Immobilized Escherichia coli BL21 as a catalyst for the synthesis of adenine and hypoxanthine nucleosides

Different supports, such as alginate, agar, agarose, and polyacrylamide, were used to immobilize Escherichia coli BL 21 by entrapment techniques. The transglycosylation reaction involved in the synthesis of adenosine from uridine and adenine was chosen as a model system to study the characteristics of these biocatalysts. Whole cells immobilized on agarose proved to be optimal and could be used up to 30 times without significant loss of activity. This biocatalyst was further employed to test its ability in the synthesis of other adenine and hypoxanthine nucleosides. Ribo-, 2'-deoxyribo-, and arabinonucleosides could be prepared in high yields starting from the corresponding pyrimidine nucleosides and purine bases. Similar product yields were obtained with both free and immobilized cells, though, in the latter case, a longer reaction time was necessary.     

Functional heterologous expression and purification of a mammalian methyl-CpG binding domain in suitable yield for DNA methylation profiling assays

DNA methylation is a major epigenetic modification in mammalian cells, and patterns involving methylation of cytosine bases, known as CpG methylation, have been implicated in the development of many types of cancer. Methyl binding domains (MBDs) excised from larger mammalian methyl-CpG-binding proteins specifically recognize methyl-cytosine bases of CpG dinucleotides in duplex DNA. Previous molecular diagnostic studies involving MBDs have employed Escherichia coli for protein expression with either low soluble yields or the use of time-consuming denaturation-renaturation purification procedures to improve yields. Efficient MBD-based diagnostics require expression and purification methods that maximize protein yield and minimize time and resource expenditure. This study is a systematic optimization analysis of MBD expression using both SDS-PAGE and microscopy and it provides a comparison of protein yield from published procedures to that from the conditions found to be optimal in these experiments. Protein binding activity and specificity were verified using a DNA electrophoretic mobility shift assay, and final protein yield was improved from the starting conditions by a factor of 65 with a simple, single-step purification.     

DNA Base Damage in Chromatin of γ-Irradiated Cultured Human Cells

We report on the chemical characterization of DNA base damage in chromatin of γ-irradiated cultured human cells. Chromatin was isolated from unirradiated and irradiated cells and analyzed by gas chroma-tography/mass spectrometry with selected-ion monitoring after acidic hydrolysis of chromatin and trimethylsilylation of hydrolysates. Prior to analysis of chromatin samples, experimental conditions for acidic hydrolysis were optimized by determining the relative molar response factors of modified bases under non-acidic and acidic conditions, and their release from DNA under various acidic conditions. A number of modified bases in chromatin isolated from irradiated cells were identified and quantitated. These were 5-hydroxy-5-methylhydantoin, 5-hydroxyhydantoin, 5-(hydroxymethyl)uracil, cytosine glycol, thymine glycol, 5,6-dihydroxycytosine, 4,6-diamino-5-formamidopyrimidine, 8-hydroxyadenine, 2-hydroxyadenine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, and 8-hydroxyguanine. Radiation doses ranging from 42 to 420 Gy (J . kg¹) were used. Background levels of all modified bases were observed in chromatin isolated from unirradiated cells. The radiation yields of a number of modified bases were increased significantly over their background levels at a dose as low as 42 Gy. In most cases, linear dose-yield relationships were obtained up to ≈200Gy. At radiation doses higher than 420 Gy, no additional increase in the yields of modified bases was observed. The yields of guanine-derived bases amounted to ≈ 45% of the total net yield of modified bases measured, followed by almost equal yields of adenine-, cytosine- and thymine-derived bases. Modified bases identified were typical products of hydroxyl radical attack on DNA bases, indicating the involvement of hydroxyl radical, although their induction in part by the direct effect of ionizing radiation through ionization of DNA bases cannot be excluded. The yields of modified bases were lower than those previously measured after γ-irradiation of fully expanded chromatin in aqueous buffer solutions.     

