Alkylation of nucleic acid components with ethylenimine and its derivatives. IV. Alkylation of homopolynucleotides and DNA]

Alkylation of homopolynucleotides and DNA by thio TEPA and monoaziridine diethyl phosphate was studied. The modification affected nucleic bases and terminal phosphate groups but not internucleotide phosphate groups. It was shown that the main center of modification in poly(A) was the N1 atom, whereas the products of N6- and N3-alkylations were formed in smaller amounts. In poly(G), the alkylation proceeded predominantly at the N7 and, insignificantly, at the N1 atom of guanine; the pyrimidine N3 atom is alkylated poorly in poly(C) and even worse in poly(U). In the case of DNA, the major alkylated sites are the guanine N7 and the adenine N3; this results in DNA denaturation and the subsequent formation of products modified at N1 and N6 of adenine, N1 of guanine, and N3 of cytosine. An increase in the pH and ionic strength of the solution as well as the DNA denaturation decrease the reaction rate, whereas ultrasonic fragmentation enhances it. Upon alkylation, melting temperatures decrease, CD and UV spectra change, and DNA luminescence appears. To separate the reaction mixtures and identify the DNA alkylation products, chemical hydrolysis, ion-exchange and reverse-phase HPLC, and UV spectroscopy were used.     

Formation and structure of reaction products of cis-PtCl2(NH3)2 with d(ApG) and/or d(GpA) in di-, tri- and penta-nucleotides. Preference for GpA chelation over ApG chelation

The reaction products of cis-PtCl2(NH)3)2 with several deoxyribonucleotides containing d(ApG) and/or d(GpA) have been studied. The various reaction products were separated by high-performance liquid chromatography and characterized by means of absorbance at 254 nm in combination with atomic absorption spectroscopy and 300-MHz 1H-NMR (pH dependence of the non-exchangeable base-protons, T1 relaxation time determinations). For the larger fragments the results from these techniques were confirmed by enzymatic degradation studies of the platinated fragments. The smallest of the investigated nucleotides, d(ApG) and d(GpA), both formed a variety of different platinum chelates. In the reaction with d(ApG) 15% cis-Pt(NH3)2-[d(ApG)N1(1),N7(2)] and 78% cis-Pt(NH3)2[d(ApG)N7(1),N7(2)] were found, 4% of the reacted material consisted of a 1 mol Pt/2 mol dinucleotide product, and 3% of an unidentified 1:1 product. From the main product two rotamers were found to occur: at room temperature, 81% anti,anti and 19% anti,syn product is present. With d(GpA) about equal amounts of N1,N7 and N7,N7 products were found; for both products the anti,anti and anti,syn conformations were found, respectively. Upon reaction of cis-PtCl2(NH3)2 with d(pApG) and d(pGpA) only the N7,N7 products were found; at room temperature and pH greater than 1.5 these products were present in anti,anti conformation. However, for the d(pApG)-platinum chelate at -20 degrees C a small amount (less than 5%) of a second product could be observed in NMR. For the d(pGpA)-platinum chelate a second N7,N7-coordinated product was observed when the pH of the NMR sample was lowered to 1.1 (at this pH the free 5'-phosphate group is protonated). With the larger fragments d(ApGpA), d(pApGpA) and d(TpApGpApT) the intra-molecular competition between the formation of the d(ApG) or the d(GpA) chelates could be studied. Using these nucleotides no N1-coordinated products or rotamers were observed. In the case of d(ApGpA) and d(TpApGpApT) the d(GpA) chelate (67% and 75% respectively) was favoured over the d(ApG) chelate, while with d(pApGpA) about equal amounts of both chelates were formed.     

DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4: analysis and crystal structures of multiple base pair substitution and frameshift products with the adduct 1,N2-ethenoguanine

