Collaborative Research: Role of DNA sequence and deformability on lesion recognition and excision in the base excision repair pathway

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Collaborative Research: Role of DNA sequence and deformability on lesion recognition and excision in the base excision repair pathwayDNA damage occurs often in cells and must be repaired to ensure the integrity of the genome. This project will test whether damage that occurs within a rigid region of DNA is repaired more slowly than damage that occurs within a flexible region. This knowledge will help understand key aspects of DNA repair, mutation rates, and molecular evolution. The results of this project will also provide detailed insight into how proteins that repair DNA damage interact with the DNA substrate, which is critical for maintaining cellular life. Graduate and undergraduate students will receive multidisciplinary training in chemical and biophysical techniques, including advanced spectroscopic and computational methods. A joint course in fluorescence and nuclear magnetic resonance spectroscopy will also be developed. New online undergraduate course materials for quantitative approaches in the biosciences and chemistry will be developed, and a variety of outreach and scientific literacy projects for school age children and adults are planned.DNA flexibilities and repair efficiencies will be systematically assessed for three common types of damage that are repaired by three different enzymes of the base excision repair pathway (uracil-DNA glycosylase, thymine-DNA glycosylate, and O6MeG-DNA methyltransferase). Despite differences in sequence and structure, these enzymes use a similar base flipping mechanism to recognize and remove the damaged base. By using enzyme kinetics, fluorescence, nuclear magnetic resonance and computer simulations, DNA rigidities and repair efficiencies will be systematically assessed for a large number of DNA sequences. This data will be used to quantify the link between DNA rigidity and repair efficiency, and help explain the origins of the observed sequence-dependent behavior in terms of structure, energetics and dynamics.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.