Efficient synthesis and biological evaluation of 1,2,9-trisubstituted 1,9-dihydro-6H-purin-6-ones

The carbodiimides 4, obtained from aza-Wittig reactions of iminophosphorane 3 with aromatic isocyanates, reacted with amines in the presence of a catalytic amount of RO^?Na⁺ to give the 1,2,9-trisubstituted 1,9-dihydro-6H-purin-6-ones 6 in good yields. Compound 6 exhibited cytotoxicity against various cancer cells. For example, compounds 6b showed the best inhibition activities against KB, HepG2 and OVCAR3 with IC₅₀ 9.5, 20.4 and 10.0 μM.     

A novel approach to the synthesis of oligodeoxyribonucleotide boranophosphates.

Deoxyribonucleoside 3'-boranophosphate derivatives including adenine, cytosine, guanine, and thymine bases were synthesized in good yields by the use of a new boranophosphorylation reaction. The reaction was found to be effective for the formation of internucleotidic boranophosphate linkages.     

Coulombic effects on the traceless Staudinger ligation in water

The traceless Staudinger ligation can be mediated by phosphinothiols under physiological conditions. Proximal positive charges are necessary to achieve that transformation, presumably because those charges discourage protonation of the key iminophosphorane intermediate. Here, a series of cationic phosphinothiols is used to probe Coulombic effects on the traceless Staudinger ligation in aqueous buffers. The reagent bis(m-N,N-dimethylaminomethylphenyl)phosphinomethanethiol (3) is found to be superior to others, both in its ability to mediate the traceless Staudinger ligation in water and in the efficiency of its synthesis.     

Direct radiation damage to crystalline DNA: what is the source of unaltered base release?

The radiation chemical yields of unaltered base release have been measured in three crystalline double-stranded DNA oligomers after X irradiation at 4 K. The yields of released bases are between 10 and 20% of the total free radical yields measured at 4 K. Using these numbers, we estimate that the yield of DNA strand breaks due to the direct effect is about 0.1 micromol J(-1). The damage responsible for base release is independent of the base type (C, G, A or T) and is not scavenged by anthracycline drugs intercalated in the DNA. For these reasons, reactions initiated by the hydroxyl radical have been ruled out as the source of base release. Since the intercalated anthracycline scavenges electrons and holes completely but does not inhibit base release, the possibility for damage transfer from the bases to the sugars can also be ruled out. The results are consistent with a model in which primary radical cations formed directly on the sugar-phosphate backbone react by two competing pathways: deprotonation, which localizes the damage on the sugar, and hole tunneling, which transfers the damage to the base stack. Quantitative estimates indicate that these two processes are approximately equally efficient.     

Measurements of nucleic bases released after gamma irradiation of DNA in solution in air.

The release of unaltered nucleic bases from gamma-irradiated DNA in a dilute buffered aqueous solution was studied in both salmon sperm and superhelical viral DNA. Analyses of freed bases were made by high-performance liquid chromatography. An elution protocol was developed for maximum separation of the four nucleic bases and nucleosides with a sensitivity of 10-20 pmol of nucleic base. It was found that: (i) both prompt and delayed release of bases postirradiation occur in both types of DNA; (ii) these yields (G-values) were measured to be 10-15 times higher for the salmon sperm DNA in comparison to the SV40 DNA; (iii) the A-T/G-C ratio in the DNA was not reflected in the ratios of the released base; and (iv) based on measurements made by us of DNA strand breaks in SV40 DNA (unpublished results), less than half of all breaks result in the release of an undamaged base.     

