Protein-DNA charge transport: Redox activation of a DNA repair protein by guanine radical

DNA charge transport (CT) chemistry provides a route to carry out oxidative DNA damage from a distance in a reaction that is sensitive to DNA mismatches and lesions. Here, DNA-mediated CT also leads to oxidation of a DNA-bound base excision repair enzyme, MutY. DNA-bound Ru(III), generated through a flash/quench technique, is found to promote oxidation of the [4Fe-4S](2+) cluster of MutY to [4Fe-4S](3+) and its decomposition product [3Fe-4S](1+). Flash/quench experiments monitored by EPR spectroscopy reveal spectra with g = 2.08, 2.06, and 2.02, characteristic of the oxidized clusters. Transient absorption spectra of poly(dGC) and [Ru(phen)(2)dppz](3+) (dppz = dipyridophenazine), generated in situ, show an absorption characteristic of the guanine radical that is depleted in the presence of MutY with formation instead of a long-lived species with an absorption at 405 nm; we attribute this absorption also to formation of the oxidized [4Fe-4S](3+) and [3Fe4S](1+) clusters. In ruthenium-tethered DNA assemblies, oxidative damage to the 5'-G of a 5'-GG-3' doublet is generated from a distance but this irreversible damage is inhibited by MutY and instead EPR experiments reveal cluster oxidation. With ruthenium-tethered assemblies containing duplex versus single-stranded regions, MutY oxidation is found to be mediated by the DNA duplex, with guanine radical as an intermediate oxidant; guanine radical formation facilitates MutY oxidation. A model is proposed for the redox activation of DNA repair proteins through DNA CT, with guanine radicals, the first product under oxidative stress, in oxidizing the DNA-bound repair proteins, providing the signal to stimulate DNA repair

Effects of the Photooxidant on DNA-Mediated Charge Transport

A direct comparison of DNA charge transport (CT) with different photooxidants has been made. Photooxidants tested include the two metallointercalators, Rh(phi)_2(bpy‘)^(3+) and Ru(phen)(bpy‘)(dppz)^(2+), and three organic intercalators, ethidium (Et), thionine (Th), and anthraquinone (AQ). CT has been examined through a DNA duplex containing an A_6-tract intervening between two 5‘-CGGC-3‘ sites with each of the photooxidants covalently tethered to one end of the DNA duplex. CT is assayed both through determination of the yield of oxidative guanine damage and, in derivative DNA assemblies, by analysis of the yield of a faster oxidative trapping reaction, ring opening of N^2-cyclopropylguanine (d^(CP)G) within the DNA duplex. We find clear differences in oxidative damage ratios at the distal versus proximal 5‘-CGGC-3‘ sites depending upon the photooxidant employed. Importantly, nondenaturing gel electrophoresis data demonstrate the absence of any DNA aggregation by the DNA-bound intercalators. Hence, differences seen with assemblies containing various photooxidants cannot be attributed to differential aggregation. Comparisons in assemblies using different photooxidants thus reveal characteristics of the photooxidant as well as characteristics of the DNA assembly. In the series examined, the lowest distal/proximal DNA damage ratios are obtained with Ru and AQ, while, for both Rh and Et, high distal/proximal damage ratios are found. The oxidative damage yields vary in the order Ru > AQ > Rh > Et, and photooxidants that produce higher distal/proximal damage ratios have lower yields. While no oxidative DNA damage is detected using thionine as a photooxidant, oxidation is evident using the faster cyclopropylguanosine trap; here, a complex distance dependence is found. Differences observed among photooxidants as well as the complex distance dependence are attributed to differences in rates of back electron transfer (BET). Such differences are important to consider in developing mechanistic models for DNA CT

Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms

Redox cycling of extracellular electron shuttles can enable the metabolic activity of subpopulations within multicellular bacterial biofilms that lack direct access to electron acceptors or donors. How these shuttles catalyze extracellular electron transfer (EET) within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazines mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by eDNA binding. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and can participate directly in redox reactions through DNA. In vivo, biofilm eDNA can also support rapid electron transfer between redox active intercalators. Together, these results establish that PYO:eDNA interactions support an efficient redox cycle with rapid EET that is faster than the rate of PYO loss from the biofilm

Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms

Redox cycling of extracellular electron shuttles can enable the metabolic activity of subpopulations within multicellular bacterial biofilms that lack direct access to electron acceptors or donors. How these shuttles catalyze extracellular electron transfer (EET) within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazines mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by eDNA binding. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and can participate directly in redox reactions through DNA. In vivo, biofilm eDNA can also support rapid electron transfer between redox active intercalators. Together, these results establish that PYO:eDNA interactions support an efficient redox cycle with rapid EET that is faster than the rate of PYO loss from the biofilm

The Flash−Quench Technique in Protein−DNA Electron Transfer: Reduction of the Guanine Radical by Ferrocytochrome c

