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Benzoquinone/hydroquinone redox interconversion by the reversible Os(dmb)(3)(3+/2+) couple over an extended pH range with added acids and bases has revealed the existence of seven discrete pathways. Application of spectrophotometric monitoring with stopped-flow mixing has been used to explore the role of PCET. The results have revealed a role for phosphoric acid and acetate as proton donor and acceptor in the concerted electron-proton transfer reduction of benzoquinone and oxidation of hydroquinone, respectively.

As part of the ongoing effort to describe electron transfer reactions of carbon nanotubes (CNTs), we studied the mediated electrochemical oxidation of CNTs solubilized by wrapping with a T(60) deoxyribooligonucleotide. Cyclic voltammetry revealed that the oxidation of this CNT-DNA material by electrogenerated ML(3)(3+) mediators completes a catalytic cycle that increases the oxidative current compared to that obtained by voltammetry of the mediator alone (M = Fe(III), Ru(III), or Os(III); L = 2,2'-bipyridine or 4,4'-dimethyl-2,2'-bipyridine). We observed a greater increase in current at higher nanotube concentration, slower experimental scan rate, and higher mediator redox potential (E(0)'). Using computer simulation, these observations were shown to be consistent with CNT oxidation involving the removal of multiple electrons from each CNT-DNA moiety (the T(60) oligonucleotide was chosen because it is not oxidized by any of the mediators). The data are well-described by a simulation model based on the classical catalytic mechanism (EC') with the following embellishment: three populations of CNT-DNA redox-active sites with different E(0)' and therefore different oxidation rates are employed to represent the varying redox potentials of different valence band electrons within one CNT chiral type and within the distribution of CNT types present in our sample. This modeling suggests the number of CNT-DNA sites available for oxidation increases with the E(0)' of the mediator. This result can be qualitatively interpreted in terms of CNT band theory.

Polypyridyl complexes of Co decorated with 350-Da polyether chains (Co(350)(2+)) form molten phases of nucleic acids when paired with DNA counterions (Co(350)DNA) or 25-mer oligonucleotides. Analysis of voltammetry and chronoamperometry of mixtures of these phases with complexes having ClO(4)(-) counterions (Co(350)(ClO(4))(2)) and no other diluent provides charge transport rates from the oxidation and reduction currents for the complexes. As the mole fraction of the Co(350)(ClO(4))(2) complex in the mixture is varied from ca. 0.25 to 1, the physical diffusion constants derived from the Co(III/II) wave increase from 1 x 10(-11) cm(2)/s to 5 x 10(-10) cm(2)/s, and apparent diffusion constants dominated by the Co(II/I) electron self-exchange increase from 1 x 10(-10) cm(2)/s to 2 x 10(-8) cm(2)/s. Pure Co(350)DNA melts, containing no Co(350)(ClO(4))(2) complex, do not exhibit recognizable voltammetric waves; DNA suppresses the Co(II/I) electron transfer reactions of Co complexes for which it is the counterion. There are therefore two microscopically distinct kinds of Co(350) complexes, those with DNA and those with ClO(4)(-) counterions, with respect to their Co(II/I) electron-transfer dynamics, leading to percolative behavior in their mixtures. The electron-transfer rates of the Co(II/I) couple are controlled by the diffusive relaxation of the ionic atmosphere around the reaction pair, and the inactivity of the bound Co complexes can be attributed to the very low mobility of the anionic phosphate groups in the DNA counterion. Substitution of sulfonated polystyrene for DNA produced similar results, suggesting that this phenomenon is general to other polymer counterions of low mobility. We conclude that the measured Co(II/I) charge transport and electron-transfer rate constants reflect more the diffusive mobility of the perchlorate counterion than the intrinsic Co(II/I) electron hopping rate.

Catalytic guanine oxidation using Ru(bpy)32+ as a mediator (bpy = 2,2‘-bipyridine) has been investigated electrochemically in viscous solutions containing high concentrations of poly(ethylene glyco...

The 7-deaza analogues of guanine and adenine were incorporated into polymerase chain reaction (PCR) products by substitution of the appropriate nucleotide triphosphates into the reaction. These PCR products can be immobilized on ITO electrodes and detected by catalytic cyclic voltammetry with ruthenium polypyridyl complexes. Immobilization on indium tin oxide (ITO) electrodes of 330- and 1200-base pair (bp) PCR amplicons from the E. coli dacA gene containing one or both of the 7-deazapurines was effected by precipitation from a 9:1 DMF/acetate solution. Amplicons containing the 7-deazaguanine base were detected by observing current enhancement in the cyclic voltammogram of Ru(dmb)3(3)+/2+ (dmb = 4,4'-dimethyl-2,2'-bipyridine) due to the selective oxidation of the modified base by this mediator. Oxidation of incorporated 7-deazaadenine bases in addition to native guanines gives rise to a higher current enhancement in the cyclic voltammogram of Ru(bpy)3(3)+/2+ (bpy = 2,2'-bipyridine) compared to the enhancement observed in the presence of guanine only. This strategy was employed to simultaneously detect the 330-bp sequence containing 7-deazaadenine and the 1200-bp sequence containing 7-deazaguanine on the same ITO electrode. Such a strategy may provide a means for detecting multiple genes on a single microlocation and may thereby lead to more highly multiplexed gene assays.

