Dissociation of a Model DNA Compound dApdA by Monochromatic Soft X-rays in Solids and Comments on the High Selectivity for 3′ Breakage in the Phosphoester Bond

Abstract

The dissociation products of dApdA (2′-deoxyadenylyl-(3′-5′)-2′-deoxyadenosine) irradiated in the solid state by highly monochromatic soft X-rays (energy resolution, < 10⁻³) near the K-edge of phosphorus were analysed using thin-layer chromatography. The major chemical species identified were adenine base and 5′-dAMP in approximately equal amounts, indicating that the dissociation occurred between the 3′ carbon (C_3′) of deoxypentose and its adjacent phosphorus over the energy range of 2·147–2·167 keV, including the K-edge resonance absorption of phosphorus at 2·153 keV. In conjunction with the accumulated data on the degradation of dApdA and related oligonucleotides by vacuum-UV radiation (above 7 eV), which generally indicate a simple, selective dissociation at the 3′ side of the deoxypentose as observed with the soft X-rays, an hypothesis is presented on the molecular mechanism of radiation-induced breakage of phosphoester bonds that led to the selective 3′ breakage, based on the differential flexibility of torsion angles of C_3′–O_3′–P and C_4′–C_5′–O_5′–P groups in relation to those of the sugar ring.