Multiplexed DNA-mediated electrochemistry

The aromatic core of double helical DNA possesses the unique and remarkable ability to form a conduit for electrons to travel over exceptionally long molecular distances. This core of π-stacked nucleobases creates an efficient pathway for charge transfer to proceed that is exquisitely sensitive to even subtle perturbations. Ground state electrochemistry of DNA-modified electrodes has been one of the major techniques used both to investigate and to harness the property of DNA-mediated charge transfer. DNA-modified electrodes have been an essential tool for both gaining insights into the fundamental properties of DNA and, due to the exquisite specificity of DNA-mediated charge transfer for the integrity of the π-stack, for use in next generation diagnostic sensing. Here, multiplexed DNA-modified electrodes are used to (i) gain new insights on the electrochemical coupling of metalloproteins to the DNA π-stack with relevance to the fundaments of in vivo DNA-mediated charge transfer and (ii) enhance the overall sensitivity of DNA-mediated reduction for use in the detection of low abundance diagnostic targets.

First, Methylene Blue (MB′) was covalently attached to DNA through a flexible C12 alkyl linker to yield a new redox reporter for DNA electrochemistry measurements with enhanced sensitivity. Tethered, intercalated MB′ was reduced through DNA-mediated charge transport. The redox signal intensity for MB′-dT-C12-DNA was found to be at least 3 fold larger than that of previously used Nile Blue (NB)-dT-DNA, which is coupled to the base stack via direct conjugation. The signal attenuation, due to an intervening mismatch, and therefore the degree of DNA-mediated reduction, does, however, depend on the DNA film morphology and the backfilling agent used to passivate the surface. These results highlight two possible mechanisms for the reduction of MB′ on the DNA-modified electrode that are distinguishable by their kinetics: reduction mediated by the DNA base pair stack and direct surface reduction of MB′ at the electrode. The extent of direct reduction at the surface can be minimized by overall DNA assembly conditions.

Next, a series of intercalation-based DNA-mediated electrochemical reporters were developed, using a flexible alkane linkage to validate and explore their DNA-mediated reduction. The general mechanism for the reduction of distally bound redox active species, covalently tethered to DNA through flexible alkyl linkages, was established to be an intraduplex DNA-mediated pathway. MB, NB, and anthraquinone were covalently tethered to DNA with three different covalent linkages. The extent of electronic coupling of the reporter was shown to correlate with the DNA binding affinity of the redox active species, supporting an intercalative mechanism. These electrochemical signals were shown to be exceptionally sensitive to a single intervening π-stack perturbation, an AC mismatch, in a densely packed DNA monolayer, which further supports that the reduction is DNA-mediated. Finally, this DNA-mediated reduction of MB occurs primarily via intra- rather than inter duplex intercalation, as probed through varying the proximity and integrity of the neighboring duplex DNA. Further gains to electrochemical sensitivity of our DNA-modified devices were then achieved through the application of electrocatalytic signal amplification using these solvent accessible intercalative reporters, MB-dT-C8, and hemoglobin as a novel electron sink. Electrocatalysis offers an excellent means of electrochemical signal amplification, yet in DNA based sensors, its application has been limited due to strict assembly conditions. We describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low density DNA films. Electrocatalysis of MB that is covalently tethered to the DNA by a flexible alkyl linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of single CA mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: it is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling.

Finally, we expanded the application of our multiplexed DNA-modified electrodes to the electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins that contain redox cofactors. Multiplexed analysis of EndonucleaseIII (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, elucidated subtle differences in the electrochemical behavior as a function of DNA morphology. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction. Closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. The electrochemical comparison of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster, was able to be quantitatively performed. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. Based on the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues, but also through changes in solvation near the cluster.

