Synthesis of 3'-thioamido-modified 3'-deoxythymidine-5'-triphosphates and their use as chain terminators in Sanger-DNA sequencing

The thioamide derivatives 3'-deoxy-5'-O-(4,4'-dimethoxytrityl)-3'-[(2-methyl-1-thioxo- propyl)amino]thymidine 1 and 3'-deoxy-5'-O-(4,4'-dimethoxytrityl)-3'-((6-([(9H-(fluo-ren-9- ylmethoxy)carbonyl]-amino)-1-thioxohexyl)amino) thymidine 2 were synthesized by regioselective thionation of their corresponding amides 7 and 8 with 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2,4-disulfide (Lawesson's reagent). The thioamides were converted into the corresponding 5'-triphosphates 3 and 4. Compound 3 was chosen for DNA sequencing experiments and 4 was further labelled with fluorescein.     

SYNTHESIS OF 3′-THIOAMIDO-MODIFIED 3′-DEOXYTHYMIDINE-5′-TRIPHOSPHATES AND THEIR USE AS CHAIN TERMINATORS IN SANGER-DNA SEQUENCING

The thioamide derivatives 3′-deoxy-5′-O-(4,4′-dimethoxytrityl)-3′-[(2-methyl-1-thioxo-propyl)amino]thymidine 1 and 3′-deoxy-5′-O-(4,4′-dimethoxytrityl)-3′-{{6-{[(9H-(fluo-ren-9-ylmethoxy)carbonyl]-amino}-1-thioxohexyl}amino} thymidine 2 were synthesized by regioselective thionation of their corresponding amides 7 and 8 with 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphet-ane-2,4-disulfide (Lawesson's reagent). The thioamides were converted into the corresponding 5′-triphosphates 3 and 4. Compound 3 was chosen for DNA sequencing experiments and 4 was further labelled with fluorescein.     

Facile synthesis of (R)-4-mercaptopyrrolidine-2-thione from L-aspartic acid

An SN2-type of substitution of (S)-bromide 4, which had been prepared from L-aspartic acid, with potassium thiobenzoate provided (R)-benzoylthio derivative 5 with complete inversion of the configuration. Compound 5 was converted, via iodide 6c, to (R)-4-amino-3-benzoylthiobutyric acid 8b. (R)-4-Mercapto pyrrolidine-2-thione 1 was readily obtained from 8b through cyclization with acetic anhydride, thionation with Lawesson's reagent and facile removal of the S-benzoyl group with sodium methoxide.     

Formation of 1-Alkyl-5-(hydroxymethyl)pyrrole-2-aldehydes in the Browning Reaction between Hexoses and Alkylamines

d-Glucose and butyl-, ethyl-, or methyl-amine were reacted at 100°C or 70°C in an aqueous or methanol solution neutralized with acetic acid to obtain browning reaction products, and the formation of N-substituted 5-(hydroxymethyl)pyrrole-2-aldehydes in the reaction was investigated.

At first, the reaction products were treated with 2,4-dinitrophenylhydrazine reagent and the resulting 2,4-dinitrophenylhydrazones (2,4-DNPs) were fractionated by column chromatography to isolate crystalline 2,4-DNPs. When the products obtained from d-glucose and butylamine were treated with the reagent consisting of 2,4-dinitrophenylhydrazine, sulfuric acid, water and either ethanol or methanol, 2,4-DNP of l-butyl-5-(ethoxymethyl or meth-oxymethyl)pyrrole-2-aldehyde (I or II) was isolated. In this formation ethanol or methanol was considered to be directly involved. On the other hand, 2,4-DNP of 5-hydroxymethyl derivative (III) was not detected, even when the reagent containing water alone as a solvent was used.

Secondly, in order to isolate the free pyrrolealdehyde, the above browning reaction products were extracted with ethyl acetate and the extract was chromatographed on a silica gel column. From the main carbonyl fraction was isolated 1-butyl-, ethyl-, or methyl-5-(hydroxymethyl)-pyrrole-2-aldehyde (III, IV, or V), which was characterized by elementary analyses and ultraviolet, infrared, and nuclear magnetic resonance spectra.     

