Efficient synthesis of functionalized oligodeoxyribonucleotides with base-labile groups using a new silyl linker

In this study, we developed new 3′-terminal deoxyribonucleoside-loading reagents 1 with a new silyl-type linker. These reagents could increase the efficiency of introduction of 3′-terminal deoxyribonucleoside components into polymer supports to a level of 17–29 μmol/g. The efficiency was higher than that of previous T-loading reagents because reagents 1 contain a 4-aminobutyryl residue as a spacer. Moreover, we could synthesize not only unmodified DNA oligomers but also a base-labile modified DNA oligomer using resins 9a–d in the activated phosphite method without base protection.     

New reagents for the introduction of reactive functional groups into chemically synthesized DNA probes

An efficient and versatile preparative approach is described, allowing for the preparation of DNA probes modified with an aldehyde group at the 3'- or 5'-end. The developed synthetic strategy allows for the preparation of a new family of phosphoramidites and solid supports compatible with the automated synthesis of modified oligonucleotide probes. These new reagents were prepared from intermediates 3 and 3a, obtained from the commercially available aleuritic acid 1. It was demonstrated that the new phosphoramidite reagents also could be used as new types of cleavable linkers. A new and efficient method for the production of 5' aldehyde-labeled DNA probes was developed.     

Preparation of arylzinc reagents and their use in the rhodium-catalyzed asymmetric 1,4-addition for the synthesis of 2-aryl-4-piperidones

A protocol for the catalytic asymmetric synthesis of 2-aryl-4-piperidones with high enantiomeric excess (ee) (typically > or = 99% ee) has been described here. The preparation of arylzinc reagents, which are used as nucleophiles in catalysis, is also included. The whole protocol can be completed in 10-20 h, starting from the preparation of the arylzinc reagents, depending on the reaction time of the rhodium-catalyzed process. A detailed protocol is described using the preparation of 4-fluorophenylzinc chloride and its addition to benzyl 3,4-dihydro-4-oxo-1(2H)-pyridinecarboxylate in the presence of [RhCl((R)-binap)]2 as an example.     

A new isoelectric focusing gel for two-dimensional electrophoresis constructed in microporous hollow fiber membranes

We describe the preparation of IEF tube gels inside a nonwetting microporous plastic tubing. The gel in the tube need not be extruded after the first dimension separation. Instead, the porous structure of the tubes is made wettable, and the proteins are electrophoresed "through-the-wall" into the second dimension PAGE gel. Commercial ampholytes and reagents are suitable for the procedure. A useful p/ range of 4.5-9.5 can be obtained when p/ 3-10 ampholyte mixtures are used. Because of the high surface area of the porous material, precautions must be exercised to reduce oxygen inhibition during polymerization and dehydration of the gel during storage and use. A sheath device is described that satisfies these requirements. The plastic tubes can be disposed of by incineration and pose no biohazard.     

Polymer-supported reagents for multi-step organic synthesis: application to the synthesis of sildenafil

Sildenafil 1 (Viagra), a well known and commercially important pharmaceutical drug, has been prepared using polymer-supported reagents in a multi-step, convergent process resulting in a clean and efficient preparation without the need for conventional purification methods.     

New fluorescent hydrazide reagents for the oxidized 3'-terminus of RNA

The synthesis and properties of four new fluorescent reagents capable of forming moderately stable links to the 3′ oxidized end of RNA are reported. All are hydrazide derivatives: pyrene butyric acid hydrazide, proflavine monosemicarbazide, proflavine monosuccinic acid hydrazide, and anthracene-9-carboxaldehyde carbohydrazone. In addition, procedures are given for coupling the bifunctional reagent carbohydrazide to the 3′ end of RNA. These carbohydrazide adducts can easily be coupled in turn to a wide variety of fluorescent reagents having specificity for aliphatic amino groups, including isothiocyanates and sulfonyl halides. Thus a route exists for the preparation of an enormous variety of 3′ fluorescent labeled RNAs. The carbohyrazide adducts are also useful for other synthetic procedures such as preparation of covalent tRNA dimers.     

Synthesis and testing of new modified nucleosides.

