Many DNA-processing enzymes have been shown to contain a [4Fe4S] cluster, a common redox cofactor in biology. We find using DNA electrochemistry that binding of the DNA polyanion promotes a negative shift in [4Fe4S] cluster potential, which corresponds thermodynamically to ~ 500-fold increase in DNA binding affinity for the oxidized [4Fe4S]3+ cluster versus the reduced [4Fe4S]2+ cluster. This redox switch can be activated from a distance using DNA charge transport chemistry. DNA-processing proteins containing the [4Fe4S] cluster are enumerated with possible roles for the redox switch, highlighted. A model is described where repair proteins may signal one another using DNA-mediated charge transport as a first step in their search for lesions. The redox switch in eukaryotic DNA primases appears to regulate polymerase handoff, and in DNA polymerase δ, the redox switch provides a means to modulate replication in response to oxidative stress. Thus we describe redox signaling interactions of DNA-processing [4Fe4S] enzymes as well as the most interesting potential players to consider in delineating new DNA-mediated redox signaling networks.

Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.

Recent advances have led to numerous landmark discoveries of [4Fe4S] clusters coordinated by essential enzymes in repair, replication, and transcription across all domains of life. The cofactor has notably been challenging to observe for many nucleic acid processing enzymes due to several factors, including a weak bioinformatic signature of the coordinating cysteines and lability of the metal cofactor. To overcome these challenges, we have used sequence alignments, an anaerobic purification method, iron quantification, and UV–visible and electron paramagnetic resonance spectroscopies to investigate UvrC, the dual-incision endonuclease in the bacterial nucleotide excision repair (NER) pathway. The characteristics of UvrC are consistent with [4Fe4S] coordination with 60–70% cofactor incorporation, and additionally, we show that, bound to UvrC, the [4Fe4S] cofactor is susceptible to oxidative degradation with aggregation of apo species. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 ± 20 nM and 80 ± 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with a DNA-bound midpoint potential of 90 mV vs NHE. This work highlights that the [4Fe4S] center is critical to UvrC.

Homologous recombination (HR) is an important biological phenomenon because it repairs DNA double-strand break in an error-free way and rearranges genetic information during meiosis promoting genetic diversity. HR is mediated by the Rad51/RecA family of recombinases. The essential roles of the recombinases are searching for the homologous sequence and then exchanging DNA strands. Despite decades of work, the physical basis of the homology search and strand-exchange is not well-defined. Using the single-molecule DNA curtain technique, we reveal that the strand exchange occurs in precise 3-nucleotide (nt) steps for prokaryotic RecA and eukaryotic Rad51 and Dmc1. The free energy difference between the steps is~0.3 kBT, which is also conserved from bacteria to human. Molecular dynamics simulation suggests that Watson-Crick basepairing of base triplets is the molecular basis of the triplet stepping. We also show that all the recombinases can step over an internal mismatched base in the strand exchange. But only the meiosis-specific recombinase Dmc1 can step over a mismatched base without any destabilization of base-triplets, which enhances more genetic exchange during meiosis.

Bacteriophage enzymes synthesize varied and complex DNA hypermodifications. The enzyme encoded by the phage Mu genemomis necessary for post-replicative carbamoylmethyl addition to the exocyclic amine of deoxyadenosine in DNA during the lytic phase of the viral life-cycle. The molecular details of this modification reaction, including the molecular origins of the modification itself, have long eluded understanding. Here, we demonstrate that Mom co-opts the translational machinery of the host by harvesting activated glycine from charged tRNAGlyto hypermodify adenine. Based on this insight, we report the firstin vitroreconstitution of the Mu hypermodification from purified components. Using isotope labeling, we demonstrate that the carbamoyl nitrogen of the Mom modification is derived from theN6 of adenine, indicating an on-base rearrangement of theN6 aminoacylation product, possibly via a cyclic intermediate. Informed by the X-ray crystal structure of Mom, we have probed the location of the active site, identified a novel insertion, and established substrate specificities of the Mom enzyme.