DNA radiolysis. Mapping of the gene regulation domains

Abstract

Ionizing radiations induce strand breaks and modifications of nucleotides (base and/or sugar) in DNA. In aerated solution, the damages are mainly due to the attack of DNA by the hydroxyl radicals (OH ·) issued from the radiolysis of water. The lesions occur at every nucleotides along the DNA molecule. For γ-rays, β-rays and fast neutrons, we have determined at each nucleotide the probability of strand breakage at neutral pH and the probability of base and sugar modification leading also to strand breakage after an alkaline treatment. The method of sequencing gel electrophoresis was used for this purpose. We have shown that the probability of getting a radiation induced damage at a given nucleotide is modulated by: i) the chemical nature of this nucleotide, ii) the local conformation determined by the sequence of nucleotides and by DNA strandedness (single or double stranded), iii) the type of structure to which the nucleotide belongs (right-handed B- or left-handed Z-DNA) and iv) the presence of proteins specifically (e.g. repressors) or nonspecifically (histones or histone-like) bound to DNA. Therefore, radiolysis may be a convenient tool for mapping gene regulation domains in which DNA is often in non-canonical B forms or is in interaction with regulatory proteins.