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Sample records for 5-methyl uracil

  1. Multiphoton ionization of Uracil

    NASA Astrophysics Data System (ADS)

    Prieto, Eladio; Martinez, Denhi; Guerrero, Alfonso; Alvarez, Ignacio; Cisneros, Carmen

    2016-05-01

    Multiphoton ionization and dissociation of Uracil using a Reflectron time of flight spectrometer was performed along with radiation from the second harmonic of a Nd:YAG laser. Uracil is one of the four nitrogen bases that belong to RNA. The last years special interest has been concentrated on the study of the effects under UV radiation in nucleic acids1 and also in the role that this molecule could have played in the origin and development of life on our planet.2 The MPI mass spectra show that the presence and intensity of the resulting ions strongly depend on the density power. The identification of the ions in the mass spectra is presented. The results are compared with those obtained in other laboratories under different experimental conditions and some of them show partial agreement.3 The present work was supported by CONACYT-Mexico Grant 165410 and DGAPA UNAM Grant IN101215 and IN102613.

  2. Synthesis of cyclobutane nucleosides 2-preparation of thymine and uracil analogues.

    PubMed

    Afifi, Hanan; Ebead, Abdelaziz; Pignatelli, Joseph; Lee-Ruff, Edward

    2015-01-01

    1-(2-Oxocyclobutyl-4-benzoyloxymethyl)-2,4(1H,3H)-pyrimidinedione and 1-(2-oxocyclobutyl-4-benzoyloxymethyl)-5-methyl-2,4(1H,3H)-pyrimidinedione can be prepared by reaction of uracil and thymine, respectively, with 3-benzoyloxymethyl-2-bromocyclobutanone. The N-alkylation gave both cis and trans isomers with the trans isomer predominating for uracil whereas the trans isomer was the only product which could be isolated for thymine. Both series were subjected to borohydride reduction followed by transesterification with methoxide giving the corresponding uracil and thymine nucleoside analogues. The uracil derivative 1-(2-oxocyclobutyl-4-benzoyloxymethyl)-2,4(1H,3H)-pyrimidinedione was irradiated in aqueous acetonitrile to generate isonucleoside analogues.

  3. Methylation of thymine and uracil with free methyl cations formed due to beta-decay of tritiated methane: possible implication in mutagenesis and carcinogenesis.

    PubMed

    Korsakov, M V; Bystrova, M O; Mironiuk, T A; Sinotova, E N; Ivin, B A; Nefedov, V D; Likhachev, A J

    1989-05-01

    Exposure of solid thymine and uracil at room temperature to free methyl cations, produced due to beta-decay of tritiated methane, resulted in formation of their 1-, O2-, 3-, O4-, and 6-methyl derivatives. In addition, uracil formed a 5-methyl derivative (thymine); tritium-containing thymine and uracil were also detected. Both thymine and uracil formed predominantly unidentified products which resulted presumably from their oligomerization. Incubation at -195 degrees C did not markedly change the pattern of reaction products. Aqueous-ammonia solutions of these pyrimidines formed methylated derivatives and considerable amounts of methanol and tritiated water. The possible implication of these reactions in mutagenic and carcinogenic effects of tritium-substituted hydrocarbons is discussed.

  4. Antimicrobial Cellulose: Preparation and Application of 5-Methyl-5-Aminomethylhydantoin

    DTIC Science & Technology

    2006-08-01

    AFRL-ML-TY-TP-2006-4553 PREPRINT ANTIMICROBIAL CELLULOSE: Preparation and Application of 5-methyl-5- aminomethylhydantoin L. Kou, J...TELEPHONE NUMBER (Include area code) Antimicrobial Cellulose: Preparation and Application of 5-methyl-5-aminomethylhydantoin L. Kou1, J. Liang1, S.D...periods of time [1,4,6-8,10]. Thus antimicrobial textiles and polymers are in great demand for protection against infectious disease pathogens

  5. Decameric uracil complexes around Li+.

    PubMed

    Zins, Emilie-Laure; Pepe, Claude; Schröder, Detlef

    2010-07-01

    Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li(+) ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U(10)Li(+) is formed, which was referred to as an indication for so-called 'magic number' cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas-phase structure which is compatible with all experimental findings. 2010 John Wiley & Sons, Ltd.

  6. Genetic variants in uracil processing enzymes are associated with abnormal DNA uracil content

    USDA-ARS?s Scientific Manuscript database

    Introduction. Maintenance of DNA integrity through DNA repair is critical in cancer prevention. Among the enzymes involved in DNA repair are those that prevent or correct uracil misincorporation in DNA. Repair of misincorporated uracil is important since it can cause double-stranded DNA breaks and o...

  7. Excision of uracil residues in DNA: mechanism of action of Escherichia coli and Micrococcus luteus uracil-DNA glycosylases.

    PubMed Central

    Delort, A M; Duplaa, A M; Molko, D; Teoule, R; Leblanc, J P; Laval, J

    1985-01-01

    Various octadeoxynucleotides containing uracil at different positions were synthesized and submitted to the action of Escherichia coli and Micrococcus luteus uracil-DNA glycosylases. A uracil residue situated at the 5'-end was excised by the M.luteus enzyme but not by the E.coli one. Uracil residues located at the ultimate and penultimate positions at the 3'-end were not cleaved by either enzymes. At the other central positions, uracil was eliminated with different initial velocities. Single stranded phi X 174 DNA fragments were used to study the influence of the sequence. Cytosine bases were deaminated to give uracil by bisulfite treatment. It was shown that the initial excision velocity of two vicinal uracil residues was decreased. The same observation was made for two uracils separated by one base. A hypothetical scheme is suggested to explain the mechanism of action of uracil-DNA glycosylases. Images PMID:3889834

  8. Cytosine-to-uracil deamination by SssI DNA methyltransferase.

    PubMed

    Stier, Ildikó; Kiss, Antal

    2013-01-01

    The prokaryotic DNA(cytosine-5)methyltransferase M.SssI shares the specificity of eukaryotic DNA methyltransferases (CG) and is an important model and experimental tool in the study of eukaryotic DNA methylation. Previously, M.SssI was shown to be able to catalyze deamination of the target cytosine to uracil if the methyl donor S-adenosyl-methionine (SAM) was missing from the reaction. To test whether this side-activity of the enzyme can be used to distinguish between unmethylated and C5-methylated cytosines in CG dinucleotides, we re-investigated, using a sensitive genetic reversion assay, the cytosine deaminase activity of M.SssI. Confirming previous results we showed that M.SssI can deaminate cytosine to uracil in a slow reaction in the absence of SAM and that the rate of this reaction can be increased by the SAM analogue 5'-amino-5'-deoxyadenosine. We could not detect M.SssI-catalyzed deamination of C5-methylcytosine ((m5)C). We found conditions where the rate of M.SssI mediated C-to-U deamination was at least 100-fold higher than the rate of (m5)C-to-T conversion. Although this difference in reactivities suggests that the enzyme could be used to identify C5-methylated cytosines in the epigenetically important CG dinucleotides, the rate of M.SssI mediated cytosine deamination is too low to become an enzymatic alternative to the bisulfite reaction. Amino acid replacements in the presumed SAM binding pocket of M.SssI (F17S and G19D) resulted in greatly reduced methyltransferase activity. The G19D variant showed cytosine deaminase activity in E. coli, at physiological SAM concentrations. Interestingly, the C-to-U deaminase activity was also detectable in an E. coli ung (+) host proficient in uracil excision repair.

  9. A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily

    PubMed Central

    Sang, Pau Biak; Srinath, Thiruneelakantan; Patil, Aravind Goud; Woo, Eui-Jeon; Varshney, Umesh

    2015-01-01

    Uracil DNA glycosylases (UDGs) are an important group of DNA repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from DNA. Based on two short conserved sequences (motifs A and B), UDGs have been classified into six families. Here we report a novel UDG, UdgX, from Mycobacterium smegmatis and other organisms. UdgX specifically recognizes uracil in DNA, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, and shows no detectable uracil excision. UdgX shares highest homology to family 4 UDGs possessing Fe-S cluster. UdgX possesses a conserved sequence, KRRIH, which forms a flexible loop playing an important role in its activity. Mutations of H in the KRRIH sequence to S, G, A or Q lead to gain of uracil excision activity in MsmUdgX, establishing it as a novel member of the UDG superfamily. Our observations suggest that UdgX marks the uracil-DNA for its repair by a RecA dependent process. Finally, we observed that the tight binding activity of UdgX is useful in detecting uracils in the genomes. PMID:26304551

  10. Substrate Inhibition of Uracil Phosphoribosyltransferase by Uracil Can Account for the Uracil Growth Sensitivity of Leishmania donovani Pyrimidine Auxotrophs*

    PubMed Central

    Soysa, Radika; Wilson, Zachary N.; Elferich, Johannes; Forquer, Isaac; Shinde, Ujwal; Riscoe, Michael K.; Yates, Phillip A.; Ullman, Buddy

    2013-01-01

    The pathogenic protozoan parasite Leishmania donovani is capable of both de novo pyrimidine biosynthesis and salvage of pyrimidines from the host milieu. Genetic analysis has authenticated L. donovani uracil phosphoribosyltransferase (LdUPRT), an enzyme not found in mammalian cells, as the focal enzyme of pyrimidine salvage because all exogenous pyrimidines that can satisfy the requirement of the parasite for pyrimidine nucleotides are funneled to uracil and then phosphoribosylated to UMP in the parasite by LdUPRT. To characterize this unique parasite enzyme, LdUPRT was expressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity. Kinetic analysis revealed apparent Km values of 20 and 99 μm for the natural substrates uracil and phosphoribosylpyrophosphate, respectively, as well as apparent Km values 6 and 7 μm for the pyrimidine analogs 5-fluorouracil and 4-thiouracil, respectively. Size exclusion chromatography revealed the native LdUPRT to be tetrameric and retained partial structure and activity in high concentrations of urea. L. donovani mutants deficient in de novo pyrimidine biosynthesis, which require functional LdUPRT for growth, are hypersensitive to high concentrations of uracil, 5-fluorouracil, and 4-thiouracil in the growth medium. This hypersensitivity can be explained by the observation that LdUPRT is substrate-inhibited by uracil and 4-thiouracil, but 5-fluorouracil toxicity transpires via an alternative mechanism. This substrate inhibition of LdUPRT provides a protective mechanism for the parasite by facilitating purine and pyrimidine nucleotide pool balance and by sparing phosphoribosylpyrophosphate for consumption by the nutritionally indispensable purine salvage process. PMID:23986453

  11. Substrate inhibition of uracil phosphoribosyltransferase by uracil can account for the uracil growth sensitivity of Leishmania donovani pyrimidine auxotrophs.