2,4-Dinitrophenyl [14C]cysteinyl disulfide allows selective radioactive labeling of protein thiols under spectrophotometric control

2,4-Dinitrophenyl [1-14C]cysteinyl disulfide readily introduces by disulfide exchange [14C]cysteine as a label into proteins with exposed thiols. The release of an equivalent amount of colored 2,4-dinitrothiophenolate allows the labeling reaction to be followed spectrophotometrically. In reaction with two cysteine residues of rabbit skeletal muscle actin, the thiol selectivity of the reagent corresponded to that of 5,5'-dithiobis(2-nitrobenzoic acid) (Ellman's reagent) and was superior to that of N-[14C]ethylmaleimide. Labeling of single SH groups of actin and papain proceeded faster than titration with Ellman's reagent under the same conditions. The [14C]cysteine label could be removed under mild conditions, e.g., with dithiothreitol, but proved to be stable during cyanogen bromide degradation of the protein and peptide purification. 2,4-Dinitrophenyl cysteinyl disulfide can be easily prepared within a few hours.     

Unusual thionation of a cyclic hexapeptide. Conformational changes and dynamics.

One carbonyl oxygen of the cyclic hexapeptide cyclo(-Gly1-Pro2-Phe3-Val4-Phe5-Phe6-) (A) can be selectively exchanged with sulphur using Yokoyama's reagent. Surprisingly it was not the C=] of Gly1 but that of Phe5 which was substituted and cyclo(-Gly1-Pro2-Phe3-Val4-Phe5 psi [CS-NH]Phe6-) (B) was obtained. Thionation results in a conformational change of the peptide backbone although the C=O of Phe5 and the corresponding C=S are not involved in internal hydrogen bonds. Two isomers in slow exchange, containing a cis Gly1-Pro2 bond in a beta VIa-turn (minor) and a trans Gly-Pro bond in a beta II'-turn (major), were analyzed by restrained molecular dynamics in vacuo and in DMSO as well as using time dependent distance constraints. It is impossible to fit all experimental data to a static structure of each isomer. Interpreting the conflicting NOEs, local segment flexibility is found. MD simulations lead to a dynamic model for each structure with evidence of an equilibrium between a beta I- and beta II-turn about the Val4-Phe5 amide bond in both the cis and trans isomers. Additionally proton relaxation rates in the rotating frame (R1 rho) were measured to verify the assumption of this fast beta I/beta II equilibrium within each isomer. Significant contributions to R1 rho-rates from intramolecular motions were found for both isomers. Therefore it is possible to distinguish between at least four conformers interconverting on different time scales based on NMR data and MD refinement. This work shows that thionation is a useful modification of peptides for conformation-activity investigations.     

Properties of 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate--an intermediate in the non-mevalonate isoprenoid biosynthesis

Extraction and purification from the biomass of Corynebacterium ammoniagenes of 2-C-methyl-D-erhythritol 2,4-cyclopyrophosphate (MEC) was associated with its spontaneous transformation into a number of derivatives (which was due to pyrophosphate bond lability and the formation of complexes with metals). These derivatives included 1,2-cyclophospho-4-phosphate, 2,4-diphosphate, 2,3-cyclophosphate, 1,4-diphosphate, and 3,5-diphosphate (identified by 1H, 31P, and 13C NMR spectroscopy) and accounted for about 10% MEC. When added to a solution of DNA in the presence of the Fenton reagent, MEC prevented DNA decomposition. In addition, MEC slowed down the interaction of the reagent with tempol radicals, which indicates that complexation of ferrous ions by MEC attenuates their ability to catalyze the formation of hydroxyl radicals from hydrogen peroxide. In the presence of 0.23 mM MEC, the rate of respiration of rat liver mitochondria increased 1.8 times. At 0.1-1.0 mM, MEC activated in vitro proliferation of human Vgamma9 T-cells. It is suggested that MEC acts as an endogenous stabilizing agent for bacterial cells subjected to oxidative stress and as an immunomodulator for eukaryotic hosts.     

