Date of Award

7-16-2009

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Physics and Astronomy

First Advisor

Dr. William H. Nelson - Chair

Second Advisor

Dr. Stuart A. Allison

Third Advisor

Dr. Douglas Gies

Fourth Advisor

Dr. Gary Hastings

Fifth Advisor

Dr. Vadym Apalkov

Abstract

When proteins and DNA interact, arginine and lysine are the two amino acids most often in close contact with the DNA. In order to understand the radiation damage to DNA in vivo, which is always associated with protein, it is important to learn the radiation chemistry of arginine and lysine independently, and when complexed to DNA. This work studied X-irradiated single crystals of L-lysine monohydrochloride dihydrate (L-lysine·HCl·2H2O) and L-arginine monohydrochloride monohydrate (L-arginine·HCl·H2O) with EPR, ENDOR, EIE techniques and DFT calculations. In both crystal types irradiated at 66K, the carboxyl anion radical and the decarboxylation radical were detected. DFT calculations supported these assignments. Specifically, the calculations performed on the cluster models for the carboxyl anion radicals reproduced the proton transfers to the carboxyl group from the neighboring molecules through the hydrogen bonds. Moreover, computations supported the identification of one radical type as the guanidyl radical anion with an electron trapped by the guanidyl group. In addition, the radical formed by dehydrogenation of C5 was identified in the L-arginine·HCl·H2O crystals irradiated at 66K. For both crystal types, the deamination radicals and the dehydrogenation radicals were identified following irradiation at 298K. Different conformations of main-chain deamination radicals were detected at 66K and at 298K. In L-lysine·HCl·2H2O, these conformations are the result of the different rotation angles of the side chain. In L-arginine·HCl·H2O, one conformation at 66K has no O-H dipolar protons while the others have two O-H dipolar protons. In L-lysine·HCl·2H2O, two radicals with very similar sets of hyperfine couplings were identified as the result of dehydrogenation from C3 and C5. Two other radicals in low concentration detected only at 66K, were tentatively assigned as the radical dehydrogenated from C3 and the side-chain deamination radical. In L-argnine·HCl·H2O, the radicals from dehydrogenation at C5 and C2 also were identified. DFT calculations supported these assignments and reproduced conformations of these radicals.Finally, based on the radicals detected in the crystal irradated at 66K and at 298K, the annealing experiments from the irradiation at 66K, and the previous studies on the irradiated amino acids, the mechanisms of the irradiation damage on lysinie and arginine were proposed.

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