nihms-49861.pdf

Biological Contexts for DNA Charge Transport Chemistry

Edward J. Merino

Amie K. Boal

, and

Jacqueline K. Barton

Division of Chemistry and Chemical Engineering California Institute of Technology, Pasadena,

California 91125

SUMMARY

Many experiments have now shown that double helical DNA can serve as a conduit for efficient

charge transport (CT) reactions over long distances

in vitro

. These results prompt the

consideration of biological roles for DNA-mediated CT. DNA CT has been demonstrated to occur

in biologically relevant environments such as within the mitochondria and nuclei of HeLa cells as

well as in isolated nucleosomes. In mitochondria, DNA damage that results from CT is funneled to

a critical regulatory element. Thus DNA CT provides a strategy to funnel damage to particular

sites in the genome. DNA CT might also be important in long range signaling to DNA-bound

proteins. Both DNA repair proteins, containing Fe-S clusters, and the transcription factor, p53,

which is regulated through thiol-disulfide switches, can be oxidized from a distance through

DNA-mediated CT. These observations highlight a means through which oxidative stress may be

chemically signaled in the genome over long distances through CT from guanine radicals to DNA-

bound proteins. Moreover, DNA-mediated CT may also play a role in signaling among DNA-

binding proteins, as has been proposed as a mechanism for how DNA repair glycosylases more

efficiently detect lesions inside the cell.

Introduction

The double helical structure adopted by B-form DNA, where a negatively charged sugar

phosphate backbone surrounds a

-stacked array of heterocyclic aromatic base-pairs, allows

it to serve as an efficient medium for long-range charge transport (CT) [1]. This chemistry

has now been well established as a property of DNA. DNA CT can be rapid and it can occur

over long molecular distances if the reaction is initiated by oxidants or reductants that are

intercalated or otherwise well-coupled into the base-pair stack. The observation that even

very subtle changes to the structure of the base-pair stack, for instance, the presence of a

single mismatched or damaged base, can drastically attenuate the efficiency of DNA-

mediated CT further highlights the importance of the DNA base pair

-stack in these

reactions. While many features of DNA CT under a variety of experimental conditions have

now been elucidated, the role of DNA CT in biological processes requires more

consideration. This review describes recent efforts to explore biological contexts and

opportunities for DNA-mediated CT.

to whom correspondence should be addressed. jkbarton@caltech.edu.

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Author Manuscript

Curr Opin Chem Biol

. Author manuscript; available in PMC 2011 November 30.

Published in final edited form as:

Curr Opin Chem Biol

. 2008 April ; 12(2): 229–237. doi:10.1016/j.cbpa.2008.01.046.

NIH-PA Author Manuscript

DNA Damage over Long Range

It was first shown that DNA CT can promote damage to DNA from a distance in a DNA

assembly containing a tethered rhodium intercalator, a potent photooxidant, spatially

separated from two low energy guanine doublets [2]. Guanines are the bases that are most

easily oxidized in DNA, and the 5’-G's of guanine doublets have a particularly low oxidation

potential [3, 4]. Since then long range oxidative DNA damage has been extensively

characterized using a variety of photooxidants. It has become clear that electron holes,

oxidizing equivalents injected into the DNA through a host of damaging agents, formed at

any site along the DNA duplex will migrate to low energy guanine sites. The distance range

over which holes can migrate and whether guanine radicals, once generated, provide a

chemical signal for oxidative stress throughout the genome via DNA-mediated CT are

questions that need to be addressed (Figure 1).

This long range migration was explored in DNA oligonucleotides of defined length and

sequence using covalently tethered photooxidants as initiators of oxidative damage. Using

[Rh(phi)

bpy]

, (phi = 9,10-phenanthrenequinone diimine), as the photooxidant, guanine

doublet sites throughout the duplex show intense levels of damage even when the oxidant is

located 200 Å away [5]. CT over similar distances has also been observed with other

photooxidants [6]. Longer distances have not been systematically examined, but, given the

very shallow distance dependences observed thus far, efficient DNA CT over longer

distance regimes is likely possible. Recently, in a Rh-tethered assembly containing an

extended adenine tract, the distance dependence of DNA CT was shown to be essentially

flat, with no change in damage over 5 nm [7] (Figure 2). Therefore, holes can migrate over

long molecular distances to form permanent DNA lesions far from the oxidant binding site.