Propterol B,a further 1,3-diarylpropan-2-ol from Pterocarpus marsupium

The structure of propterol B, a heartwood extract of Pterocarpus marsupium, has been established as the hitherto unreported 1-(2,4-dihydroxyphenyl)-3-(4-hydroxyphenyl)propan-2-ol. The trimethyl ether of propterol B on oxidation with Jones reagent gave 1-(2,4-dimethoxyphenyl)-3-(4-methoxyphenyl)propan-2-one.     

Hydroxylated metabolites of 2,4-dichlorophenol imply a fenton-type reaction in Gloeophyllum striatum

While degrading 2,4-dichlorophenol, two strains of Gloeophyllum striatum, a basidiomycetous fungus causing brown rot decay of wood, simultaneously produced 4-chlorocatechol and 3,5-dichlorocatechol. These metabolites were identified by comparing high-performance liquid chromatography retention times and mass spectral data with those of chemically synthesized standards. Under similar conditions, 3-hydroxyphthalic hydrazide was generated from phthalic hydrazide, a reaction assumed to indicate hydroxyl radical formation. Accordingly, during chemical degradation of 2,4-dichlorophenol by Fenton's reagent, identical metabolites were formed. Both activities, the conversion of 2,4-[U-(14)C]dichlorophenol into (14)CO(2) and the generation of 3-hydroxyphthalic hydrazide, were strongly inhibited by the hydroxyl radical scavenger mannitol and in the absence of iron. These results provide new evidence in favor of a Fenton-type degradation mechanism operative in Gloeophyllum.     

Resonance Raman assignment and evidence for noncoupling of individual 2- and 4-vinyl vibrational modes in a monomeric cyanomethemoglobin

We have investigated the resonance Raman spectra of monomeric insect cyanomethemoglobins (CTT III and CTT IV) reconstituted with (1) protohemes IX selectively deuterated at the 4-vinyl as well as the 2,4-divinyls, (2) monovinyl-truncated hemes such as pemptoheme (2-hydrogen, 4-vinyl) and isopemptoheme (2-vinyl, 4-hydrogen), (3) symmetric hemes such as protoheme III (with 2- and 3-vinyls) and protoheme XIII (with 1- and 4-vinyls), and (4) hemes without 2- and 4-vinyls such as mesoheme IX, deuteroheme IX, 2,4-dimethyldeuteroheme IX, and 2,4-dibromodeuteroheme IX. Evidence is presented that the highly localized vinyl C = C stretching vibrations at the 2- and 4-positions of the heme in these cyanomet CTT hemoglobins are noncoupled and inequivalent; i.e., the 1631- and 1624-cm-1 lines have been assigned to 2-vinyl and 4-vinyl, respectively. The elimination of the 2-vinyl (in pemptoheme) or the 4-vinyl (in isopemptoheme) does not affect the C = C stretching frequency of the remaining vinyl. Furthermore, two low-frequency vinyl bending modes at 412 and 591 cm-1 exhibit greatly different resonance Raman intensities between 2-vinyl and 4-vinyl. The observed intensity at 412 cm-1 is primarily derived from 4-vinyl, whereas the 591-cm-1 line results exclusively from the 2-vinyl. Again, there is no significant coupling between 2-vinyl and 4-vinyl for these two bending modes.     

Anaerobic biodegradation of 2,4-dichlorophenol in freshwater lake sediments at different temperatures

