Role of adenine in thymine-dimer repair by reduced flavin-adenine dinucleotide

We present a study of excited-state behavior of reduced flavin cofactors using femtosecond optical transient absorption spectroscopy. The reduced flavin cofactors studied were in two protonation states: flavin-adenine dinucleotide (FADH2 and FADH-) and flavin-mononucleotide (FMNH2 and FMNH-). We find that FMNH- exhibits multiexponential decay dynamics due to the presence of two bent conformers of the isoalloxazine ring. FMNH2 exhibits an additional fast deactivation component that is assigned to an iminol tautomer. Reduced flavin cofactors also exhibit a long-lived component that is attributed to the semiquinone and the hydrated electron that are produced in photoinduced electron transfer to the solvent. The presence of adenine in FADH2 and FADH- further changes the excited-state dynamics due to intramolecular electron transfer from the isoalloxazine to the adenine moiety of cofactors. This electron transfer is more pronounced in FADH2 due to pi-stacking interactions between two moieties. We further studied cyclobutane thymine dimer (TT-dimer) repair via FADH- and FMNH- and found that the repair is much more efficient in the case of FADH-. These results suggest that the adenine moiety plays a significant role in the TT-dimer repair dynamics. Two possible explanations for the adenine mediation are presented: (i) a two-step electron transfer process, with the initial electron transfer occurring from flavin to adenine moiety of FADH-, followed by a second electron transfer from adenine to TT-dimer; (ii) the preconcentration of TT-dimer molecules around the flavin cofactor due to the hydrophobic nature of the adenine moiety.     

Capillary electrophoresis of nicotinamide—adenine dinucleotide and nicotinamide—adenine dinucleotide phosphate derivatives in coated tubular columns

HPCE was shown to be an effective and convenient method for the determination of nicotinamide—adenine dinucleotide (oxidized, NAD⁺; reduced, NADH), nicotinamide—adenine dinucleotide phosphate (oxidized, NADP; reduced, NADPH) and their synthetic derivatives. The coenzymes were easily separated among themselves and from their degradation products, which are inhibitors of dehydrogenases, in 15 min in a coated capillary. Several coenzyme derivatives such as N⁶-(2-aminoethyl)-NAD(P)⁺ and N(1)-(2-aminoethyl)-NAD(P)⁺ were separated by zone electrophoresis in uncoated or coated capillaries using 50 mM 3-(N-morpholino)propanesulphonic acid (pH 7.0) or Tris—HCl (pH 8.0) as buffer systems. Capillary zone electrophoresis and micellar electrokinetic capillary chromatography can also be used to monitor continuously coenzyme chemical modifications.     

Photochemical generation of cyclopentadienyliron dicarbonyl anion by a nicotinamide adenine dinucleotide dimer analogue

Irradiation of the absorption band of an NAD (nicotinamide adenine dinucleotide) dimer analogue, 1-benzyl-1,4-dihydronicotinamide dimer, (BNA)(2), in acetonitrile containing a cyclopentadienyliron dicarbonyl dimer, [CpFe(CO)(2)](2), results in generation of 2 equiv of the cyclopentadienyliron dicarbonyl anion, [CpFe(CO)(2)](-), accompanied by the oxidation of (BNA)(2) to yield 2 equiv of BNA(+). The studies on the quantum yields, the electrochemistry, and the transient absorption spectra have revealed that the photochemical generation of [CpFe(CO)(2)](-) by (BNA)(2) proceeds via photoinduced electron transfer from the triplet excited state of (BNA)(2) to [CpFe(CO)(2)](2).     

Ultrasensitive and selective detection of nicotinamide adenine dinucleotide by target-triggered ligation-rolling circle amplification

An ultrasensitive fluorescence assay for nicotinamide adenine dinucleotide (NAD(+)) was developed by target-triggered ligation-rolling circle amplification (L-RCA). This novel approach can detect as low as 1 pM NAD(+), much lower than those of previously reported biosensors, and exhibits high discrimination ability even against 200 times excess of NAD(+) analogs.     

Metal-intercalator-mediated self-association and one-dimensional aggregation in the structure of the excised major DNA adduct of a platinum-acridine agent

The crystal structure of the excised major DNA monoadduct, [Pt(en)(ACRAMTU-S)(dGuo-N7)]3+ ("dGuo*"; en = ethane-1,2-diamine; ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea, acridinium cation; dGuo = 2'-deoxyguanosine), of a platinum-acridine cytotoxic agent is reported. The adduct dGuo*, previously identified in enzymatic digests of native DNA treated with this drug, is partially deprotonated and dimerizes through formation of a rare GG- mismatch base pair, which is sandwiched between the planar chromophores of the acridine nonleaving groups linked to platinum. NMR evidence exists that indicates that the dimeric form persists in neutral aqueous solution. The one-dimensional pi-stack produced by the dimers in the solid state is reminiscent of a coordinative-intercalative DNA binding mode.     

