Linear Substrates Research Articles

Rationally designed multifunctional supramolecular iminium catalysis: direct vinylogous Michael addition of unmodified linear dienol substrates.

The development of a direct vinylogous Michael addition of linear nucleophilic substrates is a long-standing challenge because of the poor reactivity and the considerable difficulty in controlling regioselectivity. By employing a rationally designed multifunctional supramolecular iminium catalysis strategy, the first direct vinylogous Michael addition of unmodified linear substrates to α,β-unsaturated aldehydes, to afford chiral 1,7-dioxo compounds with good yields and excellent regio- as well as enantioselectivity, has been developed.

Rationally Designed Multifunctional Supramolecular Iminium Catalysis: Direct Vinylogous Michael Addition of Unmodified Linear Dienol Substrates

AbstractThe development of a direct vinylogous Michael addition of linear nucleophilic substrates is a long‐standing challenge because of the poor reactivity and the considerable difficulty in controlling regioselectivity. By employing a rationally designed multifunctional supramolecular iminium catalysis strategy, the first direct vinylogous Michael addition of unmodified linear substrates to α,β‐unsaturated aldehydes, to afford chiral 1,7‐dioxo compounds with good yields and excellent regio‐ as well as enantioselectivity, has been developed.

Assembly, structure, and reactivity of Cu₄S and Cu₃S models for the nitrous oxide reductase active site, Cu(Z)*.

Bridging diphosphine ligands were used to facilitate the assembly of copper clusters with single sulfur atom bridges that model the structure of the Cu(Z)* active site of nitrous oxide reductase. Using bis(diphenylphosphino)amine (dppa), a [Cu(I)4(μ4-S)] cluster with N-H hydrogen bond donors in the secondary coordination sphere was assembled. Solvent and anion guests were found docking to the N-H sites in the solid state and in the solution phase, highlighting a kinetically viable pathway for substrate introduction to the inorganic core. Using bis(dicyclohexylphosphino)methane (dcpm), a [Cu(I)3(μ3-S)] cluster was assembled preferentially. Both complexes exhibited reversible oxidation events in their cyclic voltammograms, making them functionally relevant to the Cu(Z)* active site that is capable of catalyzing a multielectron redox transformation, unlike the previously known [Cu(I)4(μ4-S)] complex from Yam and co-workers supported by bis(diphenylphosphino)methane (dppm). The dppa-supported [Cu(I)4(μ4-S)] cluster reacted with N3(-), a linear triatomic substrate isoelectronic to N2O, in preference to NO2(-), a bent triatomic. This [Cu(I)4(μ4-S)] cluster also bound I(-), a known inhibitor of Cu(Z)*. Consistent with previous observations for nitrous oxide reductase, the tetracopper model complex bound the I(-) inhibitor much more strongly and rapidly than the substrate isoelectronic to N2O, producing unreactive μ3-iodide clusters including a [Cu3(μ3-S)(μ3-I)] complex related to the [Cu4(μ4-S)(μ2-I)] form of the inhibited enzyme.

Cloning and expression of a Baeyer–Villiger monooxygenase oxidizing linear aliphatic ketones from Dietzia sp. D5

A Baeyer–Villiger monooxygenase has been identified in the genome sequence of Dietzia sp. D5. Sequence similarity search revealed that the enzyme belongs to a group of BVMOs that are closely related to ethionamide monooxygenase from Mycobacterium tuberculosis (EthA). The BVMO was expressed in E. coli BL21-CodonPlus(DE3)-RP and the best expression was achieved when the E. coli cells were cultivated in terrific broth (TB) at 15°C and induced with 0.1mM of IPTG. Since the purified enzyme did not show any measurable activity, the substrate scope of the BVMO has been determined using whole-cell and crude cell extract systems. The enzyme was most active towards linear aliphatic substrates. However, it has shown a moderate degree of conversion for cyclobutanone, 2-methylcyclohexanone, bicyclo[3.2.0]hept-2-en-6-one, phenylacetone and thioanisole. There was no detectable conversion of ethionamide, cyclohexanone and acetophenone.

