One-electron oxidation of DNA oligomers that lack guanine: reaction and strand cleavage at remote thymines by long-distance radical cation hopping

The anthraquinone (AQ) photosensitized one-electron oxidation of DNA introduces a radical cation (electron "hole") that migrates through the duplex by hopping. The radical cation normally is trapped irreversibly by reaction at guanine. We constructed AQ-linked DNA oligomers composed exclusively of A/T base pairs. Their irradiation led to reaction and strand cleavage primarily at thymines. Long-distance radical cation hopping to distant thymines was demonstrated by the distance dependence of the process and by experiments with DNA oligomers that contain a single remote GG step. The reaction of the radical cation at thymine was shown to involve its 5-methyl group by the replacement of selected thymines with uracils. These findings show that the reactivity of radical cations in DNA cannot be explained simply by exclusive reliance on the relative oxidation potential of the nucleobases. Instead, the site of reaction is determined in accord with the Curtin-Hammett principle for reactive species in rapid equilibrium.     

Long-distance radical cation transport in DNA: Horizontal charge hopping in a dimeric quadruplex

A series of DNA hairpins were synthesized and shown to associate to form quadruplexes formed by stacking five G-quartets in an antiparallel orientation. One of the hairpins in the quadruplex was linked covalently at the 5'-end to an anthraquinone (AQ) group and a 32P label was incorporated either at the 3'-terminus of the AQ-containing hairpin or on its partner hairpin in the quadruplex. Irradiation of the AQ group with UV light leads to the one-electron oxidation of the DNA and concomitant introduction of a radical cation into the DNA. Analysis by PAGE and autoradiography shows that the radical cation reacts at guanines both on the AQ-containing strand and with its partner hairpin in the quadruplex. This observation demonstrates that charge migration in DNA occurs vertically along a DNA chain and horizontally within a G-quartet.     

One-electron oxidation of DNA: the effect of replacement of cytosine with 5-methylcytosine on long-distance radical cation transport and reaction

One-electron oxidation of duplex DNA generates a radical cation that migrates through the nucleobases until it is trapped by an irreversible reaction with water or oxygen. The trapping site is often a GG step, because this site has a relatively low ionization potential and this causes the radical cation to pause there momentarily. Modifications to guanine that lower its ionization potential convert it to a better trap for the radical cation. One such modification is the formation of the Watson-Crick base pair with cytosine, which is reported to very significantly decrease its ionization potential. Methylation of cytosine to form 5-methylcytosine (5-MeC) is a naturally occurring reaction in genomic DNA that may be associated with regions of enhanced oxidative damage. The G.5-MeC base pair is reported to be more rapidly oxidized than normal G.C base pairs. We examined the oxidation of DNA oligomers that were substituted in part with 5-MeC. Irradiation of a covalently linked anthraquinone group injects a radical cation into the DNA and results in strand cleavage after piperidine treatment. For the sequences examined, substitution of 5-MeC for C has no measurable effect on the reactions. Cytosine methylation is not a general cause of enhanced oxidative damage in DNA.     

Suppression of DNA-mediated charge transport by BamHI binding

A guanine radical cation produced by one-electron DNA oxidation migrates over long distances through the DNA pi-stack. Fundamental questions regarding the likelihood of charge transport in genomic DNA, the effects of protein binding, and its biological consequences arise as the next issues of study. Electronic effects of protein binding on the efficiency of charge transport were investigated for the endonuclease BamHI-DNA complex. Direct contact of a positively charged guanidium group of BamHI to guanines in the recognition sequence 5'-GGATCC-3' completely suppressed one-electron oxidation of the guanine in the protein binding site and dramatically lowered the charge transport efficiency through the sequence. Electronically insulated guanines, by the hydrogen bonding contact of a guanidium group in BamHI, no longer function as a stepping stone in the charge transport through the DNA pi-stack.     

