Stabilisation of a nucleic acid three-way junction by an oligonucleotide containing a single 2'-C to 3'-O-phosphate butylene linkage prepared by a tandem RCM-hydrogenation method

A cyclic dinucleotide with a butylene linker between the upper 2'-C position and the 3'-O-phosphate linkage was synthesised from simple nucleoside building blocks via a tandem ring-closing metathesis and hydrogenation procedure. The major of two phosphorus epimers was incorporated into an oligodeoxynucleotide, as well as into an LNA-DNA mixmer oligonucleotide. These were evaluated as parts in three different secondary structures, a duplex, a bulged duplex and a three-way junction, with both DNA and RNA complements. In the DNA:RNA hybrid molecule, the oligodeoxynucleotide containing this single 2'-C to 3'-O-phosphate butylene linkage was found to stabilise a three-way junction.     

A Framework for Characterizing Structural Uncertainty in Large-Eddy Simulation Closures

Motivated by the sizable increase of available computing resources, large-eddy simulation of complex turbulent flow is becoming increasingly popular. The underlying filtering operation of this approach enables to represent only large-scale motions. However, the small-scale fluctuations and their effects on the resolved flow field require additional modeling. As a consequence, the assumptions made in the closure formulations become potential sources of incertitude that can impact the quantities of interest. The objective of this work is to introduce a framework for the systematic estimation of structural uncertainty in large-eddy simulation closures. In particular, the methodology proposed is independent of the initial model form, computationally efficient, and suitable to general flow solvers. The approach is based on introducing controlled perturbations to the turbulent stress tensor in terms of magnitude, shape and orientation, such that propagation of their effects can be assessed. The framework is rigorously described, and physically plausible bounds for the perturbations are proposed. As a means to test its performance, a comprehensive set of numerical experiments are reported for which physical interpretation of the deviations in the quantities of interest are discussed.     

A simple multifunctional valve for flow injection analysis

A simple and versatile pneumatically-operated two-layer rotary valve is described for simultaneous introduction of sample and diversion of analytical streams in flow injection analysis. Examples of application include valve configuration with time-controlled sample volume and with loop-controlled sample volumes in one or two loops; both configurations are useful in routine analyses of samples of highly varying analyte concentrations. The usefulness of the valve for ion-exchange preconcentration procedure is also demostrated.     

Direct Access to Aryl Bis(trifluoromethyl)carbinols from Aryl Bromides or Fluorosulfates: Palladium‐Catalyzed Carbonylation

A palladium‐catalyzed carbonylative approach for the direct conversion of (hetero)aryl bromides into their α,α‐bis(trifluoromethyl)carbinols is described, and it employs only stoichiometric amounts of carbon monoxide and trifluoromethyltrimethylsilane. In addition, aryl fluorosulfates proved highly compatible with these reaction conditions. The method is tolerant of a diverse set of functional groups, and it is adaptable to late‐stage carbon‐isotope labeling.     

Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305

Flp provides a unique opportunity to apply the tools of chemical biology to phosphoryl transfer reactions. Flp and other tyrosine recombinases catalyze site-specific DNA rearrangements via a phosphotyrosine intermediate. Unlike most related enzymes, Flp's nucleophilic tyrosine derives from a different protomer than the remainder of its active site. Because the tyrosine can be supplied exogenously, nonnatural synthetic analogs can be used. Here we examine the catalytic role of Flp's conserved H305. DNA cleavage was studied using a peptide containing either tyrosine (pKa congruent with 10) or 3-fluoro-tyrosine (pKa congruent with 8.4). Religation was studied using DNA substrates with 3'-phospho-cresol (pKa congruent with 10) or 3'-para-nitro-phenol (pKa congruent with 7.1). In both cases, the tyrosine analog with the lower pKa specifically restored the activity of an H305 mutant. These results provide experimental evidence that this conserved histidine functions as a general acid/base catalyst in tyrosine recombinases.     

A tetrathiafulvalene–perylene diimide conjugate prepared via click chemistry

A new tetrathiafulvalene (TTF)–perylene diimide (PDI) conjugate is prepared from an azide-functionalized TTF and an acetylenic PDI employing a Cu(I)-catalyzed Huisgen-Meldal-Sharpless reaction (‘click chemistry’). Thus, the TTF donor and PDI acceptor units are linked together by a 1,2,3-triazole unit. The molecules are found to assemble on a mica surface, forming fibrilar structures.     

Synthesis of hydroxymethyl branched [3.2.0]bicyclic nucleosides using a regioselective oxetane ring-formation

Two [3.2.0]bicyclic nucleosides, 35 and 34, with one and two hydroxymethyl substituents, respectively, have been efficiently synthesized. A protected (3'-C-vinyl-beta-D-allofuranosyl)thymine derivative 28 was easily prepared from diacetone-D-glucose and the thymine moiety was protected with a BOM-group. After the introduction of a leaving group in the 2'-position, the subsequent nucleoside 31 was used as the substrate for a stereoselective dihydroxylation and a regioselective oxetane ring-formation to give after deprotection the bicyclic nucleoside 34. The surprisingly efficient formation of an oxetane was first discovered by serendipity on a corresponding methylfuranoside derivative. The allo-configured bicyclic nucleoside 34 was easily shortened to a ribo-configured analogue 35 by a diol-cleaving reaction and subsequent reduction. Both 34 and 35 are conformationally restricted in the important intermediate 04'-endo conformation.     

A cyclic dinucleotide with a four-carbon 5'-C-to-5'-C connection; synthesis by RCM, NMR-examination and incorporation into secondary nucleic acid structures

A 5'-C-allylthymidine derivative was prepared from thymidine by the application of a stereoselective allylation procedure and its 5'(S)-configuration was confirmed. From this nucleoside derivative, appropriately protected building blocks were prepared and coupled using standard phosphoramidite chemistry to afford a dinucleotide with two 5'-C-allylgroups. This molecule was used as a substrate for a ring-closing metathesis (RCM) reaction and after deprotection, a 1 : 1 mixture of E- and Z-isomers of a cyclic dinucleotide with an unsaturated 5'-C-to-5'-C connection was obtained. Alternatively, a hydrogenation of the double bond and deprotection afforded a saturated cyclic dinucleotide. An advanced NMR-examination confirmed the constitution of this molecule and indicated a restriction in its overall conformational freedom. After variation of the protecting group strategy, a phosphoramidite building block of the saturated cyclic dinucleotide with the 5'-O-position protected as a pixyl ether and the phosphate protected as a methyl phosphotriester was obtained. This building block was used in the preparation of two 14-mer oligonucleotides with a central artificial bend due to the cyclic dinucleotide moiety. These were found to destabilise duplexes, slightly destabilise bulged duplexes but, to some extent, stabilise a three-way junction in high Mg(2+)-concentrations.