1,N(2)-Etheno(epsilon)guanine is a mutagenic DNA lesion derived from lipid oxidation products and also from some chemical carcinogens. Gel electrophoretic analysis of the products of primer extension by Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) indicated preferential incorporation of A opposite 3'-(1,N(2)-epsilon-G)TACT-5', among the four dNTPs tested individually. With the template 3'-(1,N(2)-epsilon-G)CACT-5', both G and A were incorporated. When primer extension was done in the presence of a mixture of all four dNTPs, high pressure liquid chromatography-mass spectrometry analysis of the products indicated that (opposite 3'-(1,N(2)-epsilon-G)CACT-5') the major product was 5'-GTGA-3' and the minor product was 5'-AGTGA-3'. With the template 3'-(1,N(2)-epsilon-G)TACT-5', the following four products were identified by high pressure liquid chromatography-mass spectrometry: 5'-AATGA-3', 5'-ATTGA-3', 5'-ATGA-3', and 5'-TGA-3'. An x-ray crystal structure of Dpo4 was solved (2.1 A) with a primer-template and A placed in the primer to be opposite the 1,N(2)-epsilon-G in the template 3'-(1,N(2)-epsilon-G)TACT 5'. The added A in the primer was paired across the template T with classic Watson-Crick geometry. Similar structures were observed in a ternary Dpo4-DNA-dATP complex and a ternary Dpo4-DNA-ddATP complex, with d(d)ATP opposite the template T. A similar structure was observed with a ddGTP adjacent to the primer and opposite the C next to 1,N(2)-epsilon-G in 3'-(1,N(2)-epsilon-G)CACT-5'. We concluded that Dpo4 uses several mechanisms, including A incorporation opposite 1,N(2)-epsilon-G and also a variation of dNTP-stabilized misalignment, to generate both base pair and frameshift mutations.     

The structure of the carbohydrate backbone of the lipopolysaccharides from Bordetella hinzii and Bordetella bronchiseptica.

The structure of the core-lipid A region of the lipopolysaccharides from Bordetella hinzii and Bordetella bronchiseptica has been analyzed. Lipopolysaccharides were deacylated using strong alkaline hydrolysis, the products were separated by high performance anion-exchange chromatography and analyzed by NMR and mass spectrometry. The following structure of the products can be deduced from the experimental results: where for the product from Bordetella hinzii N = H, R = H, beta-FucN4N- or partially N-acetylated Sug-(1-3)-beta-FucN4N and for the product from Bordetella bronchiseptica N = alpha-Hep, R = H, beta-FucN4N, beta-FucN4NMe or partially N-acetylated Sug-(1-3)-beta-FucN4N or Sug-(1-3)-beta-FucN4NMe; Sug = 2,3-diamino-2,3, 4-trideoxy-hex-4-enuronopyranosyl.     

Reaction of N3-benzoyl-3',5'-O-(di-tert-butylsilanediyl)uridine with hindered electrophiles: intermolecular N3 to 2'-O protecting group transfer

The compound N3-benzoyl-3',5'-O-(di-tert-butylsilanediyl)uridine 2 was alkylated with various alkyl iodides in CH3CN in the presence of base. Normal 2'-O-alkylated products were obtained with methyl or benzyl iodide. If hindered alkyl iodides with beta-branching such as 2-ethylbutyl iodide were used as electrophiles under the same conditions, N3-alkyl-2'-O-benzoyl uridine derivatives were produced. This unexpected transformation is usually dormant with reactive alkylating agents, but expressed with sterically hindered, less reactive electrophiles. This unwanted reaction gives isomeric products whose spectra differ in only subtle ways from target compounds.     

3-hydroxykynurenine-mediated modification of human lens proteins: structure determination of a major modification using a monoclonal antibody

Tryptophan can be oxidized in the eye lens by both enzymatic and non-enzymatic mechanisms. Oxidation products, such as kynurenines, react with proteins to form yellow-brown pigments and cause covalent cross-linking. We generated a monoclonal antibody against 3-hydroxykynurenine (3OHKYN)-modified keyhole limpet hemocyanin and characterized it using 3OHKYN-modified amino acids and proteins. This monoclonal antibody reacted with 3OHKYN-modified N(alpha)-acetyl lysine, N(alpha)-acetyl histidine, N(alpha)-acetyl arginine, and N(alpha)-acetyl cysteine. Among the several tryptophan oxidation products tested, 3OHKYN produced the highest concentration of antigen when reacted with human lens proteins. A major antigen from the reaction of 3OHKYN and N(alpha)-acetyl lysine was purified by reversed phase high pressure liquid chromatography, which was characterized by spectroscopy and identified as 2-amino-3-hydroxyl-alpha-((5S)-5-acetamino-5-carboxypentyl amino)-gamma-oxo-benzene butanoic acid. Enzyme-digested cataractous lens proteins displayed 3OHKYN-derived modifications. Immunohistochemistry revealed 3OHKYN modifications in proteins associated with the lens fiber cell plasma membrane. The low molecular products (<10,000 Da) isolated from normal lenses after reaction with glucosidase followed by incubation with proteins generated 3OHKYN-derived products. Human lens epithelial cells incubated with 3OHKYN showed intense immunoreactivity. We also investigated the effect of glycation on tryptophan oxidation and kynurenine-mediated modification of lens proteins. The results showed that glycation products failed to oxidize tryptophan or generate kynurenine modifications in proteins. Our studies indicate that 3OHKYN modifies lens proteins independent of glycation to form products that may contribute to protein aggregation and browning during cataract formation.     