The electrocatalytic and stoichiometric oxidation chemistry of binuclear ruthenium complexes incorporating the anionic tripod ligand {(η5-C5H5)Co[P(OCH3)2(=O)]3}-

The anionic tripod ligand NaLoMe (L_(oMe) - = [(η^5-C_5H_5)Co{P(O)(OCH_3)_2}_3]^-) reacts with RuO_4 in a biphasic reaction mixture of 1% H_2SO_4 and CCI_4 to afford [(L_(oMe) (HO)Ru^(IV) (µ-O)_2Ru ^(IV)(OH)(L_(oMe)] (1), which is treated with aqueous CF_3S0_3H to generate [(L_(oMe)(H_2O)Ru^(IV) (µ-O)_2R^(IV) (OH_2)(L_(oMe)][CF_3SO_3]_2 ([H_21][CF_3SO_3]_2). Addition of iodosobenzene to an acetonitrile solution of this salt yields [(L_(oMe)(O)Ru^v(µ-0)2Ru^v-(O)(_(LoMe)] (2). The dimer 1 can be reduced chemically or electrochemically to the Ru^(III)- Ru^(III) dimers [(L_(oMe)(H_20)Ru^(III) (µ-OH)_2Ru^(III) (OH_2)(L_(oMe)) ]^2+ and [(L_(oMe)) ^(III) (µ-0Hh(µ-0H2)Ru^(III) (L_(oMe)]^2+ which interconvert in aqueous media. Two electron processes dominate both the bulk chemistry and the electrochemistry of 1. Among these processes are the quasi-reversible Ru^(IV) - Ru^(IV)/Ru^(III)- Ru^(III) and Ru^(III)- Ru^(III)/ Ru^(II)- Ru^(II) reductions and a largely irreversible Ru^(V) - Ru^(V)/ Ru^(IV) - Ru^(IV)/oxidation. The dioxo dimer 2 oxidizes alcohols and aldehydes in organic media to afford 1 and the corresponding aldehydes and acids. Analogously, the Ru^(V) - Ru^(V)/ Ru^(IV)- Ru^(IV) redox wave mediates the electrooxidation of alcohols and aldehydes in aqueous buffer. In this system, substrates can be oxidized completely to CO_2. The kinetic behavior of these oxidations was examined by UV-vis and chronoamperometry, respectively, and the chemistry is typical of metal-oxo complexes, indicating that electronic coupling between two metal centers does not dramatically affect the metal-oxo chemistry. Dimer [H_21]^(2+) also reacts with alcohols, aldehydes, and triphenylphosphine in CH_3CN to afford Ru^(III)- Ru^(III) products including [(L_(oMe))CH_3CN) Ru^(III) (µ-OH)_2 Ru^(III) (NCCH_3)( L_(oMe))][CF_3SO_3]2 (characterized by X-ray crystallography) and the corresponding organic products. Reaction of 1 with formaldehyde in aqueous buffer quantitatively affords the triply bridged dimer [(L_(oMe)Ru^(III) (µ-OH)2- (µ-HCOO) Ru^(III) (L_(oMe)][CF_3SO_3] (characterized by X-ray crystallography). This reaction evidently proceeds by two parallel inner-sphere pathways, one of which is autocatalytic. Neither pathway exhibits a primary isotope effect suggesting the rate determining process could be the formation of an intermediate, perhaps a Ru^(IV) - Ru^(IV) formate adduct. The Ru^(III)- Ru^(III)formate adduct is easily oxidized to the Ru^(IV) - Ru^(IV) analog [(L_(oMe)Ru^(IV)(µ-OH)_2-(µ-HCOO) Ru^(IV) (L_(oMe)][CF_3SO_3], which, after isolation, reacts slowly with aqueous formaldehyde to generate free formate and the Ru^(III)- Ru^(III) formate adduct. These dimers function as catalysts for the electrooxidation of formaldehyde at low anodic potentials (+0.0 V versus SCE in aqueous buffer, pH 8.5) and enhance the activity of Nafion treated palladium/carbon heterogeneous fuel cell catalysts.

Expanding the repertoire of DNA-mediated signaling in DNA repair

DNA damage is extremely detrimental to the cell and must be repaired to protect the genome. DNA is capable of conducting charge through the overlapping π-orbitals of stacked bases; this phenomenon is extremely sensitive to the integrity of the π-stack, as perturbations attenuate DNA charge transport (CT). Based on the E. coli base excision repair (BER) proteins EndoIII and MutY, it has recently been proposed that redox-active proteins containing metal clusters can utilize DNA CT to signal one another to locate sites of DNA damage.

To expand our repertoire of proteins that utilize DNA-mediated signaling, we measured the DNA-bound redox potential of the nucleotide excision repair (NER) helicase XPD from Sulfolobus acidocaldarius. A midpoint potential of 82 mV versus NHE was observed, resembling that of the previously reported BER proteins. The redox signal increases in intensity with ATP hydrolysis in only the WT protein and mutants that maintain ATPase activity and not for ATPase-deficient mutants. The signal increase correlates directly with ATP activity, suggesting that DNA-mediated signaling may play a general role in protein signaling. Several mutations in human XPD that lead to XP-related diseases have been identified; using SaXPD, we explored how these mutations, which are conserved in the thermophile, affect protein electrochemistry.

