Two-dimensional 1H NMR study of two cyclobutane type photodimers of thymidylyl-(3′→5′)-thymidine

2D NMR spectroscopy and J coupling constant analysis are applied to resolve the structure of two photoproducts of thymidylyl-(35)-thymidine. These products are cyclobutane type thymine dimers possessing the cis-syn (the predominant one) and trans-syn geometry. The cis-syn is formed in an ANTI-ANTI conformation about the N-glycosyl linkages and resembles the normal base-stacked configuration. The glycosidic conformation in solution of the 5 terminal fragment differs from the crystal in which the less common SYN conformation is observed. In this isomer only the sugar pucker of the 3 terminal fragment is changed substantially with respect to the dinucleotide. The trans-syn isomer is formed in a SYN-ANTI glycosidic conformation. In this isomer the sugar puckers of both deoxyribose rings are affected and a preference for a pure 2-endo conformation is observed.Abbreviations dTpdT 2-deoxythymidylyl-(35)-2-deoxythymidine - dTp[]dT cyclobutane type photodimers of dTpdT - dTp- and dTp[]- their 5' terminal fragments (fragment A) - -pdT and-[]pdT their 3 terminal fragments (fragment B) - RP-HPLC reversed-phase high-performance liquid chromatography - COSY two-dimensional correlated spectroscopy - 2D NOE two-dimensional nuclear Overhauser spectroscopy     

The formation of peptides from the 2′(3′)-glycyl ester of a nucleotide

Summary We have synthesized 2(3)-O-(glycyl)-adenosine-5-(O-methylphos-phate), an analogue of the 3-terminus of aminoacylated tRNA. A 0.4M solution of this compound maintained at pH 8.2, yields 5.5% of diglycine and 11.5% of diketopiperazine, in addition to the hydrolysis products glycine and adenosine-5-(O-methylphosphate). Under the same conditions, glycine ethyl ester reacts much more slowly, but ultimately gives similar yields of diglycine and diketopiperazine.The aminolysis of 2(3)-O-(glycyl)-adenosine-5-(O-methylphosphate) by free glycine is relatively inefficient, but serine reacts 20 times more rapidly and yields up to 50% of N-glycylserine. The prebiotic significance of these reactions is discussed.Abbreviations MepA adenosine-5-(O-methylphosphate) - MepA-gly 2(3)-O-(glycyl)-adenosine-5-(O-methylphosphate) - MepA-bis-gly 2,3-O-(bis-glycyl)-adenosine-5-(O-methylphosphate) - DKP diketopiperazine - gly Et glycine ethyl ester - gly-ser N-glycylserine - O-gly-ser O-glycylserine - O-(gly)-gly-ser O-(glycyl)-glycylserine - Boc-gly N-tert-butyloxycarbonylglycine - MepA-Boc-gly 2(3)-O-(Boc-glycyl)-adenosine-5-(O-methylphosphate) - MepA-bis-Boc-gly 2,3-O-(bis-Boc-glycyl)-adenosine-5(O-methylphosphate) - (gly)₂ diglycine - (gly)₃ triglycine     

Microbiological synthesis of 5-ethyl- and (E)-5-(2-bromovinyl)-2′-deoxyuridine

Summary The title compounds were prepared by an enzymatic transdeoxyribosylation from 2 dGuo or 2 dThd to the respective heterocyclic bases, 5-ethyluracil and (E)-5-(2-bromovinyl)uracil, using the whole bacterial cells ofEscherichia coli as a biocatalyst.     

