PROBING PHOTODYNAMIC DAMAGE IN NUCLEIC ACIDS WITH A DAMAGE-SPECIFIC DNA BINDING PROTEIN: A COMPARISON OF THE B and Z DNA CONFORMATIONS

—We have employed a damage-specific DNA binding protein from human cells as a probe for base damage in polymers irradiated with white light in the presence of methylene blue. Protein-recognizable damage is introduced only into guanine-containing polymers and quenching of damage introduction by H₂O and sodium azide suggest the involvement of a singlet oxygen mechanism. Using poly d(G-m⁵C), we have demonstrated that the left-handed double helical Z conformation is much less susceptible to guanine photooxidation than is the usual B conformation. We speculate that this difference in reactivity may reflect steric hindrance at the purine C-4 position and could provide some insight into the initial steps of the reaction between singlet oxygen and guanine in nucleic acid polymers.     

Ion atmosphere relaxation and percolative electron transfer in Co bipyridine DNA molten salts

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.     

On choosing a reference redox system for electrochemical measurements: a cautionary tale

The potential of a quasi-reference electrode can be determined by introducing an internal reference redox system (IRRS) which comprises either the oxidizable or reducible form of a reversible (and, ideally, outer-sphere) redox couple and then observing the cyclic voltammetric responses. The objective is to choose the IRRS so that the cyclic voltammetric response for the simultaneously present electroactive analyte system (ANS) can be observed independently of the IRRS response. We identify three fundamental paradigms describing the relative positioning of the IRRS and ANS on the potential scale, the operative redox components for the IRRS and ANS, and the starting potential (E _start), reversing potential (E _rev), and ending potential (E _end) for the cyclic voltammetric scan as follows: paradigm A, an optimal paradigm which can produce completely independent cyclic voltammetric responses for the IRRS or for ANS; paradigm B, a less-than-optimal paradigm which can produce an independent cyclic voltammetry (CV) response for the ANS or a mixed response for the IRRS with that response on top of the ANS response; paradigm C, a problematic paradigm that can produce an independent CV response for the IRRS or a mixed response for the ANS with that response on top of the IRRS response; and any mixed response produces a thermodynamically favored redox cross-reaction which couples the IRRS and ANS systems and which can complicate the analysis of the ANS and IRRS responses. The conclusion is that paradigm C is to be avoided.     

Non-linear dynamic phenomena in the behaviour of a railway wheelset model

A dicone moving on a pair of cylindrical rails can be considered as a simplified model of a railway wheelset. Taking into account the non-linear friction laws of rolling contact, the equations of motion for this non-linear mechanical system result in a set of differential-algebraic equations. Previous simulations performed with the differential-algebraic solver DASSL, [2], and experiments, [7], indicated non-linear phenomena such as limit-cycles, bifurcations as well as chaotic behaviour. In this paper the non-linear phenomena are investigated in more detail with the aid of special in-house software and the path-following algorithm PATH [10]. We apply Poincaré sections and Poincaré maps to describe the structure of periodic, quasiperiodic and chaotic motions. The analyses show that part of the chaotic behaviour of the non-linear system can be fully understood as a non-linear iterative process. The resulting stretching and folding processes are illustrated by series of Poincaré sections.     

Identification of the radical anions of C2N4S2 and P2N4S2 rings by in situ EPR spectroelectrochemistry and DFT calculations