Anaerobic degradation of 2,4-dichlorophenol (2,4-DCP) between 5 and 72 degrees C was investigated. Anaerobic sediment slurries prepared from local freshwater pond sediments were partitioned into anaerobic tubes or serum vials, which then were incubated separately at the various temperatures. Reductive 2,4-DCP dechlorination occurred only in the temperature range between 5 and 50 degrees C, although methane was formed up to 60 degrees C. In sediment samples from two sites and at all tested temperatures from 5 to 50 degrees C, 2,4-DCP was transformed to 4-chlorophenol (4-CP). The 4-CP intermediate was subsequently degraded after an extended lag period in the temperature range from 15 to 40 degrees C. Adaptation periods for 2,4-DCP transformation decreased between 5 and 25 degrees C, were essentially constant between 25 and 35 degrees C, and increased in the tubes incubated at temperatures between 35 and 40 degrees C. The degradation rates increased exponentially between 15 and 30 degrees C, had a second peak at 35 degrees C, and decreased to about 5% of the peak activity by 40 degrees C. In tubes from one sediment sample, incubated at temperatures above 40 degrees C, an increase in the degradation rate was observed following the minimum at 40 degrees C. This suggests that at least two different organisms were involved in the transformation of 2,4-DCP to 4-CP. Storage of the original sediment slurries for 2 months at 12 degrees C resulted in increased adaptation times, but did not affect the degradation rates.     

Anaerobic biodegradation of 2,4-dichlorophenol in freshwater lake sediments at different temperatures.

Anaerobic degradation of 2,4-dichlorophenol (2,4-DCP) between 5 and 72 degrees C was investigated. Anaerobic sediment slurries prepared from local freshwater pond sediments were partitioned into anaerobic tubes or serum vials, which then were incubated separately at the various temperatures. Reductive 2,4-DCP dechlorination occurred only in the temperature range between 5 and 50 degrees C, although methane was formed up to 60 degrees C. In sediment samples from two sites and at all tested temperatures from 5 to 50 degrees C, 2,4-DCP was transformed to 4-chlorophenol (4-CP). The 4-CP intermediate was subsequently degraded after an extended lag period in the temperature range from 15 to 40 degrees C. Adaptation periods for 2,4-DCP transformation decreased between 5 and 25 degrees C, were essentially constant between 25 and 35 degrees C, and increased in the tubes incubated at temperatures between 35 and 40 degrees C. The degradation rates increased exponentially between 15 and 30 degrees C, had a second peak at 35 degrees C, and decreased to about 5% of the peak activity by 40 degrees C. In tubes from one sediment sample, incubated at temperatures above 40 degrees C, an increase in the degradation rate was observed following the minimum at 40 degrees C. This suggests that at least two different organisms were involved in the transformation of 2,4-DCP to 4-CP. Storage of the original sediment slurries for 2 months at 12 degrees C resulted in increased adaptation times, but did not affect the degradation rates.     

Synthesis of 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-substituted-benzene thymidine mimics, some related alpha-anomers, and their evaluation as antiviral and anticancer agents

A group of unnatural 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluorobenzenes having a variety of C-5 substituents (H, Me, F, Cl, Br, I, CF3, CN, NO2, NH2), designed as thymidine mimics, were synthesized for evaluation as anticancer and antiviral agents. The coupling reaction of 3,5-bis-O-(p-chlorobenzoyl)-2-deoxy-alpha-D-ribofuranosyl chloride with an organocadmium reagent [(2,4-difluorophenyl)2Cd] afforded a mixture of the alpha- and beta-anomeric products (alpha:beta = 3:1 to 10:1 ratio). Treatment of the alpha-anomer with BF3.Et2O in nitroethane at 110-120 degrees C for 30 min was developed as an efficient method for epimerization of the major alpha-anomer to the desired beta-anomer. The 5-substituted (H, Me, Cl, I, NH2) beta-anomers exhibited negligible cytotoxicity in a MTT assay (CC50 = 10(-3)-10(-4) M range), relative to thymidine (CC50 = 10(-3)-10(-5) M range), against a variety of cancer cell lines. In contrast, the 5-NO2 derivative was more cytotoxic (CC50 = 10(-5)-10(-6) M range). A number of 5-substituted beta-anomers, and some related alpha-anomers, that were evaluated using a wide variety of antiviral assay systems [HSV-1, HSV-2, varicella-zoster virus (VZV), vaccinia virus, vesicular stomatitis, cytomegalovirus (CMV) and human immunodeficiency (HIV-1, HIV-2) viruses], showed that this class of unnatural C-aryl nucleoside mimics are inactive antiviral agents.     

