Direct H atom abstraction from spore photoproduct C-6 initiates DNA repair in the reaction catalyzed by spore photoproduct lyase: evidence for a reversibly generated adenosyl radical intermediate

Spore photoproduct (SP) lyase, which catalyzes the direct reversal of SP (5-thyminyl-5,6-dihydrothymine) to thymine monomers, is the only identified nonphotoactivatable pyrimidine dimer lyase. Unlike DNA photolyase, SP lyase does not contain a flavin cofactor and does not require light for activation. Instead, preliminary studies point to the presence of an iron-sulfur cluster in SP lyase and the requirement for S-adenosylmethionine (AdoMet) for catalytic activity, suggesting that SP lyase belongs to the growing group of iron-sulfur cluster and AdoMet-dependent radical enzymes. Here we provide evidence for the role of AdoMet as a reversible deoxyadenosyl radical generator, which initiates repair by hydrogen atom abstraction from C-6 of SP. Reaction of 6-(3)H-SP, but not methyl-(3)H-SP, with SP lyase and AdoMet results in transfer of (3)H to AdoMet, while no tritiated 5'-deoxyadenosine is observed. When 5'-tritiated AdoMet is used in the reaction with unlabeled SP, transfer of (3)H into the repaired thymine monomers is observed. These results point to the reversible generation of a 5'-deoxyadenosyl radical intermediate, which reacts directly with the DNA lesion to initiate a radical-mediated beta-scission. We also demonstrate that AdoMet is a catalytic cofactor that is not consumed during turnover. Together, these results support a novel radical-based mechanism for the repair of UV-induced DNA damage.     

Characterization of the DNA repair spore photoproduct lyase enzyme from Clostridium acetobutylicum: A radical-SAM enzyme

Spore photoproduct lyase (SPL) is a “Radical-SAM” repair enzyme which catalyzes the cleavage of spore photoproduct (SP, 5-thyminyl-5,6-dihydrothymine), a specific lesion found in bacterial spore DNA, to thymine monomers by a free-radical mechanism. The enzyme requires S-adenosyl-l-methionine (SAM) and a [4Fe–4S] cluster for activity. SPL from Bacillus subtilis has been difficult to isolate and characterize due to problems with the solubility and stability of the overexpressed protein in Escherichia coli and the lability of the [Fe–S] cluster, even if the protein was purified under strictly anaerobic conditions. In order to overcome these problems we searched for another SPL enzyme and we found that the recombinant SPL enzyme from Clostridium acetobutylicum, isolated either aerobically or anaerobically from overexpressing E. coli, behaves more stably than the B. subtilis one. We report here a complete spectroscopic and biochemical characterization of this enzyme. In particular we show for the first time that, using HYSCORE spectroscopy, SAM binds to the cluster as observed in the case of other members of the “Radical-SAM” enzyme family such as the activases of pyruvate formate lyase and ribonucleotide reductase.     

The sugar conformation governs (6-4) photoproduct formation at the dinucleotide level

The LNA dinucleotide mimic of TpT whose two-sugar puckers are locked in the C3'-endo conformation selectively produces the corresponding cyclobutane pyrimidine dimer under 254 nm irradiation. In the natural series (TpT) the sugar puckers are in a major C2'-endo sugar conformation and the (6-4) photoproduct is also produced. Consequently, this study demonstrates that the C2'-endo conformation of the sugar pucker is necessary for (6-4) photoproduct formation.     

Study of mechanism of prins reaction employing the method of labeled molecules

Conclusions The use of radiocarbon to study the Prins reaction in aqueous medium disclosed that it proceeds consecutively with the formation of a 1,3-diol as the intermediate product.Deceased.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1870–1872, August, 1973.     

Probing the reaction mechanism of aristolochene synthase with 12,13-difluorofarnesyl diphosphate

12,13-Difluorofarnesyl diphosphate, prepared using Suzuki-Miyaura chemistry, is a potent inhibitor of aristolochene synthase (AS), indicating that the initial cyclisation during AS catalysis generates germacryl cation in a concerted reaction.     