The previously unknown radical anions of unsaturated E2N4S2 ring systems (E=RC, R2NC, R2P) can be generated voltammetrically by the one-electron reduction of the neutral species and, despite half-lives on the order of a few seconds, have been unambiguously characterized by electron paramagnetic resonance (EPR) spectroelectrochemistry using a highly sensitive in situ electrolysis cell. Cyclic voltammetric studies using a glassy-carbon working electrode in CH3CN and CH2Cl2 with [nBu4N][PF6] as the supporting electrolyte gave reversible formal potentials for the [E2N4S2]0/- process in the range of -1.25 to -1.77 V and irreversible peak potentials for oxidation in the range of 0.66 to 1.60 V (vs the Fc+/0 couple; Fc=ferrocene). Reduction of the neutral compound undergoes an electrochemically reversible one-electron transfer, followed by the decay of the anion to an unknown species via a first-order (chemical) reaction pathway. The values of the first-order rate constant, kf, for the decay of all the radical anions in CH2Cl2 have been estimated from the decay of the EPR signals for (X-C6H4CN2S)2*-, where X=4-OCH3 (kf=0.04 s(-1)), 4-CH3 (kf=0.02 s(-1)), 4-H (kf=0.08 s(-1)), 4-Cl (kf=0.05 s(-1)), 4-CF3 (kf=0.05 s(-1)), or 3-CF3 (kf=0.07 s(-1)), and for [(CH3)3CCN2S]2*- (kf=0.02 s(-1)), [(CH3)2NCN2S]2*- (kf=0.05 s(-1)), and [(C6H5)2PN2S]2*- (kf=0.7 s(-1)). Values of kf for X=4-H and for [(CH3)2NCN2S]2*- were also determined from the cyclic voltammetric responses (in CH2Cl2) and were both found to be 0.05 s(-1). Possible pathways for the first-order anion decomposition that are consistent with the experimental observations are discussed. Density functional theory calculations at the UB3LYP/6-31G(d) level of theory predict the structures of the radical anions as either planar (D2h) or folded (C2v) species; the calculated hyperfine coupling constants are in excellent agreement with experimental results. Linear correlations were observed between the voltammetrically determined potentials and both the orbital energies and Hammett coefficients for the neutral aryl-substituted rings.     

pH-dependence of the aqueous electrochemistry of the two-electron reduced alpha-[Mo18O54(SO3)] sulfite Dawson-like polyoxometalate anion derived from its triethanolammonium salt

The electrochemistry of the Dawson-like sulfite polyoxometalate anion alpha-[Mo18O54(SO3)2]6-, derived from the TEAH6{alpha-[Mo18O54(SO3)2]} salt (TEAH+ is the triethanolammonium cation; pKa=7.8), has been investigated in aqueous media using cyclic and rotated disk voltammetry at glassy carbon electrodes and bulk electrolysis, with a focus on the pH-dependence for oxidation to alpha-[Mo18O54(SO3)2]4-. In buffered media at pH>or=4, the cyclic voltammetric response for alpha-[Mo18O54(SO3)2]6- reveals two partially resolved one-electron oxidation processes corresponding to the sequential generation of alpha-[Mo18O54(SO3)2]5- and alpha-[Mo18O54(SO3)2]4-. At lower pH, using electrolytes containing sulfuric acid, the two waves coalesce but the individual apparent E0' reversible formal potential values for the two processes can be extracted down to pH 2 by assuming that reversible protonation accompanies fast electron transfer. The results for 2相似文献   

An informative subtlety of itemperature-jump or coulostatic responses for surface-attached species

Theoretical relationships are developed to describe the open-circuit responses associated with the indirect laser-induced temperature-jump (ILIT) method, a method for measuring fast electron-transfer rate constants of surface-attached redox species. The analysis is also applicable to data obtained using the coulostatic charge-injection method. The unique relationship between k_m, the relaxation rate constant for the ILIT (or coulostatic) response, and E_i, the potential at which the system is initially poised, exhibits a surprising sensitivity to the values of k₀, E_i^0′ (the standard rate constant and formal potential for the redox couple), α (the transfer coefficient in the Butler–Volmer equation) and γ (a dimensionless parameter which is directly proportional to the total surface concentration of the redox moiety). ILIT data for several examples of surface-attached ferrocene moieties confirm the theoretically predicted k_m vs E_i behavior. Values of E_i^0′ and γ extracted from the ILIT data agree well with the values obtained from cyclic voltammetric data thereby confirming that the ILIT and cyclic voltammogram (CV) experiments are sampling the same ferrocene population.     

Heterogeneous electron-transfer kinetics for ruthenium and ferrocene redox moieties through alkanethiol monolayers on gold

