Syntheses and Characterizations of Modified Nucleosides and Their Incorporation into Oligodeoxynucleotides

ABSTRACT OF THE DISSERTATIONSyntheses and Characterizations of Modified Nucleosides and Their Incorporation into OligodeoxynucleotidesbyMario Rolando VargasDoctor of Philosophy, Graduate Program in ChemistryUniversity of California, Riverside, May 2011Dr. Yinsheng Wang, Chairperson Tobacco-specific nitrosamines, N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), are found in tobacco and its smoke. Both compounds can generate the same intermediate upon metabolic activation by cytochrome P450, which can then form mutagenic DNA adducts. These adducts have been detected in the DNA of lung cancer patients. One of the most persistent and abundant adduct that has been detected in several tissues of rats that have been treated with NNN, is O2-(pyridyloxobutyl)-thymidine (O2-POBdT). N3-POBdT a new adduct that has never been detected in genomic DNA. Chapter 2 of this dissertation reports on the syntheses of O2-POBdT and N3-POBdT and their incorporation into oligodeoxynucleotides (ODNs) for conducting biological studies. 5-Hydroxymethyl-2-deoxycytidine (hmdC) is a modified nucleotide that has recently been detected genomic DNA. Tet enzymes oxidize 5-methylcytosine (mC) to generate hmdC. Recently, it has been discovered that hmdC plays a crucial role in stem cell development. Like hmdC, 5-formyl-dC (fdC) has also recently been detected in genomic DNA. Its levels are lower than hmdC and its exact role remains to be determined. Chapter 3 of this dissertation reports on the syntheses of hmdC and fdC and their incorporation into ODNs. 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) is an oxidized lesion found in genomic DNA. It is weakly mutagenic in vitro and in vivo, causing G→T transversions. 2'-Deoxyribonolactone (dL) is an oxidized abasic site found in damaged DNA. If left unrepaired it can produce single- and double-strand breaks, and dL is also mutagenic. Generation of the dL in short ONDs can be readily be accomplished from insertion of a precursor, 7-nitroindole, d(7-Ni), followed by UV irradiation. Chapter 4 of this dissertation reports on the syntheses of 8-oxodG and d(7-Ni) and their incorporation into ODNs