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Aadarsh Raghunathan

Aadarsh Raghunathan supervised by Dr. Krishnan Marimuthu  received his Master of Science – Dual Degree in Computational and Natural Science  (CND). Here’s a summary of his research work on  Recognition, Repair, and Repression of UV-Induced DNA Damage: AComputational Perspective:

Solar UV radiation challenges the integrity of the genome, causing severe mutations and potentially leading to cancer. Regulatory regions of DNA are particularly important for transcription, and hence preventing damage formation in those regions is essential. When UV damage occurs, it triggers various response systems in the body, the most common being nucleotide excision repair (NER). Global genome nucleotide excision repair (GGNER) takes a broad approach to the repair process, with proteins like Xeroderma Pigmentosum C (XPC) scanning the entire genome for lesions. The mechanism by which XPC identify damage sites from a long, perfectly matched DNA duplex is still not completely resolved. In this thesis, we examine three stages of handling DNA damage: (A) prevention, (B) recognition, and (C) binding to repair protein XPC. Experimentally, it has been found that histone methyltransferase ASH1L prevents the formation of cyclobutane pyrimidine dimers (CPD) in enhancer regions of DNA. Our simulations show that ASH1L binding distorts the geometry of adjacent base pairs, disfavoring the induction of CPD lesions. Subsequently, we studied how the induction of mismatch damage affects the dynamics of DNA fluctuations. FRET lifetime and efficiency analysis has shown that mismatches well recognized by XPC exhibit different intrinsic fluctuations compared to poorly recognized mismatches. We computationally calculated the FRET efficiency for different mismatches from MD simulations. Further, umbrella sampling simulations showed that the fluctuations in the CCC mismatch (a well repaired mismatch) can be mapped to a metastable state not accessible to matched DNA or poorly recognized lesions. This suggests a conformational selection mechanism of repair by XPC. Lastly, we investigated the mechanism by which XPC binds to sites of damage. For this study, we used the crystal structure of RAD4 (the yeast ortholog of XPC) bound to pyrimidine (6-4) pyrimidone photoproducts (64pp) to determine the mechanism of RAD4 binding. Using the nudged elastic band method, we determined the minimum energy pathway between the unbound and productively bound states of RAD4. The obtained pathway reveals that the β hairpins of RAD4 cause the DNA to sample multiple twist states, finally reaching a stable twist angle that is favorable for binding. Furthermore, using enhanced sampling in conjunction with our minimum energy path, we determined the energetic cost of some of the key binding events.

August 2024