I-OmiI and I-OmiII: Two intron-encoded homing endonucleases within the Ophiostoma minus rns gene

The mitochondrial small subunit ribosomal RNA (rns) gene of the ascomycetous fungus Ophiostoma minus [strain WIN(M)371] was found to contain a group IC2 and a group IIB1 intron at positions mS569 and mS952 respectively. Both introns have open reading frames (ORFs) embedded that encode double motif LAGLIDADG homing endonucleases (I-OmiI and I-OmiII respectively). Codon-optimized versions of I-OmiI and I-OmiII were synthesized for overexpression in Escherichia coli. The in vitro characterization of I-OmiII showed that it is a functional homing endonuclease that cleaves the rns target site two nucleotides upstream (sense strand) of the intron insertion site generating 4 nucleotide 3′ overhangs. The endonuclease activity of I-OmiII was tested using linear and circular substrates and cleavage activity was evaluated at various temperatures. The I-OmiI protein was expressed in E. coli, but purification was difficult, thus the endonuclease activity of this protein was tested via in vivo assays. Overall this study showed that there are many native forms of functional homing endonucleases yet to be discovered among fungal mtDNA genomes.

Highly Versatile Pd–Thioether–Phosphite Catalytic Systems for Asymmetric Allylic Alkylation, Amination, and Etherification Reactions

A Pd-furanoside thioether-phosphite catalytic system that can create new C-C, C-N, and C-O bonds in several substrate types using a wide range of nucleophiles in high yields and enantioselectivities has been identified. Of particular note are the excellent enantioselectivities obtained in the etherification of linear and cyclic substrates. The potential application of the new Pd-thioether-phosphite catalytic systems was also demonstrated by the synthesis of the chiral carbo- and heterocycles.

RF Performance of SOI CMOS Technology on Commercial 200-mm Enhanced Signal Integrity High Resistivity SOI Substrate

RF performance of a 200-mm commercial-enhanced signal integrity high resistivity silicon-on-insulator (eSI HR-SOI) substrate is investigated and compared with its counterpart HR-SOI wafer. By measuring coplanar waveguide lines and substrate crosstalk structures, it is demonstrated that losses are completely suppressed leading to virtually lossless linear substrate. Moreover, a reduction of the second harmonic distortion by more than 25 dB is measured on eSI HR-SOI wafer compared with HR-SOI. Excellent matching between experimental dc and RF characteristics of fully depleted SOI MOSFETs measured on top of HR-SOI and eSI HR-SOI is demonstrated. Furthermore, digital substrate noise is reduced by more than 25 dB on eSI HR-SOI compared with HR-SOI, when injected noise varies from 500 kHz to 50 MHz. The eSI HR-SOI substrate is fully compatible with the CMOS process and could be considered as a promising solution for the RF front-end-modules integration and system-on-chip applications.

Synthesis of arborescent polystyrene‐g‐[poly(2‐vinylpyridine)‐b‐polystyrene] core–shell–corona copolymers

ABSTRACTArborescent copolymers with a core‐shell‐corona (CSC) architecture, incorporating a polystyrene (PS) core, an inner shell of poly(2‐vinylpyridine), P2VP, and a corona of PS chains, were obtained by anionic polymerization and grafting. Living PS‐b‐P2VP‐Li block copolymers serving as side chains were obtained by capping polystyryllithium with 1,1‐diphenylethylene before adding 2‐vinylpyridine. A linear or arborescent (generation G0 – G3) PS substrate, randomly functionalized with acetyl or chloromethyl coupling sites, was then added to the PS‐b‐P2VP‐Li solution for the grafting reaction. The grafting yield and the coupling efficiency observed in the synthesis of the arborescent PS‐g‐(P2VP‐b‐PS) copolymers were much lower than for analogous coupling reactions previously used to synthesize arborescent PS homopolymers and PS‐g‐P2VP copolymers from the same types of coupling sites. It was determined from static and dynamic light scattering analysis that PS‐b‐P2VP formed aggregates in THF, the solvent used for the synthesis. This presumably hindered coupling of the macroanions with the substrate, and explains the low grafting yield and coupling efficiency observed in these reactions. Purification of the crude products was also problematic due to the amphipolar character of the CSC copolymers and the block copolymer contaminant. A new fractionation method by cloud‐point centrifugation was developed to purify copolymers of generations G1 and above. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014, 52, 1075–1085

Strand-specific Recognition of DNA Damages by XPD Provides Insights into Nucleotide Excision Repair Substrate Versatility

Recognition and removal of DNA damages is essential for cellular and organismal viability. Nucleotide excision repair (NER) is the sole mechanism in humans for the repair of carcinogenic UV irradiation-induced photoproducts in the DNA, such as cyclobutane pyrimidine dimers. The broad substrate versatility of NER further includes, among others, various bulky DNA adducts. It has been proposed that the 5'-3' helicase XPD (xeroderma pigmentosum group D) protein plays a decisive role in damage verification. However, despite recent advances such as the identification of a DNA-binding channel and central pore in the protein, through which the DNA is threaded, as well as a dedicated lesion recognition pocket near the pore, the exact process of target site recognition and verification in eukaryotic NER still remained elusive. Our single molecule analysis by atomic force microscopy reveals for the first time that XPD utilizes different recognition strategies to verify structurally diverse lesions. Bulky fluorescein damage is preferentially detected on the translocated strand, whereas the opposite strand preference is observed for a cyclobutane pyrimidine dimer lesion. Both states, however, lead to similar conformational changes in the resulting specific complexes, indicating a merge to a "final" verification state, which may then trigger the recruitment of further NER proteins.

