A novel approach to the stereocontrolled synthesis of C-vinyl beta-D-galactopyranosides

Reaction of a lithiated dithiinyl reagent with a O-perbenzylated D-glycono-delta-lactone readily generates the corresponding masked C-vinyl galactosides in high yields and full beta-selectivity. Removal of the sulfur mask renders the free vinyl aglycone with the vinyl group in either the Z or E configuration, depending on the desulfurization conditions chosen.     

Synthesis of dinucleoside boranophosphates by a boranophosphotriester approach

Dinucleoside boranophosphates including four kinds of nucleobases were synthesized by a boranophosphotriester method in good yields. In the present boranophosphotriester method, side-reactions at the nucleobases, which caused by a borane reagent, were completely avoided.     

Stereoselective synthesis of dinucleoside boranophosphates by an oxazaphospholidine method

A stereoselective synthesis of dinucleoside boranophosphates by using nucleoside 3'-oxazaphospholidine derivatives is described. The diastereoselectivity of the internucleotidic bond formation reactions varied with the nucleobase used. (Rp)- and (Sp)-dithymidine boranophosphates were synthesized with excellent diastereoselectivity both in solution and on a solid-support, whereas a loss of diastereopurity was observed for the 2'-deoxycytidine derivative having an unprotected nucleobase amino group. On the other hand, complete chemoselectivity of the 3'-oxazaphospholidine derivatives toward hydroxy groups over amino groups was serendipitously found during the study. This unique chemoselectivity of the 3'-oxazaphospholidine derivatives was investigated by comparing them with the conventional nucleoside 3'-phosphoramidite.     

Pre-activation strategy for oligodeoxyribonucleotide synthesis using triaryloxydichlorophosphoranes in the phosphotriester method.

Triaryloxydichlorophosphoranes were tested as condensing agents for oligodeoxyribonucleotide synthesis in the phosphotriester method. Tris(2,4,6-tribromophenoxy)dichlorophosphorane (BDCP) was found to be a relatively stable crystalline material which could be used as a chemical reagent. A notable feature of the BDCP-promoted condensation reaction was studied by 31P-NMR. A small amount of BDCP compared to the conventional condensing agent was effective for the generation of active nucleotide intermediates and BDCP itself was quantitatively converted into an inert material, tris(2,4,6-tribromophenyl)phosphate (2). Thus, BDCP enabled us to separate the activation step from the condensation process in the phosphotriester method. This preactivation method was applied to the solid-phase synthesis.     

Characterization of oligodeoxyribonucleotide synthesis on glass plates

Achieving high fidelity chemical synthesis on glass plates has become increasingly important, since glass plates are substrates widely used for miniaturized chemical and biochemical reactions and analyses. DNA chips can be directly prepared by synthesizing oligonucleotides on glass plates, but the characterization of these micro-syntheses has been limited by the sub-picomolar amount of material available. Most DNA chip syntheses have been assayed using in situ coupling of fluorescent molecules to the 5′-OH of the synthesized oligonucleotides. We herein report a systematic investigation of oligonucleotide synthesis on glass plates with the reactions carried out in an automated DNA synthesizer using standard phosphoramidite chemistry. The analyses were performed using ³²P gel electrophoresis of the oligonucleotides cleaved from glass plates to provide product distribution profiles according to chain length of oligonucleotides. 5′-Methoxythymidine was used as the chain terminator, which permits assay of coupling reaction yields as a function of chain length growth. The results of this work reveal that a major cause of lower fidelity synthesis on glass plates is particularly inefficient reactions of the various reagents with functional groups close to glass plate surfaces. These problems cannot be detected by previous in situ fluorescence assays. The identification of this origin of low fidelity synthesis on glass plates should help to achieve improved synthesis for high quality oligonucleotide microarrays.     