New efficient routes for the high-yielding synthesis of several classes of modified nucleosides have been developed. We have prepared both the D- and L-enantiomers of the methylene-expanded oxetanocin isonucleosides 1a-c and the L-2',3'-dideoxy isonucleosides 2abc (both the oxa and thia analogues) as well as new routes for the preparation of L-ribose and 2-deoxy L-ribose 3ab and their modified nucleosides 4.     

Development of a new ultraporous polymer as support in organic synthesis

This paper describes the preparation and post-functionalisation of a new polymeric support based on emulsion-derived foams and called polyHIPEs. The remaining pendant vinylic bonds are easily functionalised by a free radical mechanism. The large pores and channels of this material allow an easy access of the reagent in solution toward the grafted species. PolyHIPE-supported thiol, in the presence of an excess of triethylsilane, showed a good activity and selectivity toward reductive cyclisation of 6-bromohex-1-ene and 1-allyloxy-2-bromobenzene.     

Glycosynthases: new enzymes for oligosaccharide synthesis

The mutation of putative acid/base and nucleophile of the active sites of retaining glycosyl hydrolases, together with kinetic analysis of the mutants, and stereochemical identification of products lead to useful information for the understanding of the reaction mechanism of these enzymes. This was the preliminary and fundamental step toward the preparation of new enzymatic activities called glycosynthases. Direct exploitation of this information has been possible, leading to the design of four new enzymes for oligosaccharides synthesis. The interest for these biocatalysts rises from the fact that the yield of the reaction can be increased and selectivity can be interpreted as key characteristic of the transfer reaction instead of a balance of hydrolytic and transferring pathways followed either by substrates and products. These new biocatalysts possess different specificities and are promising and useful tools in the construction of oligosaccharide molecules of great biological interest. This short review focused the attention on different glycosynthases obtained from four glycosyl hydrolases highlighting on the preparation and development of these new enzymes.     

Multiple oligonucleotide synthesis in tandem on solid-phase supports for small and large scale synthesis

Multiple oligonucleotides linked end-to-end in tandem can be synthesized by adding a nucleoside to the 5'-OH end of a prior sequence. Nucleosides with 3'-succinyl or Q-Linker arms are coupled with HBTU/DMAP. Alternatively, new phosphoramidite reagents with 3'-ester linkages can be used. Hydroxyl or amino supports can also be used as universal starting materials. Treatment with NH4OH cleaves the 3'-ester to yield only 3'-OH groups and no unwanted 3'-phosphorylated products occur.     

Graphite-epoxy composites as a new transducing material for electrochemical genosensing

The use of a rigid carbon-polymer composite material as an electrochemical transducer in hybridisation genosensors is reported. Graphite-epoxy composites (GEC) have an uneven surface where DNA can be adsorbed using a simple dry-adsorption procedure. Single-stranded-DNA binds strongly to GEC in a way that prevents the strands from self-associating, while permitting hybridisation with complementary DNA. Hybridisation has been detected through biotin-streptavidin interaction using a streptavidin conjugated to horseradish peroxidase. Non-specific adsorption onto GEC is almost non-existent even when the surface has not been treated by blocking reagents. The analytical signal obtained was higher when compared with other electrochemical genosensors. Results can be achieved in 150 min, and the detection limit is in the order of fmol. Additionally, surface regeneration is possible using a simple polishing procedure, allowing for multiple use. The new genosensor based on GEC fulfils the requirements desired for these devices: ease of preparation as dry-adsorption of DNA is very simple and easily automated, robustness, sensitivity, low cost of production, ease of miniaturisation and simple use and fast response. Additionally, it can be used for field measurements and can be produced as a genosensor kit. Also, this material can be implemented for screen-printing procedures for the mass production of genosensors. The utility of the genosensor based on GEC is also illustrated with the detection of a sequence related to novel determinant of beta-lactamase resistance in Staphylococcus aureus.     