In all of these experiments, strong damage is observed at the 5’-G of GG sites. Thus, 5’-G

damage at a GG site has become the hallmark of one electron oxidative damage arising

through DNA CT.

While DNA CT proceeds over long distances, the reaction is exquisitely sensitive to

mismatches, base lesions and other perturbations to the DNA base pair stack. This was

evident first in the finding that DNA bulges can interfere with long range oxidative damage.

Intervening mismatches, particularly those where local stacking is highly perturbed, also

attenuate long range oxidative damage. Thus, while DNA CT can occur over remarkably

long distances, it is a reaction that is modulated by the intervening sequence-dependent

structure and dynamics of DNA.

Interestingly, fewer experiments have been carried out to explore electron transfer through

DNA [8]. DNA-mediated electrochemistry, involving ground state DNA-mediated

reductions, exhibits a very shallow distance dependence with a remarkable sensitivity to

intervening mismatches and lesions [9,10]. Recent solution experiments, where electron and

hole transfer are compared using the same DNA and photoactivated group demonstrate that

electron transfers through DNA are similarly characterized by these two important features:

(i) a shallow distance dependence and (ii) a sensitivity to perturbations in the base pair stack

[11].

The constant assault on DNA by endogenous and exogenous oxidizing agents often leads to

covalent modification of DNA, and due to DNA-mediated CT, these modifications may not

necessarily arise at the site of first collision [12]. Oxidative reactions in DNA have

important implications for the generation of mutations and subsequent pathogenesis. The

most common biological oxidant, iron, undergoes Fenton chemistry to produce hydroxyl

radicals and other species that can readily react with the DNA bases. Additionally, radicals

generated on the sugar-phosphate backbone can lead to hole formation on the DNA bases

[13]. Importantly, once a hole is produced in double stranded DNA, DNA CT can funnel the

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hole to low oxidation potential sites, where the hole reacts irreversibly with O

and H

The oxidative reaction of DNA bases with O

and H

O leads to the formation of mutagenic

DNA lesions [12, 14]. Further oxidation of DNA base lesions yields products that bypass the

repair machinery and exacerbate DNA damage.

Funneling Oxidative Damage to Specific DNA Regions

The involvement of DNA CT in promoting oxidative lesions suggests that DNA damage

products may not be uniformly distributed within a genome but may instead be funneled to

specific sites. This hypothesis is supported by analysis of genomic DNA showing that

introns and exons contain differential amounts of low oxidation potential sites [15]. Further

examination of eight eukaryotic genomes illustrates that DNA CT may drive non-uniform

distribution of oxidative DNA lesions [16]. For instance, exons contain a 50 fold decrease in

oxidation prone guanine. Therefore protein coding regions may be protected from DNA

lesions by appropriately placing low oxidation potential sites such that DNA CT can funnel

damage out of the exons and into introns. Telomeres, the ends of chromosomes, represent

hot spots for DNA damage, and these telomeric regions represent sites of particularly high

guanine content. Moreover, the DNA telomeres may also adopt a quadruplex structure, and

it has been shown that holes are preferentially shuttled to guanines within these structures

[17, 18].

