Oligonucleotide chip assay for quantification of gamma ray-induced single strand breaks

An oligonucleotide chip assay was designed for direct quantification of single strand breaks (SSBs) induced by gamma-ray irradiation. The oligonucleotides used were 20-mers, which were short enough to produce only a single strand break within a single oligonucleotide. The two ends of the oligonucleotides were labeled with fluorescein and biotin, respectively. The biotinylated ends of the oligonucleotides were immobilized on a silicon wafer chip treated with (3-aminopropyl)triethoxysilane (APTES), glutaraldehyde, and avidin. The DNA fragments cleaved by gamma-ray irradiation were detected by a laser-induced fluorescence (LIF) detection system. The gamma-ray-induced SSBs were quantified using a calibration curve (fluorescence intensity versus gamma-ray dose) without the need for complicated mathematical calculation based on gel-based separation. The experimentally determined gamma-ray-induced SSBs yield was almost equal to the theoretical value derived from gel electrophoresis of plasmid DNAs and DNA surface coverage.