Electrospray ionization tandem mass spectrometric techniques for the analysis of drug/DNA complexes

Many anticancer and antibacterial therapies are based on the interaction of small molecule drugs with DNA. Increasing interest in the development of DNA-interactive agents has fostered the need for sensitive and versatile analytical techniques that are capable of characterizing the DNA/ligand interactions and are compatible with librarybased screening methods. Electrospray ionization mass spectrometry (ESI-MS) has emerged as a useful technique for the analysis of non-covalent complexes formed between DNA and small molecules due to its low sample consumption and fast analysis time. The work presented in this dissertation is aimed at exploring, optimizing, and validating ESI-MS methods for characterizing DNA-ligand interactions. ESI-MS is first used to assess the binding of threading bis-intercalators to duplexes containing different sequences to determine high affinity binding sites of the ligands. Preliminary DNAse footprinting experiments identified possible specific binding sites of the ligands and ESI-MS experiments revealed that the ligands bound to DNA duplexes containing the respective specific binding sequences. The metal-mediated binding of benzoxazole ligands with different side chains to duplex DNA is also examined. Cu²⁺ and Ni⁺ were found to promote the most dramatic increase in ligand binding, and ligands exhibiting the most dramatic metal-mediated or metal-enhanced binding were also determined to be the most cytotoxic. The quadruplex DNA binding selectivity of perylene diimides is evaluated by screening the binding of the ligands to quadruplex, duplex and single strand DNA by ESI-MS. Three ligands, one containing basic side chains, one containing anionic sidechains, and one benzannulated compound were determined to be the most-quadruplex selective. The ESI-MS results correlated well with spectroscopic experiments. The relative gas-phase stabilities of different quadruplex DNA structures were investigated using molecular dynamics simulations and ESI-MS. The stabilities from the E[subscript 1/2] values generally paralleled the RMSD and relative free energies of the quadruplexes based on MD energy analysis. Finally an ESI-MS technique employing the KMnO₄ reaction with DNA to determine conformational changes to the duplex structure upon ligand binding is detailed. Thymines in most intercalator/duplex complexes are more susceptible to oxidation by KMnO₄ than those in duplex DNA. CAD and IRMPD experiments are used to identify the site of oxidation.