Whether DNA CT is important in funneling damage to discrete locations could be resolved

by determining the location of oxidative lesions in a genome. Visualizing the sequence

details of oxidative damage on a genome is difficult, however, due to their size and low

copy number. Most methods only interrogate the total level of damaged DNA adducts by

mass spectrometry as well as a variety of other techniques but do not yield the location in

the sequence of the lesions produced. Ligation-mediated PCR has, however, been utilized to

determine the sequence details of oxidative damage in DNA genomes [19]. DNA CT was

shown to occur in isolated nuclei from HeLa cells using ligation-mediated PCR in

conjunction with [Rh(phi)

bpy]

; the complex binds to DNA without sequence specificity,

and upon photoactivation, either promotes strand breaks directly at the oxidant site or

induces one electron oxidative damage [20]. The pattern of oxidative lesions reveals

hallmarks of DNA CT, with damage occurring predominately at guanine-rich low oxidation

potential sites, the 5’-G of guanine doublets and triplets. Moreover the results showed that

while oxidative damage was found preferentially at guanine doublets, the rhodium

photooxidant was bound primarily at distant sites. Hence the damage must have occurred

through DNA-mediated CT. This work established that CT can occur in DNA within the

nucleus.

Another biologically important target for oxidative stress is the mitochondrion.

Mitochondria contain an abundance of reactive oxygen species as a result of oxidative

phosphorylation and also contain their own DNA [21]. Mutations in mitochondrial DNA

have been found in a variety of tumors and are associated with other diseases, while other

DNA perturbations, like large scale rearrangments, are common in mitochondrial DNA.

Oxidative damage to extracted mitochondrial DNA [22] as well as to mitochondrial DNA

within functioning mitochondria [23] promoted by the rhodium photooxidant reveals that

DNA lesions can arise from a distance using DNA CT. Again, this damage from a distance

was demonstrated by comparing sites of Rh binding versus guanine oxidation. The spatial

separation between the Rh binding sites and one electron guanine oxidation sites is striking;

oxidation can occur more than 70 bases away from the nearest bound oxidant. Again these

data support long range CT through DNA within a cellular organelle, here the

mitochondrion (Figure 3).

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Some interesting biological consequences of DNA CT emerged from these studies. First,

sites of base oxidation by DNA CT in mitochondrial DNA overlap with known mutational

hot spots associated with cancers. The correlation between mutation frequency [24] and

lesions produced [22] suggests that DNA CT may be a major contributor to mitochondrial

oxidative lesions

in vivo

. Secondly, one highly damaged position found is a regulatory

element known as conserved sequence block II that is vital for DNA replication. Conserved

sequence block II contains a seven guanosine repeat, the largest guanosine repeat on the

mitochondrial genome. Positioning such a low oxidation potential site as a regulatory

element can be advantageous since each mitochondrion contains many copies of its genome.

Funneling damage to a regulatory element, via DNA CT, could decrease the likelihood that

damaged mitochondrial genomes will be replicated by the formation of an oxidative lesion

that perturbs the replication machinery. These lesions could signal the level of damage in a

particular genome. DNA CT may thus provide a protection mechanism to exclude damaged

DNA from the replication cycle in mitochondria.

Long Range CT in the presence of DNA-bound Proteins

Since it is apparent that DNA-mediated CT can take place in the crowded environment of a

cell, it becomes important to ask systematically what are the effects of DNA-binding

proteins on DNA CT? Moreover, within many organisms, DNA is packaged into chromatin

or chromatin-like higher order structures via interactions with histone proteins. How does

the nucleosome structure, containing DNA-bound histones, affect DNA CT?

Several studies of DNA CT in the presence of specific DNA-binding proteins have been

carried out. Experiments to monitor CT through the DNA base pair stack is unaltered when

a protein, such as a helix-turn helix protein, is bound in such a way that it induces little

structural change in the DNA [25]. Proteins that perturb the structure of DNA, however,

have a profound effect on the yield of CT [26]. Uracil DNA glycosylase, a DNA repair

enzyme that flips uracil residues out of the base-pair stack, does not allow CT to proceed

beyond the protein binding site. TATA-binding protein, a transcription factor that kinks the

DNA helix by > 90 degrees, also diminishes CT efficiency to guanine doublets. This

sensitivity of DNA-mediated CT to protein binding has actually led to the application of

DNA electrochemistry as a sensitive probe for DNA binding by base-flipping proteins as

well as proteins like TATA-binding protein [26, 27].

