Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Low energy secondary electron induced damage of condensed nucleotides

Abstract

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 smallmore » 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.« less

Authors:
ORCiD logo [1];  [1];  [2];  [1]; ORCiD logo [1]
+ Show Author Affiliations
  1. Georgia Inst. of Technology, Atlanta, GA (United States)
  2. Argonne National Lab. (ANL), Lemont, IL (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1559940
Alternate Identifier(s):
OSTI ID: 1523698
Grant/Contract Number:  
AC02-06CH11357; FG02-02ER15337
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 150; Journal Issue: 20; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
74 ATOMIC AND MOLECULAR PHYSICS; XPS; electrons; nucleotides; radiation damage

Citation Formats

McKee, A. D., Schaible, M. J., Rosenberg, R. A., Kundu, S., and Orlando, Thomas M. Low energy secondary electron induced damage of condensed nucleotides. United States: N. p., 2019. Web. doi:10.1063/1.5090491.
Copy to clipboard
McKee, A. D., Schaible, M. J., Rosenberg, R. A., Kundu, S., & Orlando, Thomas M. Low energy secondary electron induced damage of condensed nucleotides. United States. https://doi.org/10.1063/1.5090491
Copy to clipboard
McKee, A. D., Schaible, M. J., Rosenberg, R. A., Kundu, S., and Orlando, Thomas M. Tue . "Low energy secondary electron induced damage of condensed nucleotides". United States. https://doi.org/10.1063/1.5090491. https://www.osti.gov/servlets/purl/1559940.
Copy to clipboard
@article{osti_1559940,
title = {Low energy secondary electron induced damage of condensed nucleotides},
author = {McKee, A. D. and Schaible, M. J. and Rosenberg, R. A. and Kundu, S. and Orlando, Thomas M.},
abstractNote = {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.},
doi = {10.1063/1.5090491},
journal = {Journal of Chemical Physics},
number = 20,
volume = 150,
place = {United States},
year = {Tue May 28 00:00:00 EDT 2019},
month = {Tue May 28 00:00:00 EDT 2019}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1063/1.5090491
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 9 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Electron Attachment to Microhydrated Deoxycytidine Monophosphate
journal, April 2018

  • Kočišek, Jaroslav; Sedmidubská, Barbora; Indrajith, Suvasthika
  • The Journal of Physical Chemistry B, Vol. 122, Issue 20
  • DOI: 10.1021/acs.jpcb.8b03033

Understanding the Interaction between Low-Energy Electrons and DNA Nucleotides in Aqueous Solution
journal, July 2015

  • McAllister, Maeve; Smyth, Maeve; Gu, Bin
  • The Journal of Physical Chemistry Letters, Vol. 6, Issue 15
  • DOI: 10.1021/acs.jpclett.5b01011

The measurement of molecular fragments from DNA components using synchrotron radiation
journal, March 2003

X-ray induced damage in DNA monitored by X-ray photoelectron spectroscopy
journal, August 2008

  • Ptasińska, Sylwia; Stypczyńska, Agnieszka; Nixon, Tony
  • The Journal of Chemical Physics, Vol. 129, Issue 6
  • DOI: 10.1063/1.2961027

The relationship between interfacial bonding and radiation damage in adsorbed DNA
journal, January 2014

  • Rosenberg, R. A.; Symonds, J. M.; Vijayalakshmi, K.
  • Phys. Chem. Chem. Phys., Vol. 16, Issue 29
  • DOI: 10.1039/c4cp01649a

The interaction of a protein–DNA surface complex with low-energy electrons
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
journal, November 1976

  • Henke, Burton L.; Smith, Jerel A.; Attwood, David T.
  • Applied Physics Letters, Vol. 29, Issue 9
  • DOI: 10.1063/1.89176

Inelastic electron interaction (attachment/ionization) with deoxyribose
journal, May 2004

  • Ptasińska, S.; Denifl, S.; Scheier, P.
  • The Journal of Chemical Physics, Vol. 120, Issue 18
  • DOI: 10.1063/1.1690231

Mechanism and Site of Attack for Direct Damage to DNA by Low-Energy Electrons
journal, May 2005

Chemical Basis of DNA Sugar−Phosphate Cleavage by Low-Energy Electrons
journal, November 2005