Anthraquinone-sensitized photooxidation of 5-methylcytosine in DNA leading to piperidine-induced efficient strand cleavage

One-electron photooxidations of 5-methyl-2'-deoxycytidine (d(m)C) and 5-trideuteriomethyl-2'-deoxycytidine ([D(3)]d(m)C) by sensitization with anthraquinone (AQ) derivatives were investigated. Photoirradiation of an aerated aqueous solution containing d(m)C and anthraquinone 2-sulfonate (AQS) afforded 5-formyl-2'-deoxycytidine (d(f)C) and 5-hydroxymethyl-2'-deoxycytidine (d(hm)C) in good yield through an initial one-electron oxidation process. The deuterium isotope effect on the AQS-sensitized photooxidation of d(m)C suggests that the rate-determining step in the photosensitized oxidation of d(m)C involves internal transfer of the C5-hydrogen atom of a d(m)C-tetroxide intermediate to produce d(f)C and d(hm)C. In the case of a 5-methylcytosine ((m)C)-containing duplex DNA with an AQ chromophore that is incorporated into the backbone of the DNA strand so as to be immobilized at a specific position, (m)C underwent efficient direct one-electron oxidation by the photoexcited AQ, which resulted in an exclusive DNA strand cleavage at the target (m)C site upon hot piperidine treatment. In accordance with the suppression of the strand cleavage at 5-trideuterio-methylcytosine observed in a similar AQ photosensitization, it is suggested that deprotonation at the C5-methyl group of an intermediate (m)C radical cation may occur as a key elementary reaction in the photooxidative strand cleavage at the (m)C site. Incorporation of an AQ sensitizer into the interior of a strand of the duplex enhanced the one-electron photooxidation of (m)C, presumably because of an increased intersystem crossing efficiency that may lead to efficient piperidine-induced strand cleavage at an (m)C site in a DNA duplex.     

Mechanism for radical cation transport in duplex DNA oligonucleotides

We investigated the photoinduced one-electron oxidation of a series of DNA oligomers having a covalently linked anthraquinone group (AQ) and containing [(A)(n)GG](m) or [(T)(n)GG](m) segments. These oligomers have m GG steps, where m = 4 or 6, separated by (A)(n) or (T)(n) segments, where n = 1-7 for the (A)(n) set and 1-5 for the (T)(n) set. Irradiation with UV light that is absorbed by the AQ causes injection of a radical cation into the DNA. The radical cation migrates through the DNA, causing chemical reaction, primarily at GG steps, that leads to strand cleavage after piperidine treatment. The uniform, systematic structure of the DNA oligonucleotides investigated permits the numerical solution of a kinetic scheme that models these reactions. This analysis yields two rate constants, k(hop), for hopping of the radical cation from one site to adjacent sites, and k(trap), for irreversible reaction of the radical cation with H(2)O or O(2). Analysis of these findings indicates that radical cation hopping in these duplex DNA oligomers is a process that occurs on a microsecond time scale. The value of k(hop) depends on the number of base pairs in the (A)(n) and (T)(n) segments in a systematic way. We interpret these results in terms of a thermally activated adiabatic mechanism for radical cation hopping that we identify as phonon-assisted polaron hopping.     

Near-UV induced interstrand cross-links in anthraquinone-DNA duplexes

Anthraquinone (AQ) has been extensively used as a photosensitizer to study charge transfer in DNA. Near-UV photolysis of AQ induces electron abstraction in oligonucleotides leading to AQ radical anions and base radical cations. In general, this reaction is followed by the transport of base radical cations to sites of low oxidation potential, that is, GG, and conversion of G radical cations to DNA breaks. Here, we show that AQ also produces interstrand cross-links in DNA duplexes. About half of the cross-links collapse to single strands in hot piperidine treatment. The structure of stable interstrand cross-links was deduced by MS, NMR, and sequence substitution. The cross-links consist of a covalent link between the methyl group of T on one strand with either C6 or C7 of AQ on the other strand. The formation of interstrand cross-links decreased in O2 compared to deoxygenated solutions. In the presence of O2, the yield of breaks at GG doublets was 10-fold greater than that of cross-links for end tethered AQ, while cross-links exceeded breaks for centrally located AQ. The formation of stable cross-links can be explained by initial charge transfer from T to excited AQ, deprotonation of T radical cations, and condensation of the latter species with AQ radicals. These studies reveal a novel pathway of damage in the photolysis of AQ-DNA duplexes.     

