Where Are the Sugar Radicals in Irradiated DNA?

Abstract

Numerous sugar radicals have been observed by EPR and ENDOR spectroscopy in X-irradiated nucleosides and nucleotides. However, no sugar radicals have been observed in irradiated DNA. One possibility exists that sugar radicals may be present in relatively small abundance and therefore have so far escaped detection. Another possibility is that each of the five carbon-centered H-abstraction sugar radicals may exist in a wide range of conformations. Adding together various groups of radicals with different hyperfine couplings and anisotropic g factors may result in very broad EPR lines which would be difficult to detect. Using the crystal structure of a B-DNA dodecamer, the conformations of the five H-abstraction sugar radicals have been computed at all sites. The X-band EPR spectra for each radical were then simulated using typical alpha-proton and beta-proton couplings computed from the various radical conformations. The results suggest considerable broadenings of the EPR lines for the C2', C3' H-abstraction radicals. Composite EPR spectra were simulated by adding 15% of an H-abstraction radical to the DNA spectrum. The results indicate that the outer lines of the C1' radical are visible and should be easy to identify. The broad spectra of the C2' and C3' radicals are barely visible. The simulated spectra of the C4' and C5' radicals are basically doublets and are obscured by the DNA signal.