  • Zheng, Yi; Cloutier, Pierre; Hunting, Darel J.
  • Journal of the American Chemical Society, Vol. 127, Issue 47
  • DOI: 10.1021/ja054129q

Spur energy distributions in liquid water using a generalized oscillator strength from inelastic X-ray scattering measurements
journal, December 2017

Damage Induced to DNA by Low-Energy (0−30 eV) Electrons under Vacuum and Atmospheric Conditions
journal, July 2009

  • Brun, Émilie; Cloutier, Pierre; Sicard-Roselli, Cécile
  • The Journal of Physical Chemistry B, Vol. 113, Issue 29
  • DOI: 10.1021/jp902540k

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
journal, September 2008

  • Schyman, Patric; Laaksonen, Aatto
  • Journal of the American Chemical Society, Vol. 130, Issue 37
  • DOI: 10.1021/ja805000g

Measurement of inelastic cross sections for low-energy electron scattering from DNA bases
journal, May 2011

  • Michaud, Marc; Bazin, Marc; Sanche, Le´on
  • International Journal of Radiation Biology, Vol. 88, Issue 1-2
  • DOI: 10.3109/09553002.2011.577505

Quantitative analysis of saccharides by X-ray photoelectron spectroscopy
journal, June 2009

  • Stevens, Joanna S.; Schroeder, Sven L. M.
  • Surface and Interface Analysis, Vol. 41, Issue 6
  • DOI: 10.1002/sia.3047

Low-Energy Electron Transmission through Thin-Film Molecular and Biomolecular Solids
journal, May 2007

Dissociative electron attachment to hydrated single DNA strands
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
journal, May 2006

  • Tan, Zhenyu; Xia, Yueyuan; Zhao, Mingwen
  • Radiation and Environmental Biophysics, Vol. 45, Issue 2
  • DOI: 10.1007/s00411-006-0049-0

Lack of proportionality of total electron yield and soft x-ray absorption coefficient
journal, January 2000

  • Henneken, H.; Scholze, F.; Ulm, G.
  • Journal of Applied Physics, Vol. 87, Issue 1
  • DOI: 10.1063/1.371854

Side-by-Side Comparison of DNA Damage Induced by Low-Energy Electrons and High-Energy Photons with Solid TpTpT Trinucleotide
journal, August 2013

  • Park, Yeunsoo; Peoples, Anita R.; Madugundu, Guru S.
  • The Journal of Physical Chemistry B, Vol. 117, Issue 35
  • DOI: 10.1021/jp405397m

Absolute cross section for low-energy-electron damage to condensed macromolecules: A case study of DNA
journal, September 2012

Single, Double, and Multiple Double Strand Breaks Induced in DNA by 3−100 eV Electrons
journal, April 2003

  • Huels, Michael A.; Boudaïffa, Badia; Cloutier, Pierre
  • Journal of the American Chemical Society, Vol. 125, Issue 15
  • DOI: 10.1021/ja029527x

How Do Low-Energy (0.1−2 eV) Electrons Cause DNA-Strand Breaks?
journal, October 2006

  • Simons, Jack
  • Accounts of Chemical Research, Vol. 39, Issue 10
  • DOI: 10.1021/ar0680769

Resonant Formation of DNA Strand Breaks by Low-Energy (3 to 20 eV) Electrons
journal, March 2000

Halogen Anion Formation in 5-Halouracil Films: X Rays Compared to Subionization Electrons
journal, February 1999

  • Klyachko, Dimitri V.; Huels, Michael A.; Sanche, Léon
  • Radiation Research, Vol. 151, Issue 2
  • DOI: 10.2307/3579768

Resonant dissociation of DNA bases by subionization electrons
journal, January 1998

  • Huels, Michael A.; Hahndorf, Ina; Illenberger, Eugen
  • The Journal of Chemical Physics, Vol. 108, Issue 4
  • DOI: 10.1063/1.475503

On the mechanism of anion desorption from DNA induced by low energy electrons
journal, October 2006

  • Ptasińska, Sylwia; Sanche, Léon
  • The Journal of Chemical Physics, Vol. 125, Issue 14
  • DOI: 10.1063/1.2338320

Transport of secondary electrons through coatings of ion-irradiated metallic nanoparticles
journal, June 2018