Long-distance radical cation migration in duplex DNA: the effect of contiguous A.A and T.T mismatches on efficiency and mechanism

A series of DNA oligomers was prepared. Each oligomer contained an anthraquinone group (AQ, sensitizer) covalently linked at a 5'-end and two GG steps that surrounded a variable region. The variable region was composed of A.T base pairs or A.A or T.T mismatches. Irradiation of the AQ injected a radical cation (hole) into the DNA that migrated through the duplex, being trapped by reaction with H2O of O2 at the GG steps. The effect of substituting A.A or T.T mismatches for Watson-Crick base pairs was examined. For A.A mispairs, charge transfer through the mismatch region was as efficient as through normal DNA. For the T.T mismatches, radical cation transport was strongly distance-dependent. These findings suggest that A.A mismatches form a zipper-like motif, and charge transport proceeds by a hopping mechanism. In contrast, charge transport through the T.T mismatches (where there are no purines) may proceed by quantum mechanical tunneling.     

Selective one-electron oxidation of duplex DNA oligomers: reaction at thymines

The one-electron oxidation of duplex DNA generates a nucleobase radical cation (electron "hole") that migrates long distances by a hopping mechanism. The radical cation reacts irreversibly with H2O or O2 to form oxidation products (damaged bases). In normal DNA (containing the four common DNA bases), reaction occurs most frequently at guanine. However, in DNA duplexes that do not contain guanine (i.e., those comprised exclusively of A/T base pairs), we discovered that reaction occurs primarily at thymine and gives products resulting from oxidation of the T-C5 methyl group and from addition to its C5-C6 double bond. This surprising result shows that it is the relative reactivity, not the stability, of a nucleobase radical cation that determines the nature of the products formed from oxidation of DNA. A mechanism for reaction is proposed whereby a thymine radical cation may either lose a proton from its methyl group or H2O/O2 may add across its double bond. In the latter case, addition may initiate a tandem reaction that converts both thymines of a TT step to oxidation products.     

Role of the guanine N1 imino proton in the migration and reaction of radical cations in DNA oligomers

Oxidation of a guanine nucleobase to its radical cation in DNA oligomers causes an increase in the acidity of the N1 imino proton that may lead to its spontaneous transfer to N3 of the paired cytosine. This proton transfer is suspected of playing an important role in long-distance radical cation hopping in DNA and the decisive product-determining role in the reaction of the radical cation with H2O or O2. We prepared and investigated DNA oligomers in which certain deoxycytidines are replaced by 5-fluoro-2'-deoxycytidines (F5dC). The pKa of F5C was determined to be 1.7 units below that of dC, which causes proton transfer from the guanine radical cation to be thermodynamically unfavorable. Photoinitiated one-electron oxidation of the DNA by UV irradiation of a covalently attached anthraquinone derivative introduces a radical cation that hops throughout the oligomer and is trapped selectively at GG steps. The introduction of F5dC does not affect the efficiency of charge hopping, but it significantly reduces the amount of reaction at the GG sites, as revealed by subsequent reaction with formamidopyrimidine glycosylase. These findings suggest that transfer of the guanine radical cation N1 proton to cytosine does not play a significant role in long-range charge transfer, but this process does influence the reactions with H2O and/or O2.     

One-electron photooxidation and site-selective strand cleavage at 5-methylcytosine in DNA by sensitization with 2-methyl-1,4-naphthoquinone-tethered oligonucleotides