Lipase catalyzed synthesis of organic acid esters of lactic acid in non-aqueous media

Lipases from Rhizomucor miehei (Lipozyme IM20) and porcine pancreas (PPL) were employed as catalysts for the esterification reaction between the hydroxyl group of lactic acid and the carboxyl group of organic acids. Reactions were carried out at both shake-flask and bench-scale levels. Various parameters, such as solvent, temperature, substrate and enzyme concentrations, effect of buffer volume, buffer pH and water volume, were investigated for optimization of yields. While ethylmethyl ketone (EMK) was found to be the best solvent for shake-flask reactions, chloroform gave higher yields at bench-scale level. Detailed studies were carried out with respect to the synthesis of palmitoyl and stearoyl lactic acids. At shake-flask level, maximum yields of 37.5 and 40% were observed in case of palmitoyl and stearoyl lactic acids, respectively, with Lipozyme IM20; at bench-scale level, the maximum yields were 85.1 and 99% respectively, when PPL was employed. Of all the organic acids employed (C(2)--C(18)), only lauric, palmitic and stearic acids gave yields above 50%. At bench-scale level, PPL could be reused for up to three cycles with yields above 40%. Esters prepared were found to conform to Food Chemical Codex (FCC) specifications in terms of acid value, ester value, sodium and lactic acid contents.     

Studies on glycosphingolipids of fresh-water bivalves. V. The structure of a novel ceramide octasaccharide containing mannose-6-phosphate found in the bivalve, Corbicula sandai.

A ceramide octasaccharide containing mannose-6-phosphate was isolated from the fresh-water bivalve Corbicula sandai by solvent fractionation, followed by two types of silicic acid column chromatography, and finally QAE-Sephadex column chromatography. The structural analysis involved the following steps. (a) Gas-liquid chromatography of the component sugars, fatty acids, and long-chain bases. (b) Degradation with HCl and HF to elucidate the sugar sequence. (c) Permethylation analysis coupled with GC-MS to identify the positions of the glycosidic linkages between the sugar units. (d) Chromium trioxide oxidation to determine the anomeric configuration. (e) Smith degradation to determine the site of linkage of the ethanolamine residue. The structure of this novel glycolipid was determined to be: 4-O-MeGalp(bets1 yields 3)-GalNAcp(beta1 yields3)Fucp(alpha1 yields 4)GlcNAcp(beta1 yields 2)Manp(alpha1 yields 3)[Xylp(alpha1 yields 2)][2'-aminoethylphosphoryl(yields 6)]Manp(beta1yields 4)Glcp(beta1 yields 1)ceramide. It is very interesting that fucose was found to be internally linked in this sugar chain. To our knowledge, this is the first example of internal fucose in a glycolipid. The ceramide moiety consisted of normal saturated fatty acids, among which stearic acid was pr     

(Butylthio)carbonyl group: a new protecting group for the guanine and uracil residues in oligoribonucleotide synthesis

The protection of the O6-amide and N2-amino groups of guanosine and the N3-imide group of uridine with the (butylthio)carbonyl group is described. This group could be rapidly introduced in good yields and removed very easily under the conventional deprotective conditions of the exo-amino acyl groups of other nucleoside bases.     

Facially-selective thymine-thymine photodimerization in TTT triads

Irradiation of alkane-linked DNA hairpins possessing TTT steps with flanking purine bases yields products identified as the cis-syn (2 + 2) dimers formed between the central thymine and its 3'- and 5'-neighbors. Selective formation of the 3'-dimer is attributed to ground state conformational effects and electron transfer quenching by purine bases.     

Base liberation from nucleotides by superoxide and intramolecular enhancement effect of phosphate group

The reaction of nucleotides with superoxide gave the corresponding nucleobases in good yield. The base-release reaction of nucleotides due to superoxide was examined and compared to that of nucleosides. Hence, the phosphate moiety greatly enhances the yields, in particular those of adenine from adenosine monophosphates. Superoxide in combination with the phosphate moiety has been revealed to be more active than superoxide alone. The phosphate peroxy radical, generated in situ from superoxide and phosphate, seems to be the species responsible for the formation of the free bases.     

Liquid Phase Synthesis of Peptide Nucleic Acid (or Polyamide Nucleic Acid) Dimers

Abstract

The liquid phase synthesis of “polyamide nucleic acid” (PNA) dimers containing the purine nucleic acid bases adenine and guanine has been achieved in good yields. This strategy was elaborated in order to circumvent difficult direct coupling of protected PNA monomers. This method can be applied to the liquid phase synthesis of short protected polyPNAs fragments, which can then selectively be deprotected.     

