Enhancing the catalytic repertoire of nucleic acids: a systematic study of linker length and rigidity

The incorporation of potentially catalytic groups in DNA is of interest for the in vitro selection of novel deoxyribozymes, A series of 10 C5-modified analogues of 2'-deoxyuridine triphosphate have been synthesised that possess side chains of differing flexibility and bearing a primary amino or imidazole functionality, For each series of nucleotide analogues differing degrees of flexibility of the C5 side chain was achieved through the use of alkynyl, alkenyl and alkyl moieties, The imidazole function was conjugated to these CS-amino-modified nucleotides using either imidazole 4-acetic acid or imidazole 4-acrylic acid (urocanic acid), The substrate properties of the nucleotides (fully replacing dTTP) with Taq polymerase during PCR have been investigated in order to evaluate their potential applications for in vitro selection experiments, 5-(3-Aminopropynyl)dUTP and 5-(E-3-aminopropenyl)dUTP and their imidazole 4-acetic acid- and urocanic acid-modified conjugates were found to be substrates, In contrast, C5-amino-modified dUTPs with alkane or Z-alkene linkers and their corresponding conjugates were not substrates, The incorporation of these analogues during PCR has been confirmed by inhibition of restriction enzyme digestion using XbaI and by mass spectrometry of the PCR products.

Reactions to peripheral image motion using a head/eye platform

The authors demonstrate four real-time reactive responses to movement in everyday scenes using an active head/eye platform. They first describe the design and realization of a high-bandwidth four-degree-of-freedom head/eye platform and visual feedback loop for the exploration of motion processing within active vision. The vision system divides processing into two scales and two broad functions. At a coarse, quasi-peripheral scale, detection and segmentation of new motion occurs across the whole image, and at fine scale, tracking of already detected motion takes place within a foveal region. Several simple coarse scale motion sensors which run concurrently at 25 Hz with latencies around 100 ms are detailed. The use of these sensors are discussed to drive the following real-time responses: (1) head/eye saccades to moving regions of interest; (2) a panic response to looming motion; (3) an opto-kinetic response to continuous motion across the image and (4) smooth pursuit of a moving target using motion alone.

Kinetic multi-layer model of gas-particle interactions in aerosols and clouds (KM-GAP): linking condensation, evaporation and chemical reactions of organics, oxidants and water

We present a novel kinetic multi-layer model for gas-particle interactions in aerosols and clouds (KMGAP) that treats explicitly all steps of mass transport and chemical reaction of semi-volatile species partitioning between gas phase, particle surface and particle bulk. KMGAP is based on the PRA model framework (P¨oschl-Rudich- Ammann, 2007), and it includes gas phase diffusion, reversible adsorption, surface reactions, bulk diffusion and reaction, as well as condensation, evaporation and heat transfer. The size change of atmospheric particles and the temporal evolution and spatial profile of the concentration of individual chemical species can be modeled along with gas uptake and accommodation coefficients. Depending on the complexity of the investigated system and the computational constraints, unlimited numbers of semi-volatile species, chemical reactions, and physical processes can be treated, and the model shall help to bridge gaps in the understanding and quantification of multiphase chemistry and microphysics in atmospheric aerosols and clouds. In this study we demonstrate how KM-GAP can be used to analyze, interpret and design experimental investigations of changes in particle size and chemical composition in response to condensation, evaporation, and chemical reaction. For the condensational growth of water droplets, our kinetic model results provide a direct link between laboratory observations and molecular dynamic simulations, confirming that the accommodation coefficient of water at 270K is close to unity (Winkler et al., 2006). Literature data on the evaporation of dioctyl phthalate as a function of particle size and time can be reproduced, and the model results suggest that changes in the experimental conditions like aerosol particle concentration and chamber geometry may influence the evaporation kinetics and can be optimized for efficient probing of specific physical effects and parameters. With regard to oxidative aging of organic aerosol particles, we illustrate how the formation and evaporation of volatile reaction products like nonanal can cause a decrease in the size of oleic acid particles exposed to ozone.

