Electron tunneling pathways and role of adenine in repair of cyclobutane pyrimidine dimer by DNA photolyase

Electron tunneling pathways in enzymes are critical to their catalytic efficiency. Through electron tunneling, photolyase, a photoenzyme, splits UV-induced cyclobutane pyrimidine dimer into two normal bases. Here, we report our systematic characterization and analyses of photoinitiated three electron transfer processes and cyclobutane ring splitting by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repair and for the final electron return to restore the active cofactor and complete the catalytic photocycle. Significantly, we found that the adenine moiety of the unusual bent flavin cofactor is essential to mediating all electron-transfer dynamics through a superexchange mechanism, leading to a delicate balance of time scales. The cyclobutane ring splitting takes tens of picoseconds, while electron-transfer dynamics all occur on a longer time scale. The active-site structural integrity, unique electron tunneling pathways, and the critical role of adenine ensure the synergy of these elementary steps in this complex photorepair machinery to achieve maximum repair efficiency which is close to unity. Finally, we used the Marcus electron-transfer theory to evaluate all three electron-transfer processes and thus obtained their reaction driving forces (free energies), reorganization energies, and electronic coupling constants, concluding that the forward and futile back-electron transfer is in the normal region and that the final electron return of the catalytic cycle is in the inverted region.     

A dithienylethene-tethered beta-cyclodextrin dimer as a photoswitchable host

The binding of TSPP by a dithienylethene-tethered beta-cyclodextrin dimer can be altered reversibly by irradiation with light.     

Cyanoacetaldehyde as a building block for prebiotic formation of pyrimidines

The present study uses density functional theory to investigate the possible free radical pathways for cytosine and uracil formation from cyanoacetaldehyde in the presence of urea and ammonia. Our proposed mechanisms are characterized by a smaller number of precursors and relatively lower barriers compared to previously reported reactions with other prebiotic precursors. Thus, the proposed mechanisms are more plausible in environments like prebiotic earth and present-day Titan. Overall, this study suggests a kinetically accessible route to pyrimidine formation and will hopefully contribute toward understanding the relevance of these precursors in prebiotic reactions.     

Urinary analysis of 8-oxoguanine, 8-oxoguanosine, fapy-guanine and 8-oxo-2'-deoxyguanosine by high-performance liquid chromatography-electrospray tandem mass spectrometry as a measure of oxidative stress

A sensitive and specific assay aimed at measuring the oxidized nucleic acids, 8-oxoguanine (8-oxoGua), fapy-guanine (Fapy-Gua), 8-oxoguanosine (8-oxoGuo), 8-oxo-2'-deoxyguanosine (8-oxodG) has been developed by coupling reversed phase liquid chromatography (HPLC) with electrospray tandem mass spectrometry detection (MS/MS) and isotope dilution. The HPLC-MS/MS approach with multiple reaction monitoring (MRM) allowed for the sensitive determination of 8-oxoGua, Fapy-Gua, 8-oxoGuo, and 8-oxodG in human urine samples. There is no sample preparation needed except for the addition of buffer and (13)C- and (15)N-labeled internal standards to the urine prior to sample injection into the HPLC-MS/MS system. This method was tested in urine samples from non-smokers, smokers, non-smokers with chronic kidney disease (CKD) and smokers with CKD, to assess the level of oxidative damage to nucleic acids. Markers of both RNA and DNA damage were significantly increased in the smokers with and without CKD compared to their respective control subjects. These findings suggest that a highly specific and sensitive analytical method such as isotope dilution HPLC-MS/MS may represent a valuable tool for the measurement of oxidative stress in human subjects.     

A polymer supported manganese catalyst useful as a superoxide dismutase mimic

Polymer supported manganese was synthesized via a template polymerization involving functional monomers to afford a catalyst with superoxide dismutase activity.     