TheDictyostelium discoideum 30,000 dalton protein contributes to phagocytosis

Summary TheDictyostelium discoideum 30 kDa actin-bundling protein cross-links actin filaments into bundles in vitro, and is present in filopodia and pseudopodia in living cells. Monoclonal antibodies reactive with this protein have been isolated, and employed as specific probes for the function of this protein. The monoclonal antibody B2C blocks the interaction of the 30 kDa protein with F-actin in vitro, and decreases phagocytosis ofE. coli when introduced into livingDictyostelium cells by controlled sonication. Use of this monoclonal antibody for visualization of the 30 kDa protein by immunofluorescence microscopy reveals striking localization around food particles during the process of phagocytosis. Double staining with rhodamine-labelled phalloidin and the monoclonal antibody documents the co-localization of the 30 kDa protein and actin during formation of phagocytic cups. The dissociation of the 30 kDa protein occurs during the process of maturation to form phagolysosomes. These results support the hypothesis that this actin cross-linking protein participates in dynamic rearrangements of actin filaments accompanying phagocytosis.Abbreviations ATP adenosine 5-triphosphate - DEAE diethyl aminoethyl - EDTA (ethylenedinitrilo)-tetraacetic acid - EGTA ethylene glycol-bis(-aminoethyl ether) N,N,N,N-tetraacetic acid - PAGE polyacrylamide gel electrophoresis - PIPES piperazine-N,N-bis[2-ethanesulfonic acid] - SDS sodium dodecyl sulfate - Sorensen's buffer 2mM Na₂HPO₄+15mM KH₂PO₄, pH6.1 - Tris tris-(hydroxymethyl) aminomethane     

A novel PH-CT-COSY methodology for measuring JPH coupling constants in unlabeled nucleic acids. Application to HIV-2 TAR RNA

A quantitative analysis of J_PH scalar couplings in nucleic acids is difficult due to small couplings to phosphorus, the extreme overlap of the sugar protons and the fast relaxation of the spins involved in the magnetization transfer. Here we present a new methodology that relies on heteronuclear Constant Time Correlation Spectroscopy (CT-COSY). The three vicinal ³J_PH3, ³J_PH5 and ³J_PH5 scalar couplings can be obtained by monitoring the intensity decay of the P_i-H3_{i – 1} peak as a function of the constant time T in a 2D correlation map. The advantage of the new method resides in the possibility of measuring the two ³J_PH5 and ³J_PH5 scalar couplings even in the presence of overlapped H5/H5 resonances, since the quantitative information is extracted from the intensity decay of the P-H3 peak. Moreover, the relaxation of the H3 proton is considerably slower than that of the H5/H5 geminal protons and the commonly populated conformations of the phosphate backbone are associated with large ³J_PH3 couplings and relatively small ³J_{PH5 / H5}. These two facts lead to optimal signal-to-noise ratio for the P-H3 correlation compared to the P-H5/H5 correlation.The heteronuclear CT-COSY experiment is suitable for oligonucleotides in the 10–15 kDa molecular mass range and has been applied to the 30mer HIV-2 TAR RNA. The methodology presented here can be used to measure P-H dipolar couplings (D_PH) as well. We will present qualitative results for the measurement of P-H_base and P-H2 dipolar couplings in the HIV-2 TAR RNA and will discuss the reasons that so far precluded the quantification of the D_PHs for the 30mer RNA.     

The catalysis of nucleotide polymerization by compounds of divalent lead

Summary Soluble lead salts and a number of lead-containing minerals catalyze the formation of oligonucleotides from nucleoside 5-phosphorimidazolides. The effectiveness of lead compounds correlates strongly with their solubility. Under optimal conditions we were able to obtain 18% of pentamer and higher oligomers from ImpA. Reactions involving ImpU gave smaller yields.Abbreviations A adenosine - U uridine - Im imidazole - MeIm 1-methyl-imidazole - EDTA ethylenediaminetetraacetic acid - pA adenosine 5-phosphate - pU uridine 5-phosphate - Ap adenosine cyclic 2:3-phosphate - ATP adenosine 5-triphosphate - AppA P₁,P₂-diadenosine 5-diphosphate - pNp (N = A,U) nucleotide 2(3), 5-diphosphate - ImpA adenosine 5-phosphoreimidazolide - ImpU uridine 5-phosphorimidazolide - A ²pA adenylyl-[25]-adenosine - A ³pA adenylyl-[35]-adenosine - pA ²pA 5-phospho-adenylyl-[25]-adenosine - pA ³pA 5-phospho-adenylyl-[35]-adenosine - pUpU 5-phospho-uridylyl-uridine - pApU 5-phospho-adenylyl-uridine - pUpA 5-phospho-uridylyladenine - (pA)n (n, 2,3,4,) oligoadenylates with 5 terminal phosphate - ImpApA 5-phosphorimidazolide of adenylyl adenosine - (pA) ₅₊ pentamer and higher oligoadenylates with 5 terminal phosphate - (Ap)nA (n = 2,3,4) oligoadenylates without terminal phosphates In the following we do not specify the nature of the internucleotide linkageIn the following we do not specify the nature of the internucleotide linkage     