An in vitro one-dimensional assay to study growth factor-regulated tumor cell-macrophage interaction.

Growth factor-dependent pairing and motility between tumor cells and tumor-associated macrophages on extracellular matrix (ECM) fibers of the tumor microenvironment have been shown to enhance intravasation and metastatic spread of breast carcinomas. We describe an in vitro motility assay that combines time-lapse wide-field microscopy and micro-patterned linear adhesive substrates to reconstitute the in vivo behavior between macrophages, tumor cells, and ECM fibers in orthotopic rodent tumor models observed by intravital imaging. Commercially available linear stripes of 650 nm dye-labeled fibronectin microlithographed onto glass cover slips are sequentially plated with fluorescently labeled MTLn3 tumor cells and bone marrow-derived macrophages and time-lapse imaged for up to 8 h. Incubation with pharmacological inhibitors during the assay can identify important paracrine or autocrine signaling pathways involved in the macrophage-tumor cell interaction. This high-resolution motility assay will lead to a more detailed description of immune cell-tumor cell behavior as well as interrogating additional cell types within the tumor microenvironment which use cytokine/growth factor paracrine signaling interactions to facilitate intravasation and metastasis.

Synthesis of Arborescent Polymers by “Click” Grafting

ABSTRACTA novel method was developed for the preparation of arborescent (dendritic graft) polymers, by successive grafting reactions of linear chain segments using alkyne-azide “click” chemistry coupling. A linear polystyrene substrate was thus randomly functionalized with acetylene functionalities, by acetylation and further reaction with propargyl bromide in the presence of potassium hydroxide and 18-crown-6 in toluene. The anionic polymerization of styrene was achieved with 6-tert-butyldimethylsiloxy-hexyllithium to obtain polystyrene with a protected hydroxyl chain end. Deprotection of the hydroxyl group, followed by conversion into tosyl and azide functionalities yielded the material serving as side chains in the grafting reactions. Coupling of the azide-terminated side chains with the acetylene-functionalized substrate in the presence of a Cu(I) catalyst proceeded in up to 93% yield. Additional cycles of substrate functionalization and side chain coupling led to arborescent polymers of generations G1 and G2, with low polydispersity indices (Mw/Mn≈ 1.1), in 60-84% yield. These polymers are characterized by a very compact structure, and molecular weights increasing geometrically over successive generations. A similar methodology was also shown to work for the synthesis of arborescent polybutadiene systems, using azide-functionalized substrates and alkyne-terminated side chains. The coupling reaction proceeded in up to 76% yield under optimized conditions for these systems.

Secretion of circular proteins using sortase.

Circular proteins occur naturally and have been found in microorganisms, plants, and eukaryotes where they are commonly involved in host defense. Properties of circular proteins include enhanced resistance to exoproteases, increased thermostability, longer life spans, and increased activity. Using an enzymatic approach based on the bacterial sortase A (SrtA) transpeptidase, N- and C-termini of conventional linear proteins can be linked resulting in a circular protein. Circularization of bioengineered linear substrate proteins can indeed confer the desirable properties associated with circular proteins. Here, we describe how cells can be manipulated to secrete circularized proteins for substrates of choice via sortase-mediated circularization in the lumen of the endoplasmic reticulum.

