Process_DNADamage – DNA damage

Name
WID Process_DNADamage
Name DNA damage
 
Implementation
Initialization order 17 View in model
 
Reactions
Chemical reactions View in model
 
Parameters
Parameters View in model
 
Comments
Comments Simulates a spectrum of DNA lesions repaired by base excision repair, nucleotide excision repair, and homologous recombination repair: DNA strand breaks: caused by hydrolysis and beta-elimination of abasic sites ionizing radiation (alpha, beta particles, protons, electrons, gamma rays) Spontaneous base loss Base damage: caused by Spontaneous deamination oxidation -- oxygen radicals generated by metabolism, ionizing radiation, chemicals alkylation -- carbon radicals generated by metabolism, ionizing radiation, chemicals amidation -- nitrogen radicals generated by metabolism, ionizing radiation, chemicals Intrastrand cross links: caused by UV-B induced cyclization The simulation does not consider the following types of DNA damage: interstrand cross links: caused by bifunctional akylating agents psoralens DNA-protein cross links Sugar-phosphate damage other than strand breaks DNA gaps Additionally, the simulation does not consider mutiple damages per base or sugar-phosphate. Categorizes strand breaks in DNA segments (216 bases) according to scheme described in the track structure model literature [PUB_0486]: Symbol Definition NB no strand break SSB single strand break SSB+ multiple single strand breaks on segment all on same strand 2SSB single strand breaks on both strand separated by at least 10 bases on DNA segment DSB two single strand breaks on opposite strands within 10 bases DSB+ double strand break with additional strand break on DNA segment DSB++ two single strand breaks on same DNA segment References Errol C Friedberg, Graham C Walker, and Wolfram Siede (1995). DNA Repair and Mutagenesis. ASM Press: Washington, DC. [PUB_0461] Nikjoo H, O'Neill P, Goodhead DT, and Terrissol M. Computational modelling of low-energy electron-induced DNA damage by early physical and chemical events (1997). Int J Radiat Biol. 71(5): 467-83. [PUB_0486]
References
  1. Friedberg EC, Walker GC, Siede W, Wood RD, Schultz RA, Ellenberger T. DNA repair and mutagenesis. ASM Press (2006). WholeCell: PUB_0461, ISBN: 9781555813192

  2. Nikjoo H, O'Neill P, Goodhead DT, Terrissol M. Computational modelling of low-energy electron-induced DNA damage by early physical and chemical events. Int J Radiat Biol 71, 467-83 (1997). WholeCell: PUB_0486, PubMed: 9191891

 
Metadata
Created 2012-10-01 15:07:35
Last updated 2012-10-01 15:13:59