Rapid incorporation of radiobromine via the reaction of labeled sodium bromide with organoboranes

Organoboranes react with⁸²Br labeled sodium bromide in the presence of chloramine-T to yield the corresponding⁸²Br labeled alkyl and aryl bromides. The reaction is rapid, proceeds under mild conditions, and tolerates a variety of functional groups.     

Unusual nitrogen based heterocycles via allenic intermediates from the reaction of propargyl alcohols with P(III) substrates

The apparently simple reaction of the P(III) precursors [(RNH)P(μ-N-t-Bu)₂PY] (Y=NH-t-Bu, Cl), (OCH₂CMe₂CH₂O)PCl, and Ph₂PCl with functionalized propargyl alcohols is examined. In most cases, the final products are not the expected allenes but several previously unpredicted structural motifs, such as substituted oxazabenzocycloheptenones, indolinones, and fused heterocycles as revealed by X-ray crystallography. Mechanistic aspects of these novel reactions, as well as possible utility and the structural chemistry of the products are also discussed. The P–C or P–N bond cleavage of many of these compounds led to phosphorus-free 2-substituted indoles, quinolinones, and tetrahydroacridine.     

Synthesis of chiral chromium tricarbonyl labeled thymine PNA monomers via the Ugi reaction

[reaction: see text] Ugi condensation was used to synthesize the first examples of chiral racemic Ar.Cr(CO)(3) labeled peptide nucleic acid (PNA) monomers bearing the organometallic moiety linked to the alpha-carbon of the glycine unit.     

Evidence of carbon-carbon bond formation on GaAs(100) via Fischer-Tropsch methylene insertion reaction mechanism

Sequential multiple methylene (CH2) insertions into adsorbed methyl species on clean gallium-rich GaAs(100)-(4 x 1) occurs to form higher alkenes (ethene, propene, butene) and two higher alkyl iodides (iodoethane, iodopropane), not reported for a semiconductor surface previously.     

Probing phosphate ion via the europium(III)-modulated fluorescence of gold nanoclusters

Fluorescent gold nanoclusters (Au-NCs) were synthesized by a one-pot method using 11-mercaptoundecanoic acid as a reducing and capping reagent. It is found that the red fluorescence of the Au-NCs is quenched by the introduction of Eu(III) at pH 7.0, but that fluorescence is restored on addition of phosphate. The Au-NCs were investigated by transmission electron microscopy and fluorescence photographs. The effect of pH on fluorescence was studied in the range from pH 6 to 10 and is found to be strong. Based on these findings, we have developed an assay for phosphate. Ions such as citrate, Fe(CN)₆ ³⁻, SO₄ ²⁻, S₂O₈ ²⁻, Cl⁻, HS⁻, Br⁻, AcO⁻, NO₂ ⁻, SCN⁻, ClO₄ ⁻, HCO₃ ⁻, NO₃ ⁻, Cd²⁺, Ba²⁺, Zn²⁺, Mg²⁺, and glutamate do not interfere, but ascorbate and Fe³⁺ can quench Au-NCs fluorescence. The fluorescent nanocluster probe responds to phosphate in the range from 0.18 to 250 μM, and the detection limit is 180 nM. The probe also responds to pyrophosphate and ATP.

Off/on fluorescence sensor for phosphate based on Eu³⁺-modulated Au NCs thanks to the competition of oxygen-donor atoms from phosphate with those from the carboxylate groups was developed

     

Synthesis of isotopically labeled arachidonic acids to probe the reaction mechanism of prostaglandin H synthase