    PubMed

    Soysa, Radika; Wilson, Zachary N; Elferich, Johannes; Forquer, Isaac; Shinde, Ujwal; Riscoe, Michael K; Yates, Phillip A; Ullman, Buddy

    2013-10-11

    The pathogenic protozoan parasite Leishmania donovani is capable of both de novo pyrimidine biosynthesis and salvage of pyrimidines from the host milieu. Genetic analysis has authenticated L. donovani uracil phosphoribosyltransferase (LdUPRT), an enzyme not found in mammalian cells, as the focal enzyme of pyrimidine salvage because all exogenous pyrimidines that can satisfy the requirement of the parasite for pyrimidine nucleotides are funneled to uracil and then phosphoribosylated to UMP in the parasite by LdUPRT. To characterize this unique parasite enzyme, LdUPRT was expressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity. Kinetic analysis revealed apparent Km values of 20 and 99 μM for the natural substrates uracil and phosphoribosylpyrophosphate, respectively, as well as apparent Km values 6 and 7 μM for the pyrimidine analogs 5-fluorouracil and 4-thiouracil, respectively. Size exclusion chromatography revealed the native LdUPRT to be tetrameric and retained partial structure and activity in high concentrations of urea. L. donovani mutants deficient in de novo pyrimidine biosynthesis, which require functional LdUPRT for growth, are hypersensitive to high concentrations of uracil, 5-fluorouracil, and 4-thiouracil in the growth medium. This hypersensitivity can be explained by the observation that LdUPRT is substrate-inhibited by uracil and 4-thiouracil, but 5-fluorouracil toxicity transpires via an alternative mechanism. This substrate inhibition of LdUPRT provides a protective mechanism for the parasite by facilitating purine and pyrimidine nucleotide pool balance and by sparing phosphoribosylpyrophosphate for consumption by the nutritionally indispensable purine salvage process.

  12. Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils.

    PubMed

    Porecha, Rishi H; Stivers, James T

    2008-08-05

    The astonishingly efficient location and excision of damaged DNA bases by DNA repair glycosylases is an especially intriguing problem in biology. One example is the enzyme uracil DNA glycosylase (UNG), which captures and excises rare extrahelical uracil bases that have emerged from the DNA base stack by spontaneous base pair breathing motions. Here, we explore the efficiency and mechanism by which UNG executes intramolecular transfer and excision of two uracil sites embedded on the same or opposite DNA strands at increasing site spacings. The efficiency of intramolecular site transfer decreased from 41 to 0% as the base pair spacing between uracil sites on the same DNA strand increased from 20 to 800 bp. The mechanism of transfer is dominated by DNA hopping between landing sites of approximately 10 bp size, over which rapid 1D scanning likely occurs. Consistent with DNA hopping, site transfer at 20- and 56-bp spacings was unaffected by whether the uracils were placed on the same or opposite strands. Thus, UNG uses hopping and 3D diffusion through bulk solution as the principal pathways for efficient patrolling of long genomic DNA sequences for damage. Short-range sliding over the range of a helical turn allows for redundant inspection of very local DNA sequences and trapping of spontaneously emerging extrahelical uracils.

  13. Fragmentation Pathways in the Uracil Radical Cation

    SciTech Connect

    Zhou, Congyi; Matsika, Spiridoula; Kotur, Marija; Weinacht, Thomas C.

    2012-08-24

    We investigate pathways for fragmentation in the uracil radical cation using ab initio electronic structure calculations. We focus on the main fragments produced in pump–probe dissociative ionization experiments. These are fragments with mass to charge ratios (m/z) of 69, 28, 41, and 42. Barriers to dissociation along the ground ionic surface are reported, which provide an estimate of the energetic requirements for the production of the main fragments. Finally, direct and sequential fragmentation mechanisms have been analyzed, and it is concluded that sequential fragmentation after production of fragment with m/z 69 is the dominant mechanism for the production of the smaller fragments.

  14. Dynamics of Dissociative Electron Attachment to Uracil and Furane

    NASA Astrophysics Data System (ADS)

    Fonseca Dos Santos, Samantha; Douguet, Nicolas; Orel, Ann; Rescigno, Thomas

    2016-05-01

    We present the results of a theoretical study of dissociative electron attachment (DEA) to Uracil and Furan. In both cases we will present calculated angular distributions based on analysis of the entrance amplitudes obtained from the results of complex Kohn scattering calculations. For uracil, we will compare our results with available experimentally measured angular distributions obtained using the COLTRIMS method.

  15. Electron affinities of uracil: microsolvation effects and polarizable continuum model.

    PubMed

    Melicherčík, Miroslav; Pašteka, Lukáš F; Neogrády, Pavel; Urban, Miroslav

    2012-03-08

    We present adiabatic electron affinities (AEAs) and the vertical detachment energies (VDEs) of the uracil molecule interacting with one to five water molecules. Credibility of MP2 and DFT/B3LYP calculations is supported by comparison with available benchmark CCSD(T) data. AEAs and VDEs obtained by MP2 and DFT/B3LYP methods copy trends of benchmark CCSD(T) results for the free uracil and uracil-water complexes in the gas phase being by 0.20 - 0.28 eV higher than CCSD(T) values depending on the particular structure of the complex. AEAs and VDEs from MP2 are underestimated by 0.09-0.15 eV. For the free uracil and uracil-(H(2)O)(n) (n = 1,2,3,5) complexes, we also consider the polarizable continuum model (PCM) and discuss the importance of the microsolvation when combined with PCM. AEAs and VDEs of uracil and uracil-water complexes enhance rapidly with increasing relative dielectric constant (ε) of the solvent. Highest AEAs and VDEs of the U(H(2)O)(5) complexes from B3LYP with ε = 78.4 are 2.03 and 2.81 eV, respectively, utilizing the correction from CCSD(T). Specific structural features of the microsolvated uracil-(H(2)O)(n) complexes and their anions are preserved also upon considering PCM in calculations of AEAs and VDEs.

  16. Photorejuvenation using topical 5-methyl aminolevulinate and red light.

    PubMed

    Ruiz-Rodríguez, Ricardo; López, Laura; Candelas, Daniel; Pedraz, Javier

    2008-07-01

    Photodynamic therapy has been proved to be effective in skin rejuvenation. To evaluate clinical efficacy and side effects of photodynamic therapy using topical 5-methyl aminolevulinate and red light for photorejuvenation. A randomized, prospective, split-face comparison study of 10 white, adult patients with moderate photodamage, Fitzpatrick skin types 2 or 3, and no occurrence of actinic keratosis was performed. Three treatments using topical methyl aminolevulinate cream, applied for 1 hour on one half of the face and 3 hours on the other half before illumination with red light. A blinded investigator prior to treatment and 2 months after the third treatment evaluated each side of the subject's faces. A moderate improvement in fine lines, tactile roughness, and skin tightness was observed in most of the patients, mostly on the 3-hour time side. There were no changes in mottled pigmentation or telangiectasias. Side effects were observed in all subjects (erythema, edema, scaling) mainly in the 3-hour incubation time side. The small number of patients and the lack of placebo group. Methyl aminolevulinic-photodynamic therapy with red light can improve fine lines, tactile roughness and skin tightness in patients with moderate photoaging and no occurrence of actinic keratosis.

  17. Arabidopsis uracil DNA glycosylase (UNG) is required for base excision repair of uracil and increases plant sensitivity to 5-fluorouracil.

    PubMed

    Córdoba-Cañero, Dolores; Dubois, Emeline; Ariza, Rafael R; Doutriaux, Marie-Pascale; Roldán-Arjona, Teresa

    2010-03-05

    Uracil in DNA arises by misincorporation of dUMP during replication and by hydrolytic deamination of cytosine. This common lesion is actively removed through a base excision repair (BER) pathway initiated by a uracil DNA glycosylase (UDG) activity that excises the damage as a free base. UDGs are classified into different families differentially distributed across eubacteria, archaea, yeast, and animals, but remain to be unambiguously identified in plants. We report here the molecular characterization of AtUNG (Arabidopsis thaliana uracil DNA glycosylase), a plant member of the Family-1 of UDGs typified by Escherichia coli Ung. AtUNG exhibits the narrow substrate specificity and single-stranded DNA preference that are characteristic of Ung homologues. Cell extracts from atung(-/-) mutants are devoid of UDG activity, and lack the capacity to initiate BER on uracil residues. AtUNG-deficient plants do not display any apparent phenotype, but show increased resistance to 5-fluorouracil (5-FU), a cytostatic drug that favors dUMP misincorporation into DNA. The resistance of atung(-/-) mutants to 5-FU is accompanied by the accumulation of uracil residues in DNA. These results suggest that AtUNG excises uracil in vivo but generates toxic AP sites when processing abundant U:A pairs in dTTP-depleted cells. Altogether, our findings point to AtUNG as the major UDG activity in Arabidopsis.

  18. On the Electronically Excited States of Uracil

    SciTech Connect

    Epifanovsky, Evgeny; Kowalski, Karol; Fan, Peng-Dong; Valiev, Marat; Matsika, Spiridoula; Krylov, Anna

    2008-10-09

    Vertical excitation energies in uracil in the gas phase and in water solution are investigated by the equation-of-motion coupled-cluster and multi-reference configuration interaction methods. Basis set effects are found to be important for converged results. The analysis of electronic wave functions reveals that the lowest singlet states are predominantly of a singly excited character and are therefore well described by single-reference equation-of-motion methods augmented by a perturbative triples correction to account for dynamical correlation. Our best estimates for the vertical excitation energies for the lowest singlet n and are 5.0±0.1 eV and 5.3±0.1 eV, respectively. The solvent effects for these states are estimated to be +0.5 eV and ±0.1 eV, respectively. We attribute the difference between the computed vertical excitations and the maximum of the experimental absorption to strong vibronic interaction between the lowest A00 and A0 states leading to intensity borrowing by the forbidden transition.

  19. Uracil salvage pathway in Lactobacillus plantarum: Transcription and genetic studies.

    PubMed

    Arsène-Ploetze, Florence; Nicoloff, Hervé; Kammerer, Benoît; Martinussen, Jan; Bringel, Françoise

    2006-07-01

    The uracil salvage pathway in Lactobacillus plantarum was demonstrated to be dependent on the upp-pyrP gene cluster. PyrP was the only high-affinity uracil transporter since a pyrP mutant no longer incorporated low concentrations of radioactively labeled uracil and had increased resistance to the toxic uracil analogue 5-fluorouracil. The upp gene encoded a uracil phosphoribosyltransferase (UPRT) enzyme catalyzing the conversion of uracil and 5-phosphoribosyl-alpha-1-pyrophosphate to UMP and pyrophosphate. Analysis of mutants revealed that UPRT is a major cell supplier of UMP synthesized from uracil provided by preformed nucleic acid degradation. In a mutant selection study, seven independent upp mutants were isolated and all were found to excrete low amounts of pyrimidines to the growth medium. Pyrimidine-dependent transcription regulation of the biosynthetic pyrimidine pyrR1-B-C-Aa1-Ab1-D-F-E operon was impaired in the upp mutants. Despite the fact that upp and pyrP are positioned next to each other on the chromosome, they are not cotranscribed. Whereas pyrP is expressed as a monocistronic message, the upp gene is part of the lp_2376-glyA-upp operon. The lp_2376 gene encodes a putative protein that belongs to the conserved protein family of translation modulators such as Sua5, YciO, and YrdC. The glyA gene encodes a putative hydroxymethyltransferase involved in C1 unit charging of tetrahydrofolate, which is required in the biosynthesis of thymidylate, pantothenate, and purines. Unlike upp transcription, pyrP transcription is regulated by exogenous pyrimidine availability, most likely by the same mechanism of transcription attenuation as that of the pyr operon.

