Gas phase studies of hypoxanthine

Hypoxanthine is not only a naturally occurring nucleobase in tRNA but also a damaged one in DNA arising from oxidative deamination of adenine. This thesis describes studies of the intrinsic reactivity of hypoxanthine as a free base and the stability of DNA duplexes containing hypoxanthine in the gas phase versus in solution by calculation and mass spectrometry methods.;Firstly, the free base of hypoxanthine is studied as a damaged nucleobase. Hypoxanthine is one of the damaged nucleobases that can be excised by Alkyladenine DNA glycosylase (AAG) in humans. To understand the intrinsic properties of hypoxanthine, we examined the gas phase acidity and proton affinity using quantum mechanical calculations and gas-phase mass spectrometric experimental methods. We find that the N9-H of hypoxanthine is more acidic than that of adenine and guanine, pointing to a way by which AAG may discriminate damaged bases from normal bases. We hypothesize that AAG may cleave certain damaged nucleobases as anions and the active site may take advantage of a nonpolar environment to favor deprotonated hypoxanthine as a better leaving group than adenine and guanine. The acidities of AAG substrates have been compared with those of normal bases by calculations and Cooks kinetics method. In addition, the acidity differences between damaged and normal bases are enhanced in the gas phase when we compare them with the acidities in solution. These results support our hypothesis.;Secondly, to understand the effect of hypoxanthine on DNA stability, we study a series of 9-mer DNA duplexes with the sequence 5'-d(GGTTXTTGG)-3'/3'-d(CCAAYAACC)-5', where the central base X or Y = adenine (A), guanine (G), thymine (T), cytosine (C) and hypoxanthine (H). Comparison of the duplex stability in the gas phase versus in solution indicates that hypoxanthine has much less of a destabilizing effect in the gas phase versus in solution, relative to the normal complementary duplexes. The biological implications of these results are discussed in the context of hypoxanthine both as a universal base and as a damaged base.