MCA pilot PUI: biophysical methods to investigate DNA repair

The National Science Foundation Division of Emerging Frontiers awarded Missouri State University $285,999 on July 15, 2026, under the Biological Sciences program (CFDA 47.074) to investigate biophysical methods for understanding how DNA repair enzymes recognize and respond to damaged DNA. The project will focus on protein-DNA interactions using biochemical and biophysical techniques to elucidate the initial stages of damage recognition, with the hypothesis that perturbations to DNA conformational properties play a critical role in enzyme kinetics and repair initiation. The principal investigator, a full professor at the primarily undergraduate institution, will receive release time from teaching and community service responsibilities to pursue this research direction and mentor undergraduate students. The award runs through June 30, 2029, with work performed in Springfield, Missouri. Prior work supported under this funding resulted in four publications with student first authors demonstrating consistent DNA backbone perturbation across various mismatch and damage types and strong correlation between DNA conformational equilibria and enzyme kinetics, pointing toward the substrate's properties as central to early damage recognition.

Abstract

Damage to DNA happens all the time in cells and must be repaired to prevent negative outcomes such as cell death and diseases such as cancer or neurodegenerative conditions. Fortunately, there are sophisticated repair mechanisms in every cell to prevent and fix some damage events. Many details are known about DNA repair, but details of how the damage itself is initially recognized by repair enzymes remains a mystery. This project will investigate the interactions between repair proteins and damaged DNA, providing results that could be leveraged for technological development and biomedical interventions. The PI, who is a full professor at a primarily undergraduate institution, has significant teaching and community service responsibilities standard to faculty at such institutions. As part of this project, the PI will be released from some of these responsibilities to pursue this research on the repair of DNA damage. This project will also provide training opportunities for many undergraduate students. The primary goal of this program is to provide the PI with dedicated time to pursue and develop new directions to his research program utilizing biochemical and biophysical techniques to understand the initial stages of DNA repair and damage recognition. Four papers published subsequently with student first authors demonstrated consistent perturbation of the DNA backbone due to the presence of various mismatches or damage types, and a very strong correlation between the DNA backbone conformational equilibria and enzyme kinetics. This suggests an important role for the properties of the DNA substrate in the early stages of damage recognition. The projects outlined will lead to a broader array of techniques used to make connections with the PIS most recent results and add to the fundamental understanding of DNA repair and damage recognition. The PI hypothesizes that perturbation to the DNA conformational properties (structure, dynamics, thermodynamics) and perhaps the presence of high energy, sparsely-populated states, contribute to the recognition process of DNA damage. Though a connection already has been demonstrated using 31P NMR, the research plan is to expand into other techniques and more complex systems to investigate these interactions more directly. More specifically, with the greater time provided by funding from this program, the PI will 1) cultivate and expand the capability of expressing and purifying repair enzymes, 2) study thermodynamics of binding via ITC and SPR, and 3) study structural and dynamic aspects of binding by NMR and X-RAY crystallography. The PI will continue to receive direct training from collaborators on this variety of new techniques and instrumentation mentioned, as well as a suite of higher field solution NMR experiment such as relaxation dispersion, which are currently unavailable to the PI or inaccessible due to time constraints to the PIS responsibilities. Training began in the fall of 2025 during the PI?S second sabbatical, leading to successful expression and purification of apurinic endonuclease I (APE1) through direct involvement of the PIS research community and collaborators. These new experiments will lead to more publications with a variety of techniques involved by partnering with the PI?S collaborators as well as continued student training. All of these techniques offer a variety of perspectives and complementary information on biomolecular recognition, and the PI?S ongoing research will provide greater insight into the convergent biophysical details of DNA repair and contribute to the foundation of more powerful biomedical interventions relating to DNA damage and repair. 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.- subawards are planned for this award.