To further understand the electrochemical signaling of XPD, we studied the yeast S. cerevisiae Rad3 protein. ScRad3 mutants were incubated on a DNA-modified electrode and exhibited a similar redox potential to SaXPD. We developed a haploid strain of S. cerevisiae that allowed for easy manipulation of Rad3. In a survival assay, the ATPase- and helicase-deficient mutants show little survival, while the two disease-related mutants exhibit survival similar to WT. When both a WT and G47R (ATPase/helicase deficient) strain were challenged with different DNA damaging agents, both exhibited comparable survival in the presence of hydroxyurea, while with methyl methanesulfonate and camptothecin, the G47R strain exhibits a significant change in growth, suggesting that Rad3 is involved in repairing damage beyond traditional NER substrates. Together, these data expand our understanding of redox-active proteins at the interface of DNA repair.

Physical characterization of the rack effect and hydrogen bond networks in blue copper proteins

A summary of previous research is presented that indicates that the purpose of a blue copper protein's fold and hydrogen bond network, aka, the rack effect, enforce a copper(II) geometry around the copper(I) ion in the metal site. In several blue copper proteins, the C-terminal histidine ligand becomes protonated and detaches from the copper in the reduced forms. Mutants of amicyanin from Paracoccus denitrificans were made to alter the hydrogen bond network and quantify the rack effect by pK_a shifts.

The pK_a's of mutant amicyanins have been measured by pH-dependent electrochemistry. P94F and P94A mutations loosen the Northern loop, allowing the reduced copper to adopt a relaxed conformation: the ability to relax drives the reduction potentials up. The measured potentials are 265 (wild type), 380 (P94A), and 415 (P94F) mV vs. NHE. The measured pK_a's are 7.0 (wild type), 6.3 (P94A), and 5.0 (P94F). The additional hydrogen bond to the thiolate in the mutants is indicated by a red-shift in the blue copper absorption and an increase in the parallel hyperfine splitting in the EPR spectrum. This hydrogen bond is invoked as the cause for the increased stability of the C-terminal imidazole.

Melting curves give a measure of the thermal stability of the protein. A thermodynamic intermediate with pH-dependent reversibility is revealed. Comparisons with the electrochemistry and apoamicyanin suggest that the intermediate involves the region of the protein near the metal site. This region is destabilized in the P94F mutant; coupled with the evidence that the imidazole is stabilized under the same conditions confirms an original concept of the rack effect: a high energy configuration is stabilized at a cost to the rest of the protein.

Fundamental Studies of Carbon Oxygen Bond Activation in Nickel Diphosphine Ether Complexes. And, Metallomacrocycles as Ligands: Synthesis and Characterization of Aluminum-Bridged Bisglyoximato Complexes of Iron and Cobalt

In order to develop better catalysts for the cleavage of aryl-X bonds fundamental studies of the mechanism and individual steps of the mechanism have been investigated in detail. As the described studies are difficult at best in catalytic systems, model systems are frequently used. To study aryl-oxygen bond activation, a terphenyl diphosphine scaffold containing an ether moiety in the central arene was designed. The first three chapters of this dissertation focus on the studies of the nickel complexes supported by this diphosphine backbone and the research efforts in regards to aryl-oxygen bond activation.

Chapter 2 outlines the synthesis of a variety of diphosphine terphenyl ether ligand scaffolds. The metallation of these scaffolds with nickel is described. The reactivity of these nickel(0) systems is also outlined. The systems were found to typically undergo a reductive cleavage of the aryl oxygen bond. The mechanism was found to be a subsequent oxidative addition, β-H elimination, reductive elimination and (or) decarbonylation.

Chapter 3 presents kinetic studies of the aryl oxygen bond in the systems outlined in Chapter 2. Using a series of nickel(0) diphosphine terphenyl ether complexes the kinetics of aryl oxygen bond activation was studied. The activation parameters of oxidative addition for the model systems were determined. Little variation was observed in the rate and activation parameters of oxidative addition with varying electronics in the model system. The cause of the lack of variation is due to the ground state and oxidative addition transition state being affected similarly. Attempts were made to extend this study to catalytic systems.

