SEQUENCE-DEPENDENT VARIATIONS OF DNA-STRUCTURE MODULATE RADIATION-INDUCED STRAND BREAKAGE

Using a 80 base pair DNA fragment, the sequence-dependence was compare d for: (i) the probability of fast neutrons induced strand breakage, ( ii) the accessibility of the H4'- and H5'-atoms to OH. attack, (iii) t he width of the minor groove, and (iv) the probability of OH. reaction s with H4'- or H5'-atoms. The probability of strand breakage. was meas ured using sequencing gel electrophoresis. The accessibility and the p robability of reaction were calculated for the energy-minimized modell ed DNA fragment. A Monte-Carro simulation was used for calculating the probabilities of H-atom abstraction by OH.. It was observed that redu ced breakage occurs in sequences exhibiting low accessibility of H4' a nd H5'2 and low probability of H-atom abstraction by OH., due to a nar row, minor groove. This shows that the breakage probability at a given nucleotide site is not determined by the chemical nature of the nucle otide (A, T, G or C), but mainly by the local sequence-modulated intri nsic structure. Fitting the experimental results with the calculated p robabilities 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.