Prostaglandin H synthase (PGHS) catalyzes the conversion of arachidonic acid to prostaglandin G(2) in the cyclooxygenase reaction. The first step of the mechanism has been proposed to involve abstraction of the pro-S hydrogen atom from C13 to generate a pentadienyl radical spanning C11-C15. We report here the synthesis of six site-specifically deuterated arachidonic acids to investigate the structure of the radical intermediate. The preparation of these compounds was achieved using a divergent scheme that involved one advanced intermediate for all targets. The synthetic design introduced the label late in the routes and allowed the utilization of common synthetic intermediates in the preparation of various targets. Both 13(R)- and 13(S)-deuterium-labeled arachidonic acids were synthesized in high enantiomeric purity as deduced from soybean lipoxygenase assays and mass spectrometric analysis of the resulting enzymatic products. Each synthetic compound was reacted under anaerobic conditions with the wide singlet tyrosyl radical of PGHS-2 to generate a radical intermediate that was analyzed by EPR. Deuterium substitution at positions 11, 13(S), and 15 resulted in the loss of one hyperfine interaction, indicating that the protons at these positions interact with the unpaired electron. Simulation of the spectra was achieved with one set of parameters that are consistent with the assignment of a pentadienyl radical. Use of 16-[(2)H(2)]-arachidonic acid indicated that only one of the protons at C16 gives rise to a strong hyperfine interaction. The findings are discussed in the context of two proposed mechanisms for the cyclooxygenase reaction.     

Probing phosphate ion via the europium(III)-modulated fluorescence of gold nanoclusters

Fluorescent gold nanoclusters (Au-NCs) were synthesized by a one-pot method using 11-mercaptoundecanoic acid as a reducing and capping reagent. It is found that the red fluorescence of the Au-NCs is quenched by the introduction of Eu(III) at pH 7.0, but that fluorescence is restored on addition of phosphate. The Au-NCs were investigated by transmission electron microscopy and fluorescence photographs. The effect of pH on fluorescence was studied in the range from pH 6 to 10 and is found to be strong. Based on these findings, we have developed an assay for phosphate. Ions such as citrate, Fe(CN)₆ ^3?, SO₄ ^2?, S₂O₈ ^2?, Cl^?, HS^?, Br^?, AcO^?, NO₂ ^?, SCN^?, ClO₄ ^?, HCO₃ ^?, NO₃ ^?, Cd²⁺, Ba²⁺, Zn²⁺, Mg²⁺, and glutamate do not interfere, but ascorbate and Fe³⁺ can quench Au-NCs fluorescence. The fluorescent nanocluster probe responds to phosphate in the range from 0.18 to 250 μM, and the detection limit is 180 nM. The probe also responds to pyrophosphate and ATP. Figure

Off/on fluorescence sensor for phosphate based on Eu³⁺-modulated Au NCs thanks to the competition of oxygen-donor atoms from phosphate with those from the carboxylate groups was developed     

Probing the reaction of membrane proteins via infrared spectroscopies,plasmonics, and electrochemistry

Spectroelectrochemistry, in combination with plasmonic approaches and infrared spectroscopy, has emerged as a powerful tool in the study of membrane protein redox reactions, both for immobilized monolayer samples and those reintroduced into their native environment. Here the use of nanostructured electrodes for surface enhanced spectroelectrochemistry are discussed.     

Probing the mechanism of direct Mannich-type alpha-methylenation of ketoesters via electrospray ionization mass spectrometry

Reactions promoting direct Mannich-type alpha-methylenation of alpha, beta and gamma-ketoesters have been monitored via electrospray ionization mass and tandem mass spectrometric experiments. Key intermediates of the catalytical cycle of this synthetically useful reaction have been intercepted and characterized. The mechanistic information provided by electrospray ionization mass spectrometry/mass spectrometry (ESI-MS/MS) guided the optimization of reaction conditions, allowing alpha-methyleneketoesters to be prepared in high yields (80-95%) and in high-enough purity for immediate further manipulation.     

Difficult substrates in the R-hydroxynitrile lyase catalyzed hydrocyanation reaction: application of the mass transfer limitation principle in a two-phase system

The application of a number of new and/or difficult substrates in the catalyzed hydrocyanation reaction by R-hydroxynitrile lyase from almonds is described. By using an aqueous–organic two-phase system and increasing the rate of the enzymatic reaction relative to the mass transfer rate, the enantiomeric purity was improved. By fine tuning the reaction parameters (temperature, pH, and the amount of enzyme) the hydrocyanation reaction was optimized for all substrates. The general principles described here can also be applied to optimize the reaction conditions for other substrates.