Besides affecting base stacking, in studies of long range oxidation, DNA-binding proteins

have also been found to tune the oxidation potential of possible damage sites in DNA. For

example, the restriction enzyme BamHI, which binds the DNA sequence 5’-GGATCC-3’

inhibits damage at the guanine doublet located within its binding site [28]. BamHI makes

extensive hydrogen bonding contacts to the guanines in its restriction site and these

interactions are proposed to change the ionization potential, making the guanines less

susceptible to oxidation. Both mechanisms that proteins employ to perturb DNA CT,

structural alteration of the

-stack or modification of the electronic properties of specific

bases, are interesting to consider in a biological context. One could imagine DNA-binding

proteins, through a specific interaction, could insulate a particular sequence or a region of

the genome, disallowing the propagation of DNA CT. Whether such protection is actually

utilized within the cell has not, however, been established.

A question of significant interest has been whether DNA CT can proceed within the

nucleosome core particle (Figure 4). Experiments were first carried out on DNA using the

intercalating photooxidant, Rh(phi)

bpy

, in the presence and absence of bound histones

[29]. The 146 base pair DNA sequence employed in these studies was the same utilized for

the crystal structure determination of the nucleosome core particle [30], which had a distinct

kink in the DNA at its center in order to obtain consistent phasing of the DNA bound in the

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nucleosomes. We observed damage at all of the 5’-G's of guanine doublets between the Rh,

bound at the DNA terminus, and this central kink, both in the absence and presence of the

histone proteins. Thus it appears that even within the nucleosome, DNA CT may proceed.

This long range CT within DNA in the nucleosome core particle was confirmed in similar

experiments using tethered anthraquinone as the photooxidant [31]. Some variations in

relative intensities across the guanine doublets were observed for damage in the nucleosome

versus that for the free DNA when comparing anthraquinone and the Rh intercalator. These

variations may represent differences along the DNA in access to oxygen and water, required

to make the irreversible damage products from the guanine radical, and possible tuning of

local guanine oxidation potentials by the DNA-bound histones. Between Rh and

anthraquinone as photooxidants, the small variations in guanine damage observed likely

reflect differences in rates of back electron transfer for the two oxidants. Interestingly,

anthraquinone-tethered nucleosomes were also recently utilized to show DNA-protein

crosslinking that results from long range DNA CT [32].

As indicated, DNA CT was also found to occur in the mitochondrion, and here the DNA is

also bound by its native suite of proteins [23]. Mitochondrial DNA-protein interactions were

found to be altered, perhaps also through crosslinking, as a result of oxidative damage

arising via DNA CT. These results may resemble that seen in the nucleosome core particle.

Importantly, in considering DNA being packaged in the nuclesome core particle, we

generally consider that the DNA is being not only packaged but also protected from the

assault of various damaging agents. Certainly these results show that within the nucleosome,

the DNA is not protected from oxidative damage because of DNA-mediated CT.

Oxidation from a Distance of DNA-bound Proteins

Not only can proteins serve to modulate DNA CT, DNA-binding proteins can also serve to

participate in reactions at a distance through DNA-mediated CT. DNA-binding proteins

contain a variety of functional motifs with oxidation potentials similar to or lower than that

of guanine [33]. Guanine radicals generated with a ruthenium photooxidant can be

transferred to aromatic amino acid side chains (tyrosine and tryptophan) present in

positively charged peptides (Lys-Tyr-Lys and Lys-Trp-Lys) [34]. Photolyase, an enzyme

that uses CT to repair thymine dimer lesions in DNA, contains a flavin cofactor that can also

be oxidized and reduced via the DNA

-stack when probed electrochemically on DNA-

modified electrodes [35]. Additionally, appropriately positioned thiols incorporated into the

sugar-phosphate backbone can be oxidized in a DNA-mediated reaction [36].