Chapter 4 investigates aryl oxygen bond activation in the presence of additives. It was found that the addition of certain metal alkyls to the nickel(0) model system lead to an increase in the rate of aryl oxygen bond activation. The addition of excess Grignard reagent led to an order of magnitude increase in the rate of aryl oxygen bond activation. Similarly the addition of AlMe3 led to a three order of magnitude rate increase. Addition of AlMe₃ at -80 °C led to the formation of an intermediate which was identified by NOESY correlations as a system in which the AlMe3 is coordinated to the ether moiety of the backbone. The rates and activation parameters of aryl oxygen bond activation in the presence of AlMe3 were investigated.

The last two chapters involve the study of metalla-macrocycles as ligands. Chapter 5 details the synthesis of a variety of glyoxime backbones and diphenol precursors and their metallation with aluminum. The coordination chemistry of iron on the aluminum scaffolds was investigated. Varying the electronics of the aluminum macrocycle was found to affect the observed electrochemistry of the iron center.

Chapter 6 extends the studies of chapter 5 to cobalt complexes. The synthesis of cobalt dialuminum glyoxime metal complexes is described. The electrochemistry of the cobalt complexes was investigated. The electrochemistry was compared to the observed electrochemistry of a zinc analog to identify the redox activity of the ligand. In the presence of acid the cobalt complexes were found to electrochemically reduce protons to dihydrogen. The electronics of the ancillary aluminum ligands were found to affect the potential of proton reduction in the cobalt complexes. These potentials were compared to other diglyoximate complexes.

Electrocatalytic activity of transition metal substituted heteropolytungstates

The electrochemical and electrocatalytic behavior of a series of heteropolytungstate anions in which a tungsten atom in the well known Keggin structure has been replaced by an iron atom is described. All of the iron substituted ions exhibit a one electron reversible couple associated with the Fe³⁺ center and a pair of two electron waves attributed to electron addition and removal from the tungsten oxo framework. The pH and ionic strength effects upon the various electrochemical processes are discussed and interpreted in terms of a competition between protonation and ion pairing of the highly negatively charged ions.

The anions are efficient catalysts for the electroreduction of hydrogen peroxide. A catalytic mechanism involving a formally Fe(IV) intermediate is proposed. Pulse radiolysis experiments were employed to detect the intermediate and evaluate the rate constants for the reactions in which it is formed and decomposed. A chain mechanism for the catalytic decomposition of hydrogen peroxide in which the Fe center shuttles between the +2, +3, and +4 oxidation states is proposed to explain the non-integral stoichiometry observed for the iron substituted polytungstate catalyzed electroreduction of hydrogen peroxide.

The anions are also efficient electrocatalyst for the electrochemical conversion of nitric oxide to ammonia. The catalyzed reduction does not produce hydroxylamine as an intermediate and appears to depend upon the ability of the multiply reduced heteropolytungstates to deliver several electrons to the bound NO group in a concerted step. A valuable feature of the heteropolytungstates is the ease at which the formal potentials of the several redox couples they exhibit may be shifted by changing the identity of the central heteroatom. Exploitation of this feature provided diagnostic information that was decisive in establishing the mechanism of electrocatalytic reduction.

The iron substituted heteropolytungstates are not degraded by repeated cycling between their oxidized and reduced states. They also show superior activity compared to their unsubstituted analogues, indicating that the Fe center acts as a binding site that facilitates inner-sphere electron transfer processes. The basic electrochemistry of several other transition metal substituted Keggin ions is also described.

Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

DNA-mediated charge transport signaling within the cell

DNA possesses the curious ability to conduct charge longitudinally through the π-stacked base pairs that reside within the interior of the double helix. The rate of charge transport (CT) through DNA has a shallow distance dependence. DNA CT can occur over at least 34 nm, a very long molecular distance. Lastly, DNA CT is exquisitely sensitive to disruptions, such as DNA damage, that affect the dynamics of base-pair stacking. Many DNA repair and DNA-processing enzymes are being found to contain 4Fe-4S clusters. These co-factors have been found in glycosylases, helicases, helicase-nucleases, and even enzymes such as DNA polymerase, RNA polymerase, and primase across the phylogeny. The role of these clusters in these enzymes has remained elusive. Generally, iron-sulfur clusters serve redox roles in nature since, formally, the cluster can exist in multiple oxidation states that can be accessed within a biological context. Taken together, these facts were used as a foundation for the hypothesis that DNA-binding proteins with 4Fe-4S clusters utilize DNA-mediated CT as a means to signal one another to scan the genome as a first step in locating the subtle damage that occurs within a sea of undamaged bases within cells.

