Take a look at the phosphorous (gold particle) in the right corner that is being oxidized by OH and becomes mechanically separated from the backbone (single strand break). Two dash-lines show the broken bonds. The remaining H (the white particle) that was initially in OH, forms a bond with the Thymine (a base damage). The distorted thymine and sugar-ring destroys the base-pair hydrogen bonds and base stacking network. This is a real time simulation performed up to 2.5 pico-second (2.5 10^-12 s) using ReaxFF molecular dynamics. This simulation clearly demonstrates a single strand break on a realistic chunk of DNA for the first time (to the best of my knowledge). Color codes: carbon, oxygen, nitrogen, phosphorus and hydrogen atoms are shown as green, red, blue,
gold and white.
Ref: Abolfath, van Duin, Brabec, J. Phys. Chem. . A115, 11045 (2011).
2) DNA single strand break (DNA-SSB)
3) A ppt presentation on SSB chemical pathway
4) DNA single strand break (DNA-SSB). Another view.
3) DNA double strand break (DNA-DSB) by OH free radicals produced by ionizing radiation, mega-voltage X-ray and/or gamma-ray. Two pair of dash-lines show sites of damage.
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