Similarly, many DNA-binding proteins contain cysteine residues that are redox-active, and

these too may be oxidized at a distance through DNA CT [37]. One example is p53, a redox-

modulated transcription factor that contains ten conserved cysteine residues in its DNA-

binding domain [38]. We prepared a DNA-assembly containing a pendant photooxidant, and

the consensus sequence for binding p53 [37]. As illustrated in Figure 5, we observe that

photoactivation of the anthraquinone promotes oxidative dissociation of p53 from the DNA.

The presence of an intervening mismatch, moreover, inhibits this DNA-mediated reaction.

Analysis of the p53 crystal structure reveals several candidates for thiol oxidation close to

the DNA, and mass spectrometry of trypsin digests of p53 after photolysis is consistent with

disulfide bond formation in the DNA-bound protein. Hence DNA-bound p53 can be

oxidized and induced to dissociate from its bound site from a distance through DNA-

mediated CT.

The oxidation of p53 through DNA CT was also probed within the cellular environment.

Human HCT cells were treated with the Rh photooxidant and irradiated to generate high

levels of guanine radicals. A new oxidized form of p53 was detected via western blot that

could be reversed by addition of exogenous thiols, consistent with disulfide bond formation.

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In fact, the same oxidized p53 was produced upon addition of hydrogen peroxide. This

oxidized p53 appears under conditions of oxidative stress.

The promoter sequences for p53 are diverse and can include those that control expression of

important apoptotic or developmental genes. Biologically, p53 must distinguish between

various promoters depending upon cellular stresses [39]. Further investigation reveals that

the DNA-mediated oxidation of p53 and subsequent dissociation is promoter-specific [37].

On a promoter involved in apoptosis, p21, p53 does not dissociate with photoactivation from

a distance, although dissociation is observed on a promoter involved in DNA repair. We

hypothesize that under high levels of oxidative stress, formation of guanine radicals via

DNA CT occurs frequently, signaling that the DNA repair pathway is futile. When bound to

DNA repair promoters, p53 oxidation followed by dissociation occurs, though p53 remains

bound to promoters to activate cell cycle arrest under the high oxidative stress. Importantly,

these results taken together provide a chemical rationale for the cellular response of p53 to

oxidative stress through long range signaling using DNA-mediated CT.

The Possibility of DNA-mediated Signaling among Proteins

DNA repair proteins are another major class of DNA-binding proteins that could modulate

or participate in DNA CT events. Given the well established sensitivity of DNA CT to a

wide variety of damaged bases [10], it is interesting to consider that DNA repair proteins

could harness CT to search DNA for damaged sites. We have studied the DNA-mediated

electron transfer properties of several repair proteins that contain [4Fe4S] clusters, a cofactor

capable of being oxidized by guanine radicals [40, 41]. Two of these, MutY and

Endonuclease III (EndoIII), are glycosylases in the base-excision repair (BER) pathway and

are highly conserved in a wide variety of organisms [42]. MutY is an adenine glycosylase,

primarily removing A mispaired with 8-oxo-guanine, while EndoIII removes a broad

spectrum of oxidized pyrimidines from DNA. The [4Fe4S] cluster in the isolated proteins is

found in the 2+ oxidation state and was originally demonstrated to be redox-inert and, thus,

likely a structural element [43]. Notably, most of these early characterization attempts were

executed in the absence of DNA; when bound to DNA, the [4Fe4S] moiety could be in a

different environment, conferring upon it different redox properties.

DNA-mediated oxidation of the [4Fe4S]

cluster in MutY and EndoIII has been explored

in solution using a variety of experimental techniques [44, 45]. The electron lost upon

oxidation of the [4Fe4S]

cluster can be trapped in DNA by a uridine base modified with a

nitroxide spin label. The resulting nitroxide radical species is detected with electron

paramagnetic resonance spectroscopy [44]. Similarly, a guanine radical cation, generated

with a ruthenium photooxidant and monitored spectroscopically or with gel electrophoresis,

can be quenched by MutY, resulting in formation of a [4Fe4S]

cluster [45]. Importantly,

guanine radicals are the first products of oxidative DNA damage inside the cell, and these

results indicate that base radicals could provide the driving force

in vivo

to initiate DNA-

mediated CT signaling among [4Fe4S] BER glycosylases.