  20. Uracil Salvage Pathway in Lactobacillus plantarum: Transcription and Genetic Studies

    PubMed Central

    Arsène-Ploetze, Florence; Nicoloff, Hervé; Kammerer, Benoît; Martinussen, Jan; Bringel, Françoise

    2006-01-01

    The uracil salvage pathway in Lactobacillus plantarum was demonstrated to be dependent on the upp-pyrP gene cluster. PyrP was the only high-affinity uracil transporter since a pyrP mutant no longer incorporated low concentrations of radioactively labeled uracil and had increased resistance to the toxic uracil analogue 5-fluorouracil. The upp gene encoded a uracil phosphoribosyltransferase (UPRT) enzyme catalyzing the conversion of uracil and 5-phosphoribosyl-α-1-pyrophosphate to UMP and pyrophosphate. Analysis of mutants revealed that UPRT is a major cell supplier of UMP synthesized from uracil provided by preformed nucleic acid degradation. In a mutant selection study, seven independent upp mutants were isolated and all were found to excrete low amounts of pyrimidines to the growth medium. Pyrimidine-dependent transcription regulation of the biosynthetic pyrimidine pyrR1-B-C-Aa1-Ab1-D-F-E operon was impaired in the upp mutants. Despite the fact that upp and pyrP are positioned next to each other on the chromosome, they are not cotranscribed. Whereas pyrP is expressed as a monocistronic message, the upp gene is part of the lp_2376-glyA-upp operon. The lp_2376 gene encodes a putative protein that belongs to the conserved protein family of translation modulators such as Sua5, YciO, and YrdC. The glyA gene encodes a putative hydroxymethyltransferase involved in C1 unit charging of tetrahydrofolate, which is required in the biosynthesis of thymidylate, pantothenate, and purines. Unlike upp transcription, pyrP transcription is regulated by exogenous pyrimidine availability, most likely by the same mechanism of transcription attenuation as that of the pyr operon. PMID:16788187

  1. Poxvirus uracil-DNA glycosylase-An unusual member of the family I uracil-DNA glycosylases: Poxvirus Uracil-DNA Glycosylase

    SciTech Connect

    Schormann, Norbert; Zhukovskaya, Natalia; Bedwell, Gregory; Nuth, Manunya; Gillilan, Richard; Prevelige, Peter E.; Ricciardi, Robert P.; Banerjee, Surajit; Chattopadhyay, Debasish

    2016-11-02

    We report that uracil-DNA glycosylases are ubiquitous enzymes, which play a key role repairing damages in DNA and in maintaining genomic integrity by catalyzing the first step in the base excision repair pathway. Within the superfamily of uracil-DNA glycosylases family I enzymes or UNGs are specific for recognizing and removing uracil from DNA. These enzymes feature conserved structural folds, active site residues and use common motifs for DNA binding, uracil recognition and catalysis. Within this family the enzymes of poxviruses are unique and most remarkable in terms of amino acid sequences, characteristic motifs and more importantly for their novel non-enzymatic function in DNA replication. UNG of vaccinia virus, also known as D4, is the most extensively characterized UNG of the poxvirus family. D4 forms an unusual heterodimeric processivity factor by attaching to a poxvirus-specific protein A20, which also binds to the DNA polymerase E9 and recruits other proteins necessary for replication. D4 is thus integrated in the DNA polymerase complex, and its DNA-binding and DNA scanning abilities couple DNA processivity and DNA base excision repair at the replication fork. In conclusion, the adaptations necessary for taking on the new function are reflected in the amino acid sequence and the three-dimensional structure of D4. We provide an overview of the current state of the knowledge on the structure-function relationship of D4.

  2. Inelastic collisions of the uracil molecules with electrons.

    PubMed

    Shafranyosh, I I; Sukhoviya, M I

    2012-11-14

    Ionization and excitation of the uracil molecules by electron impact is investigated. Production of positive ions of uracil molecules (nucleic acid base) was studied using a crossed electron and molecular beam technique. The method developed by the authors enabled the molecular beam intensity to be measured and the electron dependences and the absolute values of the total cross sections of production of both positive ions to be determined. It is shown that the total positive uracil ion production cross section reaches its maximal value of (1.0 ± 0.1) × 10(-15) cm(2) at the 95 eV electron energy. Dissociative ionization cross sections were also determined. The luminescence spectra of isolated uracil molecules in the wavelength range of 200-500 nm under the influence of slow electrons are obtained. In the spectrum, more than 20 spectral bands and lines at 100 eV electron energy are observed. It is shown that the uracil radiation spectrum is formed by the processes of molecules dissociative excitation, dissociative excitation with ionization, excitation of electronic levels of the initial molecule and molecular ion.

  3. Serum "uracil+uridine" levels in pernicious anaemia.

    PubMed

    Parry, T E; Blackmore, J A

    1976-12-01

    The serum "uracil+uridine" level, expressed as uracil, has been measured in 21 cases of vitamin B12 deficiency, in which the serum folate was normal, and compared with the level in 97 normal subjects. The level in the vitamin B12 deficient group (11.9 mumol/1). was significantly lower than in the controls (15.7 mumol/1., P less than 0.005). Nine of the former were complicated by stystemic illness but the clinical and haematological features in the remaining 12 were consistent with the diagnosis of pernicious anaemia in relapse. The serum uracil level in this group was even lower (10.21 mumol/1., P less than 0.01). This finding is unexpected in view of the generally accepted indirect role of vitamine B12 in the methylation of deoxyuridine monophosphate to deoxythymidine monophosphate. Reasons are given for not accepting these results as reflecting the main biochemical lesion in vitamin B12 deficiency. Although they do not give direct support to an impairment in the methylation of deoxyuridine monophosphate, they do not exclude it as they test only one possible metabolic pathway and moreover they could represent the result of more than one action of vitamin B12 on uracil metabolism. They do show, however, that some aspect of uracil metabolism other than methylation is affected in vitamin B12 deficiency in man.

  4. Effects of microsolvation on uracil and its radical anion: Uracil.(H2O)n (n=1-5)

    NASA Astrophysics Data System (ADS)

    Kim, Sunghwan; Schaefer, Henry F.

    2006-10-01

    Microsolvation effects on the stabilities of uracil and its anion have been investigated by explicitly considering the structures of complexes of uracil with up to five water molecules at the B3LYP /DZP++ level of theory. For all five systems, the global minimum of the neutral cluster has a different equilibrium geometry from that of the radical anion. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of uracil are predicted to increase gradually with the number of hydrating molecules, qualitatively consistent with experimental results from a photodetachment-photoelectron spectroscopy study [J. Schiedt et al., Chem. Phys. 239, 511 (1998)]. The trend in the AEAs implies that while the conventional valence radical anion of uracil is only marginally bound in the gas phase, it will form a stable anion in aqueous solution. The gas-phase AEA of uracil (0.24eV) was higher than that of thymine by 0.04eV and this gap was not significantly affected by microsolvation. The largest AEA is that predicted for uracil•(H2O)5, namely, 0.96eV. The VDEs range from 0.76to1.78eV.

  5. Electronic structure of uracil-like nucleobases adsorbed on Si(001): uracil, thymine and 5-fluorouracil

    NASA Astrophysics Data System (ADS)

    Molteni, Elena; Onida, Giovanni; Cappellini, Giancarlo

    2016-04-01

    We study the electronic properties of the Si(001):Uracil, Si(001):Thymine, and Si(001):5-Fluorouracil systems, focusing on the Si dimer-bridging configuration with adsorption governed by carbonyl groups. While the overall structural and electronic properties are similar, with small differences due to chemical substitutions, much larger effects on the surface band dispersion and bandgap show up as a function of the molecular orientation with respect to the surface. An off-normal orientation of the molecular planes is favored, showing larger bandgap and lower total energy than the upright position. We also analyze the localization of gap-edge occupied and unoccupied surface states. Supplementary material in the form of one pdf file available from the Journal web page at http://dx.doi.org/10.1140/epjb/e2016-70011-1

  6. The regioselective iodination of quinolines, quinolones, pyridones, pyridines and uracil.

    PubMed

    Dutta, Uttam; Deb, Arghya; Lupton, David W; Maiti, Debabrata

    2015-12-28

    A radical based direct C-H iodination protocol for quinolines, quinolones, pyridones, pyridines, and uracil has been developed. The iodination occurs in a C3 selective manner for quinolines and quinolones. Pyridones and pyridines undergo C3 and C5 iodination, while dimethyl uracil undergoes C5 iodination. Scope of the method was demonstrated through the rapid synthesis of both electron rich as well as electron poor heteroaromatic iodides. The protocol was found to be scalable and general, while a mechanism has been proposed.

  7. Biochemical Characterization of Uracil Phosphoribosyltransferase from Mycobacterium tuberculosis

    PubMed Central

    Villela, Anne Drumond; Ducati, Rodrigo Gay; Rosado, Leonardo Astolfi; Bloch, Carlos Junior; Prates, Maura Vianna; Gonçalves, Danieli Cristina; Ramos, Carlos Henrique Inacio; Basso, Luiz Augusto; Santos, Diogenes Santiago

    2013-01-01

    Uracil phosphoribosyltransferase (UPRT) catalyzes the conversion of uracil and 5-phosphoribosyl-α-1-pyrophosphate (PRPP) to uridine 5′-monophosphate (UMP) and pyrophosphate (PPi). UPRT plays an important role in the pyrimidine salvage pathway since UMP is a common precursor of all pyrimidine nucleotides. Here we describe cloning, expression and purification to homogeneity of upp-encoded UPRT from Mycobacterium tuberculosis (MtUPRT). Mass spectrometry and N-terminal amino acid sequencing unambiguously identified the homogeneous protein as MtUPRT. Analytical ultracentrifugation showed that native MtUPRT follows a monomer-tetramer association model. MtUPRT is specific for uracil. GTP is not a modulator of MtUPRT ativity. MtUPRT was not significantly activated or inhibited by ATP, UTP, and CTP. Initial velocity and isothermal titration calorimetry studies suggest that catalysis follows a sequential ordered mechanism, in which PRPP binding is followed by uracil, and PPi product is released first followed by UMP. The pH-rate profiles indicated that groups with pK values of 5.7 and 8.1 are important for catalysis, and a group with a pK value of 9.5 is involved in PRPP binding. The results here described provide a solid foundation on which to base upp gene knockout aiming at the development of strategies to prevent tuberculosis. PMID:23424660

  8. Uracil misincorporation into DNA and folic acid supplementation

    USDA-ARS?s Scientific Manuscript database

    BACKGROUND: Folate deficiency decreases thymidylate synthesis from deoxyuridylate, which results in an imbalance of deoxyribonucleotide that may lead to excessive uracil misincorporation (UrMis) into DNA during replication and repair. OBJECTIVE: We evaluated the relation between UrMis in different ...