Herein we describe a role for 4Fe-4S clusters in DNA-mediated charge transport signaling among EndoIII, MutY, and DinG, which are from distinct repair pathways in E. coli. The DinG helicase is an ATP-dependent helicase that contains a 4Fe-4S cluster. To study the DNA-bound redox properties of DinG, DNA-modified electrochemistry was used to show that the 4Fe-4S cluster of DNA-bound DinG is redox-active at cellular potentials, and shares the 80 mV vs. NHE redox potential of EndoIII and MutY. ATP hydrolysis by DinG increases the DNA-mediated redox signal observed electrochemically, likely reflecting better coupling of the 4Fe-4S cluster to DNA while DinG unwinds DNA, which could have interesting biological implications. Atomic force microscopy experiments demonstrate that DinG and EndoIII cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Knocking out DinG in CC104 cells leads to a decrease in MutY activity that is rescued by EndoIII D138A, but not EndoIII Y82A. DinG, thus, appears to help MutY find its substrate using DNA-mediated CT, but do MutY or EndoIII aid DinG in a similar way? The InvA strain of bacteria was used to observe DinG activity, since DinG activity is required within InvA to maintain normal growth. Silencing the gene encoding EndoIII in InvA results in a significant growth defect that is rescued by the overexpression of RNAseH, a protein that dismantles the substrate of DinG, R-loops. This establishes signaling between DinG and EndoIII. Furthermore, rescue of this growth defect by the expression of EndoIII D138A, the catalytically inactive but CT-proficient mutant of EndoIII, is also observed, but expression of EndoIII Y82A, which is CT-deficient but enzymatically active, does not rescue growth. These results provide strong evidence that DinG and EndoIII utilize DNA-mediated signaling to process DNA damage. This work thus expands the scope of DNA-mediated signaling within the cell, as it indicates that DNA-mediated signaling facilitates the activities of DNA repair enzymes across the genome, even for proteins from distinct repair pathways.

In separate work presented here, it is shown that the UvrC protein from E. coli contains a hitherto undiscovered 4Fe-4S cluster. A broad shoulder at 410 nm, characteristic of 4Fe-4S clusters, is observed in the UV-visible absorbance spectrum of UvrC. Electron paramagnetic resonance spectroscopy of UvrC incubated with sodium dithionite, reveals a spectrum with the signature features of a reduced, [4Fe-4S]+1, cluster. DNA-modified electrodes were used to show that UvrC has the same DNA-bound redox potential, of ~80 mV vs. NHE, as EndoIII, DinG, and MutY. Again, this means that these proteins are capable of performing inter-protein electron transfer reactions. Does UvrC use DNA-mediated signaling to facilitate the repair of its substrates?

UvrC is part of the nucleotide excision repair (NER) pathway in E. coli and is the protein within the pathway that performs the chemistry required to repair bulky DNA lesions, such as cyclopyrimidine dimers, that form as a product of UV irradiation. We tested if UvrC utilizes DNA-mediated signaling to facilitate the efficient repair of UV-induced DNA damage products by helping UvrC locate DNA damage. The UV sensitivity of E. coli cells lacking DinG, a putative signaling partner of UvrC, was examined. Knocking out DinG in E. coli leads to a sensitivity of the cells to UV irradiation. A 5-10 fold reduction in the amount of cells that survive after irradiation with 90 J/m2 of UV light is observed. This is consistent with the hypothesis that UvrC and DinG are signaling partners, but is this signaling due to DNA-mediated CT? Complementing the knockout cells with EndoIII D138A, which can also serve as a DNA CT signaling partner, rescues cells lacking DinG from UV irradiation, while complementing the cells with EndoIII Y82A shows no rescue of viability. These results indicate that there is cross-talk between the NER pathway and DinG via DNA-mediated signaling. Perhaps more importantly, this work also establishes that DinG, EndoIII, MutY, and UvrC comprise a signaling network that seems to be unified by the ability of these proteins to perform long range DNA-mediated CT signaling via their 4Fe-4S clusters.