A novel approach for the solid phase synthesis of DNA-peptide conjugates

The strategy of this study involves automated synthesis of oligonucleotides on a CPG support using standard cyanoethyl phosphoramidite chemistry followed by covalent linkage to peptide fragments bearing a free terminal alpha-amino group and residues with protected side chains. Conjugation was formed through an alkyldiisocyanate linker. Conjugates were isolated by cleavage from the solid support and deprotection in one step.     

A novel approach to solid phase chemical synthesis of oligonucleotide mRNA cap analogs

A novel approach for the synthesis of 5-capped 2'-O-methyloligoribonucleotides on a disulfide-tethered solid support is described. The key step of the synthesis is ZnCl2 promoted coupling of m7GDP imidazolide to a fully deprotected oligonucleotide 5'-phosphate on-support. By this methodology m7G5'pppm2'Apm2'Upm2'Ap has been prepared.     

A novel theoretical approach to the analysis of dendritic transients.

A novel theoretical framework for analyzing dendritic transients is introduced. This approach, called the method of moments, is an extension of Rall's cable theory for dendrites. It provides analytic investigation of voltage attenuation, signal delay, and synchronization problems in passive dendritic trees. In this method, the various moments of a transient signal are used to characterize the properties of the transient. The strength of the signal is measured by the time integral of the signal, its characteristic time is determined by its centroid ("center of gravity"), and the width of the signal is determined by a measure similar to the standard deviation in probability theory. Using these signal properties, the method of moments provides theorems, expressions, and efficient algorithms for analyzing the voltage response in arbitrary passive trees. The method yields new insights into spatiotemporal integration, coincidence detection mechanisms, and the properties of local interactions between synaptic inputs in dendritic trees. The method can also be used for matching dendritic neuron models to experimental data and for the analysis of synaptic inputs recorded experimentally.     

A combinatorial approach to the synthesis of cystine based organogelators.

A solid-phase approach was used to prepare 20 cystine amide derivatives with disulfide bond formation resulting from an intra-site reaction between neighbouring cysteine residues. Library members were screened as potential organogelators in a range of solvent mixtures and resulted in the identification of a potent gelator able to rigidify water/DMSO mixtures at concentrations as low as 1.3 mM.     

Application of allyloxycarbonyl group as a protecting group to oligodeoxyribonucleotide synthesis

The allyloxycarbonyl (AOC) group, known as an efficient amino protective group in solution-phase synthesis of nucleotides, has been used for the first time in solid-phase oligonucleotide synthesis. The efficiency of the new procedure is compared with that of the conventional N-acyl protection.     

A psoralen-conjugated triplex-forming oligodeoxyribonucleotide containing alternating methylphosphonate-phosphodiester linkages: synthesis and interactions with DNA.

A psoralen-conjugated oligodeoxyribopyrimidine (1443), PS-pTTTTCTTTTCTTCTT, where PS is trimethylpsoralen and C is 5-methyl-2'-deoxycytidine, that contains alternating methylphosphonate-phosphodiester internucleotide linkages was synthesized. The ability of 1443 to form triple-stranded complexes with a purine tract in a synthetic DNA duplex was studied. Irradiation of solutions containing the DNA target and 10 microM 1443 or 0.25 microM of a similar psoralen-conjugated oligodeoxyribonucleotide that contained all phosphodiester linkages, (1193), with long-wavelength UV light resulted in approximately 80% formation of interstrand cross-links at pH 7.0, 37 degrees C, in the presence of 20 mM magnesium chloride. The extent of triplex formation as monitored by photo-cross-linking decreased over the pH range 5.5-8.0, and the apparent pK of the 5-methylcytosines (C) in 1443 was approximately one-half of a pH unit less than that of the 5-methylcytosines in 1193. Oligomer 1443 formed triplexes in the absence of magnesium, and maximum triplex formation was observed in solutions containing 2.5 mM magnesium, whereas maximal triplex formation by the fully charged 1193 was not observed until the magnesium concentration was 10 mM or higher. Unlike the all-phosphodiester backbone of 1193, the alternating methylphosphonate-phosphodiester backbone of 1193 is resistant to hydrolysis by exonucleases in fetal calf serum. The nuclease resistance of 1443 and its ability to form triplexes at very low magnesium concentrations suggests that triplex-forming oligomers with alternating methylphosphonate-phosphodiester backbones may be good candidates for use as antigene reagents in cell culture.     