  9. Time-resolved radiation chemistry: Dynamics of electron attachment to uracil following UV excitation of iodide-uracil complexes

    SciTech Connect

    King, Sarah B.; Yandell, Margaret A.; Stephansen, Anne B.; Neumark, Daniel M.

    2014-12-14

    Electron attachment to uracil was investigated by applying time-resolved photoelectron imaging to iodide-uracil (I{sup –}U) complexes. In these studies, an ultraviolet pump pulse initiated charge transfer from the iodide to the uracil, and the resulting dynamics of the uracil temporary negative ion were probed. Five different excitation energies were used, 4.00 eV, 4.07 eV, 4.14 eV, 4.21 eV, and 4.66 eV. At the four lowest excitation energies, which lie near the vertical detachment energy of the I{sup –}U complex (4.11 eV), signatures of both the dipole bound (DB) as well as the valence bound (VB) anion of uracil were observed. In contrast, only the VB anion was observed at 4.66 eV, in agreement with previous experiments in this higher energy range. The early-time dynamics of both states were highly excitation energy dependent. The rise time of the DB anion signal was ∼250 fs at 4.00 eV and 4.07 eV, ∼120 fs at 4.14 eV and cross-correlation limited at 4.21 eV. The VB anion rise time also changed with excitation energy, ranging from 200 to 300 fs for excitation energies 4.00–4.21 eV, to a cross-correlation limited time at 4.66 eV. The results suggest that the DB state acts as a “doorway” state to the VB anion at 4.00–4.21 eV, while direct attachment to the VB anion occurs at 4.66 eV.

  10. Establishment of uracil auxotrophic dikaryotic strains of Lentinula edodes by crossbreeding

    PubMed Central

    Zhou, Chenli; Xi, Liping; Mao, Wenjun; Wan, Jianing; Li, Yan; Wang, Ying; Bao, Dapeng

    2017-01-01

    The uracil auxotrophic monokaryotic strain 423-9 of Lentinula edodes was crossed with nine monokaryons (cro2-2-9, W66-1, xd2-3-2, QingKe 20A, 241-1-1, 9015-1, L66-2, 241-1-2, and Qing 23A) derived from wild type strains of L. edodes. Nine dikaryotic hybrids were established from these crosses. These hybrids were fruited and 496 single spore isolates were obtained. Among these single spore isolates, 166 were identified as monokaryons under a microscope. We screened these monokaryons on selective medium and obtained 19 uracil auxotrophic monokaryons. By using the Monkaryon-monkaryon crossing method among the uracil auxotrophic monokaryons, 56 uracil auxotrophic dikaryotic strains were established on selective medium. These dikaryotic strains were unable to grow on minimal medium without uracil and exhibited slow growth rates on PDA plates compared to the wild type strain. The uracil auxotrophic dikaryotic strains also showed more vigorous growth on sawdust cultivation medium containing uracil than that without uracil. The fruiting tests showed that they formed normal fruiting bodies on the sawdust medium containing uracil. The results show that the uracil auxotrophic dikaryotic strain of L. edodes could be produced by mating, and will provide a valuable resource for future genetic studies and for spawn protection and identification. PMID:28588390

  11. Establishment of uracil auxotrophic dikaryotic strains of Lentinula edodes by crossbreeding.

    PubMed

    Zhou, Chenli; Xi, Liping; Mao, Wenjun; Wan, Jianing; Li, Yan; Wang, Ying; Bao, Dapeng

    2017-03-01

    The uracil auxotrophic monokaryotic strain 423-9 of Lentinula edodes was crossed with nine monokaryons (cro2-2-9, W66-1, xd2-3-2, QingKe 20A, 241-1-1, 9015-1, L66-2, 241-1-2, and Qing 23A) derived from wild type strains of L. edodes. Nine dikaryotic hybrids were established from these crosses. These hybrids were fruited and 496 single spore isolates were obtained. Among these single spore isolates, 166 were identified as monokaryons under a microscope. We screened these monokaryons on selective medium and obtained 19 uracil auxotrophic monokaryons. By using the Monkaryon-monkaryon crossing method among the uracil auxotrophic monokaryons, 56 uracil auxotrophic dikaryotic strains were established on selective medium. These dikaryotic strains were unable to grow on minimal medium without uracil and exhibited slow growth rates on PDA plates compared to the wild type strain. The uracil auxotrophic dikaryotic strains also showed more vigorous growth on sawdust cultivation medium containing uracil than that without uracil. The fruiting tests showed that they formed normal fruiting bodies on the sawdust medium containing uracil. The results show that the uracil auxotrophic dikaryotic strain of L. edodes could be produced by mating, and will provide a valuable resource for future genetic studies and for spawn protection and identification.

  12. Targeting tumors with nonreplicating Toxoplasma gondii uracil auxotroph vaccines

    PubMed Central

    Fox, Barbara A.; Sanders, Kiah L.; Chen, Shan; Bzik, David J.

    2013-01-01

    Toxoplasma gondii is an intracellular parasite that has evolved to actively control its invaded host cells. Toxoplasma triggers then actively regulates host innate IL-12 and interferon-γ responses that elicit T cell control of infection. A live, nonreplicating avirulent uracil auxotroph vaccine strain (cps) of Toxoplasma triggers novel innate immune responses that stimulate amplified CD8+ T cell responses and life-long immunity in vaccinated mice. Here, we review recent reports showing that intratumoral treatment with cps activated immune-mediated regression of established solid tumors in mice. We speculate that a better understanding of host-parasite interaction at the molecular level and applying improved genetic models based on Δku80 Toxoplasma strains will stimulate development of highly effective immunotherapeutic cancer vaccine strategies using engineered uracil auxotrophs. PMID:23928100

  13. Carbonic anhydrase inhibitory properties of some uracil derivatives.

    PubMed

    Alper Türkoğlu, Emir; Şentürk, Murat; Supuran, Claudiu T; Ekinci, Deniz

    2017-12-01

    Inhibitors of carbonic anhydrase (CA) have been carried out in many therapeutic applications, especially antiglaucoma activity. In this study, we investigated some uracil derivatives (4-12) to inhibit human CA I (hCA I) and II (hCA II) isoenzymes. The KI values of the compounds 4-12 are in the range of 0.085-428 µM for hCA I and of 0.1715-645 µM against hCA II, respectively. It is concluded from the kinetic investigations, all compounds used in the study act as competitive inhibitors with substrate, 4-NPA. Uracil derivatives are emerging agents for the inhibiton of carbonic anhydrase which could be used in biomedicine.

  14. Energy Transfer in Microhydrated Uracil, 5-Fluorouracil, and 5-Bromouracil.

    PubMed

    Poštulka, J; Slavíček, P; Fedor, J; Fárník, M; Kočišek, J

    2017-09-28

    Experiment and theory are combined to study the interaction of low energy electrons with microhydrated uracil and its halogenated analogues 5-fluorouracil and 5-bromouracil. We report electron ionization (EI) and electron attachment (EA) mass spectra for the uracils with different degrees of hydration. Both EI and EA lead to evaporation of water molecules. The number of evaporated molecules serves as a measure of the energy transferred to the solvent. Upon EI, the amount of energy transferred to neighboring water molecules is similar for all three studied species. On the other hand, the energy transferred upon EA rises significantly from uracil to 5-fluorouracil and 5-bromouracil. 5-Bromouracil is the only studied molecule that undergoes dissociative electron attachment after hydration at the studied energy of 1.2 eV. Theoretical modeling of the energetics for the electron attachment process allows for setting the energy transferred to the solvent on the absolute scale. We discuss the importance of this energy for the radiosensitization.

  15. Shape resonance spectra of uracil, 5-fluorouracil, and 5-chlorouracil

    SciTech Connect

    Kossoski, F.; Varella, M. T. do N.; Bettega, M. H. F.

    2014-01-14

    We report on the shape resonance spectra of uracil, 5-fluorouracil, and 5-chlorouracil, as obtained from fixed-nuclei elastic scattering calculations performed with the Schwinger multichannel method with pseudopotentials. Our results are in good agreement with the available electron transmission spectroscopy data, and support the existence of three π* resonances in uracil and 5-fluorouracil. As expected, the anion states are more stable in the substituted molecules than in uracil. Since the stabilization is stronger in 5-chlorouracil, the lowest π* resonance in this system becomes a bound anion state. The present results also support the existence of a low-lying σ{sub CCl{sup *}} shape resonance in 5-chlorouracil. Exploratory calculations performed at selected C–Cl bond lengths suggest that the σ{sub CCl{sup *}} resonance could couple to the two lowest π* states, giving rise to a very rich dissociation dynamics. These facts would be compatible with the complex branching of the dissociative electron attachment cross sections, even though we cannot discuss any details of the vibration dynamics based only on the present fixed-nuclei results.

  16. Shape resonance spectra of uracil, 5-fluorouracil, and 5-chlorouracil

    NASA Astrophysics Data System (ADS)

    Kossoski, F.; Bettega, M. H. F.; Varella, M. T. do N.

    2014-01-01

    We report on the shape resonance spectra of uracil, 5-fluorouracil, and 5-chlorouracil, as obtained from fixed-nuclei elastic scattering calculations performed with the Schwinger multichannel method with pseudopotentials. Our results are in good agreement with the available electron transmission spectroscopy data, and support the existence of three π* resonances in uracil and 5-fluorouracil. As expected, the anion states are more stable in the substituted molecules than in uracil. Since the stabilization is stronger in 5-chlorouracil, the lowest π* resonance in this system becomes a bound anion state. The present results also support the existence of a low-lying σ _CCl^* shape resonance in 5-chlorouracil. Exploratory calculations performed at selected C-Cl bond lengths suggest that the σ _CCl^* resonance could couple to the two lowest π* states, giving rise to a very rich dissociation dynamics. These facts would be compatible with the complex branching of the dissociative electron attachment cross sections, even though we cannot discuss any details of the vibration dynamics based only on the present fixed-nuclei results.

  17. Bis(5-methyl­pyrazine-2-carboxyl­ato)­diphenyl­tin(IV)

    PubMed Central

    Gao, Zhongjun

    2008-01-01

    In the mol­ecule of the title compound, [Sn(C6H5)2(C6H5N2O2)2], two O and one N atoms from the two 5-methyl­pyrazine-2-carboxyl­ate ligands and one C atom of a phenyl group form a distorted square-planar arrangement in the equatorial plane around the Sn atom, while the distorted octa­hedral coordination is completed by an N atom of one of the 5-methyl­pyrazine-2-carboxyl­ate ligands and a C atom of the other phenyl group in the axial positions. In the crystal structure, inter­molecular C—H⋯O hydrogen bonds link the mol­ecules into centrosymmetric dimers. PMID:21202741

  18. The dipole bound-to-covalent anion transformation in uracil

    NASA Astrophysics Data System (ADS)

    Hendricks, J. H.; Lyapustina, S. A.; de Clercq, H. L.; Bowen, K. H.