The oxidizability of substituted nucleobases was evaluated through theoretical calculations and the ability of individual bases to induce current enhancement in the cyclic voltammograms of metal complexes. Formation of the guanine derivatives 7-deazaguanine and 8-oxoguanine is known to lower the energy for oxidation of guanine. The similar derivatives of adenine were examined and gave lower predicted redox energies as well as current enhancement with Ru(bpy)32+ (7-deazaadenine) and Fe(bpy)32+ (8-oxoadenine). Oxidizable, substituted pyrimidines were identified using a computational library that gave 5-aminocytosine and 5-aminouracil as promising electron donors. Again, these predictions were verified using catalytic electrochemistry. In addition, the computations predicted that 6-aminocytosine would be redox-active but not as easily oxidized as 5-aminocytosine, which was also confirmed experimentally. In addition to calculating the relative one-electron redox potentials, we used calculations to evaluate th...

Oligonucleotides containing the guanine nucleobase were adsorbed onto ITO electrodes from mixtures of DMF and acetate buffer. Chronocoulometry and chronoamperometry were performed on the modified electrodes in both phosphate buffer and buffer containing low concentrations of the inorganic complex Ru(bpy)3(2+) (bpy = 2,2' bipyridine), which catalyzes guanine oxidation. The charge and current evolution with and without the catalyst were compared to the charge and current evolution for electrodes that were treated with identical oligonucleotides that were substituted at every guanine with the electrochemically inert nucleobase hypoxanthine. Chronocoulometry over 2.5 s shows that roughly 2 electrons per guanine were transferred to the electrode in both the presence and absence of Ru(bpy)3(2+), although at a slower rate for the uncatalyzed process. Chronoamperograms measured over 250 ms can be fit to a double exponential decay, with the intensity of the fast component roughly 6-20 times greater than that of the slow component. First- and second-order rate constants for catalytic and direct guanine oxidation were determined from the fast component. The maximum catalytic enhancement for immobilized guanine was found to be i(cat)/i(d) = 4 at 25 microM Ru(bpy)3(2+). The second-order rate constant for the catalyzed reaction was 1.3 x 10(7) M(-1) s(-1), with an apparent dissociation constant of 8.8 microM. When compared to parallel studies in solution, a smaller value of the dissociation constant and a larger value of the second-order rate constant are observed, probably due to distortion of the immobilized DNA, an increase in the local negative charge due to the oxygen sites on the ITO surface, and redox cycling of the catalyst, which maintains the surface concentration of the active form.

The oxidation of guanines in DNA by Ru(III) is investigated by catalytic electrochemistry and stopped-flow spectrophotometry. The reactions of calf thymus DNA (20% guanine) and herring testes DNA (25% guanine) with Ru(bpy)3(3+) (bpy = 2,2'-bipyridine) show biexponential decays in stopped-flow spectrophotometric experiments with the fast and slow components in 2:1 ratios and average rate constants in 880 mM NaCl ofk= 18,700 M-1 s-1 for calf thymus DNA andk= 24,600 M-1 s-1 for herring testes DNA. The higher rate constant for the more guanine-rich DNA is possibly due to a higher density of electron-rich guanine multiplets. The observation of a biexponential decay is incorporated into digital simulations of the catalytic voltammograms observed for Ru(bpy)3(2+) in the presence of DNA. For both DNAs, the rates observed by voltammetry are somewhat slower than those observed by stopped-flow spectrophotometry and the dependence of the rate constants on scan rate using the biexponential model is less pronounced than when only one decay is treated, supporting the notion that the scan rate dependence arises from the multiphasic decay. At low salt concentrations, where binding of the metal complex to DNA increases the effective catalytic rate constant, rates can be measured by stopped-flow spectrophotometry only with a less oxidizing complex, Fe(bpy)3(3+/2+), which yields trends in the rate constants similar to those observed for the case of Ru(bpy)3(3+/2+) at high ionic strength. Oligonucleotides based on the trinucleotide repeat sequences (AGT)n and (GAA)n produce significant catalytic currents, which are readily interpreted in terms of the guanine concentration and the secondary structure discerned from gel electrophoresis experiments. These experiments may provide a basis for sensing secondary structures and repeat numbers in biologically relevant DNAs.

