DNA Charge Transport: from Chemical Principles to the Cell

Abstract

The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology.

Figure 1. Comparison of DNA and graphite structures

Spacing between adjacent base pairs in DNA (3.4 Å) is similar to the planar spacing in graphite (z-direction). This close proximity of aromatic base-pairs allows for significant oribital overlap along the DNA helix, resulting in π-stacking of the DNA bases. The structural similarity between graphite, a known conductive material, and DNA was an initial clue to the conductivity of DNA. PDB file 3BSE (DNA).

Figure 2. Solution platforms for studying DNA CT

Top: In the initial studies of DNA CT, electron transfer between metal complexes via the DNA could be detected by monitoring the quenching of the fluorescence from a tethered ruthenium metal complex (green) by a distally tethered rhodium complex (red). Bottom: DNA CT can also be detected by monitoring the oxidation of guanine by a tethered rhodium photooxidant (red) injecting holes into the DNA that localize to the distal guanines. Structure of an intercalating photooxidant [Rh(phi)₂(bpy′)]²⁺ is shown.

Figure 3. Mismatch detection on DNA-modified electrodes

Comparison of the electrochemical properties of a well-matched DNA monolayer assembled on gold electrodes to that of a monolayer containing a single base pair mismatch. A distally bound, covalent redox probe such as Nile blue can stack with the DNA bases and report on the integrity of the DNA. Cyclic voltammogram (CV) traces demonstrate that current flows from the electrode surface to the redox probe at different applied potentials in physiological buffer. Charge can flow efficiently through well-matched DNA, but when the π-stacking of the bases is disrupted by a single base pair mismatch or lesion, DNA CT is attenuated and current does not flow effectively to the redox probe.

Figure 4. Electrochemical assay for the detection of methyltransferase activity

A self-assembled monolayer of DNA tethered to methylene blue on a gold electrode can be used to measure the methyltransferase activity of assayed solutions. The electrode is first treated with either purified methyltransferases, such as human Dnmt1, or lysates from tumors. If the DNA is not fully methylated, then a restriction enzyme can cut the DNA at a restriction site, highlighted in blue, within the DNA. After washing, the electrochemical signal is turned off, leading to a low percent of signal remaining compared to the signal before treatment with the restriction enzyme. If the DNA is methylated, corresponding to high methyltransferase activity, then the DNA is protected from restriction and the electrochemical signal is unperturbed, corresponding to a high percent of signal remaining. This assay has been used to detect the methyltransferase activity from tumor lysates (right). For tumor lysates tested with this device, the percent of signal remaining after treatment with restriction enzymes is high owing to increased methyltransferase activity. Lysates from adjacent tissue, however, have low percent signal remaining. Thus, lysates from tumors and normal tissue can be distinguished using this assay.

Figure 5. Redistribution of DNA repair proteins to sites of damage via DNA-mediated CT signaling

Diffusing DNA-processing enzymes with 4Fe-4S clusters such as EndoIII, MutY, or DinG bind to DNA in the 2+ oxidation state (green) [1]. An electron can be transferred to a nearby oxidized protein in the 3+ oxidation state (blue), reducing it to the 2+ oxidation state, promoting its dissociation from DNA owing to a decreased binding affinity [2]. The protein can then take advantage of 3D diffusion in order to search the genome elsewhere for damage [3]. If there is an intervening lesion or substrate that attenuates or blocks DNA CT such as a DNA lesion or R-loop, the proteins stay bound to the DNA and use 1D diffusion to locate the substrate to be processed [4]. This mechanism provides a means for proteins to locate DNA damage within a sea of undamaged bases in the genome.

Figure 6. DNA electrochemistry of WT and Y82A EndoIII

DNA-binding proteins with redox-active cofactors such as iron-sulfur clusters can be assayed on DNA-modified electrodes, effectively measuring their DNA-bound redox potentials. DNA binding shifts the redox potential of the [4Fe4S]^3+/2+ couple of the base excision repair protein EndoIII, activating the protein towards oxidation. The EndoIII mutant Y82A is less proficient in DNA charge transfer electrochemically, with less charge passing from the DNA through the protein to the cluster. Thus Y82A EndoIII is less able to cooperate with other iron-sulfur cluster proteins via DNA CT to scan the genome for damage.

Figure 7. Genetic experiments indicate DNA-mediated signaling among DinG, EndoIII, and MutY

Left: When EndoIII is knocked out of InvA cells that depend upon R-loop repair by DinG for growth, a significant growth defect is observed (red). When the knockout, InvA Δnth, is complemented with a plasmid encoding WT EndoIII, EndoIII D138A, or RNaseH growth is restored (blue). When InvA Δnth is complemented with an empty plasmid or a plasmid encoding EndoIII Y82A, the growth defect remains (red). Taken together this indicates that the growth defect is indeed due to silencing the nth gene, that there is signaling between EndoIII and DinG to facilitate the unwinding of R-loops, and that this signaling is DNA-mediated; the enzymatically active but CT-deficient mutant EndoIII Y82A cannot restore growth while the CT-proficient but catalytically inactive EndoIII D138A does restore growth. Right: The InvA growth assay and Lac+ reversion assays tested indicate that DNA-mediated signaling facilitates signaling among DinG, EndoIII, and MutY.

Figure 8. SoxR, Dps and p53 proteins use DNA CT to sense and respond to distant DNA damage produced by a tethered photooxidant

(A) SoxR, a bacterial transcription factor involved in response to superoxide stress, contains [2Fe2S]^2+/1+ clusters and undergoes a conformational change and transcriptional activation upon oxidation. Irradiation of a construct with covalently tethered photooxidant [Rh(phi)₂(bpy′)]³⁺ located 80 base pairs from the SoxR promoter binding site produced soxS, the target gene for SoxR. Irradiation of the photooxidant produces an excited state capable of oxidizing DNA, the injected electron hole localizes to guanine radicals, and SoxR then becomes oxidized to fill guanine radicals, resulting in transcriptional activation from a distance via DNA CT. (B) Dps proteins, bacterial mini ferritins implicated in the virulence of pathogenic bacteria, contain iron-binding ferroxidase sites and are involved in DNA protection from oxidative stress. Damage created at a low redox potential guanine triplet upon irradiation with tethered photooxidant [Ru(phen)(dppz)(bpy′)]²⁺ can be attenuated by Dps loaded with ferrous iron, but not by Apo-Dps or Dps loaded with ferric iron, which both lack reducing equivalents. Charge transfer from the ferrous iron bound at the ferroxidase sites of Dps to guanine radical holes within DNA could be an efficient mechanism of genomic protection from a distance via DNA CT. (C) p53, a human transcription factor known as the “guardian of the genome”, contains a network of redox-active cysteine residues. Irradiation of constructs with a tethered anthraquinone photooxidant separated from the p53 response element can result in oxidation of these cysteine residues and dissociation of p53 from the DNA. Specifically, when the response element contains low redox potential guanine sites, p53 can become efficiently oxidized via DNA CT, resulting in decisions regarding the cellular fate. PDB files: SoxR (2ZHG), Dps (1N1Q), p53 (3KMD).