Mononuclear palladium and heterodinuclear palladium–ruthenium complexes of semicarbazone ligands: synthesis, characterization, and application in C–C cross-coupling reactions

Reaction of salicylaldehyde semicarbazone (L-1), 2-hydroxyacetophenone semicarbazone (L-2), and 2-hydroxynaphthaldehyde semicarbazone (L-3) with [Pd(PPh3)(2)Cl-2] in ethanol in the presence of a base (NEt3) affords a family of yellow complexes (1a, 1b and 1c, respectively). In these complexes the semicarbazone ligands are coordinated to palladium in a rather unusual tridentate ONN-mode, and a PPh3 also remains coordinated to the metal center. Crystal structures of the 1b and 1c complexes have been determined, and structure of 1a has been optimized by a DFT method. In these complexes two potential donor sites of the coordinated semicarbazone, viz. the hydrazinic nitrogen and carbonylic oxygen, remain unutilized. Further reaction of these palladium complexes (1a, 1b and 1c) with [Ru(PPh3)(2)(CO)(2)Cl-2] yields a family of orange complexes (2a, 2b and 2c, respectively). In these heterodinuclear (Pd-Ru) complexes, the hydrazinic nitrogen (via dissociation of the N-H proton) and the carbonylic oxygen from the palladium-containing fragment bind to the ruthenium center by displacing a chloride and a carbonyl. Crystal structures of 2a and 2c have been determined, and the structure of 2b has been optimized by a DFT method. All the complexes show characteristic H-1 NMR spectra and, intense absorptions in the visible and ultraviolet region. Cyclic voltammetry on all the complexes shows an irreversible oxidation of the coordinated semicarbazone within 0.86-0.93 V vs. SCE, and an irreversible reduction of the same ligand within -0.96 to -1.14 V vs. SCE. Both the mononuclear (1a, 1b and 1c) and heterodinuclear (2a, 2b and 2c) complexes are found to efficiently catalyze Suzuki, Heck and Sonogashira type C-C coupling reactions utilizing a variety of aryl bromides and aryl chlorides. The Pd-Ru complexes (2a, 2b and 2c) are found to be better catalysts than the Pd complexes (1a, 1b and 1c) for Suzuki and Heck coupling reactions.

Synthesis, structural characterization and catalytic activity of a multifunctional enzyme mimetic oxoperoxovanadium(v) complex

The synthesis and structural characterization of a novel oxoperoxovanadium(v) complex [VO(O-2)(PAH)-(phen)] containing the ligands 2-phenylacetohydroxamic acid (PAHH) and 1,10-phenanthroline (phen) has been accomplished. The oxoperoxovanadium(v) complex was found to mimic both vanadate-dependent haloperoxidase (VHPO) activity as well as nuclease activity through effective interaction with DNA. The complex is the first example of a structurally characterized stable oxoperoxovanadium(v) complex with a coordinated bi-dentate hydroximate moiety (-CONHO-) from 2-phenylacetohydroximate (PAH). The oxoperoxovanadium(v) complex has been used as catalyst for the peroxidative bromination reaction of some unsaturated alcohols (e.g. 4-pentene-1-ol, 1-octene-3-ol and 9-decene-1-ol) in the presence of H2O2 and KBr. The catalytic products have been characterized by GC-MS analysis and spectrophotometric methods. The DNA binding of this complex has been established with CT DNA whereas the DNA cleavage was demonstrated with plasmid DNA. The interactions of the complex with DNA have been monitored by electronic absorption and fluorescence emission spectroscopy. Viscometric measurements suggest that the compound is a DNA intercalator. The nuclease activity of this complex was confirmed by gel electrophoresis studies.

Peroxidative bromination and oxygenation of organic compounds: synthesis, X-ray crystal structure and catalytic implications of mononuclear and binuclear oxovanadium(V) complexes containing Schiffbase ligands