Indium tin oxide electrodes were modified with DNA, and the guanines in the immobilized nucleic acid were used as a substrate for electrocatalytic oxidation by Ru(bpy)3(3+) (bpy = 2,2'-bipyridine). Nucleic acids were deposited onto 12.6-mm2 electrodes from 9:1 DMF/water mixtures buffered with sodium acetate. The DNA appeared to denature in the presence of DMF, leading to adsorption of single-stranded DNA. The nucleic acid was not removed by vigorous washing or heating the electrodes in water, although incubation in phosphate buffer overnight liberated the adsorbed biomolecule. Acquisition of cyclic voltammograms or chronoamperomograms of Ru(bpy)3(2+) at the modified electrodes produced catalytic signals indicative of oxidation of the immobilized guanine by Ru(III). The electrocatalytic current was a linear function of the extent of modification with a slope of 0.5 microA/pmol of adsorbed guanine; integration of the current-time traces gave 2.2+/-0.4 electrons/guanine molecule. Use of long DNA strands therefore gave steep responses in terms of the quantity of adsorbed DNA strand. For example, electrodes modified with a 1497-bp PCR product from the HER-2 gene produced detectable catalytic currents when as little as 550 amol of strand was adsorbed, giving a sensitivity of 44 amol/mm2.

The electron-transfer rate constants for oligonucleotides containing adjacent guanines were determined by digital simulation of cyclic voltammograms of Ru(bpy)32+ in the presence of the oligonucleotides (bpy = 2,2‘-bipyridine). These experiments showed that sequences containing an isolated guanine (included in a 5‘-AGT segment) gave a rate constant of 1.4 × 105 M-1 s-1 (in terms of guanine concentration) while sequences containing a 5‘-GG segment gave an overall rate constant of 7.5 × 105 M-1 s-1. Both rate constants were independent of DNA concentration in the simulations. By assuming that the 3‘-G of the GG doublet exhibits the same rate constant as the isolated guanine, we estimate the ratio of rate constants for the 5‘-G of the GG doublet to the 3‘-G to be kGG/kG = 12 ± 2. This value was independent of DNA concentration and scan rate. Similar experiments using oligonucleotides containing inosine (I) in place of guanosine gave the same rate constant for a 5‘-IG doublet as for isolated guanine (kIG/kG =...

The effect of polar 2‘-substituents on the oxidation of nucleic acids at the 1‘-C−H bond was investigated. Oligonucleotides with the sequence 5‘-ATI CCC2‘-X TTI CIT AT-3‘ (I = inosine, −X = −H, −NH2, − OCH3, −F) were synthesized and subjected to oxidation by Ru(tpy)(bpy)O2+ (tpy = 2,2‘:6‘,2‘ ‘-terpyridine; bpy = 2,2‘-bipyridine). High-resolution electrophoresis revealed a similar cleavage pattern for all of the sites in the oligonucleotides except for the 2‘-substituted site, which varied in the extent of cleavage relative to the other sites according to H > NH2 > OCH3 > F. Because the cleavage was monitored following piperidine treatment, this analysis could not be applied to the 2‘-hydroxy oligonucleotide. The extent of cleavage was a linear function of oxidant concentration, and the slope of this plot was used as a relative rate after normalizing to the adjacent, unsubstituted 5‘-cytosine. When the relative rates were determined using other nucleotides in the sequence for normalization, the results did...

Electrocatalytic oxidation of guanine in DNA was detected at tin-doped indium oxide electrodes modified with nylon and nitrocellulose polymers. The catalytic oxidation occurs via oxidation at the electrode of the complex Ru(bpy)32+ to the 3+ state, which is then reduced back to the 2+ state by guanine in DNA (bpy = 2,2′-bipyridine). Catalysis is observed as a current enhancement in the cyclic voltammogram of Ru(bpy)32+ when DNA is immobilized in the film. As seen in solution, the catalytic enhancement in the nitrocellulose film is lower at 800 mM NaCl than without added salt because electrostatic binding of the Ru(bpy)32+ to the DNA at low salt increases the catalytic rate constant. The cyclic voltammogram of Os(bpy)32+, which does not oxidize guanine, exhibits less current in the presence of DNA because binding to the immobilized DNA precludes communication of the metal complex with the electrode. Electrodes modified with poly[C] gave no enhancement; however, catalytic current was observed upon hybridization to poly[G]. Exposure of the poly[C] electrode to random single-stranded DNA gave no catalytic current. Glassy carbon electrodes modified with the membranes behaved in a manner similar to that of the metal oxide electrodes.

Photolysis of Pt2(pop)44- in the presence of duplex DNA produces strand scission via abstraction of the 4‘- and 5‘-hydrogen atoms (pop = P2O5H22-). The cleavage intensities are higher for single-stranded DNA compared to those for duplex DNA because of lower electrostatic repulsion and greater solvent accessibility in single strands. When the single-stranded oligomer d(5‘-ACTGCCTTTTTGCTGAA) was photolyzed in the presence of Pt2(pop)44-, there was no significant or systematic change in cleavage intensity as a function of temperature in the range 28 to 98 °C. Cleavage of the hairpin d(5‘-ATCCTATTTTTTAGGAT) showed a higher cleavage intensity in the 5‘-TTTTT loop region compared to that for the base-paired nucleotides. Thermal denaturation of the hairpin gave a less selective cleavage pattern. The increase in cleavage at the duplex nucleotides could be used to estimate the Tm for the folded hairpin; thus, the cleavage pattern reflects the thermal denaturation of individual nucleotides. This concept was tested ...