Photosensitized one-electron oxidation was applied to discriminate a specific base site of 5-methylcytosine (mC) generated in DNA possessing a partial sequence of naturally occurring p53 gene, using a sensitizing 2-methyl-1,4-naphthoquinone (NQ) chromophore tethered to an interior of oligodeoxynucleotide (ODN) strands. Photoirradiation and subsequent hot piperidine treatment of the duplex consisting of mC-containing DNA and NQ-tethered complementary ODN led to oxidative strand cleavage selectively at the mC site, when the NQ chromophore was arranged so as to be in close contact with the target mC. The target mC is most likely to be one-electron oxidized into the radical cation intermediate by the sensitization of NQ. The resulting mC radical cation may undergo rapid deprotonation and subsequent addition of molecular oxygen, thereby leading to its degradation followed by strand cleavage at the target mC site. In contrast to mC-containing ODN, ODN analogs with replacement of normal cytosine, thymine, adenine, or guanine at the mC site underwent less amount of such an oxidative strand cleavage at the target base site, presumably due to occurrence of charge transfer and charge recombination processes between the base radical cation and the NQ radical anion. Furthermore, well designed incorporation of the NQ chromophore into an interior of ODN could suppress a competitive strand cleavage at consecutive guanines, which occurred as a result of positive charge transfer. Thus, photosensitization by an NQ-tethered ODN led to one-electron oxidative strand cleavage exclusively at the target mC site, providing a convenient method of discriminating mC in naturally occurring DNA such as human p53 gene as a positive band on a sequencing gel.     

Cytosine-gated hole creation and transfer in DNA in aqueous solution

The selenite radical, SeO3-, has been found to selectively produce the cytosyl radical upon one-electron oxidation of duplex DNA. This is at first a surprising result as SeO3- can only oxidize guanine of the DNA bases, implying that the transiently formed guanyl radical cation must transpose into the neutral cytosyl radical with loss of a proton. Back oxidation to produce the neutral guanyl radical, in competition with another fixation reaction, is observed.     

Synthesis and photooxidation of oligodeoxynucleotides containing 5-dimethylaminocytosine as an efficient hole-trapping site in the positive-charge transfer through DNA duplexes

We have designed and synthesized DNA duplexes containing 5-dimethylaminocytosine ((DMA)C) to investigate the effects of C(5)-substituted cytosine bases on the transfer and trapping of positive charge (holes) in DNA duplexes. Fluorescence quenching experiments revealed that a (DMA)C base is more readily one-electron oxidized into a radical cation intermediate as compared with other natural nucleobases. Upon photoirradiation of the duplexes containing (DMA)C, the photosensitizer-injected hole migrated through the DNA bases and was trapped efficiently at the (DMA)C sites, where an enhanced oxidative strand cleavage occurred by hot piperidine treatment. The (DMA)C radical cation formed by hole transfer may undergo specific hydration and subsequent addition of molecular oxygen, thereby leading to its decomposition followed by a predominant strand cleavage at the (DMA)C site. This remarkable property suggests that the modified cytosine (DMA)C can function as an efficient hole-trapping site in the positive-charge transfer in DNA duplexes.     

Photoinduced charge separation in titania nanotubes

The photocatalytic one-electron oxidation reaction of an aromatic compound during UV light irradiation of titania nanotubes and nanoparticles was investigated using time-resolved diffuse reflectance spectroscopy. Remarkably long-lived radical cations of the aromatic compound and trapped electrons were observed for the nanotubes when compared to those for nanoparticles. The influences of the morphology on the one-electron oxidation process of an aromatic compound adsorbed on the surface were discussed in terms of the charge recombination dynamics between the radical cation and electrons in TiO2.     

Long-range oxidative damage to DNA: protection of guanines by a nonspecifically bound disulfide

One-electron oxidation of DNA generates a base radical cation ("hole") that migrates through the duplex and causes damage at guanines. Unrepaired damage may lead to mutations. It has been suggested that "sacrificial guanines" in intron regions of DNA might serve to protect genes from damage. We have investigated the ability of a noncovalently bound sacrificial reagent to protect DNA from damage. Irradiation of an anthraquinone (AQ)-linked DNA duplex injects a radical cation into the DNA that causes reactions at GG steps close to and farther from the AQ. Bis[2-(3-(aminopropyl)amino)ethyl]disulfide, an analogue of spermine, binds to duplex DNA. Irradiation of the AQ-linked DNA in the presence of this disulfide suppresses the reaction at both GG steps and protects the DNA from damage. It is suggested that evolutionary pressure for the preservation of genomic integrity would yield disulfide-containing compounds optimized to bind to DNA and neutralize base radical cations.     

