Synthesis and RNA-selective hybridization of α-l-ribo- and β-d-lyxo-configured oligonucleotides

Three α-l-ribofuranosyl analogues of RNA nucleotides (α-l-RNA analogues) have been synthesized and incorporated into oligonucleotides using the phosphoramide approach on an automated DNA synthesizer. The 4′-C-hydroxymethyl-α-l-ribofuranosyl thymine monomer was furthermore synthesized. Relative to the unmodified duplexes, incorporation of a single α-l-RNA monomer into a DNA strand leads to reduced thermal stability of duplexes with DNA complements but unchanged thermal stability of duplexes with RNA complements, whereas incorporation of more than one α-l-RNA monomer lead to moderately decreased thermal stability also of duplexes with RNA complements. Efficient hybridization with an RNA complement and no melting transition with a DNA complement were observed with stereoregular chimeric oligonucleotides composed of a mixture of α-l-RNA and affinity enhancing α-l-LNA monomers (α-l-ribo-configured locked nucleic acid). Furthermore, duplexes formed between oligodeoxynucleotides containing an α-l-RNA monomer and complementary RNA were good substrates for Escherichia coli RNase H. RNA-selective hybridization was also achieved by the incorporation of 1-(4-C-hydroxymethyl-β-d-lyxofuranosyl)thymine monomers into a DNA strand, whereas stable duplexes were formed with both complementary DNA and RNA when these monomers were incorporated into an RNA strand.     

Locked and unlocked nucleosides in functional nucleic acids

Nucleic acids are able to adopt a plethora of structures, many of which are of interest in therapeutics, bio- or nanotechnology. However, structural and biochemical stability is a major concern which has been addressed by incorporating a range of modifications and nucleoside derivatives. This review summarizes the use of locked nucleic acid (LNA) and un-locked nucleic acid (UNA) monomers in functional nucleic acids such as aptamers, ribozymes, and DNAzymes.     

Volume and heat capacity of model non-aqueous self-assembly systems

Blends of immiscible polymers are often stabilized by block copolymers which can form non-aqueous micelles and microemulsions in the liquid polymers. The phase diagrans, apparent volumes and apparent heat capacities of model non-aqueous binary and ternary systems were studied in order to investigate the conditions under which such self-assembly systems could form. 1,2-Hexanediol, which can cosolubilize hexane and ethyleneglycol, forms inverse micelles in hexane and weak microaggregates in ethyleneglycol. Genapol X-060, a commercial alcoholic surfactant containing on the average an aliphatic chain of 13 carbons and 6 oxyethylenes (C₁₃E₆), forms microaggregates in poly(ethyleneglycol) 400. These self-assembly systems are strengthen in the presence of a third component which has an affinity for the inner phase.Presented at the Symposium, 76^th CSC Congress, Sherbrooke, Quebec, May 30–June 3, 1993, honoring Professor Donald Patterson on the occasion of his 65^th birthday.     

Voltage-dependent anion channel transports calcium ions through biomimetic membranes

The mitochondrial outer membrane channel (VDAC), a central player in mitochondria and cell death, was reconstituted in polymer-supported phospholipid bilayers. Highly purified VDAC was first reconstituted in vesicles; channel properties and NADH-ferricyanide reductase activity were ascertained before deposition onto solid substrates. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1,2-distearoyl-sn-glycero-3-phosphoethanolamine-poly(ethylene glycol)-N-hydroxysuccinimide mixed vesicles containing VDAC were linked onto amine-grafted surfaces (glass and gold) and disrupted to form a VDAC-containing polymer-tethered planar bilayer. Surface plasmon spectroscopy, fluorescence microscopy, and atomic force microscopy measurements ascertained the membrane thickness, fluidity, and continuity. VDAC reconstituted in bilayers efficiently transported calcium ions and was modulable by two channel blockers, 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid and l-glutamate. The novel setup may allow the study of the assembly of a polyprotein complex centered on VDAC and its role in mitochondrial biology, calcium fluxes, and apoptosis.     

In vitro determination of the release kinetics of peptides and free amino acids during the digestion of food proteins

The kinetics of peptide release during in vitro digestion of 4 protein sources (casein, cod protein, soy protein, and gluten) were investigated. Samples were sequentially hydrolyzed with pepsin (30 min) and pancreatin (2, 4, or 6 h) in a dialysis cell with continuous removal of digestion products. Nondialyzed digests were fractionated by ion-exchange chromatography and ultrafiltration. Animal proteins were digested at a greater rate than plant proteins. Target amino acids of specific enzymes appeared more rapidly in the dialyzed fractions when compared to other amino acids. Throughout the hydrolysis, nondialyzed digests contained a higher proportion of peptide mixtures with basic-neutral properties. Except for gluten, peptide fractions with molecular weights that exceeded 10 kDa (basic-neutral, BN > 10) were rapidly hydrolyzed during the first 2 h of pancreatin digestion. The kinetics of release and the composition of peptide fractions were different when the protein sources were compared. The analysis of amino acids revealed that threonine and proline proportions were relatively high in BN > 10 and in peptide fractions with molecular weight between 10-1 kDa (BN 10-1), while tyrosine, phenylalanine, lysine, and arginine predominated in the low molecular weight (<1 kDa) fractions. More resistant peptides were generally rich in proline and glutamic acid. The role of in vitro digestion assays in dietary protein quality evaluation is discussed.     

On third-order limiter functions for finite volume methods

In this article, we propose a finite volume limiter function for a reconstruction on the three-point stencil. Compared to classical limiter functions in the MUSCL framework, which yield 2^nd-order accuracy, the new limiter is 3^rd-order accurate for smooth solution. In an earlier work, such a 3^rd-order limiter function was proposed and showed successful results [2]. However, it came with unspecified parameters. We close this gap by giving information on these parameters.     

Interfacial tension between low molecular weight polymers from the static analysis of cylindrical drops and their break-up dynamics

A spinning drop tensiometer was used to measure the interfacial tension between the coexisting phases of mixtures of low molecular weight polypropylene glycol, M_w = 1000, and polyethylene glycol, M_w = 300, 400, or 550. Two types of experiments gave concordant interfacial tensions. First, the static analysis of the equilibrium diameter of cylindrical drops according to Vonnegut and, second, Tomotika's dynamic analysis of Rayleigh instabilities caused by a sharp decrease of the angular speed. The end-pinching process also lead to the break-up of the drops and it was characterized by a rapid expansion of the hemispherical ends followed by a slower pinching step. The pinching rate increases as the final angular speed decreases while the growth rate of Rayleigh instabilities shows no definite trends in the range 118-245 rad · s^?1. It is shown that the end-pinching of long cylindrical drops can be analyzed in terms of short fiber retraction to get the interfacial tension. © 1995 John Wiley & Sons, Inc.