Transgenic tobacco plants overexpressing a cold-adaptive nitroreductase gene exhibited enhanced 2,4-dinitrotoluene detoxification rate at low temperature

Abstract

Plants encounter many environmental factors such as low and high temperatures during phytoremediation processes. In this study, our aim was to produce the transgenic tobacco plants by using a newly characterized bacterial nitroreductase, Ntr, which was active at a broad range temperature in order to detoxify 2,4-dinitrotoluene (2,4-DNT) at lower temperature. The presence of Ntr and its heterologous expression was verified in T1 transgenic plants and their growing ability were determined under toxic amount of 2,4-DNT (35?µM). Fresh weight and dry weight of transgenic plants were significantly higher than wild type (WT) under toxic 2,4-DNT at 22?°C, indicating higher growth capacity of the transgenics. Transgenic plants also showed a higher tolerance than WT when exposed to 2,4-DNT at 15?°C. Moreover, transformation rate of 2,4-DNT was gradually decreased through decreasing temperatures in WT media, however, it was increased through decreasing temperatures in transgenic plant TR3-25 media and it had the highest transformation rate (54%) of 2,4-DNT at 4?°C. Correlatively, 2,4-DNT treatment at 4?°C led to a significant decrease in H₂O₂ level in transgenic plants. Thus, transgenic plants overexpressing nitroreductase might have an important advantage for phytoremediation of toxic nitroaromatic compounds in field applications at low temperatures.     

Use of 4-Nitrophenoxyacetic Acid for Detection and Quantification of 2,4-Dichlorophenoxyacetic Acid (2,4-D)/(alpha)-Ketoglutarate Dioxygenase Activity in 2,4-D-Degrading Microorganisms

Purified 2,4-dichlorophenoxyacetic acid (2,4-D)/(alpha)-ketoglutarate dioxygenase (TfdA) was shown to use 4-nitrophenoxyacetic acid (K(infm) = 0.89 (plusmn) 0.04 mM, k(infcat) [catalytic constant] = 540 (plusmn) 10 min(sup-1)), producing intensely yellow 4-nitrophenol. This reagent was used to develop a rapid, continuous, colorimetric assay for the detection of TfdA and analogous activities in 2,4-D-degrading bacterial cells and extracts.     

Solid phase synthesis of a GHRP analog containing C-terminal thioamide group

[Lyst6]GHRP, the C-terminally thionated analog of the highly potent growth hormone releasing hexapeptide His-D-Trp-Ala-Trp-D-Phe-Lys-NH2 was prepared by using solid support. The success of the synthesis showed that Lawesson's reagent can be used for selective thionation of an amide group not only in solution but also on the surface of a resin. The C-terminal thioamide group proved to be stable under the conditions of the solid phase synthesis.     

Synthesis of 4-deoxy analogues of 2-acetamido-2-deoxy-D-glucose and 2-acetamido-2-deoxy-D-xylose and their effects on glycoconjugate biosynthesis

4-Deoxy analogues of 2-acetamido-2-deoxy-D-glucose and 2-acetamido-2-deoxy-D-xylose were synthesized and evaluated as inhibitors of glycoconjugate biosynthesis. Methyl 2-acetamido-2,4-dideoxy-beta-D-xylo-hexopyranoside (11) showed a reduction in [3H]GlcN and [14C]Leu incorporation into hepatocyte cellular glycoconjugates by 89 and 88%, of the control cells, respectively, at 20 mM, whereas the free sugars, 2-acetamido-2,4-dideoxy-alpha,beta-D-xylo-hexopyranoses (15), showed a reduction of [3H]GlcN and [14C]Leu incorporation by 75 and 64%, respectively, at 20 mM. The acetylated analogues of 11 and 15, namely methyl 2-acetamido-3,6-di-O-acetyl-2,4-dideoxy-beta-D-xylo-hexopyranoside and 2-acetamido-1,3,6-tri-O-acetyl-2,4-dideoxy-alpha,beta-D-xylo-hexopyra noses, showed a greater inhibition of [3H]GlcN and [14C]Leu incorporation at 1 mM compared with their non-acetylated counterparts, but were toxic to hepatocytes at concentrations of 10 and 20 mM. Corresponding derivatives of 2-acetamido-2,4-dideoxy-L-threo-pentopyranose showed no biological effect up to 20 mM, suggesting that the C-6 substituent is important for the biological activity.     