  • Haume, Kaspar; de Vera, Pablo; Verkhovtsev, Alexey
  • The European Physical Journal D, Vol. 72, Issue 6
  • DOI: 10.1140/epjd/e2018-90050-x

Quantitative analysis of complex amino acids and RGD peptides by X-ray photoelectron spectroscopy (XPS): Quantitative XPS analysis of amino acids and RGD peptides
journal, April 2013

  • Stevens, Joanna S.; de Luca, Alba C.; Pelendritis, Michalis
  • Surface and Interface Analysis, Vol. 45, Issue 8
  • DOI: 10.1002/sia.5261

Unified Mechanism for the Generation of Isolated and Clustered DNA Damages by a Single Low Energy (5–10 eV) Electron
journal, January 2017

  • Shao, Yu; Dong, Yanfang; Hunting, Darel
  • The Journal of Physical Chemistry C, Vol. 121, Issue 4
  • DOI: 10.1021/acs.jpcc.6b12110

Low-energy electron diffraction and induced damage in hydrated DNA
journal, May 2008

  • Orlando, Thomas M.; Oh, Doogie; Chen, Yanfeng
  • The Journal of Chemical Physics, Vol. 128, Issue 19
  • DOI: 10.1063/1.2907722

Detection of energy-selected secondary electrons in coincidence with energy-loss events in thin carbon foils
journal, November 1991

Precursors of Solvated Electrons in Radiobiological Physics and Chemistry
journal, June 2012

  • Alizadeh, Elahe; Sanche, Léon
  • Chemical Reviews, Vol. 112, Issue 11
  • DOI: 10.1021/cr300063r

Damage to Model DNA Fragments from Very Low-Energy (<1 eV) Electrons
journal, May 2004

  • Berdys, Joanna; Anusiewicz, Iwona; Skurski, Piotr
  • Journal of the American Chemical Society, Vol. 126, Issue 20
  • DOI: 10.1021/ja049876m

Damage to amino acid–nucleotide pairs induced by 1 eV electrons
journal, January 2010

  • Ptasińska, Sylwia; Li, Zejun; Mason, Nigel J.
  • Physical Chemistry Chemical Physics, Vol. 12, Issue 32
  • DOI: 10.1039/b926267a

Probing low-energy electron induced DNA damage using single photon ionization mass spectrometry
journal, November 2008

  • Chen, Yanfeng; Aleksandrov, Alexandr; Orlando, Thomas M.
  • International Journal of Mass Spectrometry, Vol. 277, Issue 1-3
  • DOI: 10.1016/j.ijms.2008.07.003

Energy Thresholds of DNA Damage Induced by UV Radiation: An XPS Study
journal, April 2015

  • Gomes, P. J.; Ferraria, A. M.; Botelho do Rego, A. M.
  • The Journal of Physical Chemistry B, Vol. 119, Issue 17
  • DOI: 10.1021/acs.jpcb.5b01439

Low energy electron-driven damage in biomolecules
journal, August 2005

Adsorption of carbonyl compounds on clean and modified Cu(110) surfaces: A combined eels-ups study
journal, May 1990

DNA Damage Induced by Low-Energy Electrons: Electron Transfer and Diffraction
journal, May 2006

Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays
journal, December 2014

  • Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie
  • Scientific Reports, Vol. 4, Issue 1
  • DOI: 10.1038/srep07391

Cleavage Enhancement of Specific Chemical Bonds in DNA by Cisplatin Radiosensitization
journal, April 2013

  • Xiao, Fangxing; Luo, Xinglan; Fu, Xianzhi
  • The Journal of Physical Chemistry B, Vol. 117, Issue 17
  • DOI: 10.1021/jp400852p

Mechanism for Damage to DNA by Low-Energy Electrons †
journal, August 2002

  • Barrios, Robyn; Skurski, Piotr; Simons, Jack
  • The Journal of Physical Chemistry B, Vol. 106, Issue 33
  • DOI: 10.1021/jp013861i

Thermal Stability and Reducibility of Oxygen-Containing Functional Groups on Multiwalled Carbon Nanotube Surfaces: A Quantitative High-Resolution XPS and TPD/TPR Study
journal, October 2008

  • Kundu, Shankhamala; Wang, Yuemin; Xia, Wei
  • The Journal of Physical Chemistry C, Vol. 112, Issue 43
  • DOI: 10.1021/jp804413a