High-Speed Imaging/Mapping Spectroscopic Ellipsometry for In-Line Analysis of Roll-to-Roll Thin-Film Photovoltaics

An expanded-beam spectroscopic ellipsometer has been developed and applied toward in situ high-speed imaging/mapping analysis of large area spatial uniformity for multilayer coated substrates in roll-to-roll thin-film photovoltaics (PV). Slower speed instrumentation available in such analyses applies a 1-D detector array for spectroscopic mapping and involves width-wise translation of the ellipsometer optics over the moving coated substrate surface, measuring point-by-point in a time-consuming process. The expanded-beam instrument employs instead a 2-D detector array with no moving optics, exploiting one array index for spectroscopy and the second array index for line imaging across the width of a large area sample. Thus, the instrument enables imaging width-wise and mapping length-wise for uniformity evaluation at the high linear substrate speeds required for real-time, in situ, and online analysis in roll-to-roll thin-film PV. In this investigation, we employ the expanded beam technique to characterize the uniformity of the Ag, ZnO, and n-type hydrogenated amorphous silicon (a-Si:H) layers of an a-Si:H n-i-p structure deposited on a flexible polyimide substrate in the roll-to-roll configuration. Spectroscopic ellipsometry data across a line image were collected as the substrate was translated by a roll-to-roll mechanism. Coated areas as large as 12 cm × 45 cm were analyzed in this study for layer thickness and optical properties by applying the appropriate analytical models for the complex dielectric functions of the Ag, ZnO, and n-type a-Si:H layers.

Dispersion characteristics of surface plasmon polariton modes in a metallic slab waveguide with nonlinear magnetic cladding

We investigate the propagation characteristics of surface plasmon polaritons along a slab waveguide with a nonlinear magnetic cladding characterized by permeability μ =μl+μnlH2 and a linear substrate. The dispersion relation for the surface plasmon polariton modes supported by the structure was derived and numerically solved. The dependance of mode behavior on input power was studied. As the input power increases, the propagation constant of the modes increases. The effect of self focussed peak on the mode confinement near the interface and the resulting propagation characteristics of the plasmon modes were investigated. Increase in metal film thickness lifts the degeneracy of nonlinear plasmon modes supported by the waveguide. It has been observed that the propagation length is not a single valued function of input power which is crucial in understanding optical nano-switches.

Functional characterisation of three members of the Vitis viniferaL. carotenoid cleavage dioxygenase gene family

BackgroundIn plants, carotenoids serve as the precursors to C13-norisoprenoids, a group of apocarotenoid compounds with diverse biological functions. Enzymatic cleavage of carotenoids catalysed by members of the carotenoid cleavage dioxygenase (CCD) family has been shown to produce a number of industrially important volatile flavour and aroma apocarotenoids including β-ionone, geranylacetone, pseudoionone, α-ionone and 3-hydroxy-β-ionone in a range of plant species. Apocarotenoids contribute to the floral and fruity attributes of many wine cultivars and are thereby, at least partly, responsible for the “varietal character”. Despite their importance in grapes and wine; carotenoid cleavage activity has only been described for VvCCD1 and the mechanism(s) and regulation of carotenoid catabolism remains largely unknown.ResultsThree grapevine-derived CCD-encoding genes have been isolated and shown to be functional with unique substrate cleavage capacities. Our results demonstrate that the VvCCD4a and VvCCD4b catalyse the cleavage of both linear and cyclic carotenoid substrates. The expression of VvCCD1, VvCCD4a and VvCCD4b was detected in leaf, flower and throughout berry development. VvCCD1 expression was constitutive, whereas VvCCD4a expression was predominant in leaves and VvCCD4b in berries. A transgenic population with a 12-fold range of VvCCD1 expression exhibited a lack of correlation between VvCCD1 expression and carotenoid substrates and/or apocarotenoid products in leaves, providing proof that the in planta function(s) of VvCCD1 in photosynthetically active tissue is distinct from the in vitro activities demonstrated. The isolation and functional characterisation of VvCCD4a and VvCCD4b identify two additional CCDs that are functional in grapevine.ConclusionsTaken together, our results indicate that the three CCDs are under various levels of control that include gene expression (spatial and temporal), substrate specificity and compartmentalisation that act individually and/or co-ordinately to maintain carotenoid and volatile apocarotenoid levels in plants. Altering the expression of VvCCD1 in a transgenic grapevine population illustrated the divergence between the in vitro enzyme activity and the in planta activity of this enzyme, thereby contributing to the efforts to understand how enzymatic degradation of carotenoids involved in photosynthesis occurs. The identification and functional characterisation of VvCCD4a and VvCCD4b suggest that these enzymes are primarily responsible for catalysing the cleavage of plastidial carotenoids.

Pd(II)-Catalyzed Intramolecular 1,2-Aminoalkylation of Conjugated 1,3-Dienes for the Synthesis of Pyrrolizidines

A palladium(II)-catalyzed tandem cyclization reaction involving an intramolecular 1,2-aminoalkylation of N-4,6-dienyl β-keto amides has been developed. This process provides an efficient method for the rapid assembly of pyrrolizidines starting from linear substrates in moderate to good yields and high to excellent diastereoselectivities.