Further optimization of detritylation in solid-phase oligodeoxyribonucleotide synthesis

Various conditions for optimum detritylation (i.e., the removal of 5'-O-trityl protecting groups) during solid-phase synthesis of oligodeoxyribonucleotides were investigated. Di- and tri-chloroacetic acids of variable concentrations were used to study the removal of the 4,4'-dimethoxytrityl (DMTr) group. It was found that the DMTr group could be completely removed under much milder acidic conditions than what are currently used for automated solid-phase synthesis. The 2,7-dimethylpixyl (DMPx) is proposed as an alternative and more readily removable group for the protection of the 5'-OH functions both in solid- and solution-phase synthesis. The improved detritylation conditions are expected to minimize the waste and offer a protocol for incorporation of acid sensitive building-blocks in oligonucleotides.     

A new approach for the synthesis of novel 5-substituted isodeoxyuridine analogs

Cyclic sulfates of carbohydrates provide excellent synthons for the preparation of isodeoxyuridines through direct nucleophilic substitution reactions. These substitution reactions have exceptional regioselectivity. The products of the reactions served as key precursors for the synthesis of 5-substituted isodeoxyuridines via the Stille and Heck coupling reactions. Interestingly, unprotected nucleosides could be used in these metal-mediated functionalizations. The methodologies are general and allow ready access to a variety of C-5 functionalized isomeric deoxyuridines, but also have the potential to be extended to other nucleoside analogs.     

A new approach to the synthesis of efaroxan

Efaroxan was synthetised by cyclisation of the tertiary alcohol 2 which was prepared by the ring opening of the gem-disubstituted epoxide 3 with ortho-metallated fluorobenzene.     

A novel approach to insertional mutagenesis of Haemophilus influenzae.

Insertional mutagenesis of the Haemophilus influenzae chromosome was accomplished by a novel method employing a 2.2-kbp element, TSTE. This element, consisting of the neo gene of Tn5 flanked by Haemophilus-specific uptake sequences, was ligated to circularized chromosomal fragments before transformation into the homologous strain. Eight mutants defective in the production of haemocin were detected. This strategy provides an efficient mechanism for the insertional mutagenesis of H. influenzae.     

A computational approach to the synthesis of dirithromycin

Dirithromycin is a macrolide antibiotic derived from erythromycin A. Dirithromycin is synthesized by the condensation of 9(S)-erythromycylamine with 2-(2-methoxyethoxy)-acetaldehyde. To gain insight into the synthesis, the condensation mechanism has been analyzed computationally by the AM1 method in the gas phase. First, the formation of the Schiff bases of dirithromycin and epidirithromycin from 9(S)-erythromycylamine and 2-(2-methoxyethoxy)-acetaldehyde were modeled. Then, the tautomerization of the Schiff bases to dirithromycin and epidirithromycin were considered. Finally, the epimerization of the Schiff base of epidirithromycin to the Schiff base of dirithromycin was investigated. Our results show that, even though carbinolamine forms faster for epidirithromycin than the corresponding structure for dirithromycin, dirithromycin is the major product of the synthesis. Figure Synthesis of dirithromycin     

A novel approach to the distortion assessment of denture impression trays.

A novel method to treat and interpret distortion of denture impression trays has been proposed. When compared with the conventional method this approach, based on the general least squares principle, offers a significant advantage since the displacement for each individual point can be traced providing more profound insight into the character of the overall deformation itself. The method was applied to study dental impression trays manufactured of self-curing acrylic. The results indicate the existence of a large degree of individuality and non-uniform behaviour of a specific tray material. The method developed here can be applied to specimens of any arbitrary size and shape and it is not limited by the number of the reference points.