title: The Influence of DNA Configuration on the Direct Strand Break Yield.
abstract: OBJECTIVE
  To study the influence of DNA configuration on the direct damage yield. No indirect effect has been accounted for.
  
  
  METHODS
  The GEANT4-DNA code was used to simulate the interactions of protons and alpha particles with geometrical models of the A-, B-, and Z-DNA configurations. The direct total, single, and double strand break yields and site-hit probabilities were determined. Certain features of the energy deposition process were also studied.
  
  
  RESULTS
  A slight increase of the site-hit probability as a function of the incident particle linear energy transfer was found for each DNA configuration. Each DNA form presents a well-defined site-hit probability, independently of the particle linear energy transfer. Approximately 70% of the inelastic collisions and ~60% of the absorbed dose are due to secondary electrons. These fractions are slightly higher for protons than for alpha particles at the same incident energy.
  
  
  CONCLUSIONS
  The total direct strand break yield for a given DNA form depends weakly on DNA conformation topology. This yield is practically determined by the target volume of the DNA configuration. However, the double strand break yield increases with the packing ratio of the DNA double helix; thus, it depends on the DNA conformation.
authors.affiliation: Gleb Wataghin Institute of Physics, State University of Campinas, 13083-859 Campinas, SP, Brazil.
authors.forename: M A
authors.initials: MA
authors.lastname: Bernal
authors.affiliation: Radiological Sciences Laboratory, State University of Rio de Janeiro, 20550-900 Rio de Janeiro, RJ, Brazil.
authors.forename: C E
authors.initials: CE
authors.lastname: deAlmeida
authors.affiliation: Centre d'Etudes Nucléaires de Bordeaux-Gradignan, University of Bordeaux, 33175 Gradignan, France.
authors.forename: S
authors.initials: S
authors.lastname: Incerti
authors.affiliation: Centre d'Etudes Nucléaires de Bordeaux-Gradignan, University of Bordeaux, 33175 Gradignan, France.
authors.forename: C
authors.initials: C
authors.lastname: Champion
authors.affiliation: Ecoanalytica, Moscow 119899, Russia ; Geant4 Associates International Ltd., West Yorkshire HX7 7BT, UK.
authors.forename: V
authors.initials: V
authors.lastname: Ivanchenko
authors.affiliation: Department of Physics, Faculty of Sciences, Saint Joseph University, Beirut 1107 2050, Lebanon.
authors.forename: Z
authors.initials: Z
authors.lastname: Francis
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D053903:DNA Breaks, Double-Stranded / Q000528:radiation effects*; D044704:DNA, A-Form / Q000737:chemistry* / Q000528:radiation effects; D059371:DNA, B-Form / Q000737:chemistry* / Q000528:radiation effects; D043542:DNA, Z-Form / Q000737:chemistry* / Q000528:radiation effects; D006801:Humans; D018499:Linear Energy Transfer; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D011336:Probability; D012984:Software
chemical_list: D044704:DNA, A-Form; D059371:DNA, B-Form; D043542:DNA, Z-Form