A unique surface membrane anchored purine-salvage enzyme is conserved among a group of primitive eukaryotic human pathogens

Previously, we isolated and characterized the gene encoding the 3-Nucleotidase/Nuclease (Ld3NT/NU) from the human pathogen, Leishmania donovani. This unique cell surface enzyme has been shown to be involved in the salvage of host-derived purines, which are essential for the survival of this important protozoan parasite. In this report, we assessed whether the 3-Nucleotidase/Nuclease was conserved amongst other pathogenic Leishmania and related trypanosomatid parasites. Results of pulsed field gel electrophoresis and Southern blotting showed that a Ld3NT/NU gene homolog was present in each of the visceral and cutaneous Leishmania species tested (i.e. isolates of L. donovani, L. infantum, L. tropica, L. major and L. mexicana, respectively). Further, results of colorimetric assays using 3-adenosine monophosphate as substrate demonstrated that each of these organisms also expressed significant levels of 3-nucleotidase enzyme activity. In addition, we showed that a Ld3NT/NU gene homolog was expressed in each of these Leishmania species as a > 40 kDa 3-nucleotidase enzyme activity. A Ld3NT/NU gene homolog was also identified in two Crithidia species (C. fasciculata and C. luciliae) and Leptomonas seymouri but was only marginally detectable in Trypanosoma brucei, Trypanosoma cruzi and Phytomonas serpens. Cumulatively, results of this study showed that an Ld3NT/NU homolog was conserved amongst pathogenic Leishmania sp. which suggests that this enzyme must play an critical role in purine salvage for all members of this group of human pathogens.     

DNA sequence analysis of spontaneous mutation in a PolA1 strain of Escherichia coli indicates sequence-specific effects

Summary The sequences of a collection of 261 spontaneous lacI^- mutants recovered in a PolA^- strain of Escherichia coli have indicated an increase in the frequency of most classes of mutation in this strain. Among base substitutions in lacI, a preference for transversions over transitions was observed. In addition, a single transition in the lac operator was enhanced 8-fold. More significantly, of 18 frameshifts, 12 occurred adjacent to a 5-GTGG-3 sequence. Likewise, 15 of 24 deletions and 2 of 10 duplications had 5-GTGG-3 sequences at one or both endpoints. We speculate that the prevalence of mutations at these specific sequences reflects the persistence of strand discontinuities that enhance the opportunity for mutagenic mishaps. Further, 5-GTGG-3 sequences apparently represent sites where DNA polymerase I is involved in some aspect of DNA metabolism. These results strengthen the view that DNA context contributes an important component to spontaneous mutagenesis and indicate an anti-mutagenic role for DNA polymerase I.     

Geometry of the dry-state oligomerization of 2′,3′-cyclic phosphates

Summary Evaporation of a solution of thymidine plus either theexo or theendo diastereomer of uridine cyclic 2,3-O, O-phosphorothioate (U > p(S) in 1,2-diaminoethane hydrochloride buffer gave the 2,5 and 3,5 isomers of (P-thio) uridylylthymidine (Up(S)dT) in a ratio of 1:2 with a combined yield of about 20%. These isomers were re-converted to U > p(S) and dT by a reaction that is known to proceed by an in-line mechanism. Both the 2,5 and 3,5 isomers gave as product the same diastereomer of U > p(S) that had been used originally in their formation. These dry-state prebiotic reactions (Verlander, Lohrmann, and Orgel 1973) are thus shown to be stereospecific, and both the 2,5 and 3,5 internucleotide bonds are formed by an in-line mechanism.Abbreviations DAE 1,2-diaminoethane - HPLC high pressure liquid chromatography - RNase bovine pancreatic ribonuclease A, EC 3.1.4.22 - TEAB triethylammonium bicarbonate - tris tris(hydroxymethyl)aminomethane - UMP(S) uridine monophosphorothioate - U > p uridine cyclic 2,3-phosphate - U > p(S) uridine cyclic 2,3-O, O-phosphorothioate - Up(S)dT (P-thio)uridylylthymidine - U2p(R_p-S)5dT (P-thio)uridylylthymidine with theR configuration at phosphorous, and a 2,5 internucleotide linkage     

Restoration of the wild-type locus in an RuBP carboxylase/oxygenase mutant of Synechocystis PCC 6803 via targeted gene recombination.

