Sequence-dependent variations of DNA structure modulate radiation-induced strand breakage

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Abstract
Using a 80 base pair DNA fragment, the sequencedependence was compared for: (i) the probability of fast neutrons induced strand breakage, (ii) the accessibility of the H4- and H5-atoms to OH attack, (iii) the width of the minor groove, and (iv) the probability of OH reactions with H4- or H5- atoms. The probability of strand breakage was measured using sequencing gel electrophoresis. The accessibility and the probability of reaction were calculated for the energy-minimized modelled DNA fragment. A Monte-Carlo simulation was used for calculating the probabilities of H-atom abstraction by OH. It was observed that reduced breakage occurs in sequences exhibiting low accessibility of H4 and H5 2 and low probability of H-atom abstraction by OH, due to a narrow, minor groove. This shows that the breakage probability at a given nucleotide site is not determined by the chemical nature of the nucleotide (A, T, G or C), but mainly by the local sequence-modulated intrinsic structure. Fitting the experimental results with the calculated probabilities of reaction suggests that a C4-centered radical evolves towards a strand break three times more efficiently than the C5 one, and that half of the breaks occur via the 4-path and half via the 5-path.