Detailed electron paramagnetic resonance and electron nuclear double resonance experiments on the co-crystalline complex of 1-methylthymine:9-methyladenine (MTMA) have revealed that the major radiation induced products at low temperatures (10 K) are MTMA1, a radical formed by net hydrogen abstraction from the C5 methyl group on thymine, and MTMA2, a radical formed by net hydrogen abstraction of the N1 methyl group on thymine. The following four minor products were also observed: MTMA3, the C4-OH protonated anion of thymine, MTMA4, the C6 H-addition product of thymine, and MTMA5 and MTMA6, radicals formed by net H-addition to C2 and C8 of the adenine base. The geometries, energetics and hyperfine properties of all possible radicals of MT and MA, the primary anions and cations, as well as radicals formed via net hydrogen atom abstraction (deprotonated cations) or addition (protonated anions) were investigated theoretically. All systems were optimized using the hybrid Hartree-Fock density functional theory functional B3LYP, in conjunction with the 6-31G(d,p) basis set of Pople and co-workers. Calculations of the anisotropic hyperfine couplings for all the radicals observed in MTMA are presented, and are shown to compare favorably with the experimentally measured hyperfine couplings. The calculated ionizations potentials indicate that MA would be the preferred oxidation site. However, in MTMA neither the adenine cation nor its N4-deprotonated derivative were observed. The adenine cation in MTMA is not stabilized by deprotonation, and is thus likely subject to recombination. The calculated electron affinities indicate that MT would be the preferred reduction site. Reduction of MT is believed to result in protonation of the anion at C4=O. The calculated hyperfine couplings for the MT anion are very similar to those of the C4-OH protonated anion, and therefore, the theoretical calculations are not useful in deciding the actual protonation state of this reduction product.

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The thesis describes over-expression, purification and crystallization of three proteins from Staphylococcus aureus (S. aureus). S. aureus is an important human pathogen and methicillin-resistant S. aureus (MRSA) is a serious problem in hospitals nowadays. The crystal structure of 3-Methyladenine DNA glycosylase I (TAG) was determined by single-wavelength anomalous diffraction (SAD) method. TAG is responsible for DNA repair and is an essential gene for both MRSA and methicilin-susceptible S. aureus (MSSA). The structure was also determined in complex with 3-methyladenine (3-MeA) and was solved using molecular replacement (MR) method. An assay was carried out and the molecular basis of discrimination between 3-MeA and adenosine was determined. The native crystal structure of fructose 1-phosphate kinase (PFK) from S. aureus was determined to 2.30 Å and solved using molecular replacement method. PFK is an essential enzyme involved in the central metabolism of MRSA. Despite extensive efforts no co-complex was determined, although crystals were obtained they diffracted poorly. An assay which can be used to test for inhibitors has been developed. Mevalonate Kinase (MK) is another essential enzyme in MRSA and is a key drug target in the mevalonate pathway. Native data diffracting to 2.2 Å was collected. The structure was solved using multiple isomorphorus replacement (MIR) method. A citrate molecule was bound at the MK active site, arising from the crystallization condition. The citrate molecule indicates how substrate might bind. The protein was kinetically characterized. A thermodynamic analysis using fluorescence-based method was carried out on each protein to investigate binding interactions of potential fragments and thus a drug design starting point.