Summary The interaction between homologous DNA sequences, distant from each other in the chromosome, was examined in the cyanobacterium Synechocystis PCC 6803. Most of the rbcL gene encoding the large subunit of ribulose bisphosphate carboxylase/oxygenase (Rubisco) was duplicated in the genome by a targeted insertion of a 3-truncated gene copy into the psbA-I locus. Both rbcL genes, in the psbA-I region and at the rbc locus, were non-functional; The former due to the 3 truncation, and the latter due to a deletion in the 5-region (creating a 5 truncation) and a mutation associated with an insertion of the Rhodospirillum rubrum rbc gene, yielding a high-CO₂-requiring mutant (cyanorubrum). The 3 and the 5 truncated rbcL genes were linked to chloramphenicol and kanamycin resistance markers, respectively. Decreasing the kanamycin selective pressure concomitantly with exposure of the double resistance mutant to air, resulted in air-growing colonies. Analysis of their genomes, Rubisco proteins, and their ultrastructure revealed: 1) Reconstitution of a full-length cyanobacterial rbcL gene at the rbc locus; 2) simultaneous synthesis of the cyanobacterial (L₈S₈) and R. rubrum L₂) enzymes in meroploids containing both mutated and reconstituted rbcL genes; 3) reappearance of carboxysomes. Our results indicate extensive recombinatorial interactions between the homologous sequences at both loci leading to reconstitution of the cyanobacterial rbcL gene.     

Occurrence of pppApp-synthesizing activity in actinomycetes and isolation of purine nucleotide pyrophosphotransferase

The occurrence of adenosine 5-triphosphate-3-diphosphate-synthesizing activity was detected in five strains of actinomycetes; Streptomyces morookaensis, Streptomyces aspergilloides, Streptomyces hachijoensis, Actinomyces violascens and Streptoverticillium septatum, out of 825 strains of actinomycetes, bacteria, fungi and imperfecti. Purine nucleotide pyrophosphotransferase were extracellularly excreted associating with the cell growth, and were purified partially or to apparent homogeniety from the culture filtrate. The enzymes are a monomeric protein with a molecular weight of 18000–26000 and synthesize adenosine, guanosine and inosine 5-phosphate (mono, di or tri)-3-diphosphate such as pApp, ppApp, pppApp, pGpp, ppGpp, pppGpp and pppIpp by transferring a pyrophosphoryl group from the 5-position of ATP, dATP and pppApp to the 3-position of purine nucleotides in the presence of a divalent cation and in alkaline state.Abbreviations pppApp adenosine 5-triphosphate 3-diphosphate - ppApp adenosine 5-diphosphate 3-diphosphate - pApp adenosine 5-monophosphate 3-diphosphate - pppGpp guanosine 5-triphosphate 3-diphosphate     

Microtubular structures developed in response to a carbamate herbicide in plant mitosis

Summary Indirect immunodetection of tubulin showed that the herbicide carbetamide activated silent signals left by the preprophase band (PPB) and by old phragmoplasts. Thus, after half an hour of treatment, 5.3% of anaphases inAllium cepa L. meristems showed spindle microtubules pointing to sites of the longitudinal cell membranes which, under control conditions, would only start attracting microtubules from the growing phragmoplast at late telophase. After 2 h, 12.8% of the telophases showed not only the expected phragmoplast between the two sister nuclei, but one or two additional phragmoplasts, at one or both cell tips, the sites of the phragmoplasts from the telophases of previous cycles. A few binucleate cells, obtained by aborting phragmoplast formation by a short caffeine treatment, developed three phragmoplasts in their next mitosis (bimitosis) in the presence of carbetamide: one between each sister pair of telophasic nuclei plus an extra one. The latter also occupied the site of the phragmoplast of the telophase of the previous cycle.Abbreviations PPB preprophase band of microtubules - EGTA ethylene glycol-bis(-amino-ethyl-ether)-N,N,N,N-tetraacetic acid - PMSF phenylmethylsulfonyl-fluoride - PIPES piperazine-N,N-bis(2-ethane sulphonic acid) - PBS phosphate-buffered saline - DAPI 4,6-diamidino-2-phenylindole     

