Date of Award

December 2022

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Department

Chemistry

First Advisor

Xiaohua Peng

Committee Members

James Cook, M.Mahmun Hossain, Arsenio Pacheco, Mark Dietz

Abstract

DNA interstrand cross-link (ICL) can covalently bind two DNA strands, preventing DNA strands separation, and therefore, blocking DNA transcription and replication, which are essential biological processes for cell division. Among different methods to induce DNA interstrand cross-linking, photoinduction is an important way to activate the cross-linking reactions due to its many characteristics, such as non-invasive, controllability, selectivity and biorthogonality. My research mainly focuses on developing novel binaphthalene compounds which can be activated by 350 nm UV light to produce DNA interstrand cross-linking via alkylation. We designed and synthesized a series of binaphthalene analogues with different substituents at the position-4’ on the naphthalene rings (1a-1e, 12a-12g, 22a,b, 23a-23d and 24a-24d) and/or various leaving groups, including triphenylphosphonium salts (1a-1e), amine functional groups (12c-12e), ether functional groups (12b, 22a,b, 23a-23d, and 24a-24d), acetate (12a), phenylthio group (12f), and phenylselenide (12g) (Scheme 1). The reactivity of these novel compounds towards DNA have been studied by DNA interstrand cross-linking assay. The efficiency and mechanism of DNA ICL formation have been investigated. Most of these compounds showed higher DNA cross-linking yields than previously reported binaphthalene bononates. Both substituents (R) and leaving groups (L) affect their reactivity towards DNA ICL.With triphenylphosphonium (TPP+) salts as a leaving group, 1a-e showed not only various efficiency of ICL formation but also different reaction rates due to different substituents at the position-4 of the naphthalene ring. The electron-withdrawing groups facilitate the ICL reaction, such as 1b and 1d, while the electron-donating groups slow down the cross-linking process, like 1e. Although 1d showed a fast ICL reaction rate possibly due to its strong UV absorption, its ICL formation efficiency was low because of the bulky size of the phenyl group that might prevent the DNA interstrand cross-linking. The study indicated that the electronic effect, steric effect and UV-absorption combine to influence the final ICL formation. In addition, the aromatic substituents influenced the reactivity of these compounds towards dG and dA. Compound 1b showed the poorest photo-reactivity toward dA, while 1d was the most reactive toward dA. The 2-naphthalenylmethyl cations photo-generated from 1a-e can alkylate dC, dG and dA while DNA interstrand cross-linking reaction only occurred with dG-dC base pairs. We also observed that different leaving groups greatly influence the DNA ICL formation and the photo-reactivity toward DNA. Bromo-substituted binaphthalene analogues 12a-j with different leaving groups showed different cross-linking reaction rates and ICL formation efficiency. The photo-reactivity toward dA and dG was also affected by different leaving groups. For example, alkylation took place with dAs and dGs for 12a and 12g while other compounds (show compound number here) only alkylated dGs. In addition, DNA ICL formation mainly occurred at dG sites for all compounds while monoalkylation took place with dG or dG/dA, which depends on the leaving groups. For 22a, b, 23a-d, 24a-d, different substituents and leaving groups combine to influence the DNA ICL formation. The mechanism investigation of ICL formation indicated that all binaphthalene analogues generated naphthalenylmethyl free radicals (6) that were spontaneously transformed to the corresponding cations (7) directly producing DNA ICL products via alkylation (Scheme 2). Furthermore, we found that the DNA ICL formation of 12g was greatly improved in the presence of hydrogen peroxide. It is likely that H2O2 can convert a poor leaving group (-SePh) to a better leaving group (-SeOPh) by oxidation, which promote photo-induced DNA ICL formation (Scheme 3). ICL Mechanism investigation suggested that both carbocations and free radicals were involved in DNA cross-linking process induced by 350 nm irradiation in the presence of H2O2. Finally, we designed and synthesized three BINOL analogues 34-36 with different configurations (R-, S- and Rac-) to investigate the chirality effect on DNA ICL formation (Scheme 4). It was found that different organic solvents affected the DNA interstrand cross-linking efficiency. Compounds dissolved in acetonitrile (CH3CN) can induce higher DNA ICL yields with less DNA damage than those dissolved in dimethylformamide (DMF) or dimethyl sulfoxide (DMSO). We further observed that the chirality of BINOL precursors didn’t influence DNA ICL formation. For example, similar ICL yields were observed for 34a-c. It is likely due to the small size of these molecules, different configurations do not affect their binding interaction with DNA double helixes.

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