    1998-01-01

    Nucleic acid base anions play an important role in radiation-induced mutagenesis. Recently, it has been shown that isolated (gas-phase) nucleobases form an exotic form of negative ions, namely, dipole bound anions. These are species in which the excess electrons are bound by the dipole fields of the neutral molecules. In the condensed phase, on the other hand, nucleobase anions are known to be conventional (covalent) anions, implying the transformation from one form into the other due to environmental (solvation) effects. Here, in a series of negative ion photoelectron spectroscopic experiments on gas-phase, solvated uracil cluster anions, we report the observation of this transformation.

  19. HYDROGEN-BONDED DIMERS OF ADENINE AND URACIL DERIVATIVES.

    PubMed

    HAMLIN, R M; LORD, R C; RICH, A

    1965-06-25

    In concentrated solutions of either 9-ethyladenine or 1-cyclohexyluracil in deuterochloroform, absorption bands in the infrared spectrum demonstrate hydrogen bonding of the adenine and uracil derivatives with themselves. In dilute solutions, there is very little hydrogen bonding. However, when dilute solutions of 9-ethyladenine and 1-cyclohexyluracil are mixed, a series of bands appear which show that these molecules are hydrogen-bonding with each other much more strongly than with themselves. A study of the stoichiometry of this association indicates formation of 1:1 hydrogen-bonded pairs in solution.

  20. The presence of nuclear and mitochondrial uracil-DNA glycosylase in extracts of human KB cells.

    PubMed Central

    Anderson, C T; Friedberg, E C

    1980-01-01

    Extracts of human KB cells contain detectable uracil-DNA glycosylase activity. The majority of the activity is located within the nuclear fraction, however we present evidence for the presence of identifiable uracil-DNA glycosylase activity associated with the mitochondrial fraction of these cells. PMID:6253928

  1. Uracil as an index of lactic acid bacteria contamination of tomato products.

    PubMed

    Hidalgo, Alyssa; Pompei, Carlo; Galli, Antonietta; Cazzola, Sara

    2005-01-26

    The aim of this research was to evaluate the suitability of uracil as an hygienic quality index of tomato products. Whereas uridine was naturally present throughout tomato fruits' ripening, uracil appeared only after microbial contamination. In tomato pulp inoculated with nine different microbial strains, all five lactic acid bacteria (LAB) studied released relevant quantities of uracil (150-1040 mg/kg of dm), with a correlated partial or total decrease of uridine. Uracil production by yeasts and molds was very low or nonexistent; the starting uridine concentration (approximately 960 mg/kg of dm) remained constant or increased. Uracil thermostability was also verified. Twenty-six samples of tomato paste (30 degrees Brix) were collected from bag-in-drums produced in an industrial processing plant, some with evident swelling symptoms. All of the samples with high microbial count presented uracil. Uracil was also present in samples with microbial contamination under the detection limit and Howard mold count below legislation limits, implying the reprocessing, at least partial, of altered tomato product. The results indicate that uracil presence in tomato products is an index of LAB contamination that has occurred before heat treatment.

  2. Intermolecular associations of some biologically interesting pyrimidines in aqueous solution: caffeine-uracil

    NASA Astrophysics Data System (ADS)

    Iza, N.; Gil, M.; Montero, J. L.; Morcillo, J.

    1986-03-01

    Ultraviolet absorption spectra of aqueous solutions of caffeine-uracil mixt ures at C T=0.004 M have been obtained. An apparent hyperchromic effect has been observed for both bases at two bands. The hyperchromic effect attributed solely to caffeine has been evaluated at 290 nm, where uracil absorption is minimum. From this value, uracil contribution has been determinated. It results about 10% relative hyperchromism for caffeine and about -7, 5% relative hypochromism for uracil. The data obtained indicate the presence of complexes having caffeine-uracil ratio of 1:1 and higher complexes. The association constant K (CAF-U) is found to be 76± 12 M -1 from an equation where K (CAF-CAF) = 102± 6 M -1 and K (U-U) = =68±5 M -1, have been enclosed.

  3. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-halogenated uracils (5-X-uracils; X=F, Cl, Br, I).

    PubMed

    Singh, J S

    2014-01-03

    Raman (200-4000 cm(-1)) and FT-IR (400-4000 cm(-1)) spectra of uracil and 5-halogenated uracils (5-X-uracils; X=F, Cl, Br, I) have been recorded and analyzed in the range 200-4000 cm(-1). The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Ab initio and DFT calculations [using Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP)] were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-halogenated uracils by employing Gaussian-03 program. Gauss View software was used to make the vibrational analysis. Raman and IR spectra have been computed theoretically for the uracil and 5-halogenated molecules. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. Quantum chemical calculations helped in the reassignments of some fundamental vibrational modes. Most of the B3LYP/6-311++G(**) vibrational frequencies are in excellent agreement with available experimental assignments. The ring breathing and kekule stretching modes are found to lower magnitudes compared to those for uracil which could be due to mass effect of halogen atom in place of the hydrogen atom. The C-X (X=F, Cl, Br, I) stretching frequency is distinctly separated from the CH/NH ring stretching frequencies on the pyrimidine ring. All other bands have also been assigned different fundamentals/overtones/combinations.

  4. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-halogenated uracils (5-X-uracils; X = F, Cl, Br, I)

    NASA Astrophysics Data System (ADS)

    Singh, J. S.

    2014-01-01

    Raman (200-4000 cm-1) and FT-IR (400-4000 cm-1) spectra of uracil and 5-halogenated uracils (5-X-uracils; X = F, Cl, Br, I) have been recorded and analyzed in the range 200-4000 cm-1. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Ab initio and DFT calculations [using Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP)] were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-halogenated uracils by employing Gaussian-03 program. Gauss View software was used to make the vibrational analysis. Raman and IR spectra have been computed theoretically for the uracil and 5-halogenated molecules. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. Quantum chemical calculations helped in the reassignments of some fundamental vibrational modes. Most of the B3LYP/6-311++G∗∗ vibrational frequencies are in excellent agreement with available experimental assignments. The ring breathing and kekule stretching modes are found to lower magnitudes compared to those for uracil which could be due to mass effect of halogen atom in place of the hydrogen atom. The C-X (X = F, Cl, Br, I) stretching frequency is distinctly separated from the CH/NH ring stretching frequencies on the pyrimidine ring. All other bands have also been assigned different fundamentals/overtones/combinations.

  5. Fingerprinting DNA oxidation processes: IR characterization of the 5-methyl-2'-deoxycytidine radical cation.

    PubMed

    Bucher, Dominik B; Pilles, Bert M; Pfaffeneder, Toni; Carell, Thomas; Zinth, Wolfgang

    2014-02-24

    Methylated cytidine plays an important role as an epigenetic signal in gene regulation. Its oxidation products are assumed to be involved in active demethylation processes but also in damaging DNA. Here, we report the photochemical production of the 5-methyl-2'-deoxycytidine radical cation via a two-photon ionization process. The radical cation is detected by time-resolved IR spectroscopy and identified by band assignment using density functional theory calculations. Two final oxidation products are characterized with liquid chromatography coupled to mass spectrometry. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. EPR spectroscopy of gamma-irradiated single crystals of 5-methyle-2-nitrophenol

    NASA Astrophysics Data System (ADS)

    Aras, E.; Asik, B.; Buyum, M.; Birey, M.

    2006-01-01

    The electron paramagnetic resonance of gamma-irradiated single crystals of 5-methyle-2-nitrophenol has been studied for different orientations of the crystals in a magnetic field. The radicals produced by gamma irradiation have been investigated at temperatures between 120 and 330 K. The spectra were found to be temperature dependent, and radiation damage centers were attributed to [GRAPHICS] radicals. The principal values of the g-tensor were determined. The results were found to be in good agreement with the existing literature data and theoretical predictions.

  7. Antimicrobial N-brominated hydantoin and uracil grafted polystyrene beads.

    PubMed

    Farah, Shady; Aviv, Oren; Laout, Natalia; Ratner, Stanislav; Domb, Abraham J

    2015-10-28

    Hydantoin-N-halamine derivatives conjugated on polystyrene beads are promising disinfectants with broad antimicrobial activity affected by the gradual release of oxidizing halogen in water. The objective of this work was to identify and test of hydantoin-like molecules possessing urea moiety, which may provide N-haloamines releasing oxidizing halogens when exposed to water at different rates and release profiles for tailored antimicrobial agents. In this work, several hydantoin (five member ring) and for the first time reported, uracil (six member ring) derivatives have been conjugated to polystyrene beads and tested for their lasting antimicrobial activity. Four molecules of each series were conjugated onto polystyrene beads from the reaction of the N-potassium hydantoin or uracil derivatives onto chloromethylated polystyrene beads. A distinct difference in bromine loading capacity and release profiles was found for the different conjugated derivatives. All tested materials exhibit strong antimicrobial activity against Escherichia coli and bacteriophages MS2 of 7 and ~4 log reduction, respectively. These results highlight the antimicrobial potential of halogenated cyclic molecules containing urea groups as water disinfection agents. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Death of Bacillus subtilis Auxotrophs Due to Deprivation of Thymine, Tryptophan, or Uracil

    PubMed Central

    Pritikin, William B.; Romig, W. R.

    1966-01-01

    Pritikin, William B. (University of California, Los Angeles), and W. R. Romig. Death of Bacillus subtilis auxotrophs due to deprivation of thymine, tryptophan, or uracil, J. Bacteriol. 92:291–296. 1966.—Auxotrophic mutants of Bacillus subtilis 168 that require either tryptophan, uracil, or thymine died rapidly when deprived of any of these compounds. Phage PBS1 was produced by infected B. subtilis 168 (thy try-2) deprived of thymine. Phage PBS1 was not produced by infected B. subtilis 168 (try-2) deprived of tryptophan or infected B. subtilis 168-15 (try-2 ura) deprived of uracil. B. subtilis 168 thy try-2 and 168-15 could be transduced by phage PBS1 after prolonged deprivation of tryptophan or uracil, respectively. When B. subtilis 168-15 was transduced to uracil independence by phage PBS1, the uracil-independent transductants became immune to uracil-less death within 10 min of exposure to phage, and began to multiply within 2 hr after exposure to phage at an incubation temperature of 46 C. PMID:16562109

  9. Death of Bacillus subtilis Auxotrophs Due to Deprivation of Thymine, Tryptophan, or Uracil.

    PubMed

    Pritikin, W B; Romig, W R

    1966-08-01

    Pritikin, William B. (University of California, Los Angeles), and W. R. Romig. Death of Bacillus subtilis auxotrophs due to deprivation of thymine, tryptophan, or uracil, J. Bacteriol. 92:291-296. 1966.-Auxotrophic mutants of Bacillus subtilis 168 that require either tryptophan, uracil, or thymine died rapidly when deprived of any of these compounds. Phage PBS1 was produced by infected B. subtilis 168 (thy try-2) deprived of thymine. Phage PBS1 was not produced by infected B. subtilis 168 (try-2) deprived of tryptophan or infected B. subtilis 168-15 (try-2 ura) deprived of uracil. B. subtilis 168 thy try-2 and 168-15 could be transduced by phage PBS1 after prolonged deprivation of tryptophan or uracil, respectively. When B. subtilis 168-15 was transduced to uracil independence by phage PBS1, the uracil-independent transductants became immune to uracil-less death within 10 min of exposure to phage, and began to multiply within 2 hr after exposure to phage at an incubation temperature of 46 C.