The standard heterogeneous electron-transfer rate constants between substrate gold electrodes and either ferrocene or pentaaminepyridine ruthenium redox couples attached to the electrode surface by various lengths of an alkanethiol bridge as a constituent of a mixed self-assembled monolayer were measured as a function of temperature. The ferrocene was either directly attached to the alkanethiol bridge or attached through an ester (CO(2)) linkage. For long bridge lengths (containing more than 11 methylene groups) the rate constants were measured using either chronoamperometry or cyclic voltammetry; for the shorter bridges, the indirect laser induced temperature jump technique was employed to measure the rate constants. Analysis of the distance (bridge length) dependence of the preexponential factors obtained from an Arrhenius analysis of the rate constant versus temperature data demonstrates a clear limiting behavior at a surprisingly small value of this preexponential factor (much lower than would be expected on the basis of aqueous solvent dynamics). This limit is independent of both the identity of the redox couple and the nature of the linkage of the couple to the bridge, and it is definitely different (smaller) from the limit derived from an equivalent analysis of the rate constant (versus temperature) data for the interfacial electron-transfer reaction through oligophenylenevinylene bridges between gold electrodes and ferrocene. There are a number of possible explanations for this behavior including, for example, the possible effects of bridge conformational flexibility upon the electron-transfer kinetics. Nevertheless, conventional ideas regarding electronic coupling through alkane bridges and solvent dynamics are insufficient to explain the results reported here.     

Systematic approach to the quantitative voltammetric analysis of the FeIII/FeII component of the [alpha2-Fe(OH2)P2W17O61]7-/8- reduction process in buffered and unbuffered aqueous media

The one-electron reduction of [alpha(2)-Fe(III)(OH(2))P(2)W(17)O(61)](7-) at a glassy carbon electrode was investigated using cyclic and rotating-disk-electrode voltammetry in buffered and unbuffered aqueous solutions over the pH range 3.45-7.50 with an ionic strength of approximately 0.6 M maintained. The behavior is well-described by a square-scheme mechanism P + e(-) <--> Q (E(1)(0/) = -0.275 V, k(1)(0/) = 0.008 cm s(-1), and alpha(1) = 1/2), PH(+) + e(-) <--> QH(+) (E(2)(0/) = -0.036 V, k(2)(0/) = 0.014 cm s(-1), and alpha(2) = 1/2), PH(+) <--> P + H(+) (K(P) = 3.02 x 10(-6) M), and QH(+) <--> Q + H(+) (K(Q) = 2.35 x 10(-10) M), where P, Q, PH(+), and QH(+) correspond to [alpha(2)-Fe(III)(OH)P(2)W(17)O(61)](8-), [alpha(2)-Fe(II)(OH)P(2)W(17)O(61)](9-), [alpha(2)-Fe(III)(OH(2))P(2)W(17)O(61)](7-), and [alpha(2)-Fe(II)(OH(2))P(2)W(17)O(61)](8-), respectively; E(1)(0)' and E(2)(0)' are the formal potentials, k(1)(0)' and k(2)(0)' are the formal (standard) rate constants, and K(P) and K(Q) are the acid dissociation constants for the relevant reactions. The analysis for the buffered media is based on the approach of Laviron who demonstrated that a square scheme with fully reversible protonations, reversible or quasi reversible electron transfers with the assumption that alpha(1) = alpha(2), can be well-described by the behavior of a simple redox couple, ox + e(-) <--> red, whose formal potential, E(app)(0)', and standard rate constant, k(app)(0)', are straightforwardly derived functions of pH, as are the values of E(1)(0)', k(1)(0)', E(2)(0)', k(2)(0)', and K(P) (only three of the four thermodynamic parameters in a square scheme can be specified). It was assumed that alpha(app) = 1/2, and the simulation program DigiSim was used to determine the values of E(app)(0)' and k(app)(0)', which are required to describe the cyclic voltammograms obtained in buffered media in the pH range from 3.45 to 7.52 (buffer-related reactions which effect general acid-base catalysis are included in the simulations). DigiSim simulations of cyclic voltammograms obtained in unbuffered media yielded the values of E(1)(0)' and k(1)(0)'; K(Q) was then directly computed from thermodynamic constraints. These simulations included additional reactions between the redox species and H(2)O. The value of the diffusion coefficient of the [alpha(2)-Fe(III)(OH(2))P(2)W(17)O(61)](7-), 2.92 x 10(-6) cm(2) s(-1), was determined using DigiSim simulations of voltammograms at a rotating disk electrode in buffered and unbuffered media at pH 3.45. The diffusion coefficients of all redox species were assumed to be identical. When the pH is greater than 6, instability of P (i.e., [alpha(2)-Fe(III)(OH)P(2)W(17)O(61)](8-)) led to the loss of the reactant and precluded lengthy experimentation.