Novel photoacid generators for photodirected oligonucleotide synthesis

Photodirected oligonucleotide synthesis uses either direct or indirect light-dependent 5'-deprotection. Both have been reported to give lower stepwise synthetic yields than conventional methods. The deficiency appears to be due to incomplete deprotection at the oligonucleotide 5'-position and, additionally in the case where photodirection is indirect and uses photogenerated photoacid to effect 5'-detritylation, the depurinating effects of strong acid. We have developed novel photosensitive-2-nitrobenzyl esters that on irradiation with near UV light generate alpha-chloro-substituted acetic acids, such as trichloroacetic acid, which are widely and successfully used in conventional solid-phase oligonucleotide synthesis. alpha-Phenyl-4,5-dimethoxy-2-nitrobenzyltrichloroacetate and alpha-phenyl-4,5-dimethoxy-2,6-dinitrobenzyltrichloroacetate showed appropriate photochemical characteristics and were used for photodirected synthesis of a variety of oligonucleotides, including (T)(5), TATAT, TGTGT, (T)(10), (AT)(5), (CT)(5) (GT)(5), and (TGCAT)(2) on a modified Millipore Expedite DNA synthesizer. The outcomes were compared with those obtained by use of directly added trichloroacetic acid (conventional synthesis). The stepwise yields for the two methods were essentially identical.     

The surface characteristics of polycrystalline cobalt electrooxidised in sulfuric acid solutions

The oxidation of cobalt electrodes has been carried out by means of cyclic voltammetry and coulometry under controlled potential in sulfuric acid solutions of different concentrations. The electrochemical scanning tunneling microscope/scanning tunneling microscope (ECSTM/STM) systems constructed by the authors and scanning electron microscopy (SEM) with the SEM-EDX system of surface analysis of the elements have been used. The procedure applied in this work made it possible to observe the fragments of the same surface by means of SEM and ECSTM/STM. The most typical images for a polycrystalline Co electrode with a ±10% accuracy at the scales of 4800 nm × 4800 nm and 100 nm × 100 nm are presented and the results are discussed. In a diluted electrolyte (0.1 M), irregular forms of a stable cobalt oxide with Co:O ratio ∼1:1 appear. Unreproducible results have been obtained in a 1.0 M H₂SO₄ solution. Compact and relatively regular layers of cobalt oxide of the same ratio have been obtained in 0.1 M H₂SO₄, as well as in 10.0 M sulfuric acid solution, under controlled oxidation potential at the passivation range. Received: 6 January 1999 / Accepted: 5 May 1999     

Chlorella virus pyrimidine dimer glycosylase excises ultraviolet radiation- and hydroxyl radical-induced products 4,6-diamino-5-formamidopyrimidine and 2,6-diamino-4-hydroxy-5-formamidopyrimidine from DNA

A DNA glycosylase specific for UV radiation-induced pyrimidine dimers has been identified from the Chlorella virus Paramecium Bursaria Chlorella virus-1. This enzyme (Chlorella virus pyrimidine dimer glycosylase [cv-pdg]) exhibits a 41% amino acid identity with endonuclease V from bacteriophage T4 (T4 pyrimidine dimer glycosylase [T4-pdg]), which is also specific for pyrimidine dimers. However, cv-pdg possesses a higher catalytic efficiency and broader substrate specificity than T4-pdg. The latter excises 4,6-diamino-5-formamidopyrimidine (FapyAde), a UV radiation- and hydroxyl radical-induced monomeric product of adenine in DNA. Using gas chromatography-isotope-dilution mass spectrometry and y-irradiated DNA, we show in this work that cv-pdg also displays a catalytic activity for excision of FapyAde and, in addition, it excises 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua). Kinetic data show that FapyAde is a better substrate for cv-pdg than FapyGua. On the other hand, cv-pdg possesses a greater efficiency for the extension of FapyAde than T4-pdg. These two enzymes exhibit different substrate specificities despite substantial structural similarities.     

1,3-Dipolar cycloaddition-decarboxylation reactions of an azomethine ylide with isatoic anhydrides: formation of novel benzodiazepinones

A nonstabilized azomethine ylide reacts with a wide range of substituted isatoic anhydrides to afford novel 1,3-benzodiazepin-5-one derivatives, which are generally isolated in high yield. The transformations involve 1,3-dipolar cycloaddition reactions of the ylide with the anhydrides to give transient, and in a representative case spectroscopically observable, oxazolidine intermediates that undergo ring-opening-decarboxylation-ring-closing reaction cascades to yield the 1,3-benzodiazepin-5-one products.     