  10. Lewis Acid Triggered Regioselective Magnesiation and Zincation of Uracils, Uridines, and Cytidines.

    PubMed

    Klier, Lydia; Aranzamendi, Eider; Ziegler, Dorothée; Nickel, Johannes; Karaghiosoff, Konstantin; Carell, Thomas; Knochel, Paul

    2016-03-04

    The Lewis acid MgCl2 allows control of the metalation regioselectivity of uracils and uridines. In the absence of the Lewis acid, metalation of uracil and uridine derivatives with TMPMgCl·LiCl occurs at the position C(5). In the presence of MgCl2, zincation using TMP2Zn·2LiCl·2MgCl2 occurs at the position C(6). This metalation method provides easy access to functionalized uracils and uridines. Using TMP2Zn·2LiCl·2MgCl2 also allows to functionalize cytidine derivatives at the position C(6).

  11. Dynamics of UV-excited uracil, thymine, and cytosine

    NASA Astrophysics Data System (ADS)

    Hudock, Hanneli

    The excited state dynamics of nucleic acids has been a subject of much experimental and theoretical interest. Nucleic acid bases readily absorb UV radiation, which can lead to mutagenic dimer formation. The dynamics of UV-excited nucleic acids is an important step in understanding how these dimers form. The pyrimidine bases (uracil, thymine, and cytosine) have been studied with ab initio multiple spawning molecular dynamics and high level electronic structure methods. This work has involved both gas-phase and aqueous dynamics as well as simulation of the time-resolved photoelectron spectrum, transient absorption, fluorescence, and reaction rates. With these findings, complete relaxation mechanisms are proposed for the pyrimidines and comparisons are made directly to experimental results.

  12. Bis-(2-amino-5-methyl-pyridinium) fumarate-fumaric acid (1/1).

    PubMed

    Hemamalini, Madhukar; Fun, Hoong-Kun

    2010-07-24

    In the crystal structure of the title compound, C(6)H(9)N(2) (+)·0.5C(4)H(2)O(4) (2-)·0.5C(4)H(6)O(4), the fumarate dianion and fumaric acid mol-ecule are located on inversion centres. The 2-amino-5-methyl-pyrimidinium cation inter-acts with the carboxyl-ate group of the fumarate anion through a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. These motifs are centrosymmetrically paired via N-H⋯O hydrogen bonds, forming a complementary DDAA array. The carboxyl groups of the fumaric acid mol-ecules and the carboxyl-ate groups of the fumarate anions are hydrogen bonded through O-H⋯O hydrogen bonds, leading to a supra-molecular chain along [101]. The crystal structure is further stabilized by weak C-H⋯O hydrogen bonds.

  13. Effect of amino substitution on the excited state dynamics of uracil.

    PubMed

    Bányász, Akos; Gustavsson, Thomas; Keszei, Erno; Improta, Roberto; Markovitsi, Dimitra

    2008-07-01

    The excited state deactivation of two amino-substituted uracils, 5-aminouracil (5AU) and 6-aminouracil (6AU) in aqueous solution was studied by femtosecond fluorescence upconversion. The fluorescence of 6AU decays as fast as that of uracil with a unique time constant of about 100 femtoseconds. The fluorescence of 5AU exhibits a more complex behavior, fundamentally different from what we found in any other uracils: the decays are globally slower (up to several picoseconds) and depend strongly on the wavelength. This difference is attributed to the particular character of the amino group, affecting the out-of-plane motion of the 5-substituent which has been shown to be crucial for the ultrafast internal conversion occurring in uracils. Our observations indicate instead the formation of a transient fluorescent state which in turn is deactivated by a different relaxation process specific to the amino group.

  14. Production of uracil from methane by a newly isolated Methylomonas sp. SW1.

    PubMed

    Kim, Sangwoo; Lee, Wangjun; Song, Insu; Kwon, Yuhyun; Yun, Seokhun; Park, Soohyun; Cho, Sukhyeong; Oh, Byung-Keun; Oh, Han Bin; Lee, Jinwon

    2016-12-20

    Methane is an abundant, inexpensive one-carbon feedstock and one of the most powerful greenhouse gases. Because it does not compete with food demand, it is considered a promising carbon feedstock for the production of valuable products using methanotrophic bacteria. Here, we isolated a novel methanotrophic bacterium, Methylomonas sp. SW1, from a sewage sample obtained from Wonju City Water Supply Drainage Center, Republic of Korea. The conditions for uracil production by Methylomonas sp. SW1, such as Cu(2+) concentration and temperature were investigated and optimized. As a result, Methylomonas sp. SW1 produced uracil from methane as a sole carbon source with a titer of 2.1mg/L in 84h without genetic engineering under the optimized condition. The results in this study demonstrate the feasibility of using Methylomonas sp. SW1 for the production of uracil from methane. This is the first report of uracil production from gas feedstock by methanotrophic bacteria.

  15. Calculation of Positron Binding Energies and Implications for Feshbach-Resonant Positron-Uracil Annihilation

    NASA Astrophysics Data System (ADS)

    Wanniarachchi, Indika; Morgan, Caroline

    2010-04-01

    Here we investigate by first-principles calculations the possible role of vibrational Feshbach resonances in enhancing positron annihilation for low-energy positron beams incident on uracil, a base found in RNA. Geometries, vibrational polarizabilities, and dipole moments for uracil and 5-halouracils are calculated with density functional theory, DFT-B3LYP with a 6-31G+(d, p) basis set, and are used to determine positron-uracil and positron-5-halouracil binding energies. The energy of the Feshbach resonances is then determined by the law of energy conservation. Experimental work on positron interactions with uracil and 5-halouracils in conjunction with the theoretical work reported here is underway.

  16. Carbon nanotube-nucleobase hybrids: nanorings from uracil-modified single-walled carbon nanotubes.

    PubMed

    Singh, Prabhpreet; Toma, Francesca Maria; Kumar, Jitendra; Venkatesh, V; Raya, Jesus; Prato, Maurizio; Verma, Sandeep; Bianco, Alberto

    2011-06-06

    Single-walled carbon nanotubes (SWCNTs) have been covalently functionalized with uracil nucleobase. The hybrids have been characterized by using complementary spectroscopic and microscopic techniques including solid-state NMR spectroscopy. The uracil-functionalized SWCNTs are able to self-assemble into regular nanorings with a diameter of 50-70 nm, as observed by AFM and TEM. AFM shows that the rings do not have a consistent height and thickness, which indicates that they may be formed by separate bundles of CNTs. The simplest model for the nanoring formation likely involves two bundles of CNTs interacting with each other via uracil-uracil base-pairing at both CNT ends. These nanorings can be envisaged for the development of advanced electronic circuits.

  17. Barrier-Free Intermolecular Proton Transfer Induced by Excess Electron Attachment to the Complex of Alanine with Uracil

    SciTech Connect

    Dabkowska, Iwona; Rak, Janusz; Gutowski, Maciej S.; Nilles, J.M.; Stokes, Sarah; Bowen, Kit H.

    2004-04-01

    The photoelectron spectrum of the uracil-alanine anionic complex (UA)- has been recorded with 2.540 eV photons. This spectrum reveals a broad feature with a maximum between 1.6-2.1 eV. The vertical electron detachment energy is too large to be attributed to an (UA)- anionic complex in which an intact uracil anion is solvated by alanine, or vice versa. The neutral and anionic complexes of uracil and alanine were studied at the B3LYP and second order Moeller-Plesset level of theory with 6-31++G** basis sets. The neutral complexes form cyclic hydrogen bonds and the three most stable neutral complexes are bound by 0.72, 0.61 and 0.57 eV. The electron hole in complexes of uracil with alaninie is localized on uracil, but the formation of a complex with alanine strongly modulates the vertical ionization energy of uracil. The theoretical results indicate that the excess electron in (UA)- occupies a p* orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of alanine to the O8 atom of uracil. As a result, the four most stable structures of the uracil-alanine anionic complex can be characterized as the neutral radical of hydrogenated uracil solvated by the anion of deprotonated alanine. Our current results for the anionic complex of uracil with alanine are similar to our previous results for the anion of uracil with glycine [Eur. Phys. J. D 20, 431 (2002)], and together they indicate that the BFPT process is not very sensitive to the nature of the amino acid's hydrophobic residual group. The BFPT to the O8 atom of uracil may be relevant to the damage suffered by nucleic acid bases due to exposure to low energy electrons.

  18. Uracil-Containing DNA in Drosophila: Stability, Stage-Specific Accumulation, and Developmental Involvement

    PubMed Central

    Békési, Angéla; Pukáncsik, Mária; Hodoscsek, Barbara; Merényi, Gábor; Róna, Gergely; Batki, Júlia; Kiss, István; Jankovics, Ferenc; Vilmos, Péter; Erdélyi, Miklós; Vértessy, Beáta G.

