A novel methodology for characterizing strand-break termini and damaged bases in plasmid DNA exposed to ionizing radiation

Localization estimation of ionizing radiation-induced abasic sites in DNA in the solid state using fluorescence resonance energy transfer

Clustered DNA damage is considered an important factor in determining the biological consequences of ionizing radiation. In this study, we successfully estimated the localization of abasic sites (APs) in DNA exposed to ionizing radiation using fluorescence resonance energy transfer (FRET) without any involvement of repair enzyme functions. A linearized plasmid (pUC19 digested by Sma I) was irradiated with: (60)Co γ rays; (4)He(2+) (2.0 MeV/u) particles; and the (12)C(5+) (0.37 MeV/u) particles in the solid state. A donor or acceptor fluorescent probe with a nucleophilic O-amino group was used to label APs. The results showed that the (12)C(5+) particle likely produced close APs within a track. The apparent distance calculated from the observed FRET efficiency (E) of around 0.10 was estimated to be approximately 17 base pairs. On the other hand, E values of (60)Co γ rays and the (4)He(2+) beam were less than those of the (12)C(5+) beam, increased with increasing AP density (the average number of APs per base pair), and were slightly greater than those of randomly distributed APs. We propose that the FRET method provides a degree of localization regardless of whether an AP cluster is single-stranded or bistranded DNA damage.

A methodology for estimating localization of apurinic/apyrimidinic sites in DNA using fluorescence resonance energy transfer

We have developed a methodology for estimating localization of lesions on double-stranded DNA using fluorescence resonance energy transfer (FRET). We focused on apurinic/apyrimidinic (AP) sites, which are typical DNA lesions induced by radiation and chemicals and produced spontaneously under physiological conditions. Donor-acceptor fluorescent probes with O-amino groups (Alexa Fluor 350-Alexa Fluor 488 dye pair) were used for selectively labeling AP sites. pUC19 plasmid subjected to heat treatment (pH 5.2, 70 °C) was used as a model double-stranded DNA containing AP sites. The results of both FRET analysis and theoretical study enabled us to prove that AP sites induced by the heat treatment are distributed almost randomly along the DNA molecule. This methodology will be useful for estimating the risk of ionizing radiation and chemicals (e.g., pollutants and anticancer agents) based on the probability of producing "clustered DNA damage sites," which are considered to be less easily repairable and, therefore, more harmful to living systems.

Characterization of lesions induced in linear-formed plasmid DNA by valence ionization and Auger decay at carbon, nitrogen and oxygen

PURPOSE

To study the DNA lesions induced by the Auger decay of carbon, nitrogen, and oxygen using ultrasoft X-rays (USX) that are expected to be important with the DNA repair system of living cells.

MATERIALS AND METHODS

pUC19 plasmid DNA dry samples were irradiated with USX photons at 270 and 560 eV and (60)Co gamma-rays in vacuum at room temperature. The amounts of unaltered base release by the direct radiation effects were quantified using high-performance liquid chromatography. To quantify and characterize the strand break termini the rate at which snake venom phosphodiesterase (SVPD) digested irradiated DNA pretreated with and without calf intestine alkaline phosphatase was measured. Moreover, the piperidine-labile base lesions and abasic sites of the irradiated DNA were estimated using the SVPD method.

RESULTS

The yields of unaltered base release for 270, 560 eV photons and (60)Co gamma-rays were 0.016, 0.014, and 0.018 micromol/J, respectively. The total 3' termini for the three kinds of photons were around 0.1 micromol/J. The production of 3' termini with phosphate was found to be predominant with respect to that of 3'OH termini for the three kinds of radiation. The yield of piperidine-labile sites for 270 eV ( approximately 0.1 micromol/J) was slightly larger than that for 560 eV ( approximately 0.07 micromol/J) and also for gamma-rays ( approximately 0.082 micromol/J).

CONCLUSION

Although the Auger process in DNA-constituent atoms was expected to induce Auger-specific lesions in the molecule the chemical endpoints would have been covered with a large number of lesions produced from secondary electrons in the surrounding bulk DNA molecules. The present results, however, suggest that a low-energy electron field produced by the USX photons in the bulk DNA is basically not at all specific to DNA damage being produced when compared with the high-energy electron field produced by (60)Co gamma-rays.