Unique Biochemical Tools Offer New Opportunities to Interrogate DNA Repair Processes

Abstract

Environmental assaults and internal stressors pose continual threats to our genome integrity through the risk of cancer development. Fortunately, our body contains the necessarily DNA repair proteins to correct cancer-causing mutations on a biologically-relevant timescale. Recently, these proteins have been discovered to contain redox-active cofactors such as [4Fe4S] clusters and flavins. However, the biological roles of these cofactors have been elusive, and some coworkers suggested that these [4Fe4S] motifs might be ancient structural relics. Recent bioinformatics studies on the biogenesis of these redox cofactors hinted otherwise; suggesting that these cofactors might play vital functional roles in living organisms. Our work using atomic force microscopy (AFM), microscale thermophoresis (MST), and DNA-modified electrodes showed that the oxidation states of [4Fe4S] clusters control the DNA binding strengths of these bioinorganic repair proteins. By changing the DNA binding affinity, these [4Fe4S] clusters in turn modulate the ability of these proteins to carry out their respective enzymatic actions, such as DNA damage detection. We further developed a biophysical model based on the electrostatic interactions between bioinorganic [4Fe4S] cluster and DNA to describe the empirically-determined change in DNA binding affinity upon switching the oxidation state of the [4Fe4S] cofactor. Our data also demonstrated that DNA-processing proteins with disparate biological functions but with similar redox potentials can work together to trace and identify DNA lesions. The distance of this redox signaling event and its implication in biological magnetosensing will also be discussed. Taken together, these experiments highlight the exquisite redox properties of these bioinorganic proteins. In particular, our results establish that the redox cofactors regulate the ability of repair proteins to find and fix DNA damage in a timely fashion (Figure 1). Our work delineates a distinct role for these bioinorganic proteins in sensing and repairing DNA damage for cancer prevention and treatment.