Fluorescent labelling of sequencing primers for automated oligonucleotide synthesis.

A fluorescein derivative is described which can be used as a normal phosphoramidite in oligonucleotide synthesis, giving high yields of fluorescein labelled sequencing primers. The labelled primers were used in automated DNA-sequence analysis without modification of existing protocols, the computer-processed sequences being reproducibly readable up to 400 bases. The procedure described makes the fluorescent labelling of oligonucleotides much easier, and the time of labelling can be significantly reduced. It speeds up the "primer walking" approach of automated DNA sequencing.     

Microwave-assisted Ribosylation of modified heterocyclic bases by Vorbrüggen method

During the last decades the nucleoside synthesis has proven to be important. The modified silyl-Hilbert-Johnson nucleoside synthesis modified by Vorbrüggen is one of the most often used methods. We have studied N-glycosilation of modifieded heterocyclic bases by Vorbrüggen method with microwave irradiation and we were able to shorten the reaction time and obtain higher yields. The method was demonstrated by fluoroquinolone and purine.     

Microwave-assisted ribosylation of modified heterocyclic bases by Vorbrüggen method

During the last decades the nucleoside synthesis has proven to be important. The modified silyl-Hilbert-Johnson nucleoside synthesis modified by Vorbrüggen is one of the most often used methods. We have studied N-glycosilation of modifieded heterocyclic bases by Vorbrüggen method with microwave irradiation and we were able to shorten the reaction time and obtain higher yields. The method was demonstrated by fluoroquinolone and purine.     

Photochemistry of pyrimidine bases as studied by e.s.r. and spin-trapping

The direct photoexcitation of pyrimidine bases in D2O solutions yields free radicals which could be conveniently identified by spin-trapping with 2-methyl-2-nitrosopropane. Most of the radicals formed were attributed to D-addition to one end of the 5,6 double bond. However, orotic acid and iso-orotic acid yielded N(3) centred free radicals, formed by homolytic cleavage of the N-H bond. No indication could be found for a free radical involvement in the photocleavage of cyclobutane-type pyrimidine dimers.     

Efficient synthesis and biological evaluation of some 2,4-diamino-furo[2,3-d]pyrimidine derivatives

The carbodiimides 2, obtained from aza-Wittig reactions of iminophosphorane 1 with aromatic isocyanates, reacted with ammonia to give ethyl 3,4-dihydro-6-methyl-4-oxo-2-arylamino-furo[2,3-d]pyrimidine-5-carboxylate 3. Further reaction of 3 with POCl₃ and various amines generated ethyl 4-alkylamino-2-arylamino-6-methyl-furo[2,3-d]pyrimidine-5-carboxylate 5 in good yields. Their structures were confirmed by ¹H NMR, EI-Ms, IR and elemental analysis. Compound 5b was further analyzed by single crystal X-ray diffraction. Compound 5 exhibited cytotoxicity against two lung cancer cell lines. For example, compound 5a showed the best inhibition activities against A459 with IC₅₀ 0.8 μM.     

Cognate base‐pair selectivity of hydrophobic unnatural bases in DNA ligation by T4 DNA ligase

We present cognate base pair selectivity in template‐dependent ligation by T4 DNA ligase using a hydrophobic unnatural base pair (UBP), Ds‐Pa. T4 DNA ligase efficiently recognizes the Ds‐Pa pairing at the conjugation position, and Ds excludes the noncognate pairings with the natural bases. Our results indicate that the hydrophobic base pairing is allowed in enzymatic ligation with higher cognate base‐pair selectivity, relative to the hydrogen‐bond interactions between pairing bases. The efficient ligation using Ds‐Pa can be employed in recombinant DNA technology using genetic alphabet expansion, toward the creation of semi‐synthetic organisms containing UBPs.