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In January 2008, the journal and knowledge environment Science 's STKE was renamed Science Signaling , and primary research papers were first published later that year. To mark this anniversary, Thorp and Yaffe reflect on the importance of basic research to scientific progress.

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.

The binding of small molecules to distinctive three-dimensional structures in mRNA provides a new dimension in RNA control, previously limited to the targeting of secondary structures with antisense and RNA interference; such targeting can modulate mRNA function and rates of protein biosynthesis. Small molecules that selectively bind the iron-responsive element (IRE), a specific three-dimensional structure in the noncoding region of the ferritin mRNA model that is recognized by the iron-regulatory protein repressor, were identified by using chemical footprinting. The assay used involved an oxoruthenium(IV) complex that oxidizes guanine bases in RNA sequences. Small molecules that blocked oxidation of guanines in the internal loop region were expected to selectively increase the rate of ferritin synthesis, because the internal loop region of the ferritin IRE is distinctive from those of other IREs. The natural product yohimbine was found (based on gel mobility shifts) to block cleavage of the internal loop RNA site by >50% and seemed to inhibit protein binding. In the presence of yohimbine, the rate of biosynthesis of ferritin in a cell-free expression system (rabbit reticulocyte lysate) increased by 40%. Assignment of the IRE–yohimbine interaction as the origin of this effect was supported by a similar increase in synthesis of luciferase protein in a chimera of the IRE and luciferase gene. The identification of a small, drug-like molecule that recognizes a naturally occurring three-dimensional mRNA structure and regulates protein biosynthesis rates raises the possibility that small molecules can regulate protein biosynthesis by selectively binding to mRNA.

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.

Absolute quantification of Rak nuclear tyrosine kinase mRNA in breast tissue samples was determined by competitive RT-PCR. The total RNA from the same samples was also chemically amplified through conventional RT-PCR, and the relative amounts of these amplified RT-PCR products were determined by adsorption onto an indium tin oxide (ITO) electrode followed by electrochemical detection. The electrochemical detection was performed using the inorganic metal complex Ru(bpy)(3)(2+) (bpy = 2,2' bipyridine) to catalyze the oxidation of the guanine residues of the immobilized RT-PCR products. Using the competitive RT-PCR values as standards, it was found that an optimized conventional RT-PCR coupled with electrochemical detection provides a simple method for measuring relative gene expression among a series of mRNA samples from breast tumors. The use of electrochemical detection potentially eliminates the need for gel electrophoresis and fluorescent or radioactive labels in detecting the target genes.

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 ...

There is considerable enthusiasm over electrochemical techniques in biotechnology, including the development of electrochemical biosensors for DNA hybridisation. The development of assay techniques that have the convenience of solid-phase hybridisation and are rapid, sensitive and readily multiplexed will have a significant impact on diagnostics and genomics. Because electrochemistry requires a solid electrode, there is a natural marriage between electrode detection and surface hybridisation. Modern electrochemical approaches include the detection of hybridisation at electrode surfaces using duplex-specific indicators and the shuttling of electrons from surface-bound nucleic acids to solid electrodes using soluble mediators with polentials matched to that of guanine.

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.

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

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 emission properties of [ReO2(py)4]+ in Nafion perfluorosulfonated membranes have been investigated. The excited state of [ReO2(py)4]+is a sensitive probe of microheterogeneous environments in aqueous solution (Thorp el al. (1989) J. Am. Chem. SOC. 111,4364–4368). The absorption and emission maxima indicate that the interior of the membrane is quite polar, similar to ethylene glycol (Z-85). Two well-resolved emission components show different lifetimes (τ1(H2O) = 250 ns, τ2,(H20) = 1.3 μs) and isotope effects (3.0, 2.4), indicative of varying degrees of solvent accessibility. The evidence suggests that [ReO2(py)4]+ occupies two distinct regions in the polymer film, assigned as the interfacial region and the ion-cluster region based on previous electrochemical studies involving other metal ions.

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.

