Using this award funded by the Chemical of Life Processes Program of the Division of Chemistry, Professor James Stivers from the Johns Hopkins University seeks to elucidate the fundamental basis for how a paradigm DNA repair protein, namely human 8-oxoguanine DNA glycosylase, translocates along a DNA chain to find damage. Present models suggest that DNA sliding, where the protein remains in constant contact with the DNA chain, is the primary mode for damage recognition. However, these models are based on the results of single-molecule imaging methods that do not have the temporal or spatial resolution to detect important microscopic tracking events of the protein on DNA such as chain hopping. Professor Stivers uses a kinetic approach that allows quantification of both sliding and hopping events involved in protein translocation on DNA. The research aims to elucidate how nonspecific electrostatic interactions promote chain sliding by using chemical modifications of the DNA backbone, specifically neutral methylphosphonate substitutions, and by appending cationic peptide tails to the protein through expressed protein ligation. The results of this research are expected to facilitate a fundamental understanding of how nonspecific protein-nucleic acid electrostatic interactions underline the kinetics and mechanism of the search, and to provide data useful for the interpretation of the results of single molecule measurements of DNA sliding.
The efficient binding between biomolecules is a fundamental requirement of life that is governed by the chemical properties of the partners that participate in the binding. For proteins that interact with genomic DNA, the formation of specific complexes that result in DNA repair, replication or transcription takes advantage of the linear chain structure of DNA. Thus, proteins can bind to DNA a great distance from a specific target site and use the DNA chain as a track to find the target site. This work will examine the interactions that a DNA repair protein uses to track along DNA to find a damaged site, which would result in mutation and disease if not repaired. The techniques developed from this award will provide investigative methods to other scientists and contribute to general knowledge of protein-DNA recognition. This program is also designed to encourage young people to pursue training in biophysics and related sciences. Undergraduate and high school researchers (including students from groups underrepresented in STEM careers) will participate in summer research internships guided by Professor Stivers. Professor Stivers will continue to participate in- and organize- a variety of multidisciplinary conferences, workshops and summer courses through which his and others research results are disseminated to the scientific community.