    2012-01-01

    Base-excision repair and control of nucleotide pools safe-guard against permanent uracil accumulation in DNA relying on two key enzymes: uracil–DNA glycosylase and dUTPase. Lack of the major uracil–DNA glycosylase UNG gene from the fruit fly genome and dUTPase from fruit fly larvae prompted the hypotheses that i) uracil may accumulate in Drosophila genomic DNA where it may be well tolerated, and ii) this accumulation may affect development. Here we show that i) Drosophila melanogaster tolerates high levels of uracil in DNA; ii) such DNA is correctly interpreted in cell culture and embryo; and iii) under physiological spatio-temporal control, DNA from fruit fly larvae, pupae, and imago contain greatly elevated levels of uracil (200–2,000 uracil/million bases, quantified using a novel real-time PCR–based assay). Uracil is accumulated in genomic DNA of larval tissues during larval development, whereas DNA from imaginal tissues contains much less uracil. Upon pupation and metamorphosis, uracil content in DNA is significantly decreased. We propose that the observed developmental pattern of uracil–DNA is due to the lack of the key repair enzyme UNG from the Drosophila genome together with down-regulation of dUTPase in larval tissues. In agreement, we show that dUTPase silencing increases the uracil content in DNA of imaginal tissues and induces strong lethality at the early pupal stages, indicating that tolerance of highly uracil-substituted DNA is also stage-specific. Silencing of dUTPase perturbs the physiological pattern of uracil–DNA accumulation in Drosophila and leads to a strongly lethal phenotype in early pupal stages. These findings suggest a novel role of uracil-containing DNA in Drosophila development and metamorphosis and present a novel example for developmental effects of dUTPase silencing in multicellular eukaryotes. Importantly, we also show lack of the UNG gene in all available genomes of other Holometabola insects, indicating a potentially

  19. Opposite effects of uracil and adenine nucleotides on the survival of murine cardiomyocytes

    PubMed Central

    Mazzola, Alessia; Amoruso, Emanuela; Beltrami, Elena; Lecca, Davide; Ferrario, Silvia; Cosentino, Simona; Tremoli, Elena; Ceruti, Stefania; Abbracchio, Maria P

    2008-01-01

    Abstract We previously showed that the human heart expresses all known P2X and P2Y receptors activated by extra-cellular adenine or uracil nucleotides. Despite evidence that, both in humans and rodents, plasma levels of ATP and UTP markedly increase during myocardial infarction, the differential effects mediated by the various adenine- and uracil-preferring myocardial P2 receptors are still largely unknown. Here, we studied the effects of adenine and uracil nucleotides on murine HL-1 cardiomyocytes. RT-PCR analysis showed that HL-1 cardiomyocytes express all known P2X receptors (except for P2X2), as well as the P2Y2,4,6,14 subtypes. Exposure of cardiomyocytes to adenine nucleotides (ATP, ADP or BzATP) induced apoptosis and necrosis, as determined by flow-cytometry. Cell death was exacerbated by tumour necrosis factor (TNF)-α, a cytokine implicated in chronic heart failure progression. Conversely, uracil nucleotides (UTP, UDP and UDPglucose) had no effect ‘per se’, but fully counteracted the deleterious effects induced by adenine nucleotides and TNF-α, even if added to cardiomyocytes after beginning exposure to these cell death-inducing agents. Thus, exposure of cardiomyocytes to elevated concentrations of ATP or ADP in the presence of TNF-α contributes to cell death, an effect which is counteracted by uracil-preferring P2 receptors. Cardiomyocytes do not need to be ‘primed’ by uracil nucleotides to become insensitive to adenine nucleotides-induced death, suggesting the existence of a possible ‘therapeutic’ window for uracil nucleotides-mediated protection. Thus, release of UTP during cardiac ischaemia and in chronic heart failure may protect against myocardial damage, setting the basis for developing novel cardioprotective agents that specifically target uracil-preferring P2Y receptors. PMID:18419595

  20. Scaffold hopping: exploration of acetanilide-containing uracil analogues as potential NNRTIs.

    PubMed

    Babkov, Denis A; Valuev-Elliston, Vladimir T; Paramonova, Maria P; Ozerov, Alexander A; Ivanov, Alexander V; Chizhov, Alexander O; Khandazhinskaya, Anastasia L; Kochetkov, Sergey N; Balzarini, Jan; Daelemans, Dirk; Pannecouque, Christophe; Seley-Radtke, Katherine L; Novikov, Mikhail S

    2015-03-01

    In order to identify novel nonnucleoside inhibitors of HIV-1 reverse transcriptase two series of amide-containing uracil derivatives were designed as hybrids of two scaffolds of previously reported inhibitors. Subsequent biological evaluation confirmed acetamide uracil derivatives 15a-k as selective micromolar NNRTIs with a first generation-like resistance profile. Molecular modeling of the most active compounds 15c and 15i was employed to provide insight on their inhibitory properties and direct future design efforts.

  1. A QM/MM study of absorption spectra of uracil derivatives in aqueous solution

    NASA Astrophysics Data System (ADS)

    Nakayama, Akira

    2016-12-01

    The absorption spectra of three representative uracil derivatives (uracil, thymine, and 5-fluorouracil) in aqueous solution are investigated by the QM/MM approach, where the CASPT2 method is employed to evaluate the excitation energies. The computed absorption spectra are in good agreement with the experimental results, and in particular, the relative values of the absorption maximum between these derivatives are well reproduced in the simulations.

  2. Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells

    PubMed Central

    Hansen, Erik C; Ransom, Monica; Hesselberth, Jay R; Hosmane, Nina N; Capoferri, Adam A; Bruner, Katherine M; Pollack, Ross A; Zhang, Hao; Drummond, Michael Bradley; Siliciano, Janet M; Siliciano, Robert; Stivers, James T

    2016-01-01

    We report that a major subpopulation of monocyte-derived macrophages (MDMs) contains high levels of dUTP, which is incorporated into HIV-1 DNA during reverse transcription (U/A pairs), resulting in pre-integration restriction and post-integration mutagenesis. After entering the nucleus, uracilated viral DNA products are degraded by the uracil base excision repair (UBER) machinery with less than 1% of the uracilated DNA successfully integrating. Although uracilated proviral DNA showed few mutations, the viral genomic RNA was highly mutated, suggesting that errors occur during transcription. Viral DNA isolated from blood monocytes and alveolar macrophages (but not T cells) of drug-suppressed HIV-infected individuals also contained abundant uracils. The presence of viral uracils in short-lived monocytes suggests their recent infection through contact with virus producing cells in a tissue reservoir. These findings reveal new elements of a viral defense mechanism involving host UBER that may be relevant to the establishment and persistence of HIV-1 infection. DOI: http://dx.doi.org/10.7554/eLife.18447.001 PMID:27644592

  3. Detection of uracil within DNA using a sensitive labeling method for in vitro and cellular applications

    PubMed Central

    Róna, Gergely; Scheer, Ildikó; Nagy, Kinga; Pálinkás, Hajnalka L.; Tihanyi, Gergely; Borsos, Máté; Békési, Angéla; Vértessy, Beáta G.

    2016-01-01

    The role of uracil in genomic DNA has been recently re-evaluated. It is now widely accepted to be a physiologically important DNA element in diverse systems from specific phages to antibody maturation and Drosophila development. Further relevant investigations would largely benefit from a novel reliable and fast method to gain quantitative and qualitative information on uracil levels in DNA both in vitro and in situ, especially since current techniques does not allow in situ cellular detection. Here, starting from a catalytically inactive uracil-DNA glycosylase protein, we have designed several uracil sensor fusion proteins. The designed constructs can be applied as molecular recognition tools that can be detected with conventional antibodies in dot-blot applications and may also serve as in situ uracil-DNA sensors in cellular techniques. Our method is verified on numerous prokaryotic and eukaryotic cellular systems. The method is easy to use and can be applied in a high-throughput manner. It does not require expensive equipment or complex know-how, facilitating its easy implementation in any basic molecular biology laboratory. Elevated genomic uracil levels from cells of diverse genetic backgrounds and/or treated with different drugs can be demonstrated also in situ, within the cell. PMID:26429970

  4. P2 receptors activated by uracil nucleotides--an update.

    PubMed

    Brunschweiger, Andreas; Müller, Christa E

    2006-01-01

    Pyrimidine nucleotides, including UTP, UDP and UDP-glucose, are important signaling molecules which activate G protein-coupled membrane receptors (GPCRs) of the P2Y family. Four distinct pyrimidine nucleotide-sensitive P2Y receptor subtypes have been cloned, P2Y2, P2Y4, P2Y6 and P2Y14. P2Y2 and P2Y4 receptors are activated by UTP (the P2Y2, and the rat but not the human P2Y4 receptor are also activated by ATP), the P2Y6 receptor is activated by UDP, and the P2Y14 receptor by UDP-glucose. Furthermore, non-P2Y GPCRs, the cysteinylleukotriene receptors (CysLT1R and CysLT2R) have been described to be activated by UDP in addition to activation by cysteinylleukotrienes. While P2Y2, P2Y4, and P2Y6 receptor activation results in stimulation of phospholipase C, the P2Y14 receptor is coupled to inhibition of adenylate cyclase. Derivatives and analogs of the physiological nucleotides UTP, UDP and ATP have been synthesized and evaluated in order to obtain enzymatically stable, subtype-selective agonists. The P2Y2 receptor agonists diuridine tetraphosphate (diquafosol) and the uracil-cytosine dinucleotide denufosol are currently undergoing clinical trials for dry eye disease, retinal detachment disease, upper respiratory tract symptoms, and cystic fibrosis, respectively. The first antagonists for P2Y2 and P2Y6 receptors that appear to be selective versus other P2Y receptor subtypes have recently been described. Selective antagonists for P2Y4 and P2Y14 receptors are still lacking. Uracil nucleotide-sensitive P2Y receptor subtypes may constitute future targets for the treatment of certain cancer types, vascular diseases, inflammatory diseases, and immunomodulatory intervention. They have also been proposed to play a role in neurodegenerative diseases. This article is an updated version of "P2-Pyrimidinergic Receptors and Their Ligands" by C. E. Müller published in Curr. Pharm. Des. 2002, 8, 2353-2369.

  5. Crystal structure of dichlorobis(2-amino-5-methyl-1,3,4-thiadiazole)dicopper(I)

    SciTech Connect

    Neverov, V.A.; Biyushkin, V.N.; Nezhel'skaya, L.A.; Belichuk, N.I.; Rozhdestvenskaya, I.V.

    1987-04-01

    An x-ray diffraction investigation of dichlorobis(2-amino-5-methyl-1,3,4-thiadiazole)dicopper(I) has been carried out. The crystals are monoclinic: a = 6.365(2), b = 9.353(3), c = 11.456(3) A, el = 100.51(3), space group P21/b, Z = 2. The intensities of 1620 reflections with I > 3sigma were measured on a Syntex P21 diffractometer (Mo K radiation). The structure was refined by the least-squares method to R = 0.055. The hydrogen atoms have been located. The molecule of the complex is a flat centrosymmetric dimer, in which the N atoms of the hydrazine residues are bridging atoms and join two Cu atoms to form a six-membered metallocycle. The environment of each Cu atom is a trigonal pyramid. In its base there are two atoms and a Cl atom, and at its apex there is a Cl atom from an adjacent complex. The Cu-N distances are equal to 1.194 and 2.025, the Cu-Cl distance is equal to 2.333, and the Cu-Cl/sub apic/ distance is equal to 2.699 A. The interatomic distances in the ligand are consistent with the literature data. The five-membered heterocycles deviate 10 from the plane of the metallocycle.