The electrocatalytic reduction of nitric oxide to nitrous oxide by the iron siderophore ferrioxamine B was used as a basis for an electrochemical NO sensor. Evaporation of a Nafion film onto a glassy carbon electrode produced modified surfaces into which the ferric complex of ferrioxamine B could be exchanged. Cyclic voltammetry of this modified electrode in aqueous solution produced two peaks, one of which (−0.73 V versus SSCE) corresponded to the quasi-reversible reduction of solution-bound ferrioxamine B and the other of which (−0.42 V) corresponded to an adsorbed species. Greater catalytic enhancement was observed in the presence of NO for the solution wave than for the adsorption pre-peak. The catalytic enhancement, expressed as the ratio of peak current in the presence of NO ( i cat ) to the current in the absence of NO ( i d ) was a linear function of the solution NO concentration down to 1 μ M. Better sensitivity was precluded by decomposition of the reduced form of the catalyst in the absence of NO.

The binding specificity for the intercalating Ru(tpy)(dppz)O2+ complex (tpy = 2,2‘,2‘‘-terpyridine; dppz = dipyridophenazine) was investigated for duplex DNA, HIV-1 TAR DNA and RNA, and tRNAPhe. Unlike other dppz compounds studied to date, this compound cleaves nucleic acids at short range, and the resulting cleavage pattern can therefore be directly related to the recognition properties of the dppz ligand. To assign the intercalative recognition sites, a comparison was first made between the cleavage patterns of Ru(tpy)(dppz)O2+ and Ru(tpy)(bpy)O2+ (bpy = 2,2‘-bipyridine), which differs from Ru(tpy)(dppz)O2+ only by the absence of the intercalative dppz functionality. Cleavage sites common to both complexes were assigned to binding properties other than intercalation, whereas any additional sites observed for Ru(tpy)(dppz)O2+ were strongly implicated as the sites of intercalative recognition. It was necessary, however, to distinguish between those sites which represent a strong binding affinity and those...

Tryptophan is unique among the redox-active amino acids owing to its weakly acidic indolic proton (pK(a) ≈ 16) compared to the -O-H proton of tyrosine (pK(a) = 10.1) or the -S-H proton of cysteine (pK(a) = 8.2). Stopped-flow and electrochemical measurements have been used to explore the roles of proton-coupled electron transfer and concerted electron-proton transfer (EPT) in tryptophan oxidation. The results of these studies have revealed a role for OH(-) as a proton acceptor base in EPT oxidation of N-acetyl-tryptophan but not for other common bases. The reorganizational barrier for (N-acetyl-tryptophan)(+/•) self-exchange is also estimated.

Dramatic rate enhancements are observed for the oxidation of phenols, including tyrosine, at indium-tin oxide electrodes modified by the addition of the electron-transfer relays [M(II)(bpy)(2)(4,4'-(HO)(2)P(O)CH(2))(2)bpy)](2+) (M = Ru, Os) with clear evidence for the importance of proton-coupled electron transfer and concerted electron-proton transfer.

The quenching of the emission of the excited state of Pt 2 (pop) 4 4- (pop=P 2 O 5 H 2 2- ) by metal bind to DNA has been investigated. The quenching rate constant decreases by up to two orders of magnitude when excess DNA is added to the solution. This change in rate constant can be used to determine the binding constant the quencher to DNA. This has permitted the determination of binding constants for metal complexes where the affinity is quite high (≥10 5 M -1 ) or quite low (≤1000 M -1 )

The binding to DNA of complexes based on Ru(tpy)(L)OH 2 2+ (tpy=2,2',2''-terpyridine; L=bpy, 2,2'-bipyridine; phen, 1,10-phenanthroline; or dppz, dipyridophenazine) has been studied by viscometry, thermal denaturation, and absorbance hypochromism along with the kinetics of oxidation of DNA by the analogous Ru(tpy)(L)O 2+ complexes. These studies show that very weak binding occurs when L=bpy; however, when L=dppz, ΔT m is larger than that for ethidium bromide. Viscometry studies of the dppz complex show that the dppz complex does lengthen DNA, as occurs with intercalative binding

The system ROOH/[Mn3O4(dipy)4(OH2)2](ClO4)4 hydroxylates alkanes and converts ArCRCH2 to ArCRO with extremely high activity and good conversions and yields.

The complex cis-[Os(bpy) 2 (CO)H] + (bpy is 2,2'-bipyridine) has been found to be an electrocatalyst for the reduction of CO 2 in CH 3 CN containing 0.1 M tetra-n-butylammonium hexafluorophosphate at glassy carbon or Pt electrodes. Under anhydrous conditions CO is the dominant product, but addition of water results in up to 22% formate anion.

