NMR Study and Improvement of H-Phosphonate Oligonucleotide Synthesis

Abstract

The mechanism of the internucleotide condensation and side-reactions in H-phosphonate approach has been investigated. The modification of this method allowed to minimize side-reactions during the preactivation of the nucleotidic component has been developed.     

Evaluation of some new condensing reagents for hydrogenphosphonate diester formation

Various pivaloyltetrazoles and chlorophosphates have been investigated as potential condensing reagents for H-phosphonate diester formation. Acylating or phosphorylating properties as well as possible side-reactions triggered by these reagents were checked using TLC and 31P NMR analysis.     

Nucleoside H-Phosphonates. IX. Possible Side-Reactions During Hydrogen Phosphonate Diester Formation

Abstract

Possible side-reactions during hydrogenphosphonate diester formation in the presence of various condensing reagents (e.g. arensulfonyl derivatives, chlorophosphates and acyl chlorides) have been investigated using ³¹P NMR spectroscopy.     

老年色素类荧光物质形成的生化机理

老年色素类荧光物质是人体基本生命过程中多种生化副反应的终产物,其中主要有与脂过氧化相关的通过不饱和羰基化合物与蛋白质交职而形成的荧光物质;有通过糖基化／美拉德反应而形成的糖基化终产物;有多聚烯起源的蓄存在视网膜色素上皮中的老年色素,另外,许多α-β-不饱和醛酮与核苷酸反应也能形成老年色素类生化聚合物,通过对老年色素形成的生化过程的研究发现,羰氨反应导致生物大分子的交联进而形成老年色素的过程是生物体内极为重要的与老化丰关的生物毒化过程。     

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.     

Synthesis of Dinucleoside Boranophosphates by a Boranophosphotriester Approach

Abstract

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.     

Investigation of glycosylating properties of 1-deoxy-1-ethoxysulfonyl-hept-2-ulopyranosyl derivatives. Synthesis of a new sulfonic acid mimetic of the sialyl Lewis X tetrasaccharide

Glycosylation reactions of the ethylthio, bromo and chloro derivatives of 1-deoxy-1-ethoxysulfonyl-hept-2-ulopyranose were studied applying different acceptors under different conditions. Elimination side-reactions affording exo- and endoglycals occured in all cases, however, with different proportions. Glycosyl chloride donor was applied to glycosylate a trisaccharide acceptor obtaining a new sulfonic acid mimetic of the sialyl Lewis X tetrasaccharide in high yield.     

The quinone chemistry of bc complexes

The quinone chemistry that gives rise to the rather unusual strict bifurcation of electron transfer at the Q(o) site of the cytochrome bc complexes remains controversial. In this article, I review recent ideas and propose a "logic-gated" binding mechanism that combines classical quinone electrochemistry with specific hydrogen bonding requirements and results in a reversible reaction that minimizes unwanted side-reactions that could otherwise undermine the efficiency of the Q-cycle proton/electron coupling mechanism.     

A Stochastic Model of Nonenzymatic Nucleic Acid Replication: “Elongators” Sequester Replicators

The origin of nucleic acid template replication is a major unsolved problem in science. A novel stochastic model of nucleic acid chemistry was developed to allow rapid prototyping of chemical experiments designed to discover sufficient conditions for template replication. Experiments using the model brought to attention a robust property of nucleic acid template populations, the tendency for elongation to outcompete replication. Externally imposed denaturation-renaturation cycles did not reverse this tendency. For example, it has been proposed that fast tidal cycling could establish a TCR (tidal chain reaction) analogous to a PCR (polymerase chain reaction) acting on nucleic acid polymers, allowing their self-replication. However, elongating side-reactions that would have been prevented by the polymerase in the PCR still occurred in the simulation of the TCR. The same finding was found with temperature and monomer cycles. We propose that if cycling reactors are to allow template replication, oligonucleotide phenotypes that are capable of favorably altering the flux ratio between replication and elongation, for example, by facilitating sequence-specific cleavage within templates, are necessary; accordingly the minimal replicase ribozyme may have possessed restriction functionality.     