ChemInform Abstract: Aziridinyl Imines in Organic Synthesis: Development of Tandem Reaction Strategies and Application to Total Synthesis of Natural Products

AbstractReview: 37 refs.

Mutants of phage bIL67 RuvC with enhanced Holliday junction binding selectivity and resolution symmetry

Viral and bacterial Holliday junction resolvases differ in specificity with the former typically being more promiscuous, acting on a variety of branched DNA substrates, while the latter exclusively targets Holliday junctions. We have determined the crystal structure of a RuvC resolvase from bacteriophage bIL67 to help identify features responsible for DNA branch discrimination. Comparisons between phage and bacterial RuvC structures revealed significant differences in the number and position of positively-charged residues in the outer sides of the junction binding cleft. Substitutions were generated in phage RuvC residues implicated in branch recognition and six were found to confer defects in Holliday junction and replication fork cleavage in vivo. Two mutants, R121A and R124A that flank the DNA binding site were purified and exhibited reduced in vitro binding to fork and linear duplex substrates relative to the wild-type, while retaining the ability to bind X junctions. Crucially, these two variants cleaved Holliday junctions with enhanced specificity and symmetry, a feature more akin to cellular RuvC resolvases. Thus, additional positive charges in the phage RuvC binding site apparently stabilize productive interactions with branched structures other than the canonical Holliday junction, a feature advantageous for viral DNA processing but deleterious for their cellular counterparts.

Influence of Allosteric Regulators on Individual Steps in the Reaction Catalyzed by Mycobacterium tuberculosis 2-Hydroxy-3-oxoadipate Synthase

Allosteric regulation often controls key branch points in metabolic processes. Mycobacterium tuberculosis 2-hydroxy-3-oxoadipate synthase (HOAS), a thiamin diphosphate (ThDP)-dependent enzyme, produces 2-hydroxy-3-oxoadipate using 2-ketoglutarate and glyoxylate. The proposed chemical mechanism in analogy with other ThDP-dependent carboligases involves multiple ThDP-bound covalent intermediates. Acetyl coenzyme A is an activator, and GarA, a forkhead association domain-containing protein known to regulate glutamate metabolism, is an allosteric inhibitor of HOAS. Steady state kinetics using assays to study the first half and the full catalytic cycle suggested that the regulators act at different steps in the overall mechanism. To explore the modes of regulation and to test the effects on individual catalytic steps, we performed circular dichroism (CD) studies using a non-decarboxylatable 2-ketoglutarate analog and determined the distribution of ThDP-bound covalent intermediates during the steady state of the HOAS reaction using one-dimensional (1)H gradient carbon heteronuclear single quantum coherence NMR. The results suggest that acetyl coenzyme A acts as a mixed V and K type activator and predominantly affects the predecarboxylation steps. GarA does not inhibit the formation of the predecarboxylation analog and does not affect the accumulation of the postdecarboxylation covalent intermediate derived from 2-ketoglutarate; however, it decreases the abundance of the product ThDP adduct in the HOAS pathway. Thus, the two regulators act on different halves of the catalytic cycle in an unusual regulatory regime.

Poly(ADP-ribose)polymerases are involved in microhomology mediated back-up non-homologous end joining in Arabidopsis thaliana

Besides the KU-dependent classical non-homologous end-joining (C-NHEJ) pathway, an alternative NHEJ pathway first identified in mammalian systems, which is often called the back-up NHEJ (B-NHEJ) pathway, was also found in plants. In mammalian systems PARP was found to be one of the essential components in B-NHEJ. Here we investigated whether PARP1 and PARP2 were also involved in B-NHEJ in Arabidopsis. To this end Arabidopsis parp1, parp2 and parp1parp2 (p1p2) mutants were isolated and functionally characterized. The p1p2 double mutant was crossed with the C-NHEJ ku80 mutant resulting in the parp1parp2ku80 (p1p2k80) triple mutant. As expected, because of their role in single strand break repair (SSBR) and base excision repair (BER), the p1p2 and p1p2k80 mutants were shown to be sensitive to treatment with the DNA damaging agent MMS. End-joining assays in cell-free leaf protein extracts of the different mutants using linear DNA substrates with different ends reflecting a variety of double strand breaks were performed. The results showed that compatible 5'-overhangs were accurately joined in all mutants, that KU80 protected the ends preventing the formation of large deletions and that PARP proteins were involved in microhomology mediated end joining (MMEJ), one of the characteristics of B-NHEJ.