Base sequence effects in radical cation migration in duplex DNA: support for the polaron-like hopping model

A series of anthraquinone-linked (AQ) duplex DNA oligomers were prepared and investigated. Irradiation of the AQ injects a radical cation into the DNA. The radical cation migrates through the DNA and reacts selectively at GG steps, which leads to strand cleavage after treatment with piperidine. The oligomers investigated in this work were selected to assess the effect on long-distance charge transport of placing a T base (or bases) in a strand of repeating purine bases. With notable exceptions, the amount of strand scission decreases with the distance between the AQ and the GG step. The results are consistent only with models for long-distance transport, such as thermally activated polaron-like hopping, that incorporate radical cation delocalization over two or more adjacent bases.     

N(2)-phenyldeoxyguanosine: modulation of the chemical properties of deoxyguanosine toward one-electron oxidation in DNA

We have shown here that (1) substitution of an exocyclic amino group of dG is effective in modulating the chemical properties of dG toward one-electron oxidation and (2) decomposition of the guanine radical cation was effectively suppressed near dPhG. These results indicate that dPhG is a prototype of nucleosides functioning as an intrinsic antioxidant of duplex DNA toward one-electron oxidation.     

One-electron oxidation pathways during beta-cyclodextrin-modified TiO2 photocatalytic reactions

The photocatalytic one-electron oxidation reactions of aromatic sulfides using the carboxymethyl-beta-cyclodextrin (CM-beta-CD)-modified TiO(2) nanoparticles (TiO(2)/CM-beta-CD) were investigated by using nano- and femtosecond transient absorption spectroscopies. The one-electron oxidation processes of the substrate (S) by the valence band hole (h(VB) (+)) at the TiO(2) surface and the trapped hole at the adsorption site of the CM-beta-CD (h(CD) (+)) were examined. The transient absorption spectra and time traces observed for the charge carriers and the radical cation of S (S(.+)) revealed that the one-electron oxidation reaction of S during the nano- and femtosecond laser flash photolyses of TiO(2)/CM-beta-CD is significantly enhanced relative to bare TiO(2). The kinetics of the decay and the dimerization processes between S(.+)s are discussed on the basis of the results obtained by the pulse radiolysis technique.     

Direct observation of guanine radical cation deprotonation in duplex DNA using pulse radiolysis

The dynamics of one-electron oxidation of guanine (G) base mononucleotide and that in DNA have been investigated by pulse radiolysis. The radical cation (G+*) of deoxyguanosine (dG), produced by oxidation with SO(4)-*, rapidly deprotonates to form the neutral G radical (G(-H)*) with a rate constant of 1.8 x 10(7) s(-1) at pH 7.0, as judged from transient spectroscopy. With experiments using different double-stranded oligonucleotides containing G, GG, and GGG sequences, the absorbance increases at 625 nm, characteristic of formation of the G(-H)*, were found to consist of two phases. The rate constants of the faster ( approximately 1.3 x 10(7) s(-1)) and slower phases ( approximately 3.0 x 10(6) s(-1)) were similar for the different oligonucleotides. On the other hand, in the oligonucleotide containing G located at the 5'- and 3'-terminal positions, only the faster phase was seen. These results suggest that the lifetime of the radical cation of the G:C base pair (GC+*), depending on its location in the DNA chain, is longer than that of free dG. In addition, the absorption spectral intermediates showed that hole transport to a specific G site within a 12-13mer double-stranded oligonucleotide is complete within 50 ns; that is, the rate of hole transport over 20 A is >10(7) s(-1).     

long-range charge transport in duplex DNA: anthraquinone sensitization results are independent of terminal ionic distribution

Irradiation of an anthraquinone (AQ) derivative linked to a 5'-terminus of duplex DNA results in the formation of a base radical cation ("hole") that can migrate through the DNA. Reaction of the radical cation occurs primarily at the 5'-G of GG sequences. This reaction results in the formation of strand breaks when the irradiated DNA is treated with piperidine. The strand breaks are detected by polyacrylamide gel electrophoresis of samples that are labeled at the 3'- or 5'-terminus with (32)P. In contrast to a previous report in which a linked rhodium metallointercalator is used as the sensitizer to oxidize the DNA (Williams, T. T.; Barton, J. K. J. Am. Chem. Soc. 2002, 124, 1840-1841), we find that the position of the label does not affect the relative reactivity of the GG steps when AQ is the sensitizer.