Time-resolved emission of flavin adenine dinucleotide in water and water-methanol mixtures

Time-resolved fluorescence decay of flavin adenine dinucleotide (FAD) was studied at room temperature in water and water-methanol mixtures by a fluorescence upconversion technique. The observations were focused on the most initial decay phase (200 ps), before the residual fluorescence assumes a single exponential decay, typical for an extended conformation of the fluorophore. Within the first few picoseconds, where most of the electron transfer coupled quenching takes place, the emission decay curves could be fitted by a stretched exponent, compatible with the inhomogeneous distance dependent electron transfer model. This implies that the population of the excited FAD molecules exhibits a large number of non-identical states, each with its own separation between the donor (adenine) and acceptor (isoalloxazine) moieties, having its own rate of electron transfer. To evaluate the distribution of the separation between the donor-acceptor pair, we carried out molecular dynamics simulations of closed conformation of the FAD in water and water-methanol mixtures, sampling the structure at 10 fs intervals. The analysis of the dynamics reveals that within the 4 ps time frame, where most of the nonexponential fluorescence relaxation takes place, the relative motion of the donor-acceptor pair is consistent with a one-dimensional Brownian motion, where the diffusion coefficient and the shape of the confining potential well are solvent dependent. The presence of methanol enhances the diffusion constant and widens the width of the potential well. On the basis of these parameters, the relaxation dynamics was accurately reconstructed as an electron transfer reaction in an inhomogeneous system where the reactants are diffusing within the time frame of the observation.     

Differential pulse polarography as a tool for the determination of trace levels of nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+) in aqueous solution

The differential pulse polarographic behavior of NAD⁺ and NADP⁺ has been investigated in phosphate buffer. The peaks obtained at pH 8.0 are recommended for the trace determination of these compounds. Linear calibration curves are obtained over the concentration ranges from 2.6 × 10⁻⁷ to 2.6 × 10⁻⁵M for NAD⁺ and from 2 × 10⁻⁶ to 4 × 10⁻⁵ for NADP⁺.     

The electrochemical reduction and determination of reduced nicotinamide adenine dinucleotide in acidic media

The apparent reduction of reduced nicotinamide adenine dinucleotide (NADH) in acidic media at a static mercury drop electrode was investigated. A simple, quick pretreatment procedure was developed to convert the NADH to its acid-hydrated form. This adsorbs on the mercury surface during a film deposition time and the film is then reduced. The adsorption is diffusion-controlled and hence the peak currents for square-wave and linear-scan voltammetry are proportional to Ct^1/2_pAf and Ct^1/2_pAv, respectively, where t_p is the effective film deposition time, C the concentration of NADH, A the electrode area, f the square-wave frequency, and ν the linear scan rate. Several electrochemical techniques were compared for the determination of NADH; the method of choice is square-wave voltammetry, although staircase or linear scan voltammetry can also be used. The detection limit is less than 7 nM, and the range of linear response covers 2–3 orders of magnitude of NADH concentration.     

Cathodic reduction of nicotinamide adenine dinucleotide and other adenine-containing compounds in acidic media

Both nicotinamide adenine dinucleotide (NAD⁺) and acid-hydrated NADH, as well as adenine, adenosine, adenosine mono-, di-, and tri-phosphate and adenosine diphosphoribose, undergo four-electron reductions of the protonated adenine ring in acidic media. The values of αn_a (transfer coefficient times the number of electrons involved in the rate-determining step), n (total number of electron transferred), and p (number of protons involved in the rate-determining step) agree well with values previously reported for adenine. Cathodic stripping voltammetry of an adsorbed film can be applied to these compounds. Rapid scan rates are required to eliminate the slow desorption step at ?1.1 V vs. SCE for some of these compounds. Hydration of the nicotinamide ring of NADH appears to inhibit this desorption step, but does not appear to be related directly to the electroactivity of the hydration product.     

