The elastic theory of a single DNA molecule

We study the elastic responses of double-(ds) and single-stranded (ss) DNA at external force fields. A double-strand-polymer elastic model is constructed and solved by path integral methods and Monte Carlo simulations to understand the entropic elasticity, cooperative extensibility, and supercoiling property of dsDNA. The good agreement with experiments indicates that short-ranged base-pair stacking interaction is crucial for the stability and the high deformability of dsDNA. Hairpin-coil transition in ssDNA is studied with generating function method. A threshold force is needed to pull the ssDNA hairpin patterns, stabilized by base pairing and base-pair stacking, into random coils. This phase transition is predicted to be of first order for stacking potential higher than some critical level, in accordance with experimental observations.     

生物小分子与铜锌超氧化物歧化酶相互作用的波谱学研究及其应用

本工作以ESR和NMR为主要手段,并结合其它生化方法,考察了氨基酸、核酸碱基、糖等生命基本物质,和抗坏血酸等生命必需物质与钢锌超氧化物歧化酶的相互作用,实验观测到氨基酸、核酸碱基和抗坏血酸在水溶液中可以与酶中的Cu²⁺作用而使其脱离活性部位,以小分子络合物形式游离在溶液中,同时使酶失活,脱离活性部位的Cu²⁺的比例和酶的失活程度取决于小分子配体的加入量及其与Cu²⁺的络合能力。此外,首次尝试使用ESR方法,并借助氨基酸与酶的作用,考察了铜锌超氧化物歧化酶在盐酸胍变性和热变性过程中的构象变化行为,结果表明这一方法是直观而有效的。     

A two-echelon base-stock inventory model with Poisson demand and the sequential processing of orders at the upper echelon

We consider a two-echelon inventory system with a number of non-identical, independent ‘retailers’ at the lower echelon and a single ‘supplier’ at the upper echelon. Each retailer experiences Poisson demand and operates a base stock policy with backorders. The supplier manufactures to order and holds no stock. Orders are produced, in first-come first-served sequence, with a fixed production time. The supplier therefore functions as an M/D/1 queue. We are interested in the performance characteristics (average inventory, average backorder level) at each retailer. By finding the distribution of order lead time and hence the distribution of demand during order lead time, we find the steady state inventory and backorder levels based on the assumption that order lead times are independent of demand during order lead time at a retailer. We also propose two alternative approximation procedures based on assumed forms for the order lead time distribution. Finally we provide a derivation of the steady state inventory and backorder levels which will be exact as long as there is no transportation time on orders between the supplier and retailers. A numerical comparison is made between the exact and approximate measures. We conclude by recommending an approach which is intuitive and computationally straightforward.     

Precise synthesis of porphyrin array scaffolding polyisocyanides

Aryl isocyanides bearing free‐base and metallo‐porphyrins were prepared and polymerized with a Pd–Pt μ‐ethynediyl complex as the initiator to give polymers with narrow polydispersity indices. The molecular weights of the resulting polymers were precisely controlled by the initial feed ratio of the porphyrin monomer to the initiator. The UV–VIS spectra suggested that the porphyrin pendants are regularly arranged to form stacked columns. Metallo‐porphyrin polymers were also prepared by reacting free‐base porphyrin polymers with metal salts. The successive reactions of free‐base and zinc‐porphyrin monomers resulted in the formation of diblock polymers. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 585–595, 2006     

Establishing structure-property correlations and classification of base oils using statistical techniques and artificial neural networks