Fmoc-2-mercaptobenzothiazole, for the introduction of the Fmoc moiety free of side-reactions

A double side-reaction, consisting in the formation of Fmoc-beta-Ala-OH and Fmoc-beta-Ala-AA-OH, during the preparation of Fmoc protected amino acids (Fmoc-AA-OH) with Fmoc-OSu is discussed. Furthermore, the new Fmoc-2-MBT reagent is proposed for avoiding these side-reactions as well as the formation of the Fmoc-dipeptides (Fmoc-AA-AA-OH) and even tripeptides, which is another important side-reaction when chloroformates such as Fmoc-Cl is used for the protection of the alpha-amino function of the amino acids.     

Dediazoniation of p-hydroxybenzenediazonium ion in a neutral aqueous medium

The dediazoniation of p-hydroxybenzenediazonium ion (PDQ) in a neutral aqueous medium has been studied under controlled experimental conditions to prevent photochemical and/or heterolytic side-reactions. Oxygen increased the dediazoniation rate of PDQ and caused the appearance of quinone and hydroquinone. An accumulation of quinone deriving from the reduction of PDQ by hydroquinone was also observed. In ESR analyses with different spin traps, the most stable signal was identified as belonging to the adduct of the p-hydroxyphenyl radical, even in the presence of dimethylsulfoxide or ethanol. A general scheme is proposed including three pathways for the homolytic dediazoniation of PDQ. Pathway 1 represents dediazoniation induced by a hydroxyl ion, a slow process at neutral pH and an even slower one with deaerated samples; a favored quinoid structure is put forward to explain these results. In pathway 2, the formation of a semiquinone radical via the reaction of an aryl radical with oxygen is put forward to justify the increase in the dediazoniation rate in the presence of oxygen. In pathway 3, hydroquinone, produced by semiquinone dismutation, may act as a reducing agent.     

ANTABUS IN THE TREATMENT OF ALCOHOLISM IN A PRIVATE GENERAL HOSPITAL

In 35 consecutive cases in which patients were admitted to a private hospital for alcoholism, antabus was contraindicated for eight patients and administered to 27. Sixteen patients, followed three to nine months, cooperated fully with treatment and did not return to use of alcohol. In four cases there was at least one episode of drinking, but the patients continued to cooperate with treatment and attained partial success. In seven cases, including three in which antabus was stopped because of organic disease, treatment was unsuccessful. Insufficient insight and lack of family cooperation accounted for four failures.The presence of cardiovascular or hepatic diseases contraindicates antabus. As the test of reaction to alcohol after antabus has been given is hazardous, continuous supervision by nurse and physician throughout the test reaction is mandatory.Sustained results depend upon psychotherapy, family cooperation, careful follow-up, and control of side-reactions to the drug.Antabus as an antagonist to alcohol is not safe enough to permit general use of the drug.     

TERRAMYCIN IN URINARY TRACT INFECTIONS

Terramycin® is an effective agent in the control of urinary tract infections with organisms of the enteric group.The drug is tolerated by mouth and no serious side-reactions occur. In cases in which there is no organic or obstructive disease, the response to Terramycin as a urinary antiseptic is prompt and effective. In several cases in which there was severe organic and obstructive disease and the organism was highly resistant, the course of the disease was not altered by giving Terramycin.     

A two-intermediate model for imidazole-promoted peroxyoxalate chemiluminescence

A mechanism is proposed for imidazole-catalysed peroxyoxalate chemiluminescence. The reaction model includes a sequential formation of 1-aroxalylimidazole and 1,1′-oxalyldiimidazole as light-producing reaction intermediates. The suggestion is supported by the kinetic data obtained for the reaction of imidazole with bis(4-nitrophenyl) oxalate and on the recently reported ability of 1,1′-oxalyldiimidazole to function as an efficient chemiluminescence reagent. The relative contributions of different catalytic pathways and hydrolytic side-reactions are discussed © 1997 John Wiley & Sons, Ltd.     

The use of 2,3,4,6-tetra-O-benzyl-α-d-glycopyranosyl iodides in α-glycoside synthesis

2,3,4,6-Tetra-O-benzyl-α-d-gluco- and -α-d-galactopyranosyl iodides react rapidly in acetonitrile and other solvents with limited excesses of methanol, ethanol, 2-propanol, and cyclohexanol in the presence of 2,6-lutidine. The products obtained from the lower alcohols, contain a high proportion of α glycoside. The highest ratios of α- to β-anomer are obtained at low concentrations of alcohol. The high rates, stereoselectivity, and lack of side-reactions observed suggest that the alcoholysis of glycosyl iodides should be tested as a route to oligosaccharide synthesis.     