Out-of-plane vibration modes of nucleic acid bases

The out-of-plane vibration modes of uracil, cytosine and their deuterated and methylated derivatives such as 1,5-dimethyluracil (1-methylthymine), I-methylcytosine, 5-methylcytosine and 1,5-dimethylcytosine have been computed. The calculated wave-numbers have been compared to the published Raman peak and infrared band positions observed for solid or aqueous samples. The calculations have been carried out on a non-redundant set of symmetrical coordinates and a valence force field has been used. Some characteristic modes located between 750 and 800 cm^-1 found in the infrared spectra of 2-deoxycytidine, 2-deoxythymidine 5-monophosphate and polynucleotides containing cytosine and thymine bases can be interpreted from the calculated results on 1-methylthymine and 1-methylcytosine.     

Flower color modifications of Torenia hybrida by cosuppression of anthocyanin biosynthesis genes

White and blue/white varieties of Torenia hybrida were successfully obtained from the blue variety cv. Summerwave (SWB) by cosuppressing expression of two of the genes involved in anthocyanin biosynthesis; chalcone synthase (CHS) and dihydroflavonol 4-reductase (DFR). Such molecular breeding is the only precise and efficient way to create flower color variation in SWB due to its male and female sterility. Flower color and the degree of suppression varied between transgenic lines, and anthocyanin biosynthesis was more consistently suppressed in the dorsal petal lobes, ventral petal lobes and corolla tube than lateral petal lobes. A pink variety was obtained by cosuppressing the flavonoid 3,5-hydroxylase (F35H) gene. Yellow torenia was obtained from T-33, an in-house cultivar that contained both carotenoids and anthocyanins, by cosuppression of CHS or DFR genes.     

Sodium efflux from perfused giant algal cells

Internodal cells of the giant alga Chara corallina were perfused internally to replace the native cytoplasm, tonoplast and vacuole with artificial cytoplasm. Sodium efflux from perfused cells, measured by including ²²Na in the perfusion media, was increased by increasing the internal sodium concentration and by decreasing the external pH, and was inhibited by external application of the renal diuretic amiloride. The sodium efflux was markedly ATP-dependent, with a 50-fold decrease in efflux observed after perfusion with media lacking ATP. Efflux in the presence of ATP was reduced by 33% by inclusion of 10 M N,N-dicyclohexylcarbodiimide in the perfusion medium. The membrane potential of the perfused cells approximated that of intact cells from the same culture. It is suggested that sodium efflux in perfused Chara cells proceeds via a secondary antiporter with protons, regulated by ATP in a catalytic role and with the proton motive force acting as the energy source.Abbreviations DCCD N,N-dicyclohexylcarbodiimide - EGTA ethylene glycol-bis(-aminoethyl ether)-N,N,N,N-tetraacetic acid - Mes 2-(N-morpholino)ethanesulphonic acid - Mops 3(N-morpholino)propanesulphonic acid - Taps tris(hydroxymethyl)methylaminopropanesulphonic acid     

Modulation of the beta-adrenergic-response in cultured rat heart cells

Summary Subcellular fractionation studies in resting human neutrophils indicated a bimodal distribution for cytochrome b. A. major peak of cytochrome b co-sedimented with gelatinase under different experimental conditions. This localization was partially overlapped with specific granules (using lysozyme and lactoferrin as specific granule markers), but clearly resolved from azurophilic granules, plasma membrane, mitochondria, as well as from a novel alkaline phosphatase-rich intracellular organelle. A minor localization of cytochrome b was found in fractions enriched in both the plasma membrane marker 5-nucleotidase and alkaline phosphatase. A significant portion of ubiquinone cell content co-fractionated with the gelatinase-containing granules. After phorbol myristate acetate (PMA)-cell stimulation, cytochrome b was mobilized to fractions showing respiratory burst activity and enriched in 5-nucleotidase activity. This mobilization paralleled secretion of gelatinase and lysozyme to the extracellular medium. Furthermore, neutrophil stimulation with fluoride in the absence of cytochalasin B induced release of gelatinase and generation of superoxide anion with only minimal release of lysozyme. Preincubation of cells with the anion channel blocker 4,4-diisothiocyanostilbene-2,2-disulfonic acid (DIDS) prevented lysozyme release, but had only a minor effect on the release of gelatinase and did not inhibit the superoxide anion generation elicited by N-formyl-methionyl-leucyl-phenylalanine or PMA. These results suggest a main location of cytochrome b in mobilizable gelatinase-containing granules, which can constitute a subpopulation of specific granules. Furthermore, these findings show that the gelatinase-containing granule is functionally involved in the respiratory burst in neutrophils and that membrane fusion between plasma membrane and the gelatinase-containing granule occurs during activation of cells.Abbreviations DIDS 4,4-diisothiocyanostilbene-2,2-disulfonic acid - FMLP N-formyl-methionyl-leucyl-phenylalanine - PMA 4-phorbol, 12-myristate, 13-acetate     