Reduction of methyl benzoylformate by reduced nicotinamide adenine dinucleotide model in the presence of rhodizonic acid

The reduction of rhodizonic acid(RA) with 1-benzyl-1,4-dihydronicotin-amide(BNAH; NADH model) was carried out at room temperature to obtain tetra-hydroxy-p-quinone(THQ) and hexahydroxybenzene(HHB) by two-electron and four-electron reductions, respectively. The reduction of methyl benzoylformate with BNAH proceeded smoothly in the presence of RA, although it could not be reduced at all without RA.     

411 - Role of adsorption in the electrochemical behaviour of nicotinamide adenine dinucleotide at a gold electrode

The role of adsorption in the electrochemical reduction of nicotinamide adenine dinucleotide (NAD⁺) at a gold electrode was examined by cyclic voltammetry and the measurement of specular reflectivity of the electrode⋎solution interface. Reduction of the pyridine ring in NAD⁺ takes place at a less negative potential compared with its compounds such as nicotinamide mononucleotide (NMN⁺) and nicotinamide. All of these compounds are found to be adsorbed on the electrode surface around the point of zero charge from the reflectance data. NAD⁺ remains adsorbed on the electrode surface until the potential scanning attains its reduction potential, whereas NMN⁺ and nicotinamide are desorbed at potentials far prior to reduction. A possible model of the adsorbed NAD⁺ was proposed to explain how the adsorption of NAD⁺ serves to make its reduction easier than NMN⁺ and nicotinamide.     

A simple and highly sensitive DNAzyme-based assay for nicotinamide adenine dinucleotide by ligase-mediated inhibition of strand displacement amplification

Existing strategies for detecting nicotinamide adenine dinucleotide (NAD⁺) or other cofactors are commonly cumbersome and moderate sensitive. We report a novel DNAzyme-based visual assay strategy for NAD⁺ based on ligase-mediated inhibition of the strand displacement amplification (SDA). In the presence of NAD⁺, the SDA can be inhibited by the ligase reaction of two primers, which can initiate the SDA reaction in the case of no ligation, resulting in a dramatically decreasing yield of the SDA product, a G-quadruplex DNAzyme that can quantitatively catalyze the formation of a colored product. Therefore, the quantitative analysis for NAD⁺ can be achieved visually with high sensitivity. The developed strategy provides a simple colorimetric approach with high selectivity against most interferences and a detection limit as low as 50 pM. It also provides a universal platform for investigating cofactors or other related small molecules as well as quantifying the activity of DNA ligases.     

Fabrication and characterization of Meldola's blue/zinc oxide hybrid electrodes for efficient detection of the reduced form of nicotinamide adenine dinucleotide at low potential

We report the synthesis and the electrochemical properties of hybrid films made of zinc oxide (ZnO) and Meldola's blue dye (MB) using cyclic voltammetry (CV). MB/ZnO hybrid films were electrochemically deposited onto glassy carbon, gold and indium tin oxide-coated glass (ITO) electrodes at room temperature (25 ± 2 °C) from the bath solution containing 0.1 M Zn(NO₃)₂, 0.1 M KNO₃ and 1 × 10⁻⁴ M MB. The surface morphology and deposition kinetics of MB/ZnO hybrid films were studied by means of scanning electron microscopy (SEM), atomic force microscopy (AFM) and electrochemical quartz crystal microbalance (EQCM) techniques, respectively. SEM and AFM images of MB/ZnO hybrid films have revealed that the surfaces are well crystallized, porous and micro structured. MB molecules were immobilized and strongly fixed in a transparent inorganic matrix. MB/ZnO hybrid films modified glassy carbon electrode (MB/ZnO/GC) showed one reversible redox couple centered at formal potential (E⁰′) −0.12 V (pH 6.9). The surface coverage (Γ) of the MB immobilized on ZnO/GC was about 9.86 × 10⁻¹² mol cm⁻² and the electron transfer rate constant (ks) was determined to be 38.9 s⁻¹. The MB/ZnO/GC electrode acted as a sensor and displayed an excellent specific electrocatalytic response to the oxidation of nicotinamide adenine dinucleotide (NADH). The linear response range between 50 and 300 μM NADH concentration at pH 6.9 was observed with a detection limit of 10 μM (S/N = 3). The electrode was stable during the time it was used for the full study (about 1 month) without a notable decrease in current. Indeed, dopamine (DA), ascorbic acid (AA), acetaminophen (AP) and uric acid (UA) did not show any interference during the detection of NADH at this modified electrode.     