A group of seven mono- and diaquapolypyridyl complexes of Ru(II) have been shown to bind covalently to DNA by ultrafiltration, extensive dialysis, and ethanol precipitation. Incubation of the metal complex with calf thymus DNA in 50 mM phosphate buffer produces solutions of DNA exhibiting visible absorptions clearly due to the metal complex. These absorptions remain unchanged upon prolonged ultrafiltration or dialysis, demonstrating covalent binding of the metal complex to the DNA

The system ROOH/[Mn3O4(dipy)4(OH2)2](ClO4)4 hydroxylates alkanes and converts ArCRCH2 to ArCRO with extremely high activity and good conversions and yields.

Single-stranded DNA is an effective noncovalent dispersant for individual single-walled carbon nanotubes (CNTs) in aqueous solution, forming a CNT-DNA hybrid material that has advantages for CNT separations and applications. Atomic force microscopy (AFM) reveals a regular pattern on the surface of CNT-DNA. We found this pattern to be independent of the length and sequence of the wrapping DNA, yet different from the structures observed for CNTs dispersed with sodium dodecyl sulfate in the absence of DNA. We wrapped CNTs with thiol-modified DNA to form stable conjugates of CNT-DNA and core/shell CdSe/ZnS quantum dots; AFM imaging of these conjugates identified for the first time the location of DNA on the CNT-DNA nanomaterial. Our results suggest that the AFM pattern of CNT-DNA is formed by helical turns (approximately 14-nm pitch) of wrapped DNA strands that are closely arranged end-to-end in a single layer along the CNT. This work demonstrates the useful functionalization of CNTs with quantum dots in a manner that avoids direct, destructive modification of the CNT surface and suggests nearly complete surface coverage of the nanotubes with DNA.

The aqueous chemistry of a binuclear mixed-valence cluster, ((bpy){sub 2}Mn(O){sub 2}Mn(bpy){sub 2})(ClO{sub 4}){sub 3} (1), has been investigated. The cluster exists in a pH-dependent equilibrium with a higher valent trinuclear species, (Mn{sub 3}O{sub 4}(bpy){sub 4}(OH{sub 2}){sub 2}){sup 4+} (2). The trinuclear cluster is favored at low pH, conditions that favor disproportionation of 1. Evaporation of a pH 1.9 solution of 1 leads to the precipitation of red crystals of 2 in the space group P{bar 1} with a = 14.902 (5) {angstrom}, b = 15.787 (5) {angstrom}, c = 12.676 (4) {angstrom}, {alpha} = 100.22 (2){degree}, {beta} = 93.45 (3){degree}, and {gamma} = 73.98 (3){degree}. The temperature-dependent magnetic susceptibility shows strong antiferromagnetic coupling. Electrochemistry and EPR show that the concentrations of 1 and 2 are governed by a pH-dependent equilibrium. The relevance of this quantitative equilibrium to the photoactivated assembly of the manganese tetramer in photosystem II is discussed.

All higher life forms use oxygen and respiration as their primary energy source. The oxygen comes from water by solar-energy conversion in photosynthetic membranes. In green plants, light absorption in photosystem II (PSII) drives electron-transfer activation of the oxygen-evolving complex (OEC). The mechanism of water oxidation by the OEC has long been a subject of great interest to biologists and chemists. With the availability of new molecular-level protein structures from X-ray crystallography and EXAFS, as well as the accumulated results from numerous experiments and theoretical studies, it is possible to suggest how water may be oxidized at the OEC. An integrated sequence of light-driven reactions that exploit coupled electron-proton transfer (EPT) could be the key to water oxidation. When these reactions are combined with long-range proton transfer (by sequential local proton transfers), it may be possible to view the OEC as an intricate structure that is "wired for protons".

Electrocatalytic oxidation of the oligonucleotide 5'- GAA GAG GTT TTT CCT CTT CTT TTT CTT CTC C (TS) by Ru(bpy)(3)(2+) was studied by cyclic voltammetry. This oligonucleotide forms either an intramolecular triplex, hairpin, or single strand, depending on the pH (Plum, G. E.; Breslauer, K. J. J. Mol. Biol. 1995, 248, 679-695). In the triplex form, the guanine doublet in TS is buried inside the folded structure, and as such is less susceptible to oxidation by electrogenerated Ru(bpy)(3)(3+). Digital simulations of the catalytic voltammograms gave a rate constant of 3.5 +/- 0.2 x 10(2) M(-1) s(-1) for oxidation of the triplex form, while oxidation of the duplex and single-stranded forms occurred with much faster rate constants of (3.5-9.1) x 10(4) M(-1) s(-1). Experiments using a truncated form of TS that lacked the third strand of the triplex were consistent with these measurements. The Ru(bpy)(3)(3+) complex was also generated by photolyzing Ru(bpy)(3)(2+) in the presence of Fe(CN)(6)(3-). This reaction produced strand scission following piperidine treatment, which was visualized using high-resolution gel electrophoresis. These experiments showed decreased reactivity for the triplex form, and also gave an unusual reversal of a common selectivity for the 5'-G of GG doublets generally seen in B-form DNA. This reversal was ascribed to strain caused by the location of the GG doublet adjacent to the hairpin loop.