Treatment of of (R,R)-N,N-salicylidene cyclohexane 1,2-diamine(H(2)L(1)) in methanol with aqueous NH(4)VO(3) solution in perchloric acid medium affords the mononuclear oxovanadium(V) complex [VOL(1)(MeOH)]-ClO(4) (1) as deep blue solid while the treatment of same solution of (R,R)-N,N-salicylidene cyclohexane 1,2-diamine(H(2)L(1)) with aqueous solution of VOSO(4) leads to the formation of di-(mu-oxo) bridged vanadium(V) complex [VO(2)L(2)](2) (2) as green solid where HL(2) = (R,R)-N-salicylidene cyclohexane 1,2-diamine. The ligand HL(2) is generated in situ by the hydrolysis of one of the imine bonds of HL(1) ligand during the course of formation of complex [VO(2)L(2)](2) (2). Both the compounds have been characterized by single crystal X-ray diffraction as well as spectroscopic methods. Compounds 1 and 2 are to act as catalyst for the catalytic bromide oxidation and C-H bond oxidation in presence of hydrogen peroxide. The representative substrates 2,4-dimethoxy benzoic acid and para-hydroxy benzoic acids are brominated in presence of H(2)O(2) and KBr in acid medium using the above compounds as catalyst. The complexes are also used as catalyst for C-H bond activation of the representative hydrocarbons toluene, ethylbenzene and cyclohexane where hydrogen peroxide acts as terminal oxidant. The yield percentage and turnover number are also quite good for the above catalytic reaction. The oxidized products of hydrocarbons have been characterized by GC Analysis while the brominated products have been characterized by (1)H NMR spectroscopic studies.

Syntheses, structures and efficient catalysis for C–C coupling of some benzaldehyde thiosemicarbazone complexes of palladium

Reaction of the 4-R-benzaldehyde thiosemicarbazones (denoted in general as L-R; R = OCH(3), CH(3), H, Cl and NO(2)) with trans-[Pd(PPh(3))(2)Cl(2)] afforded a group of mixed-ligand complexes (denoted in general as 1-R) incorporating a N,S-coordinated thiosemicarbazone. a triphenylphosphine and a chloride. Similar reaction with Na(2)[PdCl(4)] afforded a family of bis-thiosemicarbazone complexes (denoted in general as 2-R), where each ligand is N,S-coordinated. Crystal structures of 1-CH(3), 1-NO(2), 2-OCH(3), 2-NO(2) and L-NO(2) have been determined. In all the complexes the thiosemicarbazones are coordinated to the metal center, via dissociation of the acidic proton, as bidentate N,S-donors forming five-membered chelate rings. With reference to the structure of the uncoordinated thiosemicarbazone, this coordination mode is associated with a conformational change around the C=N bond. All the 1-R and 2-R complexes display intense absorptions in the visible region. Catalytic activity of the 1-R and 2-R complexes towards some C-C coupling reactions (e.g. Suzuki, Heck and Sonogashira) has been examined and while both are found to be efficient catalysts, 1-R is much better catalyst than 2-R.

The kinetics of the gas-phase reactions of selected monoterpenes and cyclo-alkenes with ozone and the NO3 radical

The relative rate method has been used to measure the room-temperature rate constants for the gasphase reactions of ozone and NO3 with selected monoterpenes and cyclo-alkenes with structural similarities to monoterpenes. Measurements were carried out at 298 ! 2 K and 760 ! 10 Torr. The following rate constants (in units of 10"18 cm3 molecule"1 s"1) were obtained for the reaction with ozone: methyl cyclohexene (132 ! 17), terpinolene (1290 ! 360), ethylidene cyclohexane (223 ! 57), norbornene (860 ! 240), t-butyl isopropylidene cyclohexane (1500 ! 460), cyclopentene (543 ! 94), cyclohexene (81 ! 18), cyclooctene (451 ! 66), dicyclopentadiene (1460 ! 170) and a-pinene (107 ! 13). For the reaction with NO3 the rate constants obtained (in units of 10"12 cm3 molecule"1 s"1) were: methyl cyclohexene (7.92 ! 0.95), terpinolene (47.9 ! 4.0), ethylidene cyclohexane (4.30 ! 0.24), norbornene (0.266 ! 0.029), cyclohexene (0.540 ! 0.017), cyclooctene (0.513 ! 0.029), dicyclopentadiene (1.20 ! 0.10) and a-pinene (5.17 ! 0.62). Errors are quoted as the root mean square of the statistical error (95% con!dence) and the quoted error in the rate constant for the reference compound. Combining these results with previous studies, new recommendations for the rate constants are presented. Molecular orbital energies were calculated for each alkene and the kinetic data are discussed in terms of the deviation from the structureeactivity relationship obtained from the rate constants for a series of simple alkenes. Lifetimes with respect to key initiators of atmospheric oxidation have been calculated suggesting that the studied reactions play dominant roles in the night-time removal of these compounds from the atmosphere.