In this paper we report the electrochemistry of 1 [(bpy) 2 Mn(O) 2 Mn(bpy) 2 ] 3+ (1, bpy=2,2'-bipyridyl) at edge-oriented pyrolytic graphite (EOPG) and tin-doped indium oxide. These surfaces appear to mediate proton-coupled electron transfer; it is also clear that both forms of 1 adsorb at these surfaces under certain conditions

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.

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.

Genomic expansion of the triplet repeat sequences 5'-(CTG)n and 5'-(CGG)n leads to myotonic dystrophy and fragile X syndrome, respectively. Methods for determining the number of repeats in unprocessed nucleic acids would be useful in diagnosing diseases based on triplet repeat expansion. Electrochemical reactions based on the oxidation of guanine were expected to give larger signals per strand for expansion of repeats containing guanine. A novel PCR reaction was used to generate fragments containing 150, 230, 400, and 830 repeats of (CTG)n, which codes for myotonic dystrophy, and 130 and 600 repeats of (CGG)n, which codes for fragile X syndrome. These PCR fragments were immobilized to indium tin oxide electrodes, and oxidation of guanine in the fragments was realized using electrocatalysis by Ru(bpy)3(2+) (bpy = 2,2'-bipyridine). The catalytic currents due to oxidation of the immobilized guanines by Ru(bpy)3(3+) increased with the number of repeats and were a linear function of the repeat number when normalized to the number of strands immobilized. These results suggest a sensing strategy for repeat length based on the combination of the electrocatalytic strategy for determining the repeat length combined with existing methods for determining the number of strands.

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 2′-hydroxyl group of ribose imparts hydrolytic lability on RNA, which provides a mechanism for numerous biological functions. Recent evidence from chemical cleavage studies shows that this hydroxyl group also stabilizes the sugar moiety in RNA towards oxidation relative to DNA. Is this just because RNA needs to be distinguishable from DNA or does it have other evolutionary significance?

The research supported by this grant is intended to evaluate Rak mRNA expression in both tumor tissue and breast cancer cells and to determine whether inhibiting RAK is a feasible approach to breast cancer therapy. To accomplish this goal two different assays of gene expression have been devised. The first method is a traditional competitive RT-PCR system in which a homologous competitor RNA is used as a standard. The second method involves the use of an electrochemical biosensor being developed in our lab. The biosensor is designed to detect the abstraction of electrons from guanine bases in surface immobilized target RNA's or RT-PCR products. This report describes the development of a rapid electrochemical method that has detected Rak RT-PCR products. Preliminary characterization of this system has determined the sensitivity limit of this system to be 60 amol/sq mm of electrode. In addition, results from competitive RT-PCR experiments on Rak mRNA have revealed that RAK is expressed in BT-474 cells at a level of roughly 100 zmol/micrograms total RNA.

Background: The translation or stability of the mRNAs from ferritin, m-aconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of higher-solution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms. Results: Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern. Conclusions: The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes, The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.

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 photochemistry of Pt2(pop)44- with nucleic acids has been studied using radiolabeled oligomers of DNA and RNA and high-resolution electrophoresis (pop is P2O5H22-). Photolysis of Pt2(pop)44- with duplex DNA produces an even cleavage ladder and relatively little enhancement of cleavage upon treatment with piperidine. In contrast, the cleavage pattern is far less regular with single-stranded DNA, and there is a large enhancement in cleavage upon treatment with piperidine. Accordingly, photolysis of Pt2(pop)44- with the DNA hairpin 5'-d[ATCCTATTTATAGGAT] produces a much larger piperidine enhancement at the loop and end nucleotides than in the stem. There is an additional piperidine enhancement that occurs selectively at guanine residues either in RNA or in DNA at low Mg2+ concentrations that is attributed to outer-sphere electron transfer on the basis of the known excited-state redox potentials of Pt2(pop)44- and the expected oxidative chemistry of guanine. The extent of guanine oxidation is higher compared to the extent of sugar oxidation at low Mg2+ concentrations, which can be attributed to a shallower distance dependence for electron transfer compared to that for atom transfer. The effects of Mg2+ and piperidine or aniline treatment were examined on stem-loop structures of DNA and RNA and gave partial images of the expected secondary structures.

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.