白纹伊蚊细胞色素P450 CYP6家族基因多样性的研究(英文)

根据已获得的白纹伊蚊CYP6家族某成员cDNA序列片段AEDR ,设计基因特异性引物 ,以白纹伊蚊总RNA为模板 ,进行cDNA末端快速扩增 ,扩增产物经T -A克隆、测序。结果显示 :通过 5’ RACE获得 1个非全长cDNA序列 (GZS331 ) ,其与CYP6N1、CYP6N2的同源性分别为 59 8%和 59 1 % ,与CYP6N3v1 -v3同源性最高 ,达 83 9% - 84 3% ;通过 3’ RACE获得 6个非全长cDNA序列 ,其中来自抗性株的GZG0 33序列与CYP6N3v1 -v3的同源性达 98 2 % - 99 1 % ,而其余 3’ RACE克隆与CYP6N3v1 -v3的同源性则达 84 3% - 85 6%。上述所有非全长cDNA序列均与哺乳动物CYP3A1以及夜蛾CYP9A1有较高的同源性 ,分别为 2 3% - 36 1 %和 2 7 6% - 34 1 %。用PC/GENE软件所绘制的系统树显示出与同源性分析相一致的结果。所得非全长cDNA序列上报国际P450命名委员会进行统一的命名 ,并对蚊虫中细胞色素P450基因多样性及其形成原因进行了分析     

Kinetics of formation of specific styrene oxide adducts in double-stranded DNA.

The possible carcinogenicity of styrene is believed to be related to the DNA-binding properties of styrene 7,8-oxide (SO). In order to compare the intrinsic reactivity of the different nucleophilic sites in DNA towards SO and to evaluate the candidates for human biomonitoring we have determined the second-order rate constants and stabilities of several SO-adducts in double-stranded DNA. These include alpha- and beta-isomers of N7-substituted and alphaN(2)-substituted guanines, alpha- and betaN3-substituted and alphaN(6)-substituted adenines as well as betaN3- and alphaN(4)-substituted cytosines. The highest rate constants were found for the spontaneously depurinating N7-guanines being ca. 3-15-fold higher than those for the stable adducts. When the relative proportions of different alkylation products were determined in course of time, after a single addition of SO, the labile N7-guanines and N3-adenines were the major products at early time points. After 144 h of incubation at 37 degrees C, alphaN(6)-SO-adenine and alphaN(2)-SO-guanine as well as betaN3-SO-uracil were the major adducts. Regarding human biomonitoring, the N7-substituted guanines should be one of the main targets because of the high reactivity of the N7-atom of guanine. However, in the case of chronic styrene exposures the chemically more stable DNA adducts may become important.     

STUDY ON THE DIVERSITY OF CYTOCHROME P450 GENES FROM AEDES ALBOPICTUS*

Abstract Several pairs of specific primers according to the obtained cDNA sequence fragment from deltamethrin‐resistant Aedes albopktus were designed to amplify new CYP6 genes from total RNA of Aedes albopictus by rapid amplification of cDNA ends (RACE) technique. The products of RACE were cloned and selected for sequencing. The deduced amino acid sequences were subjected to homologous analysis. The results indicated that the identities of clone GZS331 sequence from 5′‐RACE products and clone GZG033 sequence from 3′‐RACE products to CYP6N3vl ‐ v3 are 83.9% ‐ 84.3% and 98.2% ‐ 99.1% respectively; while the identities of the others from 3′‐RACE products to CYP6N3v1 ‐ v3 are 84.3% ‐ 85.6%. All of these obtained cDNA sequences have a higher homology to CYP3A1 in mouse and CYP9A1 in moth. The dendrogram constructed by PC/GENE software showed similar results to homologous analysis. These obtained sequences were submitted and named by the P450 Nomenclature Committee. The diversity of cytochrome P450 genes in Culicidae species was discussed.     

Relationship between availability indices and plant uptake of nitrogen and phosphorus from organic products

A better knowledge of the plant-availability of nitrogen (N) and phosphorus (P) in organic products may help to improve the efficient use of these products as fertilizers. In the present study, availability indices for N and P of nine widely differing organic products obtained by different fractionation methods were compared with the plant uptake of N and P from these products. The fractionation methods included CaCl₂ extraction, thermal fractionation (heating of organic products), and pepsin extraction, for N, and extraction with diluted sulphuric acid, P-Bray-I, P-Olsen, and extraction using an iron oxide coated filter paper, for P. The results of pot experiments with ryegrass using a double-pot technique (Janssen, 1990) over 62 (N experiment) and 93 days (P experiment) were used as reference for plant-availabe N and P. The 0.01 M CaCl₂ extractable inorganic N reasonably predicted plant-available N only in organic products with a high inorganic N fraction. Thermal fractionation and pepsin extraction provided a reasonable index for mineralizable N in organic products having a high fraction of mineralizable N. Of the P fractionation methods, the extraction using iron oxide coated filter paper was the best indicator of plant-available P in the products.     