Determination of riboflavin, flavin mononucletide and flavin adenine dinucleotide in biological tissues by capillary zone electrophoresis and laser-induced fluorescence detection

The separation of riboflavin, flavin mononucleotide and flavin adenine dinucleotide was investigated by capillary zone electrophoresis using laser-induced fluorescence detection. In the systematic approach developed, the differential electrophoretic mobilities were first maximized by adjusting the pH. Increasing the buffer concentration improved the separation at the expense of migration times. A buffer consisting of 50 mM phosphate adjusted to pH 8.5 was found to provide a very efficient and stable electrophoretic system. Responses were linear within the range 0.1-100 micromol L(-1), and the detection limits of B2 vitamers were 0.23 nmol L(-1) or less. The method was successfully applied to a variety of biological tissues from different animals.     

Electrochemical enzymatic determinations of ethanol and -lactic acid with a carbon paste electrode modified chemically with nicotinamide adenine dinucleotide

The oxidized form of nicotinamide adenine dinucleotide (NAD⁺) is chemically immobilized at the surface of a carbon paste electrode containing n-octaldehyde. The NAD⁺ is converted to NADH by oxidation of ethanol and -lactic acid catalyzed by their respective dehydrogenases, and the NADH formed is oxidized electrochemically to the original NAD⁺, thus giving a well defined linear-sweep voltammetric peak. The peak area is linearly related to the amount of ethanol or -lactic acid in the range 0.05–2 × 10^-9 mol.     

Characterization and mechanism of formation of tandem lesions in DNA by a nucleobase peroxyl radical

5,6-Dihydro-2'-deoxyuridin-6-yl (1) was independently generated via photolysis of 3. The radical is an analogue of the major reactive species produced from thymidine upon reaction with hydroxyl radical, which is the dominant DNA-damaging agent produced by the indirect effect of gamma-radiolysis. Under aerobic conditions, the peroxyl radical (2) derived from 1 reacts approximately 82% of the time with either the 5'- or 3'-adjacent nucleotide to produce two contiguously damaged nucleotides, known as tandem lesions. The structures and distribution of tandem lesions were investigated using probes that selectively detect abasic sites, ESI-MS/MS, and competition kinetics. In addition to 2-deoxyribonolactone, nonoxidized abasic sites were detected. 18O-Labeling verified that H2O was the source of oxygen in the abasic sites, but that O2 was the source of the oxygen in the 5,6-dihydro-6-hydroxy-2'-deoxyuridine derived from 2. ESI-MS/MS experiments, in conjunction with isotopic labeling, identified several products and provided direct evidence for peroxyl radical addition to the adjacent thymine bases. Kinetic studies revealed that peroxyl radical addition to the 5'-thymine was favored by approximately 4-5-fold over C1'-hydrogen atom abstraction from the respective deoxyribose ring, and that 2-deoxyribonolactone formation accounts for approximately 11% of the total amount of tandem lesions produced. These results suggest that tandem lesions, whose biochemical effects are largely unknown, constitute a major family of DNA damage products produced by the indirect effect of gamma-radiolysis.     

G-tensors of the flavin adenine dinucleotide radicals in glucose oxidase: a comparative multifrequency electron paramagnetic resonance and electron-nuclear double resonance study

The flavin adenine dinucleotide (FAD) cofactor of Aspergillus niger glucose oxidase (GO) in its anionic (FAD*-) and neutral (FADH*) radical form was investigated by electron paramagnetic resonance (EPR) at high microwave frequencies (93.9 and 360 GHz) and correspondingly high magnetic fields and by pulsed electron-nuclear double resonance (ENDOR) spectroscopy at 9.7 GHz. Because of the high spectral resolution of the frozen-solution continuous-wave EPR spectrum recorded at 360 GHz, the anisotropy of the g-tensor of FAD*- could be fully resolved. By least-squares fittings of spectral simulations to experimental data, the principal values of g have been established with high precision: gX=2.00429(3), gY=2.00389(3), gZ=2.00216(3) (X, Y, and Z are the principal axes of g) yielding giso=2.00345(3). The gY-component of FAD*- from GO is moderately shifted upon deprotonation of FADH*, rendering the g-tensor of FAD*- slightly more axially symmetric as compared to that of FADH*. In contrast, significantly altered proton hyperfine couplings were observed by ENDOR upon transforming the neutral FADH* radical into the anionic FAD*- radical by pH titration of GO. That the g-principal values of both protonation forms remain largely identical demonstrates the robustness of g against local changes in the electron-spin density distribution of flavins. Thus, in flavins, the g-tensor reflects more global changes in the electronic structure and, therefore, appears to be ideally suited to identify chemically different flavin radicals.