Co2+/Co+ redox tuning in methyltransferases induced by a conformational change at the axial ligand

Density functional theory and quantum mechanics/molecular mechanics computations predict cob(I)alamin (Co(+)Cbx), a universal B(12) intermediate state, to be a pentacoordinated square pyramidal complex, which is different from the most widely accepted viewpoint of its tetracoordinated square planar geometry. The square pyramidality of Co(+)Cbx is inspired by the fact that a Co(+) ion, which has a dominant d(8) electronic configuration, forms a distinctive Co(+)--H interaction because of the availability of appropriately oriented filled d orbitals. This uniquely H-bonded Co(+)Cbx may have catalytic relevance in the context of thermodynamically uphill Co(2+)/Co(+) reduction that constitutes an essential component in a large variety of methyltransferases.     

Queues with Dropping Functions and Autocorrelated Arrivals

We present an analysis of the queueing system in which arriving jobs are dropped with probability depending on the queue size. The arrivals are assumed to be autocorrelated and they are modeled by the Markov-modulated Poisson process. Both transient and stationary distributions of the queue size, as well as the system loss ratio and throughput are obtained. The analytical results are accompanied with numerical examples based on the autocorrelated traffic recorded in an IP computer network.     

Non-rigid parabolic geometries of Monge type

In this paper we study a novel class of parabolic geometries which we call parabolic geometries of Monge type. These parabolic geometries are defined by gradings such that their −1 component contains a nonzero co-dimension 1 abelian subspace whose bracket with its complement is non-degenerate. We completely classify the simple Lie algebras with such gradings in terms of elementary properties of the defining set of simple roots. In addition we characterize those parabolic geometries of Monge type which are non-rigid in the sense that they have nonzero harmonic curvatures in positive weights. Standard models of all non-rigid parabolic geometries of Monge type are described by under-determined ODE systems. The full symmetry algebras for these under-determined ODE systems are explicitly calculated; surprisingly, these symmetries are all just prolonged point symmetries.     

An algorithm for the enumeration of spanning trees

Enumeration of spanning trees of an undirected graph is one of the graph problems that has received much attention in the literature. In this paper a new enumeration algorithm based on the idea of contractions of the graph is presented. The worst-case time complexity of the algorithm isO(n+m+nt) wheren is the number of vertices,m the number of edges, andt the number of spanning trees in the graph. The worst-case space complexity of the algorithm isO(n ²). Computational analysis indicates that the algorithm requires less computation time than any other of the previously best-known algorithms.     

Generalized steiner problem in series-parallel networks

The generalized Steiner problem (GSP) is concerned with the determination of a minimum cost subnetwork of a given network where some (not necessarily all) vertices satisfy certain pairwise (vertex or edge) connectivity requirements. The GSP has applications to the design of water and electricity supply networks, communication networks and other large-scale systems where connectivity requirements ensure the communication between the selected vertices when some vertices and/or edges can become inoperational due to scheduled maintenance, error, or overload. The GSP is known to be NP-complete. In this paper we show that if the subnetwork is required to be respectively biconnected and edge-biconnected, and the underlying network is series-parallel, both problems can be solved in linear time.     

Enhancement of oxygen reduction at Co-porphyrin catalyst by supporting onto hybrid multi-layered film of polypyrrole and polyoxometalate-modified gold nanoparticles

Three-dimensional multi-layered films (on glassy carbon) composed of networks of polyoxometallate (PMo₁₂O₄₀ ³⁻)-modified gold nanoparticles linked together through the alternately deposited ultra-thin layers of polypyrrole have served as active supports for Co-porphyrin catalytic centers. The hybrid organic-inorganic films (supports) have been prepared by using the layer-by-layer approach. The fact that polyanionic (phosphomolybdate) adsorbates on gold nanoparticles are attracted by positively charged sites of conducting polymer (polypyrrole) structures leads to the stabilizing effect and facilitates distribution of Au nanostructures. The systems have been characterized using scanning electron microscopy, as well as with chronoamperometric and voltammetric techniques. By supporting Co-porphyrin centers onto the hybrid film of the polymer-linked phosphomolybdate-stabilized gold nanoparticles, significant electrocatalytic enhancement effects (namely voltammetric current increases) have been observed during the electroreduction of oxygen in acid medium relative to a standard response of the simple porphyrin deposit on glassy carbon measured under analogous conditions. Among important issues is the high activity of the hybrid film (support) itself toward the reductive decomposition of hydrogen peroxide to water. When it comes to performance of the Co-porphyrin-containing system, it is reasonable to expect that the O₂ reduction process is initiated at Co-porphyrin catalytic sites (two-electron reduction to H₂O₂) and continued (two-electron reduction to H₂O) at the hybrid film containing gold nanoparticles dispersed within the highly porous cauliflower-like structures of polypyrrole multi-layers. While the gold networks facilitate charge distribution within the hybrid electrocatalytic film, non-covalent π-π interactions of porphyrin rings with polypyrrole interlayers and charge transfers between negatively charged (PMo₁₂O₄₀ ³⁻ modified) gold nanoparticles and positively charged nitrogen sites of polypyrrole could also cause synergism.