Catalysis and regulation in Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the incorporation of inorganic CO(2) into the organic molecules of life. Rubisco is extremely inefficient as a catalyst and its carboxylase activity is compromised by numerous side-reactions including oxygenation of its sugar phosphate substrate by atmospheric O(2). The reduction in the catalytic efficiency as a result of these processes has implications for crop yield, nitrogen and water usage, and for the global carbon cycle. Several aspects of Rubisco including its complex biosynthesis and multi-step catalytic reaction are subject to tight control involving light, cellular metabolites, and molecular chaperones. Numerous high-resolution crystal structures of different forms of Rubisco are now available, including structures of mutant enzymes. These provide a molecular framework for the understanding of these processes at the molecular level.     

Mechanism and energetics of proton translocation by the respiratory heme-copper oxidases

Recent time-resolved optical and electrometric experiments have provided a sequence of events for the proton-translocating mechanism of cytochrome c oxidase. These data also set limits for the mechanistic, kinetic, and thermodynamic parameters of the proton pump, which are analysed here in some detail. The analysis yields limit values for the pK of the "pump site", its modulation during the proton-pumping process, and suggests its identity in the structure. Special emphasis is made on side-reactions that may short-circuit the pump, and the means by which these may be avoided. We will also discuss the most prominent proton pumping mechanisms proposed to date in relation to these data.     

Contribution of 13C-NMR spectroscopy to the elucidation of pathways of propionate formation and degradation in methanogenic environments

Propionate is an important intermediate in the anaerobic degradation of complex organic matter to methane and carbon dioxide. The metabolism of propionate-forming and propionate-degrading bacteria is reviewed here. Propionate is formed during fermentation of polysaccharides, proteins and fats. The study of the fate of 13C-labelled compounds by nuclear magnetic resonance (NMR) spectroscopy has contributed together with other techniques to the present knowledge of the metabolic routes which lead to propionate formation from these substrates. Since propionate oxidation under methanogenic conditions is thermodynamically difficult, propionate often accumulates when the rates of its formation and degradation are unbalanced. Bacteria which are able to degrade propionate to the methanogenic substrates acetate and hydrogen can only perform this reaction when the methanogens consume acetate and hydrogen efficiently. As a consequence, propionate can only be degraded by obligatory syntrophic consortia of microorganisms. NMR techniques were used to study the degradation of propionate by defined and less defined cultures of these syntrophic consortia. Different types of side-reactions were reported, like the reductive carboxylation to butyrate and the reductive acetylation to higher fatty acids.     

Enhanced in vitro translation at reduced temperatures using a cold-shock RNA motif

Cell-free synthesis of recombinant proteins has emerged as an alternative method of protein production although protein yields still cannot compete with in vivo expression techniques. In systems based on S30 extracts of Escherichia coli unfavorable side-reactions are involved in limiting protein yields. Therefore, carrying out cell-free reactions at lower temperatures might be beneficial as side reactions should be decreased. In this study we show that by using the 5′-untranslated region of the cold-shock gene cspA from E. coli as mRNA leader in cell-free reactions, the expression temperature can be decreased and simultaneously leads to an increase in protein yields. A compensation for the lower activity of T7 RNA polymerase at lower temperatures enhances protein synthesis even further. Additionally, this 5′-untranslated region also standardizes the optimal expression temperature of different proteins.     

Paramolybdate anion-exchange resin, an improved catalyst for the C-1-C-2 rearrangement and 2-epimerization of aldoses

Aqueous solutions of molybdate at 90 degrees bring about the inversion of the C-1-C-2 fragment of aldoses having four or more carbon atoms, generating thermodynamically equilibrated mixtures of the starting aldose and its 2-epimer. In some cases, notably with the aldopentoses, substantial proportions of the 3-epimers are produced, as well as 2-epimers that have not undergone inversion of the C-1-C-2 fragment. These side-reactions can be controlled by using the paramolybdate form of an anion-exchange resin (AG MP-1) together with the formate form of the same resin. The latter acts to scavenge unbound molybdate and paramolybdate anions that appear to be responsible for the side reactions.