The electrochemical detection of nucleic acid targets at low concentrations has a number of applications in diagnostics and pharmaceutical research. Self-assembled monolayers of alkanethiol-derivatized oligonucleotides on gold electrodes provide a useful platform for such detectors, and the electrocatalytic oxidation of nucleobases included in the DNA targets is a particularly sensitive method of electrochemical detection. A strategy has been developed for combining these two aspects by substituting either 7,8-dihydro-8-oxoguanine (8G) or 5-aminouridine (5U) into DNA targets. Upon hybridization of targets containing these modified nucleobases, electrocatalytic signals at probe-modified gold electrodes are observed in the presence of Os(bpy)(3)(2+), which oxidizes both 8G and 5U upon oxidation to the Os(III) state. Self-assembled monolayers were prepared on both macro (1.6 mm) and micro (25 microm) gold electrodes using published procedures involving C6-terminated alkanethiol oligonucleotides and mercaptohexanol as the diluent. The extent of electrode modification by the modified probe was assessed using radiolabeling and a standard chronocoulometry method; both approaches gave loading levels within expected ranges ((1-6) x 10(12) molecules/cm(2)). Hybridization of the modified targets where the non-native nucleobase was incorporated by solid-phase synthesis produced electrocatalytic signals from strands that were independently detected using radiolabeling and chronocoulometry. This result was used as a basis to develop an on-electrode amplification scheme where Taq polymerase was used to extend the immobilized DNA probes from solution-phase polymeric templates using modified nucleotriphosphates. This reaction produced an electrode that was modified with extended DNA containing the appropriate modified nucleotide. Radiolabeled nucleotide triphosphates were used to confirm the desired on-electrode DNA synthesis. When these electrodes were cycled in the presence of Os(bpy)(3)(2+), electrocatalytic signals were observed when as little as 40 amol (400 fM) of the desired target was present in the hybridization solution.

A phosphoramidite containing Os(bpy)(3)(2+) (Os; bpy, 2,2'-bipyridine) with a three-carbon linker was synthesized and used to prepare oligonucleotides with the Os redox catalyst appended to the 5'-end. The electrogenerated Os(III) is capable of oxidizing 7,8-dihydro-8-oxo-guanine (8G), but 8G is not electrochemically reactive at indium tin oxide electrodes because of poor electrode kinetics for the direct reaction. The hairpin-forming oligonucleotide Os-5'-ATG TCA GAT TAG CAG GCC TGA CAT 8G was synthesized and characterized by thermal denaturation and native gel electrophoresis both in the hairpin form and when hybridized to its Watson-Crick complement. The redox potential in both forms of the appended Os(III/II) couple was 0.63 V (all potentials vs Ag/AgCl), which is identical to that for the free complex. The diffusion coefficients of the hairpin form (10.2 x 10(-)(7) cm(2)/s) and the duplex form (8.7 x 10(-)(7) cm(2)/s) were consistent with values expected from studies of noncovalently bound redox labels, which suggest that the measured diffusion coefficient should be that of the appended DNA molecule. The oligonucleotide was designed such that in the duplex form, the 8G is far from the Os(III/II) couple, but in the hairpin form, the 8G is situated close to the redox center. For the duplex form, cyclic voltammetry studies showed that mediated oxidation of the 8G nucleobase occurred only through bimolecular reaction of the electrogenerated Os(III) of one duplex with the 8G of another duplex. However, in the hairpin form, intramolecular electron transfer from 8G to Os(III) in the same molecule was apparent in both chronoamperometry and cyclic voltammetry.

Metal-to-ligand charge-transfer (MLCT) photolyses (lambdaor = 395 nm) of copper complexes of cis-1,8-bis(pyridin-3-oxy)oct-4-ene-2,6-diyne (bpod, 1), [Cu(bpod)(2)]PF(6) (2), and [Cu(bpod)(2)](NO(3))(2) (3) yield Bergman cyclization of the bound ligands. In contrast, the uncomplexed ligand 1 and Zn(bpod)(2)(CH(3)COO)(2) compound (4) are photochemically inert under the same conditions. In the case of 4, sensitized photochemical generation of the lowest energy (3)pi-pi state, which is localized on the enediyne unit, leads to production of the trans-bpod ligand bound to the Zn(II) cation by photoisomerization. Electrochemical studies show that 1, both the uncomplexed and complexed, exhibits two irreversible waves between E(p) values of -1.75 and -1.93 V (vs SCE), corresponding to reductions of the alkyne units. Irreversible, ligand-based one-electron oxidation waves are also observed at +1.94 and +2.15 V (vs SCE) for 1 and 3. Copper-centered oxidation of 2 and reduction of 3 occur at E(1/2) = +0.15 and +0.38 V, respectively. Combined with the observed Cu(I)-to-pyridine(pi) MLCT and pyridine(pi)-to-Cu(II) ligand-to-metal charge transfer (LMCT) absorption centered near approximately 315 nm, the results suggest a mechanism for photo-Bergman cyclization that is derived from energy transfer to the enediyne unit upon charge-transfer excitation. The intermediates produced upon photolysis degrade both pUC19 bacterial plasmid DNA, as well as a 25-base-pair, double-stranded oligonucleotide. Detailed analyses of the cleavage reactions reveal 5'-phosphate and 3'-phosphoglycolate termini that are derived from H-atom abstraction from the 4'-position of the deoxyribose ring rather than redox-induced base oxidation.