When investigated at DNA-modified electrodes, MutY and EndoIII are redox-active

displaying electrochemical signals with midpoint potentials (+50-100 mV versus NHE)

typical of high-potential iron proteins, proteins that can adopt either the 2+ and 3+ cluster

oxidation state [40, 41]. These proteins exhibit dramatically smaller signals at electrodes

containing an abasic site, indicating that CT to the [4Fe4S] cluster is DNA-mediated and

requires an intact

-stack. We have also electrochemically examined EndoIII in the absence

of DNA at a graphite electrode [46]. The signal associated with the 2+/3+ redox couple in

this situation is much less reversible and has a much more positive potential (~280 mV

positive shift) indicating that EndoIII is both less easily oxidized and more unstable in the

[4Fe4S]

form when the protein is not bound to DNA. Furthermore, the positive potential

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shift allows us to estimate that the protein containing the [4Fe4S]

cluster binds DNA much

more tightly than the reduced form of EndoIII; the difference in

when comparing the

[4Fe4S]

and [4Fe4S]

forms of EndoIII is at least 3 orders of magnitude.

A new role for the [4Fe4S] cluster in these glycosylase enzymes must now be considered.

The presence of a redox-active [4Fe4S] cluster could allow DNA repair proteins to use

DNA-mediated CT as a way to search quickly and efficiently for damaged bases in DNA

[41, 45, 46]. Figure 6 illustrates a model for how this search process might transpire. Here

we propose that DNA CT could help reduce the search problem faced by these enzymes,

allowing glycosylases to rapidly eliminate a search through genomic regions devoid of

lesions and instead spend most of their time bound in the vicinity of damaged sites.

Importantly, we have shown that guanine radicals can readily oxidize the [4Fe4S] cluster in

these proteins, indicating that this event could provide the driving force to trigger a DNA CT

signaling cascade among these proteins and initiating the search for lesions. Hence, DNA-

mediated CT could play a simultaneous role in funneling DNA damage to sites of low

oxidation potential and recruiting proteins to repair that damage.

The recent discovery that mutations in the human gene for MutY (

MUTYH

) can cause

predisposition to colorectal cancer [47] underscores the need to understand how repair

enzymes effectively find and repair DNA damage. Over 50 different missense and in-frame

deletion mutations in

MUTYH

have been observed in colorectal cancer patients. Many of

these single site mutants have been evaluated for their effect on MutY enzyme activity, but

it is clear that defects in the rate of excision and substrate binding affinity may not account

for all of the deficiencies observed with these mutants

in vivo

[48, 49]. An increasing body

of evidence indicates that finding the lesion is likely the limiting step in effective BER

inside the cell [50] and it is, therefore, of critical importance to understand all of the

strategies employed by these proteins to detect damage.

Conclusions

Guanine radicals are one of the first signals of oxidative stress inside a cell and DNA CT

could provide a mechanism to disseminate these radicals in genomic DNA. Given that

certain sequences have markedly low oxidation potentials, the lesions that result from this

process may be unevenly distributed throughout the genome. Thus, inside the cell, DNA CT

may play a major role in the DNA damage process by funneling damage to specific sites.

However, many fundamental characteristics of DNA CT

in vivo

still need to be addressed.

In particular, it is not known which sequences are prone to oxidative damage via DNA CT,

nor is it fully understood which distance regimes are possible for DNA CT in biological

environments.

Guanine radicals may also be important in mediating protein signaling processes. These

DNA-based radicals may transfer to low oxidation potential sites on a protein, including

amino acid side chains or protein-bound cofactors, eliciting a functional change in the

protein. Here, DNA CT could serve as an antenna for DNA damage, allowing proteins to

monitor oxidation events that occur far away and respond to them quickly. DNA CT could

also provide a mechanism for protein-protein communication and, to this end, we have

proposed that DNA repair enzymes could use DNA CT to cooperatively search for damage.