Adenine adlayers on Cu(111): XPS and NEXAFS study
journal, November 2015

  • Tsud, Nataliya; Bercha, Sofiia; Ševčíková, Klára
  • The Journal of Chemical Physics, Vol. 143, Issue 17
  • DOI: 10.1063/1.4935055

Biomolecular Damage Induced by Ionizing Radiation: The Direct and Indirect Effects of Low-Energy Electrons on DNA
journal, April 2015

Low-Energy Electron-Induced DNA Damage: Effect of Base Sequence in Oligonucleotide Trimers
journal, April 2010

  • Li, Zejun; Cloutier, Pierre; Sanche, Léon
  • Journal of the American Chemical Society, Vol. 132, Issue 15
  • DOI: 10.1021/ja9099505

Low-energy (0-10 eV) electron transmission spectra of multilayer tryptophan films
journal, September 1987

  • Leclerc, G.; Goulet, T.; Cloutier, P.
  • The Journal of Physical Chemistry, Vol. 91, Issue 19
  • DOI: 10.1021/j100303a020

Soft X-ray and Low Energy Electron-Induced Damage to DNA under N 2 and O 2 Atmospheres
journal, April 2011

  • Alizadeh, Elahe; Cloutier, Pierre; Hunting, Darel
  • The Journal of Physical Chemistry B, Vol. 115, Issue 15
  • DOI: 10.1021/jp200947g

Bringing Electrons and Microarray Technology Together
journal, September 2007

  • Solomun, T.; Sturm, H.
  • The Journal of Physical Chemistry B, Vol. 111, Issue 36
  • DOI: 10.1021/jp075338v

Low‐Energy Electron‐Induced Strand Breaks in Telomere‐Derived DNA Sequences—Influence of DNA Sequence and Topology
journal, February 2018

Image Contrast in Energy-Filtered BSE Images at Ultra-Low Accelerating Voltages
journal, April 2016

Interaction of Self-Assembled Monolayers of DNA with Electrons: HREELS and XPS Studies
journal, June 2008

  • Vilar, Manuel Rei; Botelho do Rego, Ana M.; Ferraria, Ana M.
  • The Journal of Physical Chemistry B, Vol. 112, Issue 23
  • DOI: 10.1021/jp8008207

DNA Damage Induced by Low-Energy Electrons: Conversion of Thymine to 5,6-Dihydrothymine in the Oligonucleotide Trimer TpTpT
journal, February 2011

  • Park, Yeunsoo; Li, Zejun; Cloutier, Pierre
  • Radiation Research, Vol. 175, Issue 2
  • DOI: 10.1667/rr2381.1

Damage of DNA by Low Energy Electrons (< 3 eV)
journal, July 2012

Electronic Structure of Genomic DNA: A Photoemission and X-ray Absorption Study
journal, July 2010

  • Kummer, Kurt; Vyalikh, Denis V.; Gavrila, Gianina
  • The Journal of Physical Chemistry B, Vol. 114, Issue 29
  • DOI: 10.1021/jp1013237

Low-Energy Electron Transmission Through Thin-Film Molecular and Biomolecular Solids
journal, July 2007

How Do Low-Energy (0.1—2 eV) Electrons Cause DNA-Strand Breaks?
journal, January 2007

Transport of secondary electrons through coatings of ion-irradiated metallic nanoparticles
text, January 2018

    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Electron scattering from tin tetrachloride (SnCl 4 ) molecules
    journal, August 2019

    • Możejko, Paweł; Stefanowska-Tur, Sylwia; Ptasińska-Denga, Elżbieta
    • The Journal of Chemical Physics, Vol. 151, Issue 6
    • DOI: 10.1063/1.5116307

    Clustered DNA Damages induced by 0.5 to 30 eV Electrons
    journal, July 2019

    • Zheng, Yi; Sanche, Léon
    • International Journal of Molecular Sciences, Vol. 20, Issue 15
    • DOI: 10.3390/ijms20153749

    Clustered DNA Damages induced by 0.5 to 30 eV Electrons
    journal, July 2019

    • Zheng, Yi; Sanche, Léon
    • International Journal of Molecular Sciences, Vol. 20, Issue 15
    • DOI: 10.3390/ijms20153749
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: