Synthesis and characteristics of modified DNA fragments containing thymidine glycol residues

Chemical synthesis of a series of modified oligodeoxyribonucleotides containing one or two residues of thymidine glycol (5,6-dihydro-5,6-dihydroxythymidine), the main product of oxidative DNA damage, is described. The thermal stability of DNA duplexes containing thymidine glycol residues was studied using UV spectroscopy. Introduction of even one thymidine glycol residue into the duplex structure was shown to result in its significant destabilization. Data on the interaction of DNA methyltransferases and type II restriction endonucleases with DNA ligands containing oxidized thymine were obtained for the first time. Introduction of a thymidine glycol residue in the central degenerate position of the recognition site of restriction endonuclease SsoII was found to result in an increase in the initial hydrolysis rate of the modified duplex in comparison with that of unmodified structure. The affinity of C5-cytosine methyltransferase SsoII for the DNA duplex bearing thymidine glycol was found to be twofold higher than for the unmodified substrate. However, such a modification of the DNA ligand prevents its methylation.     

Synthesis and characteristics of modified DNA fragments containing thymidine glycol residues

Chemical synthesis of a series of modified oligodeoxyribonucleotides containing one or two residues of thymidine glycol (5,6-dihydro-5,6-dihydroxythymidine), the main product of oxidative DNA damage, is described. The thermal stability of DNA duplexes containing thymidine glycol residues was studied using UV spectroscopy. Introduction of even one thymidine glycol residue into the duplex structure was shown to result in its significant destabilization. Data on the interaction of DNA methyltransferases and type II restriction endonucleases with DNA ligands containing oxidized thymine were obtained for the first time. Introduction of a thymidine glycol residue into the central degenerate position of the recognition site of restriction endonuclease SsoII was found to result in an increase in the initial hydrolysis rate of the modified duplex in comparison with that of the unmodified structure. The affinity of C5-cytosine methyltransferase SsoII for the DNA duplex bearing thymidine glycol was found to be twofold higher than for the unmodified substrate. However, such a modification of the DNA ligand prevents its methylation. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http://www.maik.ru.     

Synthesis and immunomodulating activity of new glycopeptides of glycyrrhizic acid containing residues of L-glutamic acid

New glycopeptides of glycyrrhizic acid (GA) containing Glu residues and their alpha-methyl esters, gamma-methyl esters, and alpha,gamma-dimethyl esters were synthesized using N,N'-dicyclohexylcarbodiimide in the presence of N-hydroxybenzotriazole or N-hydroxysuccinimide. Formation of amide bonds was observed on all the three COOH groups of GA, or selectively on the COOH groups of the GA carbohydrate part in dependence on the ratio of reagents and the reaction conditions. The GA glycopeptide with three residues of Glu(OH)-OMe at a dose of 2 mg/kg stimulated the production of antibody-forming cells in mouse spleen in comparison with the control. The GA glycopeptide containing Glu residues only in the GA carbohydrate part turned out to be an immunosuppressor. The glycopeptide of the 30-methyl ester of GA with residues of free Glu in its carbohydrate part increased the hemagglutinine titer at oral doses of 2 and 10 mg/kg. All the studied compounds had practically no effect on the delayed-type hypersensitivity in mice.     

Synthesis and immunomodulating activity of new glycopeptides of glycyrrhizic acid containing residues of L-glutamic acid

New glycopeptides of glycyrrhizic acid (GA) containing Glu residues and their α-methyl esters, γ-methyl esters, and α,γ-dimethyl esters were synthesized using N,N′-dicyclohexylcarbodiimide in the presence of N-hydroxybenzotriazole or N-hydroxysuccinimide. Formation of amide bonds was observed on all the three COOH groups of GA, or selectively on the COOH groups of the GA carbohydrate part in dependence on the ratio of reagents and the reaction conditions. The GA glycopeptide with three residues of Glu(OH)-OMe at a dose of 2 mg/kg stimulated the production of antibody-forming cells in mouse spleen in comparison with the control. The GA glycopeptide containing Glu residues only in the GA carbohydrate part turned out to be an immunosuppressor. The glycopeptide of the 30-methyl ester of GA with residues of free Glu in its carbohydrate part increased the hemagglutinine titer at oral doses of 2 and 10 mg/kg. All the studied compounds had practically no effect on the delayed-type hypersensitivity in mice.     

Isolation from a softwood xylan of oligosaccharides containing two 4-O-methyl-d-glucuronic acid residues

Partial hydrolysis of a larch arabino(4-O-methylglucurono)xylan afforded two series of oligouronides composed of 4-O-methyl- d-glucuronic acid and d-xylose residues. The first series included aldouronic acids up to the aldopentaouronic acid. Methylation analysis indicated that the aldopentao- and aldotetrao-uronic acids were mixtures of isomers. One aldotetraouronic acid was isolated and identified as O-β-d-Xylp-(1 → 4)-O-β-d-Xylp-(1 → 4)-O-(4-O-Me-α-d-GlcAp)-(1 → 2)-d-Xyl. The two isomeric aldotriouronic acids were separated from each other. The acids of the second series, which were composed of two uronic acids and 2-4 d-xylose residues, were identified as follows: O-β-d-Xylp-(1 → 4)-O-(4-O-Me-α-d-GlcAp)-(1 → 2)-O-β-d-Xylp-(1 → 4)-O(4-O-Me-α-d-GlcAp)-(1 → 2)-O-β-d-Xylp-(1 → 4)-d-Xyl, O-(4-O-Me-α-d-GlcAp)-(1 → 2)-O-β-d-Xylp-(1 → 4)-O-(4-O-Me-α-d-GlcAp)-(1 → 2)-O-β-d-Xylp-(1 → 4)-O-β-d -Xylp-(1 → 4)-D-Xyl, O-(4-O-Me-α-d-GlcAp)-(1 → 2)-O-β-d-Xylp-(1 → 4)-O-(4-O-Mec-α-d-GlcAp)-(1 → 2)-O-β-d-Xylp-(1 → 4)-D-Xyl, and O-(4-O-Me-α-d-GlcAp)-(1 → 2)-O-β-d-Xylp-(1 → 4)-O-(4-O-Me-α-d-GlcAp)-(1 → 2)-D-Xyl. The first three compounds were new acidic oligosaccharides. The 4-O-methyl-d-glucuronic acid in the second series was present in a larger proportion than in the first series, indicating that a large proportion of the uronic acid side-chains were located on two contiguous D-xylose residues in the backbone of the softwood xylan.     

Alkylation of deoxyribonucleic acid by carcinogens dimethyl sulphate, ethyl methanesulphonate, N-ethyl-N-nitrosourea and N-methyl-N-nitrosourea. Relative reactivity of the phosphodiester site thymidylyl(3''-5'')thymidine.

1. The ethyl phosphotriester of thymidylyl(3'-5')thymidine, dTp(Et)dT, was identified as a product from reaction of DNA with N-ethyl-N-nitrosourea, by procedures parallel to those reported previously for the methyl homologue produced by N-methyl-N-nitrosourea. 2. Enzymic degradation to yield alkyl phosphotriesters from DNA alkylated by these carcinogens and by dimethyl sulphate and ethyl methanesulphonate was studied quantitatively, and the relative yields of the triesters dTp(Alk)dT were determined. The relative reactivity of the phosphodiester group dTpdT to each of the four carcinogens was thus obtained, and compared with that of DNA overall, or with that of the N-7 atom of guanine in DNA. Relative reactivity of the phosphodiester group was lowest towards dimethyl sulphate, the least electrophilic of the reagents used, and was highest towards N-ethyl-N-nitrosourea, the most electrophilic reagent. 3. The nature of the alkyl group transferred also influenced reactivity of the phosphodiester site, since this site was relatively more reactive towards ethylation than would be predicted simply from the known Swain-Scott s values of the alkylating agents. It was therefore suggested that the steric accessibility of the weakly nucleophilic phosphodiester group on the outside of the DNA macromolecule favours its reaction with ethylating, as opposed to methylating, reagents. 4. Taking a value of the Swain-Scott nucleophilicity (n) of 2.5 for an average DNA nucleotide unit [Walles & Ehrenberg (1969) Acta Chem. Scand. 23, 1080-1084], a value of n of about 1 for the phosphodiester group was deduced, and this value was found to be 2-3 units less than that for the N-7 atom of guanine in DNA. 5. The reactivity of DNA overall was markedly high towards the alkylnitrosoureas, despite their relatively low s values. This was ascribed to an electrostatic factor that favoured reaction of the negatively charged polymer with alkyldiazonium cation intermediates.     

Reaction of diazoalkanes with 1-substituted 2, 4-dioxopyrimidines. Formation of O2, N-3 and O4-alkyl products.

In non-aqueous solution, diazomethane and diazoethane react with the O2, O4 and N-3 sites of uridine, thymidine, 1-methyluracil and 1-methylthymine. Diazoethane has a higher affinity for alkylating oxygens than does diazomethane. The relative ratio of O2:O4:N-3 methyl products is 1:2:16 and of ethyl products the ratio is 1:1:2. When the diazoethane reaction is performed in neutral buffered solution, the same proportion of O2:O4:N-3 ethyl products is found, but the extent of reaction is very low. O2-alkylation greatly labilizes the glycosidic bond of thymidine and uridine toward acid hydrolysis. All O2 and O4 alkyl 1-substituted 2,4-dioxopyrimidines are dealkylated in weak acid but the O2 alkyl group is the more stable.     

Adenovirus deoxyribonucleic acid replication. II. Synthesis of viral deoxyribonucleic acid in vitro by a nuclear membrane fraction from infected KB cells.

