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Hydrolytic Reaction (hydrolytic + reaction)

Distribution by Scientific Domains

Chemistry	60%
Life Sciences	40%

Selected Abstracts

Hydrolytic Reactions of Thymidine 5,- O -Phenyl- N -Alkylphosphoramidates, Models of Nucleoside 5,-Monophosphate Prodrugs

CHEMISTRY - A EUROPEAN JOURNAL, Issue 30 2007
Mikko Ora Dr.
Abstract To obtain detailed data on the kinetics of hydrolytic reactions of triester-like nucleoside 5,- O -aryl- N -alkylphosphoramidates, potential prodrugs of antiviral nucleoside monophosphates, the hydrolysis of diastereomeric (RP/SP) thymidine 5,-{O -phenyl- N -[(1S)-2-oxo-2-methoxy-1-methylethyl]phosphoramidate} (3), a phosphoramidate derived from the methyl ester of L -alanine, has been followed by reversed-phase HPLC over the range from H0=0 to pH,8 at 90,°C. According to the time-dependent product distributions, the hydrolysis of 3 proceeds at pH<4 by two parallel routes, namely by nucleophilic displacement of the alaninyl ester moiety by a water molecule and by hydrolysis of the carboxylic ester linkage that allows intramolecular attack of the carboxy group on the phosphorus atom, thereby resulting in the departure of either thymidine or phenol without marked accumulation of any intermediates. Both routes represent about half of the overall disappearance of 3. The departure of phenol eventually leads to the formation of thymidine 5,-phosphate. At pH>5, the predominant reaction is hydrolysis of the carboxylic ester linkage followed by intramolecular displacement of a phenoxide ion by the carboxylate ion and hydrolysis of the resulting cyclic mixed anhydride into an acyclic diester-like thymidine 5,-phosphoramidate. The latter product accumulated quantitatively without any indication of further decomposition. Hydroxide-ion-catalyzed POPh bond cleavage of the starting material 3 occurred as a side reaction. Comparative measurements with thymidine 5,-{N -[(1S)-2-oxo-2-methoxy-1-methylethyl]phosphoramidate} (4) revealed that, under acidic conditions, this diester-like compound is hydrolyzed by PN bond cleavage three orders of magnitude more rapidly than the triester-like 3. At pH>5, the stability order is reversed, with 3 being hydrolyzed six times as rapidly as 4. Mechanisms of the partial reactions are discussed. [source]

Visualization of the interaction between archaeal DNA polymerase and uracil-containing DNA by atomic force microscopy

GENES TO CELLS, Issue 1 2006
Yasuo Asami
Deamination of cytosine to uracil is a hydrolytic reaction that is greatly accelerated at high temperatures. The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. Interestingly, B-family DNA polymerases from hyperthermophilic Archaea recognize the presence of uracil in DNA and stall DNA synthesis. To better understand the recognition mechanism, the binding modes of DNA polymerase B1 of Sulfolobus solfataricus (Pol B1) to uracil-containing DNA were examined by gel mobility shift assays and atomic force microscopy. Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency was substantially enhanced by the initiation of DNA synthesis. Analysis by the atomic force microscopy showed a number of double-stranded DNA (dsDNA) in the products of DNA synthesis. The generation of ds DNA was significantly inhibited, however, by the presence of template uracil, and intermediates where monomeric forms of Pol B1 appeared to bind to uracil-containing DNA were observed. These results suggest that Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution, and that single molecules of Pol B1 bind to template uracil and stall DNA synthesis. [source]

Dinuclear Zn(II) catalysts as biomimics of RNA and DNA phosphoryl transfer enzymes: changing the medium from water to alcohol provides enzyme-like rate enhancements

JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 1 2010
R. Stan Brown
Abstract Phosphodiesters are notoriously hydrolytically inert compounds that are demonstrated to have large accelerations of P-OR cleavage promoted by transition and lanthanide metal ions in methanol and ethanol media. This review commentary describes recent findings of how a simple mononuclear and a dinuclear Zn(II) complex promote the cleavage of a series of RNA models and DNA models in alcohol media. The discussion centers on the analysis of the mechanisms of cleavage, energetics of the catalytic process, on recent findings of electrophilic assistance of leaving group departure, and the observation of a rapid hydrolytic reaction of a DNA model promoted by the dinuclear Zn(II) complex in ethanol containing less than 2% water. Copyright © 2009 John Wiley & Sons, Ltd. [source]

Enzymatic Hydrolysis of Waste Office Paper Using Viscosity as Operating Parameter

BIOTECHNOLOGY PROGRESS, Issue 2 2001
Enoch Y. Park
Enzymatic hydrolysis of waste office (WO) paper with feeding WO paper in a reactor was investigated using apparent viscosity as operating parameter. Since the apparent viscosity was correlated with the concentration of pulping WO paper, the amount of hydrolyzed WO paper was assumed by measuring the decrease in the apparent viscosity. Then the amount of hydrolysis WO paper and the amount of enzyme corresponding to the desired ratio were fed into the reactor. When the WO paper and 1% (to the amount of WO paper) enzyme were fed to the hydrolytic reaction, 87 g/L of reducing sugar (RS) with a hydrolytic yield of 42.2% was obtained for a 24-h hydrolysis. However, when nonpulping WO paper and 5% (to the amount of WO paper) enzyme were fed to the hydrolytic reaction, 120 g/L of RS with a hydrolytic yield of 40% was obtained for a 24-h hydrolysis. Therefore, the RS concentration from this hydrolysis process feeding WO paper using apparent viscosity as operating parameter may be of sufficient concentration to serve as a carbon source in microorganism culture or chemical feedstock. [source]