The Influence of Packing on Free Radical Yields in Crystalline Nucleic Acids: The Pyrimidine Bases

Abstract

The total free radical yield has been measured for crystals of five pyrimidine derivatives: thymine (T), 1-methylthymine (1MeT), 1-methyluracil (1MeU), 1-methylcytosine (1MeC) and cytosine monohydrate (C:HOH). Q-band EPR measurements were made on samples X-irradiated between 4 and 12 K. The G values in units of 10(-7) mol/J are 1MeC < 0.01, T < 0.04, 1MeU = 0.15, 1MeT = 0.25, and C:HOH = 0.8. The types of free radicals formed in these crystals are known through previous EPR investigations. A model is presented that attempts to identify the salient variables behind the large range in G values and, simultaneously, explain the variation in radical types. It is concluded that packing is a critical variable. Hydrogen-bonding networks promote the trapping of radicals through reversible proton transfer. In the absence of such a network less probable radical types are observed, such as radicals formed by irreversible protonation/deprotonation, higher-order reactions and homolytic bond cleavage. Crystals with low G values trap radicals formed predominantly by irreversible protonation/deprotonation at carbon positions and by excitation-spawned homolytic bond cleavage. In contrast, crystals with high G values trap radicals formed predominantly by reversible protonation/deprotonation at heteroatom positions. This model is extended to polynucleotides irradiated at low temperatures, where G values are typically 2-6. The high trapping efficiency seen in polynucleotides reflects highly efficient proton transfer. Consistent with this is the predominance of radicals formed by reversible protonation/deprotonation compared to those formed by irreversible protonation/deprotonation.