Purification and properties of a glycerophosphocholine phosphodiesterase from bovine brain myelin

An enzyme releasing phosphocholine from glycerophosphocholine was purified to apparent homogeneity based upon SDS-PAGE. The enzyme was liberated from lyophilized bovine myelin by differential detergent extraction and final purification was accomplished with Q-Sepharose Fast Flow chromatography yielding an apparently homogenous protein. The molecular mass based upon PAGE was approximately 14 kDa. The enzyme was also capable of releasing p-nitrophenol from p-nitrophenyl-phosphocholine. Maximal activity was obtained with 0.2 mM ZnCl₂ or 1 mM CoCl₂. p-Nitrophenylphosphocholine and phosphocholine were competitive inhibitors of glycerophosphocholine hydrolysis with Ki's of 0.028 mM and 0.03 mM respectively. Glycerophosphocholine and phosphocholine were competitive inhibitors of p-nitrophenylphosphocholine hydrolysis with Ki's of 0.5 mM and 1.75 mM respectively.Abbreviations SDS-PAGE sodium dodecylsulfate polyacrylamide gel electrophoresis - GPC glycerophosphocholine - pNPPC p-nitrophenylphosphocholine - OG octyl--glucoside - PMSF phenylmethylsulfonylfluoride - CNPase 23-cyclic nucleotide 3-phosphodiesterase     

Chemoenzymatic galactosialylation with integrated cofactor regeneration

As a precursor for the chemical synthesis of sialylated oligosaccharides, the trisaccharide glycoside Neu5Ac (2-8)Gal(1-4)GlcNAc(1-O)-pent-4-ene was synthesized starting from GlcNAc(1-O)-pent-4-ene, UDP-glucose andN-acetylneuraminic acid in a one pot reaction employing galactosyltransferase and (2-6)sialyl-transferase in a complete cofactor regeneration system.Abbreviations Neu5Ac N-acetylneuraminic acid - CMP-Neu5Ac cytidine 5-monophosphosialate - CMP cytidine 5-monophosphate - CDP cytidine 5-diphosphate - CTP cytidine 5-triphosphate - Gal galactose - GlcNAc N-acetylglucosamine - UDP uridine 5-diphosphate - UDP-Glc uridine-5-diphosphoglucose - UDP-Gal uridine-5-diphosphogalactose - PEP phosphoenolpyruvate     

Molecular gene mapping of human aldolase A (ALDOA) gene to chromosome 16

Summary Mapping of human aldolase A (ALDOA) gene was performed by molecular hybridization techniques using a panel of human-mouse cell hybrids and sorted fractions of human metaphase chromosomes besides in situ hybridization. For the purpose, three kinds of DNA probes derived from the coding region (probe-1), the 3 noncoding region (probe-2), and the coding and 3 noncoding regions (probe-3) of human aldolase A cDNA clone, pHAAL116-3, were selectively employed. The results of RNA and DNA blot analyses indicated that the human ALDOA gene is located on chromosome 16. The in situ hybridization experiment also indicated that the ALDOA gene was localized to 16q22–q24.     

Effect of adenosine monophosphates on the flowering of Impatients balsamina L., a qualitative short-day plant

Summary Adenosine monophosphates (AMPs) cause the induction of floral buds in Impatients balsamina L. under strictly non-inductive photoperiods and hasten it under inductive photoperiods, cyclic AMP being more effective than 3- or 5-AMPs in this regard.Abbreviations cyclic AMP cyclic 3,5-adenosine monophosphate