A non-covalent dimer formed in electrospray ionisation mass spectrometry behaving as a precursor for fragmentations

A non-covalent-bonded dimer was detected in the positive ion electrospray ionisation (ESI) mass spectra of a synthetic impurity. In tandem mass spectrometry (MS/MS) experiments using collision-induced dissociation (CID), the ion was found to behave as a [M+H]+-type precursor ion for fragmentation until MS5. The dimer was probably formed through multi-hydrogen bonds over a proton bridge. When the fragmentation occurred at the center of the bridge, the dimer was broken apart to give monomer fragments at MS6. However, no corresponding deprotonated dimer [2M-H]- was found in the negative ion ESI spectra. The dimer was extremely stable, and it could still be observed when a fragmentation voltage of up to 50 V was applied in the ionisation source. The formation of the non-covalent dimer was also found to be instrument-dependent, but independent of sample concentration. Accurate mass measurements of the [2M+H]+ and [M+H]+ ions, and their MSn product ions, provided the basis for assessing the fragmentation mechanism proposed for [2M+H]+. The fragmentation pathway was also illustrated for the deprotonated molecule [M-H]-.     

Novel design of a pentacyclic scaffold as structural mimic of saframycin A

The design, synthesis and evaluation of a pentacyclic scaffold, CWO-324 to mimic saframycin A is described. CWO-324 is readily synthesized in five steps from 1,4-diacetyl-piperazine-2,5-dione and 2,5-dimethoxybenzaldehyde. CWO-324 was found to scission DNA, binds to bases 69-83(5′-GCAGTCAGG CACCGT-3′) of Hind III/Rsa I from plasmid pBR322 DNA in a foot-printing study and possesses anti-tumor activity.     

A nanofabricated planar aperture as a mimic of the nerve-muscle contact during synaptogenesis

The release of synaptogenic factors by the nerve terminal plays a central role in the aggregation of neurotransmitter receptors at the postsynaptic membrane, a precisely timed and localized process that is essential for the correct formation and functioning of the synapse. This process has been difficult to re-capitulate in cell culture because present cell stimulation methods do not have sufficient spatiotemporal control of the delivery of soluble signals. We cultured myotubes atop nanofabricated planar apertures (2-8 microm diameter) to focally stimulate the muscle cell membrane with neural agrin, a synaptogenic factor released by motor neurons during development. Focal agrin delivery through the apertures after myotube fusion results in local aggregation of acetylcholine receptors (AChRs) in the vicinity of the apertures, a process reminiscent of AChR clustering at innervation sites. Since the apertures are spatially organized in microarrays, multiple experiments can be run in parallel on one device. The technique has wide applicability in cell-cell communication studies and cell-based bioassays.     

A route to dicyanomethylene pyridines and substituted benzonitriles utilizing malononitrile dimer as a precursor

The conditions of the reaction of malononitrile dimer with enaminones and arylidenemalononitrile could be adapted to yield either pyridines or benzene derivatives. A new synthesis of pyrido[1,2-a]pyrimidines from the reaction of malononitrile dimer 1 and 2-phenyl-3-piperidin-1-yl-acrylonitrile (11) is described. Compound 1 condensed with DMFDMA to yield an enaminonitrile that reacted with hydrazine hydrate to yield N',4,6-triamino-2H-pyrazolo[3,4-b]pyridine-5-carboxamidine (17).     

A dual role of phenylboronic acid as a receptor for carbohydrates as well as a quencher for neighboring pyrene fluorophore

A simple amino acid based compound (1) containing a phenyl boronic group and pyrene fluorophore showed an enhanced fluorescence in aqueous solutions at physiological pH through suppression of the photoinduced electron transfer from pyrene to boronic acid on carbohydrate binding. The compound exhibited an interesting fluorescence change depending on pH with decreased emission intensity at acidic pH but enhanced emission intensity at basic pH unlike the fluorescent carbohydrate chemosensors using a PET process with amine and aryl-boronic acid. We have characterized a dual role of phenylboronic acid as a receptor for carbohydrates as well as a quencher for the fluorescence of pyrene fluorophore.     

Photobiological effects of UVA and UVB light in zebrafish embryos: evidence for a competent photorepair system

The consequences of UVB and UVA irradiation on hatch rate, mortality, and malformation were studied in embryonic zebrafish (Danio rerio). The use of zebrafish embryos has expanded from traditional developmental models to diverse studies, including many techniques utilizing light exposure. To characterize useful indicators of photodamage, the responses and threshold limits of UV radiation as a function of embryonic stage and fish source were evaluated. Significant differences in UVB susceptibility were observed in embryos at 3, 6-7, 12, and 24h post-fertilization (hpf), with the 1000-cell stage (3 hpf) having greatest tolerance to UVB. Embryos derived from zebrafish raised in outdoor ponds were more tolerant to UVB than were embryos from laboratory-raised fish. Combinations of UVB and UVA exposure were used to confirm the presence of a competent photorepair system in zebrafish that could return otherwise malformed embryos to a normal phenotype. Overall, embryonic zebrafish had large tolerances (LD(50) of 850 J/cm(2)) to UVA, confirming their suitability for photoactivation and photorepair studies.     

