UNC-CH Physics and Astronomy PhD Defense

Zimeng Li

“Crack the Code: Triplet Repeat Expansion, DNA Mismatch Repair, and Next-gen AFM Software”

DNA Mismatch Repair protein MutSβ is involved in repairing insertion/deletion loop (IDL) errors. But studies have found that MutSβ could also promote a type of IDL containing trinucleotides repeat (TNR) sequences, leading to TNR expansion, which is key to the development of several neurodegenerative diseases such as the Huntington’s disease. To understand the molecular mechanisms of how MutSβ interacts with TNR IDLs and non-TNR IDLs, we use atomic force microscopy (AFM) to directly visualize the conforgenmations of MutSβ-DNA complexes in the initial stages of repair processing. Our data shows that when interacting with non-TNR IDLs, MutSβ adopts conformations that are consistent with a repair signaling capable formation; when interacting with TNR IDLs, MutSβ adopts very different conformations that may not be competent for repair signaling.

To facilitate AFM image analysis, we developed Image Metrics, a comprehensive software package that specializes in single molecule protein-DNA analysis and particle analysis. Building from the ground up using MATLAB, Image Metrics is the first of its kind that blends programming and automation into the core of a user-friendly interface, which frees users from the laborious tasks of repeating a preset routine while allowing them the freedom to easily implement and automate sophisticated workflows. The software is projected to be the next generation research tool for a new generation of researchers.