Two-dimensional parallel array technology as a new approach to automated combinatorial solid-phase organic synthesis

An automated, 96-well parallel array synthesizer for solid-phase organic synthesis has been designed and constructed. The instrument employs a unique reagent array delivery format, in which each reagent utilized has a dedicated plumbing system. An inert atmosphere is maintained during all phases of a synthesis, and temperature can be controlled via a thermal transfer plate which holds the injection molded reaction block. The reaction plate assembly slides in the X-axis direction, while eight nozzle blocks holding the reagent lines slide in the Y-axis direction, allowing for the extremely rapid delivery of any of 64 reagents to 96 wells. In addition, there are six banks of fixed nozzle blocks, which deliver the same reagent or solvent to eight wells at once, for a total of 72 possible reagents. The instrument is controlled by software which allows the straightforward programming of the synthesis of a larger number of compounds. This is accomplished by supplying a general synthetic procedure in the form of a command file, which calls upon certain reagents to be added to specific wells via lookup in a sequence file. The bottle position, flow rate, and concentration of each reagent is stored in a separate reagent table file. To demonstrate the utility of the parallel array synthesizer, a small combinatorial library of hydroxamic acids was prepared in high throughput mode for biological screening. Approximately 1300 compounds were prepared on a 10 μmole scale (3-5 mg) in a few weeks. The resulting crude compounds were generally >80% pure, and were utilized directly for high throughput screening in antibacterial assays. Several active wells were found, and the activity was verified by solution-phase synthesis of analytically pure material, indicating that the system described herein is an efficient means for the parallel synthesis of compounds for lead discovery. Copyright 1998 John Wiley & Sons, Inc.     

A new linkage for solid phase synthesis of oligodeoxyribonucleotides.

An aryl diisocyanate has been used to attach an appropriately protected 2'-deoxyribonucleoside bearing a free 3'-hydroxyl group, to a long chain alkylamine controlled pore glass support via a urethane moiety, in a simple two step procedure. This obviates the need for the preparation and short column chromatographic purification of the 2'-deoxyribonucleoside-3'-O-succinates required for preparation of the widely used succinyl linked supports. The greater stability of the urethane bond compared to an ester bond led to substantially higher yields of oligodeoxyribonucleotides prepared by the solid phase phosphotriester method. More than twenty oligodeoxyribonucleotides have already been synthesized on the glass support bearing the new linkage.     

Dipentafluorophenyl carbonate--a reagent for peptide synthesis

Dipentafluorophenylcarbonate, belonging to transesterifiying reagents, has been prepared and used for the synthesis of pentafluorophenyl esters of amino acids. In contrast to many other reagents of the kind, its preparation is simple, it is highly reactive and at the same time stable upon storage.     

Reagentless detection of DNA sequences on chemically modified electrodes

Microarray analysis requires complex optical instruments and numerous reagents. Several new electrochemical methods for creating sequence-selective microlocations are emerging; such approaches potentially facilitate electrochemical (electronic) readouts of microarrays. These developments parallel the migration of glucose sensing in diabetes monitoring from optical to electrochemical methods. Recent work provides a strategy that minimizes the use of added reagents and potentially produces a reusable sensor that can be applied to continuous monitoring applications.     

Synthesis and evaluation of some new spiro indoline-based heterocycles as potentially active antimicrobial agents

Several new spiro indoline-based heterocycles were synthesized by prior preparation of the 4-(2'-oxo-indol-3'-ylidene)-oxazol-5-one derivatives and subsequent reaction of the produced indol-3-ylidene based heterocycles with activated nitrile reagents. The obtained products were allowed to react with hydrazine hydrate in alcoholic basic to give the target compounds. Structure of these products was confirmed on the bases of elemental as well as spectral data. Representative compounds of the hitherto synthesized products were tested and evaluated as antimicrobial agents.     

Phosphoramidite reagents and solid-phase supports based on hydroxyprolinol for the synthesis of modified oligonucleotides

The synthesis of phosphoramidite reagents and solid-phase supports based on hydroxyprolinol for the introduction of the residues of biotin, lipoic acid, amino groups, and terminal acetylene groups at different positions of the oligonucleotide chain has been described. The efficiency of the reagents and supports has been confirmed by the synthesis of the corresponding modified oligonucleotides.     

One-pot synthesis of new A-ring fused steroidal pyridines

The preparation of pyridine rings fused to the 3,4-positions of the steroid nucleus is herein described. These new pyridine derivatives were prepared in good yields by the reaction of propargylamine with 17beta-hydroxyandrost-4-en-3-one, 17alpha-methyl-17beta-hydroxyandrost-4-en-3-one, 17beta-hydroxyestr-4-en-3-one catalyzed by Cu(II). The structure of 17beta-hydroxy-5-ene-androst-3-eno[3,4-b]pyridine was determined by X-ray analysis.