Electron transfer from a protein to oxidatively damaged DNA, specifically from ferrocytochrome c to the guanine radical, was examined using the flash−quench technique. Ru(phen)_2dppz^(2+) (dppz = dipyridophenazine) was employed as the photosensitive intercalator, and ferricytochrome c (Fe^(3+) cyt c), as the oxidative quencher. Using transient absorption and time-resolved luminescence spectroscopies, we examined the electron-transfer reactions following photoexcitation of the ruthenium complex in the presence of poly(dA-dT) or poly(dG-dC). The luminescence-quenching titrations of excited Ru(phen)_2dppz^(2+) by Fe^(3+) cyt c are nearly identical for the two DNA polymers. However, the spectral characteristics of the long-lived transient produced by the quenching depend strongly upon the DNA. For poly(dA-dT), the transient has a spectrum consistent with formation of a [Ru(phen)_2dppz^(3+), Fe^(2+) cyt c] intermediate, indicating that the system regenerates itself via electron transfer from the protein to the Ru(III) metallointercalator for this polymer. For poly(dG-dC), however, the transient has the characteristics expected for an intermediate of Fe^(2+) cyt c and the neutral guanine radical. The characteristics of the transient formed with the GC polymer are consistent with rapid oxidation of guanine by the Ru(III) complex, followed by slow electron transfer from Fe^(2+) cyt c to the guanine radical. These experiments show that electron holes on DNA can be repaired by protein and demonstrate how the flash−quench technique can be used generally in studying electron transfer from proteins to guanine radicals in duplex DNA

Fast Back Electron Transfer Prevents Guanine Damage by Photoexcited Thionine Bound to DNA

The phenothiazinium dye thionine has a high excited state reduction potential and is quenched by guanine on the femtosecond time scale. Here, we show by gel electrophoresis that irradiation of thionine with 599 nm light in the presence of an oligonucleotide duplex does not produce permanent DNA damage. Upon photoexcitation of thionine weakly associated with guanosine-5‘-monophosphate, the reduced protonated thionine radical and neutral guanine radical are detected by transient absorption spectroscopy, indicating that the quenching of thionine by guanine occurs via an electron-transfer mechanism. The observation of radical formation without permanent guanine damage indicates that fast back electron transfer plays a critical role in governing the yield of damage by DNA-binding molecules

Electron transfer between metal complexes bound to DNA: variations in sequence, donor, and metal binding mode

Using luminescence spectroscopy and single photon counting, photoinduced electron transfer (ET) reactions between photoexcited [M(phen)_2dppz ^(2+) (phen = 1,10-phenanthroline, dppz=dipyridophenazine, M=Ru or Os) and the electron acceptors Rh(phi)_2bpy^(3+) (phi=9,10-phenanthrenequinone diimine, bpy=2,2′-bipyridine) and Ru(NH_3)_6^(3+) were studied as a function of DNA sequence in long DNA polymers. In addition, the thermal back reactions between M(III) and reduced acceptor were also followed by transient absorption spectroscopy. The comparison of ET reactions of the isostructural donors Os and Ru with an intercalated acceptor, Rh(phi)_2bpy^(3+), and an externally bound acceptor, Ru(NH_3)_6^(3+), helps to elucidate which factors are important for electron transfer between DNA-bound intercalators. Ru(phen)_2dppz^(2+) and Os(phen)_2dppz^(2+) show nearly identical quenching by Rh(phi)_2bpy^(3+) for a given DNA polymer, with an efficient quenching process that occurs on a time scale much faster than the excited state lifetime. We find that Rh(phi)_2bpy^(3+) and Ru(NH_3)_6^(3+) show opposite trends for quenching of DNA-bound M(phen)_2dppz^(2+). Quenching by intercalated Rh(phi)_2bpy^(3+) is most efficient in AT-only DNA polymers and less efficient in GC-only polymers, whereas for groove-bound Ru(NH_3)_6^(3+), the reverse is observed. The intrinsic excited state lifetime of Ru(phen)_2dppz^(2+) bound to DNA and the luminescence quenching efficiency by Ru(NH_3)_6^(3+) provide indicators of the solvent accessibility of the DNA-bound dppz donor. On this basis, we attribute the difference in ET reactivity among the various DNA polymers to differences in how well M(phen)_2dppz^(2+) stacks in DNA

Os(phen)_2dppz^(2+) in Photoinduced DNA-Mediated Electron Transfer Reactions

The photoinduced electron transfer chemistry between Os(phen)_2dppz^(2+) and Rh(phi)_2bpy^(3+) bound to DNA has been characterized. Os(phen)_2dppz^(2+) serves as an isostructural analogue for Ru(phen)_2dppz^(2+) with a red-shifted emission spectrum, access to a 3+ oxidation state which is stabilized by ∼500 mV relative to the ruthenium complex, and excited-state lifetimes below 10 ns in the presence of DNA. Emission from Δ-Os(phen)_2dppz^(2+) bound to calf thymus DNA is efficiently quenched by Δ-Rh(phi)_2bpy^(3+), and a lower limit for the quenching constant is set at 7 × 10^9 s^(-1). The quenching profile over a range of quencher concentrations is found to be remarkably similar to that of the ruthenium analogue, despite an increase of ∼200 mV in ΔG for the photoinduced, forward electron transfer reaction. Such an observation may indicate the importance of the HOMO energy in the donor excited state, which is similar for both donors. Owing to the lack of spectral overlap between Os(phen)_2dppz^(2+) emission and Rh(phi)_2bpy^(3+) absorption, energy transfer does not contribute to the observed quenching, and therefore, on the basis of the similarity in quenching profiles for the osmium and ruthenium donors, we can also rule out energy transfer in the photoinduced quenching of intercalated Ru(phen)_2dppz^(2+) by Rh(phi)_2bpy^(3+). Moreover, diffusional processes are found not to contribute to quenching, since the faster intrinsic excited state of the osmium complex compared to ruthenium does not lead to a reduction in quenching efficiency. Transient absorption measurements on the microsecond time scale furthermore reveal a transient signal for this electron transfer process, and this transient intermediate has been assigned to the oxidized donor (Os(III)) on the basis of full spectral characterization and comparison to chemical oxidation of Os(II)