A dramatic isotope effect in the reaction of ClSiH with trimethylsilane-1-d: experimental evidence for intermediate complexes in silylene Si-H(D) insertion reactions

A kinetic isotope effect (kD/kH) of 7.4 has been found for the reaction of chlorosilylene with trimethysilane (Me3SiD vs Me3SiH). Such a value can be accounted for by theoretical modelling, but only if an internal rearrangement of the initially form complex is included in the mechanism. This provides the first concrete evidence for such complexes.

High yield production of a soluble bifidobacterial β-galactosidase (BbgIV) inE. coliDH5α with improved catalytic efficiency for the synthesis of prebiotic galactooligosaccharides

The bifidobacterial β-galactosidase (BbgIV) was produced in E. coli DH5α at 37 and 30 °C in a 5 L bioreactor under varied conditions of dissolved oxygen (dO2) and pH. The yield of soluble BbgIV was significantly (P < 0.05) increased once the dO2 dropped to 0–2% and remained at such low values during the exponential phase. Limited dO2 significantly (P < 0.05) increased the plasmid copy number and decreased the cells growth rate. Consequently, the BbgIV yield increased to its maximum (71–75 mg per g dry cell weight), which represented 20–25% of the total soluble proteins in the cells. In addition, the specific activity and catalytic efficiency of BbgIV were significantly (P < 0.05) enhanced under limited dO2 conditions. This was concomitant with a change in the enzyme secondary structure, suggesting a link between the enzyme structure and function. The knowledge generated from this work is very important for producing BbgIV as a biocatalyst for the development of a cost-effective process for the synthesis of prebiotic galactooligosaccharides from lactose.

Preparation and ring-opening reactions of N-diphenylphosphinyl vinyl aziridines

Predominantly (E)-N-diphenylphosphinyl vinyl aziridines are prepared by a reaction of N-diphenylphosphinyl imines with α-bromoallyllithium in the presence of freshly fused ZnCl2. These aziridines undergo a ring-opening reaction with a variety of carbon and heteronucleophiles, in good yield, and generally with good regioselectivity.

Genetic evidence for a predominant role of PI3Kβ catalytic activity in ITAM- and integrin-mediated signaling in platelets.

Phosphatidylinositol 3-kinase (PI3K) isoforms PI3Kbeta and PI3Kgamma are implicated in platelet adhesion, activation, and aggregation, but their relative contribution is still unclear or controversial. Here, we report the first comparative functional analysis of platelets from mice expressing a catalytically inactive form of PI3Kbeta or PI3Kgamma. We demonstrate that both isoforms were similarly required for maximal activation of the small GTPase Rap1b and for complete platelet aggregation upon stimulation of G protein-coupled receptors for adenosine 5'-diphosphate (ADP) or U46619. Their contribution to these events, however, was largely redundant and dispensable. However, PI3Kbeta, but not PI3Kgamma, enzymatic activity was absolutely required for Akt phosphorylation, Rap1 activation, and platelet aggregation downstream of the immunoreceptor tyrosine-based activation motif (ITAM)-bearing receptor glycoprotein VI (GPVI). Moreover, PI3Kbeta was a major essential regulator of platelet adhesion to fibrinogen and of integrin alpha(IIb)beta(3)-mediated spreading. These results provide genetic evidence for a crucial and selective role of PI3Kbeta in signaling through GPVI and integrin alpha(IIb)beta(3).

How reward and emotional stimuli induce different reactions across the menstrual cycle

Despite widespread belief that moods are affected by the menstrual cycle, researchers on emotion and reward have not paid much attention to the menstrual cycle until recently. However, recent research has revealed different reactions to emotional stimuli and to rewarding stimuli across the different phases of the menstrual cycle. The current paper reviews the emerging literature on how ovarian hormone fluctuation during the menstrual cycle modulates reactions to emotional stimuli and to reward. Behavioral and neuroimaging studies in humans suggest that estrogen and progesterone have opposing influences. That is, it appears that estrogen enhances reactions to reward, but progesterone counters the facilitative effects of estrogen and decreases reactions to rewards. In contrast, reactions to emotionally arousing stimuli (particularly negative stimuli) appear to be decreased by estrogen but enhanced by progesterone. Potential factors that can modulate the effects of the ovarian hormones (e.g., an inverse quadratic function of hormones’ effects; the structural changes of the hippocampus across the menstrual cycle) are also discussed.