The oxidative electrochemistry of truns-[Re(0)2(4-OMe-py)4]+ in the presence of DNA has been studied. The complex exhibits a reversible oxidation at E1/2(VW) = 1.00 V (vs Ag/AgCl) in buffer or in the presence of poly(dA)poly(dT). However, in the presence of calf thymus DNA or poly(dG)poly(dC), a dramatic catalytic enhancement is observed. An identical result is obtained with Fe(S-C1-~hen)3~+ (E1/2(IIIAI) = 1.02 V), but no electrocatalytic enhancement is observed with truns-[Re(0)2(py)2(dmap)2]+ (E112 = 0.90 V). Electrophoresis of plasmids electrolyzed at 1.2 V in the presence of trans-[Re(0)2(4-OMe-py)4]+ show relaxation from form I to form 11, and analogous reactions with 5'-end 32P-labeled synthetic oligonucleotides show piperidine-labile cleavage specifically at guanine. The combined results point to an electrocatalytic mechanism where the oxidized metal complex oxidizes guanine in DNA by one electron via an efficient, outer-sphere mechanism. Moreover, the experiments demonstrate a potential for the one-electron oxidation of guanine in double-helical DNA at neutral pH of between 0.90 and 1.00 V. This result should provide insight into the mechanisms of DNA oxidation by chemical agents and by ionizing radiation.

Telomeres at the ends of human chromosomes contain the repeating sequence 5'-d[(TTAGGG)(n)]-3'. Oxidative damage of guanine in DNAs that contain telomeric and nontelomeric sequence generates 7,8-dihydro-8-oxoguanine (8OG) preferentially in the telomeric segment, because GGG sequences are more reactive in duplex DNA. We have developed a general strategy for probing site-specific oxidation reactivity in diverse biological structures through substitution of minimally modified building blocks that are more reactive than the parent residue, but preserve the parent structure. In this study, 8OG was substituted for guanine at G(8), G(9), G(14), or G(15) in the human telomeric oligonucleotide 5'-d[AGGGTTAG(8)G(9)GTT AG(14)G(15)GTTAGGGTGT]-3'. Replacement of G by 8OG in telomeric DNA can affect the formation of intramolecular G quadruplexes, depending on the position of substitution. When 8OG was incorporated in the 5'-position of a GGG triplet, G quadruplex formation was observed; however, substitution of 8OG in the middle of a GGG triplet produced multiple structures. A clear correspondence between structure and reactivity was observed when oligonucleotides containing 8OG in the 5'-position of a GGG triplet were prepared in the quadruplex or duplex forms and interrogated by mediated electrocatalytic oxidation with Os(bpy)(3)(2+) (bpy = 2,2'-bipyridine). The rate constant for one-electron oxidation of a single 8OG in the 5'-position of a GGG triplet was (6.2 +/- 1.7) x 10(4) M(-1) s(-1) in the G quadruplex form. The rate constant was 2-fold lower for the same telomeric sequence in the duplex form ((3.0 +/- 1.3) x 10(4) M(-1) s(-1)). The position of 8OG in the GGG triplet affects telomerase activity and synthesis of telomeric repeat products. Telomerase activity was decreased significantly when 8OG was substituted in the 5'-position of the GGG triplet, but not when 8OG was substituted in the middle of the triplet. Thus, biological oxidation of G to 8OG in telomeres has the potential to modulate telomerase activity. Further, small molecules that inhibit telomerase by stabilizing telomeric G quadruplexes may not be as effective under oxidative stress.

Glassy carbon electrodes modified by reductive electropolymerization of a thin film of poly[Ru(vbpy)(3)(2+)] or poly[Ru(vbpy)(3)(2+)/vba] (vbpy = 4-vinyl-4'-methyl-2,2'-bipyridine and vba = p-vinylbenzoic acid) were prepared. The Ru(III/II) couples for the polymer films were reversible in nonaqueous solution but were irreversible in aqueous media. The films modified with poly[Ru(vbpy)(3)(2+)] catalyzed the oxidation of aqueous guanosine 5'-monophosphate (GMP) and poly[G], producing a current enhancement in the Ru(III/II) couple for the polymer film. The catalysis was due both to electrostatic condensation of GMP and poly[G] to the Ru-modified surface and to more facile electron transfer to the Ru(III) centers in the polymer compared to the bare electrode. The presence of GMP in solution decreased the extent of decomposition of Ru(III). When single-stranded DNA containing multiple guanines was attached to the electrode modified with the poly[Ru(vbpy)(3)(2+)/vba] copolymer, enhancement of 8-13mgr;A for the Ru(III/II) couple was observed with 8 pmol of attached DNA. This degree of enhancement corresponds to a current efficiency of 65% based on a one-electron oxidation of guanine.