Photoproducts of bacteriorhodopsin mutants: a molecular dynamics study.

Molecular dynamics simulations of wild-type bacteriorhodopsin (bR) and of its D85N, D85T, D212N, and Y57F mutants have been carried out to investigate possible differences in the photoproducts of these proteins. For each mutant, a series of 50 molecular dynamics simulations of the photoisomerization and subsequent relaxation process were completed. The photoproducts can be classified into four distinct classes: 1) 13-cis retinal, with the retinal N-H+ bond oriented toward Asp-96; 2) 13-cis retinal, with the N-H+ oriented toward Asp-85 and hydrogen-bonded to a water molecule; 3) 13,14-di-cis retinal; 4) all-trans retinal. Simulations of wild-type bR and of its Y57F mutant resulted mainly in class 1 and class 2 products; simulations of D85N, D85T, and D212N mutants resulted almost entirely in class 1 products. The results support the suggestion that only class 2 products initiate a functional pump cycle. The formation of class 1 products for the D85N, D85T, and D212N mutants can explain the reversal of proton pumping under illumination by blue and yellow light.     

32P-postlabeling of N-7, N2 and O6 2'-deoxyguanosine 3'-monophosphate adducts of styrene oxide

Adducts were prepared by reacting styrene oxide with 2-deoxyguanosine 3'-monophosphate (dGMP). Four isomeric N-7-, two diastereomeric N2- and three isomeric O6-adduct were isolated and characterized. The adducts were used as substrates in the 32P-postlabeling reaction. No phosphorylation products were seen with the N-7-alkylation products. One diastereomeric N2-adduct was labeled with 20% efficiency and the second with a markedly lower efficiency. Two of the three O6-adducts were labeled with 5% and the third with 10% labeling efficiency. The results suggest that large N-7-dGMP adducts are very poor substrates of T4 polynucleotide kinase. The diastereomeric products are labeled at different efficiencies indicating stereoselectivity in the kinase reaction.     

Synthesis and structure determination of some oxadiazole-2-thione and triazole-3-thione galactosides

The syntheses of 5-pyridyl-3(beta-D-galactopyranosyl)-1,3,4-oxadiazole-2-thiones 3a-3c and 5-pyridyl-2(beta-D-galactopyranosyl)-4-benzyl-1,2, 4-triazole-3-thiones 6a-6c are reported. The existence of N-galactosides--not S-galactosides--was proven by IR and 15N NMR spectroscopy. The structures of the final products and the intermediates were elucidated by IR, 1H, 13C and 15N NMR spectroscopy and mass spectrometry.     

Simple synthesis of a complete set of unconjugated norethisterone metabolites and their deutero-analogs

The short-step synthesis of all norethisterone (NET) hydrogenated metabolites and their deuteroanalogues has been accomplished. Reduction of NET by NaBH4 in the presence of N,N,N',N'-tetramethylethylenediamine provided 19-norpregn-20-yn-3,17-diols as a mixture of 3- and 5-epimers. The individual isomers were isolated by flash chromatography and oxidyzed by PyHCrO3Cl into 5 alpha- and 5 beta-dihydro-NET. These products were converted, on isotopic exchange with D2O--MeOD in alcaline conditions followed by reduction with NaBD4, into four stereoisomeric 2,2,3,4,4-pentadeuterated 19-norpregn-20-yn-3,17-diols; two isomeric 2,2,3,4,4,16,16,17-octadeuterated estrane-3,17-diols were also isolated as side products. All compounds obtained will be used as internal standards for chromato-mass-fragmentographic analysis.     

Synthesis of N2-alkylguanosine using Mitsunobu reaction as a key step

Peracetylated guanosine was reacted with POCl3 to give an 2-acetamido-6-chloro-9H-purine derivative, which was condensed with primary or secondary alcohols to give N2-alkylated analogues. The products were treated with mercaptoethanol in the presence of sodium methoxide to afford N2-alkylguanosines.     

A new method for the synthesis of N2-alkylguanosines using Mitsunobu reaction as a key step

Peracetylated guanosine was reacted with POCl3 to give an 2-acetamido-6-chloro-9H-purine derivative, which was condensed with primary or secondary alcohols to give N2-alkylated analogues. The products were treated with mercaptoethanol in the presence of sodium methoxide to afford N2-alkylguanosines.     

