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.     

Blending Baeyer-Villiger monooxygenases: using a robust BVMO as a scaffold for creating chimeric enzymes with novel catalytic properties

The thermostable Baeyer-Villiger monooxygenase (BVMO) phenylacetone monooxygenase (PAMO) is used as a scaffold to introduce novel selectivities from other BVMOs or the metagenome by structure-inspired subdomain exchanges. This yields biocatalysts with new preferences in the oxidation of sulfides and the Baeyer-Villiger oxidation of ketones, all while maintaining most of the original thermostability.     

Fine-tuning of a ferrocene[porphyrin]ITO redox cascade for efficient sequential electron transfer commenced by an S2 photoexcited special-pair mimic

A systematic series of ferrocene/porphyrin redox cascade architectures was assembled through a slipped-cofacial porphyrin dimer on ITO electrode in optimizing the anodic photocurrent generation to perform the highest quantum yield compared to reported values on ITO electrodes.     

A nanocarbon film electrode as a platform for exploring DNA methylation

We describe the quantitative nonlabel electrochemical detection of both cytosine (C) and methylcytosine (mC) in oligonucleotides using newly developed nanocarbon film electrodes. The film consists of nanocrystalline sp2 and sp3 mixed bonds formed by employing the electron cyclotron resonance (ECR) sputtering method. We successfully used this film to develop a simple electrochemical DNA methylation analysis technique based on the measurement of the differences between the oxidation currents of C and mC since our ECR nanocarbon film electrode can directly measure all DNA bases more quantitatively than conventional glassy carbon or boron-doped diamond electrodes. The excellent properties of ECR nanocarbon film electrodes result from the fact that they have a wide potential window while maintaining the high electrode activity needed to oxidize oligonucleotides electrochemically. Proof-of-concept experiments were performed with synthetic oligonucleotides including different numbers of C and mC. This film allowed us to perform both C- and mC-positive assays solely by using the electrochemical oxidation of oligonucleotides without bisulfite or labeling processes.     

DNA as a supramolecular scaffold for the helical arrangement of a stack of 1-ethynylpyrene chromophores

A highly organized helical pi-stacked arrangement of 1-ethynylpyrene moieties along the major groove of duplex DNA can only be achieved if more than three chromophores have been synthetically incorporated adjacent to each other.     

A label-free colorimetric platform for DNA via target-catalyzed hairpin assembly and the peroxidase-like catalytic of graphene/Au-NPs hybrids

A target-catalyzed hairpin assembly (CHA) and graphene/Au-NPs hybrids-based platform has been developed for the determination of DNA. This new sensor not only avoided any labeling but also reduced the background signal. In the absence of target, the assembly of H1 and H2 couldn't be triggered. The catalytic activity of graphene/Au-NPs hybrids was inhibited by adsorption of H1 and H2, leading to the “inactive” hybrids unable to catalyze the oxidation reaction of 3,3′,5,5′-tetramethylbenzidine (TMB). However, with the addition of target DNA, the target-catalyzed hairpin assembly was initiated and produced plenty of H1–H2 duplex, which had a weak binding affinity with the graphene/Au-NPs. Thus, the protected interface of graphene/Au-NPs hybrids became active and catalyzed the oxidation reaction of TMB accompanied with a colorless to-blue color change. This approach exhibited good sensitivity and specificity for target DNA with a detection limit of 5.74 × 10⁻¹¹ M, and realized the assay of target DNA in human serum samples. Besides, this sensor could be further expanded to detect viruses or proteins by adapting the corresponding aptamers, showing great potential in biochemical detections.     

Development of an efficient, regio- and stereoselective route to libraries based on the beta-D-glucose scaffold

The design and execution of an efficient synthetic route for the sequential functionalization of the five hydroxyl substituents of beta-D-glucose has been achieved. This strategy, based on the stereoselective glycosidation of thioglycosides, provides a new approach for the parallel construction of a wide variety of beta-D-glucose analogues and as such holds promise for solid-support library syntheses.     

A simple, efficient, and enantiocontrolled synthesis of a near-structural mimic of platensimycin

A close structural relative of platensimycin was synthesized efficiently in nine steps.     

Copper nitrate/acetic acid as an efficient synergistic catalytic system for the chemoselective tetrahydropyranylation of alcohols and phenols

Abstract  Tetrahydropyranylation of alcohols and phenols was accomplished successfully using copper nitrate and acetic acid as a synergistic catalyst at room temperature under solvent-free condition. Compared with other synergistic catalytic systems, copper nitrate/acetic acid proved to be the most efficient. Both alcohols (primary, secondary, tertiary, benzylic, cyclic, allyl, cinnamyl, and furyl) and phenols reacted smoothly in high yields. Graphical abstract        

Setting the stage for new catalytic functions in designed proteins--exploring the imine pathway in the efficient decarboxylation of oxaloacetate by an Arg-Lys site in a four-helix bundle protein scaffold