The present paper describes various classification techniques like cluster analysis, principal component (PC)/factor analysis to classify different types of base stocks. The API classification of base oils (Group I-III) has been compared to a more detailed NMR derived chemical compositional and molecular structural parameters based classification in order to point out the similarities of the base oils in the same group and the differences between the oils placed in different groups. The detailed compositional parameters have been generated using and nuclear magnetic resonance (NMR) spectroscopic methods. Further, oxidation stability, measured in terms of rotating bomb oxidation test (RBOT) life, of non-conventional base stocks and their blends with conventional base stocks, has been quantitatively correlated with their NMR and elemental (sulphur and nitrogen) data with the help of multiple linear regression (MLR) and artificial neural networks (ANN) techniques. The MLR based model developed using NMR and elemental data showed a high correlation between the ‘measured’ and ‘estimated’ RBOT values for both training (R=0.859) and validation (R=0.880) data sets. The ANN based model, developed using fewer number of input variables (only NMR data) also showed high correlation between the ‘measured’ and ‘estimated’ RBOT values for training (R=0.881), validation (R=0.860) and test (R=0.955) data sets.     

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 14

The self‐complementary tetrameric propargyl triols 8, 14, 18 , and 21 were synthesized to investigate the duplex formation of self‐complementary, ethynylene‐linked UUAA, AAUU, UAUA, and AUAU analogues with integrated bases and backbone (ONIBs). The linear synthesis is based on repetitive Sonogashira couplings and C‐desilylations (34–72% yield), starting from the monomeric propargyl alcohols 9 and 15 and the iodinated nucleosides 3, 7, 11 , and 13 . Strongly persistent intramolecular H‐bonds from the propargylic OH groups to N(3) of the adenosine units prevent the gg‐type orientation of the ethynyl groups at C(5′). As such, an orientation is required for the formation of cyclic duplexes, this H‐bond prevents the formation of duplexes connected by all four base pairs. However, the central units of the UAUA and AAUU analogues 18 and 14 associate in CDCl₃/(D₆)DMSO 10 : 1 to form a cyclic duplex characterized by reverse Hoogsteen base pairing. The UUAA tetramer 8 forms a cyclic UU homoduplex, while the AUAU tetramer 21 forms only linear associates. Duplex formation of the O‐silylated UUAA and AAUU tetramers is no longer prevented. The self‐complementary UUAA tetramer 22 forms Watson–Crick‐ and Hoogsteen‐type base‐paired cyclic duplexes more readily than the sequence‐isomeric AAUU tetramer 23 , further illustrating the sequence selectivity of duplex formation.     

Intramolecular dimers: a new design strategy for fluorescence-quenched probes

Fluorogenic probes dual-labeled with reporter and quencher dyes use a change in fluorescence to monitor biochemical events (e.g., substrate binding or enzyme digestion). Such events change the reporter-quencher distance, which affects fluorescence. Recently, it is has been shown that static quenching through intramolecular dimers is an important mechanism that can sometimes be more efficient than F?rster resonance energy transfer (FRET).     

Carbocyclic and nitrogen-containing fused CH-acids with an annelated indenyl fragment. Thermogravimetric and X-ray structural analysis of 6H-indeno[1,2-b]quinoline

Based on thermogravimetric characteristics first obtained for the model 6H-indeno [1,2-b]quinoline, the scheme of thermal conversions of this compound in the temperature range 20–700 °C has been proposed, and the limit of its thermal stability (300 °C) has been determined. This temperature is recommended as the optimum for synthesizing fused benzoaza(diaza)fluorenes. Based on the results of X-ray structural analysis, the molecules of the studied indenoquinoline form centrosymmetric pairs, which are arranged in (110) layers. The molecules are orientationally disordered. The observed self-association of these molecules is similar to the - association of fused heterocyclic systems with-excessive and ****- deficient fragments. It has been suggested that interferon-inducing and antitumor compounds with an annelated indenyl fragment have a common mechanism of action according to the intercalation model of stacking structures.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 703–709, April, 1995.     

Base-labile tert-butoxycarbonyl (Boc) group on phenols

Phenols are deprotected with weak bases from their tert-butoxycarbonyl (Boc) derivatives. Boc deprotection with bases can avoid side reactions during the deprotection with acids. We note the lability of the Boc to bases and are able to utilize it as a new cleavage condition for synthetic studies.