Many of the drugs used in cancer chemotherapy target DNA to kill malignant cells. Some of them form DNA interstrand crosslinks (ICLs), which are extremely cytotoxic lesions that block essential metabolic process such as replication, transcription and recombination by forming covalent bonds between opposite strands of DNA. Despite the importance of chemotherapeutic agents that rely on ICLs for their efficacy, the mechanisms by which these lesions are repaired remains poorly understood. A major impediment in studying ICLs repair has been the limited availability of well-defined substrates.

This dissertation describes the development of a new strategy for the synthesis of defined site-specific ICLs in high yields and purity. This strategy relies on the incorporation of ICL precursors bearing reactive aldehyde functionalities on complementary strands of DNA, followed by ICL formation via double reductive amination. We were able to synthesize different crosslinks that are isosteric to the therapeutic nitrogen mustard (NM) ICLs, introducing substitution of a few atoms to make them more stable and therefore more suitable for chemical, structural and biological studies.

The synthetic substrates were validated through molecular dynamic studies, confirming that our mimic has all the essential structural features to its natural counterpart. Modeling data also demonstrate that both the natural and the synthetic ICL induce a bend in the DNA, which could play an important role in the way the lesion is repaired. Our synthetic approach furthermore allows for the synthesis of major groove ICLs with different degrees of distortion, providing unique and valuable tools for biochemical and cell biological studies of ICL repair.