Sequence-dependent variations of DNA structure modulate radiation-induced strand breakage.
Using a 80 base pair DNA fragment, the sequence-dependence 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.
Sy
D
D
Centre de Biophysique Moléculaire, CNRS, Orléans, France.
Savoye
C
C
Begusova
M
M
Michalik
V
V
Charlier
M
M
Spotheim-Maurizot
M
M
D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000528:radiation effects*; D004249:DNA Damage; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000235:genetics
D004247:DNA