A cell-free system for the study of viral DNA replications was developed by the isolation of a nuclear membrane fraction "DNA replication complex" from adenovirus 2-infected human KB cells late after infection. This complex which possesses both DNA polymerase activity and a virus-specific endonuclease synthesizes exclusively virus-specific DNA sequences in vitro by a semiconservative mechanism. Analysis by rate zonal sedimentation in alkaline sucrose gradients showed that the products of the reaction are small DNA chains approximately 6 to 9 S, presumably "Okazaki intermediates," that are not sealed under our in vitro conditions. Analysis by rate zonal sedimentation in neutral sucrose gradients showed that labeled viral DNA fragments are hydrogen bonded to viral 18 S DNA segments, 0.25 the size of the linear, viral 31 S DNA genome. The 18 S DNA is probably a specific cleavage product of the viral endonuclease found in the replication complex and could represent intermediates in viral DNA replication or degradation products.     

Synthesis and properties of oligonucleotides containing a cholesterol thymidine monomer

Highly selective base-pair recognition makes DNA a suitable building block for orderly self-assembled structures. For some applications in nanotechnology DNA complexes need to be fixed onto surfaces. To fulfil this requirement on lipid membranes we have synthesised a thymidine monomer modified with a cholesterol moiety. Solution studies show that the melting temperature (Tm) of the duplex, with adjacent cholesterols on each strand, is much higher than that of the unmodified duplex.     

The preparation and analysis of a new trinucleotide from yeast ribonucleic acid, containing two adjacent 2′-O-methylpentose residues

Quantities of the order of 10mg of three alkali-stable trinucleotides were prepared from yeast ribonucleic acid. Analyses showed that they were of the type N1m-N2m-N3p, where m signifies 2′-O-methylation of the pentose residue. One, Am-Um-Gp, is newly described.     

Size and transforming activity of deoxyribonucleic acid in Diplococcus pneumoniae during thymidine starvation.

The transforming activity and the molecular structure of DNA from cells of Diplococcus pneumoniae during thymidine starvation have been analyzed and the effects of thymidine starvation have been compared with the effects of single-strand breaks produced by deoxyribonucleases in DNA of unstarved cells. The decrease in transforming activity of lysates from starved cells as a function of the size of DNA particles, measured by centrifugation in neutral and alkaline sucrose gradients, does not follow the kinetics observed after enzymatic degradation of DNA of unstarved cells. Moreover, a strain lacking exo- and endonuclease activities is not protected from thymineless death. These results suggest that the basic lethal mechanism of thymidine starvation might have an origin other than the activation of nucleases.     

Synthesis and activity of dermorphin analogues containing unusual amino acid residues

Solid phase syntheses of analogues of the opioidheptapeptide dermorphin(H-Tyr-dAla-Phe-Gly-Tyr-Pro-Ser-NH₂) containingin the first position 3-aminotyrosine, 3-nitrotyrosine,4-aminophenylalanine, or nucleoamino acids,3-(uracilyl-1)alanine, 3-(thyminyl-1)alanine and3-(6-methyluracilyl-1)alanine are described. Thereceptor binding properties and analgesic activity ofthe analogues were examined in comparison withdermorphin. All analogues showed low opioid activityin the binding assays with respect to µ- and-receptors. The peptide containing3-(thyminyl-1)alanine demonstrated a high analgesicactivity in different tests when administeredintracisternally in mice.     

Synthesis and activity of dermorphin analogues containing unusual amino acid residues

Summary Solid phase syntheses of analogues of the opioid heptapeptide dermorphin (H-Tyr-dAla-Phe-Gly-Tyr-Pro-Ser-NH₂) containing in the first position 3-aminotyrosine, 3-nitrotyrosine, 4-aminophenylalanine, or nucleoamino acids, 3-(uracilyl-1)alanine, 3-(thyminyl-1)alanine and 3-(6-methyluracilyl-1)alanine are described. The receptor binding properties and analgesic activity of the analogues were examined in comparison with dermorphin. All analogues showed low opioid activity in the binding assays with respect to μ- and δ-receptors. The peptide containing 3-(thyminyl-1)alanine demonstrated a high analgesic activity in different tests when administered intracisternally in mice.     

Synthesis of deoxyribonucleic acid, ribonucleic acid, and protein during sporulation of Clostridium perfringens.

The kinetics of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein synthesis as well as protein breakdown during sporulation by Clostridium perfringens were determined. Maximum levels of DNA and net RNA synthesis occurred 3 and 2 h, respectively, after inoculation of sporulation medium. The rate of RNA synthesis decreased as sporulation progressed. Deoxyadenosine increased uptake of [14C]uracil and [14C]thymine but depressed the level of sporulation and the formation of heat-resistant spores when added at concentrations above 100 mug/ml. Unlike Bacillus species, net protein synthesis, which was sensitive to chloramphenicol inhibition, continued during sporulation. The rate of protein breakdown during vegetative growth was 1%/h. During sporulation this rate increased to 4.7%/h. When added to sporulation medium at 0 time chloramphenicol reduced protein breakdown to 1%/h. If added at 3 h the rate decreased to 2.1%/h. The role of proteases in this process is discussed.