A novel type of oxygenolytic ring cleavage: 2,4-oxygenation and decarbonylation of 1H-3-hydroxy-4-oxoquinaldine and 1H-3-hydroxy-4-oxoquinoline

Abstract The utilization of quinaldine (2-methylquinoline) by Arthrobacter sp. Rü61a proceeds via 1 H -4-oxoquinaldine, 1 H -3-hydroxy-4-oxoquinaldine, and N -acetyl-anthranilic acid. By analogy, 1 H -4-oxoquinoline is degraded by Pseudomonas putida 33/1 via 1 H -3-hydroxy-4-oxoquinoline and N -formylanthranilic acid. Using the purified enzymes from both organisms, the mode of N -heterocyclic ring cleavage was investigated. The conversions of 1 H -3-hydroxy-4-oxoquinaldine and 1 H -3-hydroxy-4-oxoquinoline to N -acetyl- and N -formylanthranilic acid, respectively, were both accompanied by the release of carbon monoxide. The enzyme-catalysed transformations were performed in an [¹⁸O]O₂ atmosphere and resulted in the incorporation of two oxygen atoms into the respective products, N -acetyl- and N -formylanthranilic acid, indicating an oxygenolytic attack at C-2 and C-4 of both 1 H -3-hydroxy-4-oxoquinaldine and 1 H -3-hydroxy-4-oxoquinolone.     

Modulation of the regioselectivity of a Thermotoga neapolitana beta-glucosidase by site-directed mutagenesis

Thermotoga neapolitana beta-glucosidase (BglA) was subjected to site-directed mutagenesis in an effort to increase its ability to synthesize arbutin derivatives by transglycosylation. The transglycosylation reaction of the wild-type enzyme displays major beta(1,6) and minor beta(1,3) or beta(1,4) regioselectivity. The three mutants, N291T, F412S, and N291T/F412S, increased the ratio of transglycosylation/hydrolysis compared with the wild-type enzyme when pNPG and arbutin were used as a substrate and an acceptor, respectively. N291T and N219T/F412s had transglycosylation/hydrolysis ratios about 3- and 8-fold higher, respectively, than that of the wild-type enzyme. This is due to the decreased hydrolytic activity of the mutant rather than increased transglycosylation activity. Interestingly, N291T showed altered regioselectivity, as well as increased transglycosylation products. TLC analysis of the transglycosylation products indicated that N291T retained its beta(1,3) regioselectivity, but lost its beta(1,4) and beta(1,6) regioselectivity. The altered regioselectivity of N291T using two other acceptors, esculin and salicin, was also confirmed by TLC. The major transglycosylation products of the wild type and N291T mutant were clearly different. This result suggests that Asn-291 is highly involved in the catalytic mechanism by controlling the transglycosylation reaction.     

Properties of soluble rat brain histone lysine methyltransferase.

Histone-lysine methyltransferase has been solubilized from rat brain chromatin by repeated extraction with distilled water. The enzyme was further purified by chromatography on DEAE-cellulose and gel filtration. With chromosomal-bound histones as substrates, the enzyme methylated only the lysyl residues in histones H3 and H4. The ratio of N epsilon-mono-: N epsilon-di-: N epsilon-trimethyllysine in histone H3 was 1.8:1.0:0.45 and the ratio of N epsilon-mono-: N epsilon-dimethyllysine in histone H4 was 0.7:1.0. The enzyme loses specificity with soluble histones as substrates; however, histones H3 and H4 were still the best methyl acceptors. The pH optima for the enzyme with soluble histones H3 and H4 as substrates were 8.2 to 8.7 and 7.2 to 8.0, respectively. S-Adenosyl-L-homocysteine, one of the products of the reaction, was a competitive inhibitor with respect to S-adenosyl-L-methionine.     

Insect antifeedant compounds from Nothofagus dombeyi and N. pumilio

A bioassay-guided purification of the extracts of Nothofagus dombeyi and N. pumilio leaves yielded several triterpenes and flavonoids including 2-O-acetylmaslinic acid, 3-O-acetyl 20,24,25-trihydroxydammarane, and 3,20,24,25-tetrahydroxydammarane as new natural products. All the isolated compounds were assessed for antifeeding activity against the 5th instar larvae of Ctenopsteustis obliquana. 12-Hydroxyoleanolic lactone and pectolinarigenin from N. dombeyi and dihydrooroxylin A from N. pumilio, showed significant antifeeding activity.