Qualitative and quantitative analyses of the decomposition products that arise from the exposure of thymine to monochromatic ultrasoft X rays and 60Co gamma rays in the solid state

Side-by-side comparison of DNA damage induced by low-energy electrons and high-energy photons with solid TpTpT trinucleotide

The genotoxic effects of high-energy ionizing radiation have been largely attributed to the ionization of H2O leading to hydroxyl radicals and the ionization of DNA leading mostly to damage through base radical cations. However, the contribution of low-energy electrons (LEEs; ≤ 10 eV), which involves subionization events, has been considered to be less important than that of hydroxyl radicals and base radical cations. Here, we compare the ability of LEEs and high-energy X-ray photons to induce DNA damage using dried thin films of TpTpT trinucleotide as a simple and representative model for DNA damage. The main radiation-induced damage of TpTpT as measured by high-performance liquid chromatography (HPLC) with UV detection and HPLC coupled to tandem mass spectrometry analyses included thymine release (-Thy), strand breaks (pT, Tp, pTpT, TpTp, and TpT), and the formation of base modifications [5,6-dihydrothymine (5,6-dhT), 5-hydroxymethyluracil (5-hmU), and 5-formyluracil (5-fU)]. The global profile of products was very similar for both types of radiation indicating converging pathways of formation. The percent damage of thymine release, fragmentation, and base modification was 20, 19, and 61 for high-energy X-rays, respectively, compared to 35, 13, and 51 for LEEs (10 eV). Base release was significantly lower for X-rays. In both cases, phosphodiester bond cleavage gave mononucleotides (pT and Tp) and dinucleotides (pTpT and TpTp) containing a terminal phosphate as the major fragments. For base modifications, the ratio of reductive (5,6-dhT) to oxidative products (5-hmU plus 5-fU) was 0.9 for high-energy X-rays compared to 1.7 for LEEs. These results indicate that LEEs give a similar profile of products compared to ionizing radiation.

DNA damage induced by low-energy electrons: conversion of thymine to 5,6-dihydrothymine in the oligonucleotide trimer TpTpT

Low-energy electrons (LEE) induce single- and double-strand breaks in DNA. To investigate the mechanism of LEE-induced DNA damage, nucleotides and short oligonucleotide were irradiated with monoenergetic electrons in the solid state and the modifications were observed by chemical analyses. With 10 eV electrons and TpTpT as the target, approximately one-third of the total damage of TpTpT involves cleavage of the phosphodiester-sugar bond (C-O) and the N-glycosidic bond (C-N). Here we focus on the remaining two-thirds of the damage. The major products were observed to elute between TpT and TpTpT on the HPLC chromatogram. Of these products, three modifications were identified as XpTpT, TpXpT and TpTpX, where X  =  5,6-dihydrothymine, on the basis of comparison with standard compounds using HPLC and mass spectrometry. These results suggest that 5,6-dihydrothymine is a major product of the reaction of LEE with DNA.

“In situ” observation of guanine radicals induced by ultrasoft X‐ray irradiation around the K‐edge regions of nitrogen and oxygen

PURPOSE

In order to understand the molecular mechanism of nucleobase damage caused by ultrasoft X-ray irradiation, guanine radicals have been studied using an X-band EPR (electron paramagnetic resonance) spectrometer installed in a synchrotron soft X-ray beamline.

MATERIALS AND METHODS

Guanine pellets were irradiated under vacuum with ultrasoft X-rays obtained from a soft X-ray beamline (BL23SU) in SPring-8. The energy regions around the nitrogen (0.4 keV) and oxygen (0.5 keV) K-edges were chosen for the irradiation. The ultrasoft X-ray irradiation and EPR measurements were carried out simultaneously at low temperature, 20 K and 77 K.

RESULTS

The EPR spectrum observed during irradiation was clearly distinguishable from that of the stable radical, which still exists after exposure to ultrasoft X-rays at 77 K. The spectrum of the short-lived radicals consisted of two components, which exhibited different EPR microwave power saturation. The EPR signal intensities increased linearly with increasing dose rate (photon flux density). These signals immediately disappeared when the beam was turned off, even when irradiated at lower temperature (20 K). At the energy of the oxygen K-resonance excitation (539 eV) the signal intensity was clearly increased to more than five times that obtained on the lower energy side (526 eV). On the other hand, the enhancement was insignificant above and below the nitrogen K-edge (401 eV). The singlet EPR signal of the stable radical was similar to that reported previously in the literature for y-irradiated guanine.

CONCLUSION

The short-lived radical species observed were mainly induced as a result of the final state of the resonant Auger process on oxygen atoms existing solely in the carbonyl group in guanine. Auger events at the other atoms in guanine (namely, carbon and nitrogen) do not induce this radical process to any great extent, even though the abundance of these atoms (i.e. the sum of their photoabsorption cross sections) is dominant in the guanine molecule.

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.

Ion Desorption from DNA Components Irradiated with 0.5 keV Ultrasoft X-Ray Photons

Positive ion desorption from thin films of DNA components, 2-deoxy-d-ribose, thymine, thymidine (dThd), and thymidine 5'-monophosphate (dTMP) was investigated in the oxygen K- shell edge excitation region using synchrotron ultrasoft X rays (538 eV). A large number of molecular fragments, H(+), CH(x)(+), C(2)H(x)(+), CO(+), CH(x)O(+), C(3)H(x)(+), C(2)H(x)O(+) and C(3)H(x)O(+) (x = 1, 2 and 3), were observed as desorbed ions from 2-deoxy-d-ribose. Some of these ions are related to simultaneous bond scission at particular C-C and C-O (or C-C) bonds in the furanose ring structure in the 2-deoxy-d-ribose molecule, indicating that the impact of photons on the oxygen atom and the impact of ejected secondary electrons (e.g. Auger electrons) cause an intense destruction of the furanose ring structure. In thymine thin films, H(+), CH(x)(+), CO(+), CH(x)O(+), C(2)H(x)N(+) and CH(x)NO(+) (x = 1, 2 and 3) fragments were observed. The yields of these ions were smaller than the yields from 2-deoxy-d-ribose. The desorption of CH(3)(+) from thymine might induce a molecular conversion from thymine to uracil. The mass patterns of dThd and dTMP, and especially that of dTMP, were similar to that of 2-deoxy-d-ribose, indicating that a number of ions were generated at the sugar site, even in the nucleotide molecule. It is therefore predicted that the sugar moiety is more fragile than the thymine base.