Free radical yields in crystalline DNA X-irradiated at 4 K

Abstract

The objective of this work is to determine the extent to which various structural factors influence the yield of trapped free radicals, G(tfr), in DNA irradiated at 4 K. G(tfr) was measured in a series of 13 different oligodeoxynucleotides using electron paramagnetic resonance (EPR) spectroscopy. Each sample consisted of crystalline duplex DNA for which the crystal structure was verified to be that reported in the literature. We find that the G(tfr) of these samples is remarkably high, ranging from 0.55 to 0.75 micromol/J. The standard deviation in G(tfr) for a given crystal structure is generally small, typically less than +/-10%. Furthermore, G(tfr) does not correlate with DNA base sequence, conformation, counterion or length of base stacking. Two observations point to the importance of DNA packing: (1) The radical yields in crystalline DNA are greater than those determined previously for DNA films (0.2 to 0.5 micromol/J); and (2) the variability in G(tfr) is less in DNA crystals than in DNA films. We conclude that closely packed DNA maximizes radical trapping by minimizing the interhelical solvent space. Furthermore, the high efficiency of electron and hole trapping at 4 K is not consistent with DNA possessing properties of a metallic conductor. Indeed, it behaves as an insulator, whether it is in A-, B-, or Z-form and whether base stacking is short- (8 bp) or long-range (>1000 bp).

FIG. 1

Single-scan 40 mT Q-band EPR spectra taken at 4 K of poly-crystalline A-DNA d(GCGGGCCCGC) (II) after a dose of 22 kGy (top spectrum), polycrystalline B-DNA d(CGCGAATTCGCG) after a dose of 17 kGy (middle spectrum), and polycrystalline Z-DNA d(CGCGCG) (I) after a dose of 22 kGy (bottom spectrum). The position of g = 2.0023 is indicated by the vertical line.

FIG. 2

Free radical concentration as a function of X-ray dose for 11 different crystalline systems irradiated and measured at 4 K. The initial slopes of the individual data sets using the linear region of the data <5 kGy are plotted. From the slopes of these lines, we determine the free radical yields of the crystalline DNA samples.

FIG. 3

Model of free radical trapping in (panel a) film and (panel b) crystalline DNA. As ionizing radiation passes through the DNA matrix, it produces holes and electrons, represented by dark circles. In the film DNA, DNA spacing is expected to be variable, with the occurrence of large interstitial water spaces where increased combination reactions occur, and a lower number of free radicals are trapped on the DNA after time t. In the crystalline lattice, DNA spacing is homogeneous and large islands of solvent are absent; thus holes and electrons created in the hydration regions have increased probability of being trapped.