Ionic liquids are described that contain duplex DNA as the anion and polyether-decorated transition metal complexes based on M(MePEG-bpy)(3)(2+) as the cation (M = Fe, Co; MePEG-bpy = 4,4'-(CH(3)(OCH(2)CH(2))(7)OCO)(2)-2,2'-bipyridine). When the undiluted liquid DNA-or molten salt-is interrogated electrochemically by a microelectrode, the molten salts exhibit cyclic voltammograms due to the physical diffusion (D(PHYS)) of the polyether-transition metal complex. When M = Co(II), the cyclic voltammogram of the melt shows an oxidative wave due to the Co(III/II) couple at E(1/2) = 0.40 V (versus Ag/AgCl) and a D(PHYS) of 6 x 10(-12) cm(2)/s, which is significantly lower than that for Co(MePEG-bpy)(3)(ClO(4))(2) (D(PHYS) = 2.6 x 10(-10) cm(2)/s) due to greater viscosity provoked by the DNA polymer. When a 1:1 mixture is made of the Co(MePEG-bpy)(3).DNA and Fe(MePEG-bpy)(3)(ClO(4))(2) melts, two redox waves are observed. The first is due to the Co(III/II) couple, and the second is a catalytic wave due to oxidation of guanine in DNA by electrogenerated Fe(III) in the undiluted melt. Independent experiments show that the Fe(III) form of the complex selectively oxidizes guanine in duplex DNA. These DNA molten salts constitute a new class of materials whose properties can be controlled by nucleic acid sequence and that can be interrogated in undiluted form on microelectrode arrays.

The kinetics of oxidation of tyrosine by the series of metal complex oxidants, M(bpy)33+ (M = Os, Fe, Ru), in the presence of added bases (acetate, succinate monoanion, histidine, phosphate, and tris), were investigated in 0.5 M buffer with 0.8 M NaCl at 25 °C by utilizing a catalytic cyclic voltammetry technique. As reported in an earlier study, oxidation occurs by a series of pathwayselectron transfer followed by proton transfer (ET−PT), proton transfer followed by electron transfer (PT−ET), and concerted electron−proton transfer (EPT). The latter two occur within H-bonded association complex between tyrosine and the added base. Kinetic isolation was used to focus on the EPT pathway, in which multiple site-electron proton transfer (MS-EPT) occurs with electron transfer to the oxidant and proton transfer to the base. Measured rate constants varied from kEPT = 5.0 × 103 to 9.8 × 107 M-1 s-1. Systematic variations in RT ln kEPT with ΔG°‘ were observed with RT lnkEPT increasing with −ΔG°‘ with a slope of ∼0...

The electrical properties of single-walled carbon nanotubes (CNT) are of intense interest due to applications in nanoelectronics. Cyclic voltammetry and chronoamperometry have been used to explore the Ru(bpy)32+ electrocatalytic oxidation of DNA-solubilized carbon nanotubes. Dramatic current enhancements are observed with the addition of a CNT wrapped in an oligonucleotide sequence containing no oxidizable guanines. The current enhancement observed is solely due to the oxidation of the CNT by electrogenerated Ru(III) and subsequent recycling of the metal complex redox reaction. The chronoamperometric (CA) response is biphasic, and rate constants derived from the CA response were used to develop digital simulations of the cyclic voltammograms collected at the same CNT concentrations. Ten successive C' reactions were required to account for all of the observed signal. The oxidation of the CNT is a multielectron process, and this effect arises from the multiple electron donor sites in the carbon nanotube as well as the over oxidation of each site.

The oxidation of the amino acids tyrosine and tryptophan by complexes based on M(bpy)33+ (M = Ru, Os) was studied by monitoring the cyclic voltammetry of the metal complex in the presence of the oxidizable amino acids. Addition of both amino acids to aqueous solutions of the metal complexes in phosphate buffer produced electrocatalytic enhancement in the oxidative wave observed at indium tin oxide electrodes. The kinetics for the oxidation by the Ru(III) and Os(III) forms was determined by digital simulation. The oxidation kinetics for tryptophan were consistent with outer-sphere electron transfer, giving an expected dependence of the oxidation rate constant on the reduction potential of the metal complex. In contrast, oxidation of tyrosine at pH 7.5 did not give an appreciable dependence on the metal complex potential. These results were explained by a kinetic model where proton transfer from tyrosine to phosphate can be the rate-limiting step in competition with a concerted, multisite electron-proton-transfer pathway that is observed at lower base concentrations. These results suggest that tyrosine oxidation in enzymes can access both pathways depending on the solvent accessibility of the oxidized residue and the availability of a suitable proton acceptor.