Design and synthesis of a "click" high-mannose oligosaccharide mimic emulating Man8 binding affinity towards Con A

A dendritic "click" mannooligomer mimicking the high-mannose oligosaccharide Man(8) has been designed by replacing some of the inner mannopyranosyl subunits with triazole moieties; evaluation of its binding affinity towards the mannose-specific lectin concanavalin A revealed striking similarities between the "click" mimic and the natural Man(8).     

Novel furanoid alpha-substitued alpha-amino acid as a potent turn mimic in peptide synthesis

A stereoselective approach has been developed to the new sugar amino acid and potential potent turn mimic 5-O-(tert-butyldimethylsilyl)-3-deoxy-1,2-O-isopropylidene-3-methoxycarbonylamino-alpha-D-xylofuranose 3-C-carboxylic acid (12), via the [3,3]-sigmatropic rearrangement of allylic thiocyanates (Z)-6 and (E)-7, prepared from D-xylose. The synthesis of a new dipeptide 13 is also described.     

Triplet excited fluoroquinolones as mediators for thymine cyclobutane dimer formation in DNA

A series of fluoroquinolones (FQs), including enoxacin (ENX), pefloxacin (PFX), norfloxacin (NFX), its N(4')-acetyl derivative (ANFX), ofloxacin (OFX), and rufloxacin (RFX) have been investigated to determine their potential as DNA photosensitizers via thymine cyclobutane dimer (T<>T) formation in DNA. At fluoroquinolone concentrations and light doses insufficient to produce direct single strand breaks, ENX, PFX, and NFX were able to produce T<>T dimers in DNA, revealed by enzymatic treatment with T4 endonuclease V. By contrast, ANFX, OFX, and RFX were inefficient in this assay. The absolute values of the triplet energies of ENX, PFX, NFX, ANFX, OFX, and RFX were estimated by means of laser flash photolysis, using flurbiprofen, 4-biphenylcarboxylic acid, and naproxen as energy acceptors. They were found to be 273, 269, 269, 265, 262, and 253 kJ/mol, respectively. Other triplet excited state properties of the FQs, including quantum yields and lifetimes, were also studied. All the results indicate that the threshold ET value required for a given compound to become a potential DNA photosensitizer via T<>T formation is in the range defined by the triplet energies of NFX and ANFX (265-269 kJ/mol). This provides the basis for an alert rule: any chemical (drugs, cosmetics, pesticides, etc.) with higher ET has to be considered with regard to its potential photogenotoxicity.     

A nanoporous palladium(II) bridged coordination polymer acting as a peroxidase mimic in a method for visual detection of glucose in tear and saliva

A nanoporous coordination polymer (NPCP) was prepared from palladium(II) chloride and 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole and is shown to act as a peroxidase mimetic. It can catalyze the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB) by H₂O₂ which is formed on enzymatic oxidation of glucose by glucose oxidase. Based on these findings, a sensitive glucose test was worked out at 652 nm where the intensity if the greenish-blue product is related to the actual concentration of glucose. Figures of merit include (a) rather low Km value (30 μM) which evidences the strong binding affinity of the NPCP toward glucose, (b) a high v_(max) (8.5 M·s^?1), (c) a 47 nM detection limit, (d) a lifetime of a month, (e) a wide working pH range (2–10), and (f) a 25–80 °C temperature range. The assay was applied to non-invasive determination of glucose assay in tear, saliva where the detection limits are found to be 61 and 91 nM, respectively.

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Graphical abstract DSchematic of the mechanism of the peroxidase like catalytic activity of AHMT-Pd NPCP that was applied in a selective colorimetric method for glucose detection based on TMB oxidation in the presence of enzymatically generated H₂O₂.