Fourteen 42-residue polypeptides have been designed to identify reactive sites for the catalysis of the decarboxylation of oxaloacetate, a chemical transformation that proceeds through the formation of an imine intermediate. The sequences fold into helix-loop-helix motifs and dimerize to four-helix bundles. The catalytically active lysine residues were incorporated in several surface exposed positions, but also in positions characterised by hydrophobic properties to reduce their pKa values. The molecular environments of the Lys residues were systematically varied, to find which residues were able to stabilise and bind the imine intermediate in the decarboxylation reaction. A two-residue Arg-Lys site formed the main component of the reactive site of the helix-loop-helix dimer Decarb-K34_R33, which obeyed saturation kinetics in catalysing the reaction with a kcat/KM of 0.59 M-1S-1. The rate constant measured was nearly three orders of magnitude larger than the second-order rate constant of the butylamine-catalysed reaction (0.0011 M-1S-1), and four orders of magnitude larger than the pseudo first-order rate constant of the uncatalyzed reaction (1.3 x 10(-5) s(-1)). The sequence of Decarb-K34_R33 contained only a single lysine residue. It was flanked by an arginine in the preceding position in the sequence. A flanking Arg residue provided more efficient catalysis than a flanking Lys or Gln residue. Arginines in flanking positions in the helix, in positions four residues before or after the Lys in the sequence, are not as important in catalysis as the Arg of the Arg-Lys pair. The effect of pKa on the catalytic efficiency of the Lys residue in the decarboxylation reaction is well known. The identification of the role of the flanking Arg residue in catalysing decarboxylation, its optimal position, and the importance of conformational stability reported here sets the stage for developing a number of catalytic systems that depend on the formation of imine intermediates, but that lead to different reaction products.     

Self-quenching smart probes as a platform for the detection of sequence-specific UV-induced DNA photodamage

Molecular beacons (MBs) are sensitive probes for many DNA sequence-specific applications, such as DNA damage detection, but suffer from technical and cost limitations. We have designed smart probes with self-quenching properties as an alternative to molecular beacons to monitor sequence-specific UV-induced photodamage of oligonucleotides. These probes have similar stem-loop structural characteristics as molecular beacons, but quenching is achieved instead via photoinduced intramolecular electron transfer by neighboring guanosine residues. Our results indicate that the probes are sensitive enough to detect nanomolar target concentrations and are specific enough to discriminate single-base damage. When the probes were used to monitor UV-induced photodamage in oligonucleotide sequences that differ by a single-base mismatch, the photodamage time constant was higher for the perfectly complementary target sequences than for the mismatch sequences, indicating that these probes are specific for each target sequence. In addition, time constants obtained for oligonucleotide target sequences with both stem and loop base mismatches are lower than those with only loop mismatches, suggesting that these sequences are also specifically distinguished by the smart probes. These probes thus constitute robust, sensitive, specific, and cheaper alternatives to MBs for sequence-specific DNA damage detection.     

A mild and efficient protocol for the conversion of carboxylic acids to olefins by a catalytic decarbonylative elimination reaction

A new method for the conversion of aliphatic carboxylic acids to olefins under unprecedented mild conditions is disclosed, wherein the carboxylic acids are converted in situ with pivalic anhydride to the mixed anhydrides, which regioselectively add to a PdCl(2)-DPE-Phos catalyst. At a temperature of only 110 degrees C, smooth decarbonylation and beta-hydride elimination occur, and the corresponding olefins along with CO, CO(2) and pivalic acid are liberated.     

Cellulose supported ruthenium nanoclusters as an efficient and recyclable catalytic system for benzene hydrogenation under mild conditions

Ruthenium nanoclusters supported on biopolymer cellulose were prepared by chemical reduction technique and characterized by various experimental tools. The cellulose supported Ru catalyst effectively hydrogenates benzene under mild and solvent free conditions. The complete conversion of benzene to cyclohexane was achieved at 70°C and 2.0 MPa partial pressure of H₂ in 1 h. Effect of various parameters such as reaction temperature, H₂ partial pressure, metal loading and catalyst amount on hydrogenation of benzene was studied in detail. The catalyst was recovered from product and reused upto four times without significant loss in its catalytic activity.

     

DNA circuits as amplifiers for the detection of nucleic acids on a paperfluidic platform

This article describes the use of non-enzymatic nucleic acid circuits based on strand exchange reactions to detect target sequences on a paperfluidic platform. The DNA circuits that were implemented include a non-enzymatic amplifier and transduction to a fluorescent reporter; these yield an order of magnitude improvement in detection of an input nucleic acid signal. To further improve signal amplification and detection, we integrated the enzyme-free amplifier with loop-mediated isothermal amplification (LAMP). By bridging the gap between the low concentrations of LAMP amplicons and the limits of fluorescence detection, the non-enzymatic amplifier allowed us to detect as few as 1200 input templates in a paperfluidic format.