Synthesis of oligodeoxyribonucleoside phosphorothioates using Lawesson's reagent for the sulfur transfer step

2,4-Bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2,4-disulfide (Lawesson's reagent) efficiently converts the triphosphite intermediate used in the solid-phase synthesis of oligonucleotides into an oligodeoxyribonucleoside phosphorothioate.     

Bioconjugation of CdTe quantum dot for the detection of 2,4-dichlorophenoxyacetic acid by competitive fluoroimmunoassay based biosensor

Quantum dots (QD) are semiconductor fluorescent nanoparticles, which can be made use of for environmental monitoring with high sensitivity. In view of the alarming levels of pesticides and herbicides being used in agriculture practices, there is a need for their rapid, sensitive and specific detection in food and environmental samples, as pesticides and herbicides are harmful to living beings even at trace levels. Present study was carried out to develop a reliable and rapid method for analysis and detection of 2,4-D (herbicide) using cadmium telluride quantum dot nanoparticle (CdTe QD). Fluoroimmunoassay based on the fluorescent property of quantum dot was used along with immunoassay to detect 2,4-D. CdTe capped with mercaptopropionic acid, was conjugated using N-(3-dimethylaminopropyl)-N-ethylcarbodiimide hydrochloride (EDC) and a coupling reagent like N-hydroxysuccinimide (NHS) to alkaline phosphatase (ALP) which was in turn conjugated to 2,4-D molecule. Anti 2,4-D-IgG antibodies were immobilized in an immunoreactor column using Sepharose CL-4B as an inert matrix. The detection of 2,4-D was carried out by fluoroimmunoassay-based biosensor using competitive binding between conjugated 2,4-D-ALP-CdTe and free 2,4-D with immobilized anti 2,4-D antibodies in an immunoreactor column. It was possible to detect 2,4-D upto 250pgmL(-1). Present study also emphasizes on the resonance energy transfer between ALP and CdTe QD as a result of bioconjugation, which can be used for future biosensor development based on quantum dot-biomolecular interactions.     

Temperature-dependent biotransformation of 2,4'-dichlorobiphenyl by psychrotolerant Hydrogenophaga strain IA3-A: higher temperatures prevent excess accumulation of problematic meta-cleavage products

AIMS: The present work investigates the possibility that temperature could regulate the pattern of transformation of 2,4'-chlorobiphenyl (2,4'-CB) by psychrotolerant Hydrogenophaga sp. IA3-A. Methods AND RESULTS: Transformation of 2,4'-chlorobiphenyl to 2- and 4-chlorobenzoic acid (2- and 4-CBA), and meta-cleavage products by cells of strain IA3-A incubated at 10 degrees C, 25 degrees C, 37 degrees C or 45 degrees C were monitored by UV spectrometry, HPLC and GC-MS analyses. Cultures incubated at 10 degrees C, 25 degrees C or 37 degrees C produced low amounts of CBAs and excess levels of meta-cleavage products from 2,4'-CB. Cultures incubated at 45 degrees C transformed most of the degraded 2,4'-CB to CBAs and low level of meta-cleavage product. Culture extracts contained unusual varieties of isomeric hydroxylated metabolic products. CONCLUSIONS: Efficient transformation of 2,4'-CB to CBAs was possible in cultures incubated at 45 degrees C. Evidence for the involvement of multiple pathways in the transformation of 2,4'-CB in strain IA3-A suggests that differential regulation of the pathways at different temperatures was likely responsible for the change in the pattern of transformation of 2,4'-CB in cultures incubated at 45 degrees C. Significance AND IMPACT OF THE STUDY: It may be possible to condition cells to transform chlorinated biphenyls more efficiently without accumulating excess level of toxic intermediates.