Understanding the full range of DNA-binding proteins that could participate in these

signaling pathways, and their associated cofactors, is a major focus of investigation.

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Acknowledgments

We are grateful the NIH (GM49216) for their financial support of this work including a minority postdoctoral

fellowship to E. J. M. and to the Ralph M. Parsons Foundation for a fellowship to A. K. B. We also thank our many

coworkers and collaborators in helping to unravel this fascinating chemistry and biology.

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modified microelectrodes.

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proteins that contain a [4Fe4S] cluster, activating the proteins toward oxidation. DNA CT

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signaling by the proeins through DNA CT.]

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Protein-DNA charge transport: redox activation of a DNA repair protein by guanine radical. Proc

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the DNA through DNA CT, can oxidize MutY, a DNA repair protein that contains a [4Fe4S]

cluster. Guanine radicals, in providing an early signal of oxidative stress, may serve to activate

the DNA repair proteins to detect base lesions.]

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and absence of DNA. J Am Chem Soc. 2006; 128:12082–12083. [PubMed: 16967954] [DNA

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III by more than -200 mV, which corresponds to more than a thousand-fold difference in DNA

binding affinity for the oxidized versus reduced form of the protein.]

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containing a [4Fe4S] cluster that is redox-activated on DNA binding.]

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account for the deficiencies in these proteins

in vivo

that may lead to colon cancer.]

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associated with colorectal cancer: distinct differences in the adenine glycosylase activity and the

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importance of 8-oxoguanine for in vivo mismatch repair by MutY. Nat Chem Biol. 2008; 4:51–

58. [PubMed: 18026095] [Lesion detection is the rate-limiting step for effective DNA repair in

vivo.]

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Figure 1.

DNA charge transport (CT) in a biological environment. DNA CT could play a role in many

cellular processes ranging from funneling oxidative DNA damage to regulatory or

noncoding regions in the mitochondrion and nucleus to mediating protein signaling in DNA

repair and transcriptional regulation pathways.

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Figure 2.

DNA CT in DNA damage. Upon irradiation the intercalating Rh-oxidant accepts an electron

(arrow) giving rise to an electron hole that is funneled to low oxidation potential sites, such

as a guanine doublet (yellow), leading to formation of a guanine radical (red). Guanine

radicals can be quenched to give oxidative DNA lesions.

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Figure 3.

Funneling Damage by DNA CT in mitochondria. Each mitochondrion (grey) harbors several

mitochondrial genomes. Replication is regulated through a critical regulatory element

termed conserved sequence block II (cyan). Upon irradiation with a Rh photooxidant, CT

funnels damage to the regulatory element (blue). Oxidation of the regulatory element (top

and bottom genome) should decrease the ability of oxidized genomes to be copied, thereby

favoring replication of undamaged genomes (middle).

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Figure 4.

DNA CT in a nucleosome core particle. Photoactivation of a tethered Rh oxidant in histone-

bound DNA generates oxidative damage at a distance in the nucleosome similarly to the

DNA without histones.

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Figure 5.

DNA CT leads to the oxidative dissociation of p53 (a tetramer) from its promoter, triggered

from a distance.

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Figure 6.

A model for DNA CT in DNA repair. DNA-mediated redox activity in a class of DNA

repair proteins that contain a [4Fe4S] cluster could allow these enzymes to use DNA CT as a

damage detection strategy. Under conditions of oxidative stress, guanine radicals are

generated and these can oxidize the [4Fe4S] cluster in the repair enzyme (top). A second

protein, upon binding to DNA, becomes oxidized and transfers its lost electron, in a DNA-

mediated CT reaction to the first DNA-bound protein. The first protein becomes reduced,

subsequently loses affinity for DNA, and binds elsewhere. If a lesion is present between the

two proteins (bottom), the CT reaction occurs much less efficiently, thus the proteins remain

in the oxidized state and bound near the lesion. As illustrated here, DNA CT therefore serve

to redistribute DNA repair enzymes away from undamaged DNA and into the vicinity of

lesion sites, facilitating fast and efficient damage detection.

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