)

Electron scattering from tin tetrachloride (SnCl ₄ ) molecules Możejko, Paweł; Stefanowska-Tur, Sylwia; Ptasińska-Denga, Elżbieta The Journal of Chemical Physics, Vol. 151, Issue 6 https://doi.org/10.1063/1.5116307	journal	August 2019
Clustered DNA Damages induced by 0.5 to 30 eV Electrons Zheng, Yi; Sanche, Léon International Journal of Molecular Sciences, Vol. 20, Issue 15 https://doi.org/10.3390/ijms20153749	journal	July 2019

Similar Records

Vacuum ultraviolet photoionization of carbohydrates and nucleotides

Journal Article · Tue Jan 28 00:00:00 EST 2014 · Journal of Chemical Physics · OSTI ID:1559940

Shin, Joong-Won

Conformational characteristics of rigid cyclic nucleotides. II. The solution conformation of. cap alpha. -nucleoside 3',5'-cyclic monophosphates and the role of the 2'-hydroxyl group

Journal Article · Wed Nov 09 00:00:00 EST 1977 · J. Am. Chem. Soc.; (United States) · OSTI ID:1559940

MacCoss, M; Ezra, F S; Robins, M J; +1 more

Nitrogen K-edge x-ray absorption near edge structure of pyrimidine-containing nucleotides in aqueous solution

Journal Article · Thu May 07 00:00:00 EDT 2015 · Journal of Chemical Physics · OSTI ID:1559940

Shimada, Hiroyuki; Minami, Hirotake; Okuizumi, Naoto; +6 more

Related Subjects

74 ATOMIC AND MOLECULAR PHYSICS
XPS
electrons
nucleotides
radiation damage

Title: Low energy secondary electron induced damage of condensed nucleotides

Citation Formats

References (61)

Cited By (2)

Similar Records

Related Subjects