  6. Electroanalytical study of proflavine intercalation in 5-methyl or inosine-containing amplicons.

    PubMed

    Alexiadou, Despina K; Ioannou, Andrea K; Kouidou-Andreou, Sofia A; Voulgaropoulos, Anastasios N; Girousi, Stella Th

    2008-10-01

    Amplicons corresponding to the GC-rich p53 exon 5 and its analogues, synthesized by substituting 60% of cytosine by 5-methyl-cytosine, or 60% of guanosine by inosine and GC-poor p53 exon 6 were synthesized and investigated electrochemically, in the presence and absence of proflavine, by differential pulse voltammetry (DPV). Incorporation of base analogues and the thermal stability of the resulting amplicons were tested in the presence of a fluorescent probe (Sybr-Green). Peak current at 1.0 V was lower for methylated than for unmethylated PCR amplicons and was similarly affected by proflavine intercalation. In contrast, considerable peak current differences were observed in the presence of proflavine for unmodified exon 5 v.s. exon 6 or inosine-containing amplicons. Thermal analysis verified the expected shifts in melting temperature (T (m)) due to the base analogue incorporation and GC-content variations. In conclusion, methylated and unmethylated PCR amplicons could be distinguished in model DNA systems using differential pulse voltammetry (DPV) and use of proflavine could serve as an electrochemical probe for identifying different DNA conformations.

  7. Molecular characterization of methanogenic N(5)-methyl-tetrahydromethanopterin: Coenzyme M methyltransferase.

    PubMed

    Upadhyay, Vikrant; Ceh, Katharina; Tumulka, Franz; Abele, Rupert; Hoffmann, Jan; Langer, Julian; Shima, Seigo; Ermler, Ulrich

    2016-09-01

    Methanogenic archaea share one ion gradient forming reaction in their energy metabolism catalyzed by the membrane-spanning multisubunit complex N(5)-methyl-tetrahydromethanopterin: coenzyme M methyltransferase (MtrABCDEFGH or simply Mtr). In this reaction the methyl group transfer from methyl-tetrahydromethanopterin to coenzyme M mediated by cobalamin is coupled with the vectorial translocation of Na(+) across the cytoplasmic membrane. No detailed structural and mechanistic data are reported about this process. In the present work we describe a procedure to provide a highly pure and homogenous Mtr complex on the basis of a selective removal of the only soluble subunit MtrH with the membrane perturbing agent dimethyl maleic anhydride and a subsequent two-step chromatographic purification. A molecular mass determination of the Mtr complex by laser induced liquid bead ion desorption mass spectrometry (LILBID-MS) and size exclusion chromatography coupled with multi-angle light scattering (SEC-MALS) resulted in a (MtrABCDEFG)3 heterotrimeric complex of ca. 430kDa with both techniques. Taking into account that the membrane protein complex contains various firmly bound small molecules, predominantly detergent molecules, the stoichiometry of the subunits is most likely 1:1. A schematic model for the subunit arrangement within the MtrABCDEFG protomer was deduced from the mass of Mtr subcomplexes obtained by harsh IR-laser LILBID-MS.

  8. Androgen receptor mutations are associated with altered epigenomic programming as evidenced by HOXA5 methylation.

    PubMed

    Bens, S; Ammerpohl, O; Martin-Subero, J I; Appari, M; Richter, J; Hiort, O; Werner, R; Riepe, F G; Siebert, R; Holterhus, P-M

    2011-01-01

    Male external genital differentiation is accompanied by implementation of a long-term, male-specific gene expression pattern indicating androgen programming in cultured genital fibroblasts. We hypothesized the existence of an epigenetic background contributing to this phenomenon. DNA methylation levels in 2 normal scrotal fibroblast strains from 46,XY males compared to 2 labia majora fibroblast strains from 46,XY females with complete androgen insensitivity syndrome (AIS) due to androgen receptor (AR) mutations were analyzed by Illumina GoldenGate methylation arrays®. Results were validated with pyrosequencing in labia majora fibroblast strains from fifteen 46,XY patients and compared to nine normal male scrotal fibroblast strains. HOXA5 showed a significantly higher methylation level in complete AIS. This finding was confirmed by bisulfite pyrosequencing of 14 CpG positions within the HOXA5 promoter in the same strains. Extension of the 2 groups revealed a constant low HOXA5 methylation pattern in the controls in contrast to a highly variable methylation pattern in the AIS patients. HOXA5 represents a candidate gene of androgen-mediated promoter methylation. The constantly low HOXA5 DNA methylation level of normal male scrotal fibroblast strains and the frequently high methylation levels in labia majora fibroblast strains in AIS indicate for the first time that androgen programming in sexual differentiation is not restricted to global gene transcription but also occurs at the epigenetic level.

  9. Simultaneous determination of 2-furfural and 5-methyl-2-furfural using corona discharge ion mobility spectrometry.

    PubMed

    Jafari, M T; Khayamian, T

    2009-06-01

    A novel technique, corona discharge ion mobility spectrometry (CD-IMS), was developed for the qualitative and quantitative determination of 2-furfural (F) and 5-methyl-2-furfural (MF) in aqueous solutions. The limits of detection (LODs) were 5.3 x 10(-3) microg/mL for F and 6.7 x 10(-3) microg/mL for MF. The linear dynamic ranges of 1.16 x 10(-2) to 1.04 microg/mL and 2.20 x 10(-2) to 1.10 microg/mL were obtained for F and MF, respectively. The relative standard deviation was below 12% for both compounds. In addition to analysis of the individual compound, simultaneous determination of F and MF was also investigated. It was realized that F imposes a matrix effect on the MF signal and vice versa. The standard addition method was used to deal with the matrix effect. The recovery of the compounds in the synthetic samples validates the capability of the method.

  10. An efficient prebiotic synthesis of cytosine and uracil

    NASA Technical Reports Server (NTRS)

    Robertson, M. P.; Miller, S. L.

    1995-01-01

    In contrast to the purines, the routes that have been proposed for the prebiotic synthesis of pyrimidines from simple precursors give only low yields. Cytosine can be synthesized from cyanoacetylene and cyanate; the former precursor is produced from a spark discharge in a CH4/N2 mixture and is an abundant interstellar molecule. But this reaction requires relatively high concentrations of cyanate (> 0.1 M), which are unlikely to occur in aqueous media as cyanate is hydrolysed rapidly to CO2 and NH3. An alternative route that has been explored is the reaction of cyanoacetaldehyde (formed by hydrolysis of cyanoacetylene) with urea. But at low concentrations of urea, this reaction produces no detectable quantities of cytosine. Here we show that in concentrated urea solution--such as might have been found in an evaporating lagoon or in pools on drying beaches on the early Earth--cyanoacetaldehyde reacts to form cytosine in yields of 30-50%, from which uracil can be formed by hydrolysis. These reactions provide a plausible route to the pyrimidine bases required in the RNA world.

  11. An efficient prebiotic synthesis of cytosine and uracil

    NASA Technical Reports Server (NTRS)

    Robertson, M. P.; Miller, S. L.

    1995-01-01

    In contrast to the purines, the routes that have been proposed for the prebiotic synthesis of pyrimidines from simple precursors give only low yields. Cytosine can be synthesized from cyanoacetylene and cyanate; the former precursor is produced from a spark discharge in a CH4/N2 mixture and is an abundant interstellar molecule. But this reaction requires relatively high concentrations of cyanate (> 0.1 M), which are unlikely to occur in aqueous media as cyanate is hydrolysed rapidly to CO2 and NH3. An alternative route that has been explored is the reaction of cyanoacetaldehyde (formed by hydrolysis of cyanoacetylene) with urea. But at low concentrations of urea, this reaction produces no detectable quantities of cytosine. Here we show that in concentrated urea solution--such as might have been found in an evaporating lagoon or in pools on drying beaches on the early Earth--cyanoacetaldehyde reacts to form cytosine in yields of 30-50%, from which uracil can be formed by hydrolysis. These reactions provide a plausible route to the pyrimidine bases required in the RNA world.

  12. Effect of uracil addition on proteomic profiles and 1,3-β-glucan production in Agrobacterium sp.

    PubMed

    Jin, Li-Hua; Lee, Jung-Heon

    2014-01-01

    Uridine diphosphate (UDP)-glucose is a precursor of 1,3-β-glucan and is synthesized from glucose-1-phosphate and uridine triphosphate (UTP). Uracil was used as a precursor for UTP, which resulted in an increase in both the UDP-glucose level and the rate of 1,3-β-glucan synthesis. 1,3-β-Glucan production metabolism was reactivated after uracil addition during fermentation. 2D-PAGE was used to examine the changes in the expression level of the key metabolic enzymes in the production of 1,3-β-glucan after uracil addition. The results showed that the expression levels of UTP-glucose-1-phosphate uridylytransferase, phosphoglucomutase, and 1,3-β-glucan synthase catalytic subunit, key metabolic enzymes in the curdlan biosynthesis pathway, were increased after uracil addition by 3.5%, 30%, and 35%, respectively. Uracil phosphoribosyltransferase, which converts uracil to uridine monophosphate (UMP), was also upregulated 79% more than that without uracil addition. However, the expression levels of orotidine 5-phosphate decarboxylase, glucose-1-phosphate adenylyltransferase, and glucose-6-phosphate isomerase were decreased after uracil addition. This proteomic information is useful for predicting changes in the pathway of uracil utilization. This work provides proteomic information for the integrative analysis of bioinformatic databases, which can be used to predict and understand the metabolism of glucan synthesis at the cellular level. © 2013 International Union of Biochemistry and Molecular Biology, Inc.

  13. Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1

    DOE PAGES

    Alsøe, Lene; Sarno, Antonio; Carracedo, Sergio; ...

    2017-08-03

    Both a DNA lesion and an intermediate for antibody maturation, uracil is primarily processed by base excision repair (BER), either initiated by uracil-DNA glycosylase (UNG) or by single-strand selective monofunctional uracil DNA glycosylase (SMUG1). The relative in vivo contributions of each glycosylase remain elusive. To assess the impact of SMUG1 deficiency, we measured uracil and 5-hydroxymethyluracil, another SMUG1 substrate, in Smug1-/- mice. Here, we found that 5-hydroxymethyluracil accumulated in Smug1-/- tissues and correlated with 5-hydroxymethylcytosine levels. The highest increase was found in brain, which contained about 26-fold higher genomic 5-hydroxymethyluracil levels than the wild type. Smug1-/- mice did not accumulatemore » uracil in their genome and Ung-/- mice showed slightly elevated uracil levels. Contrastingly, Ung-/-Smug1-/- mice showed a synergistic increase in uracil levels with up to 25-fold higher uracil levels than wild type. Whole genome sequencing of UNG/SMUG1-deficient tumours revealed that combined UNG and SMUG1 deficiency leads to the accumulation of mutations, primarily C to T transitions within CpG sequences. This unexpected sequence bias suggests that CpG dinucleotides are intrinsically more mutation prone. In conclusion, we showed that SMUG1 efficiently prevent genomic uracil accumulation, even in the presence of UNG, and identified mutational signatures associated with combined UNG and SMUG1 deficiency.« less

  14. Prebiotic synthesis of 5-substituted uracils: a bridge between the RNA world and the DNA-protein world

    NASA Technical Reports Server (NTRS)

    Robertson, M. P.; Miller, S. L.

    1995-01-01

    Under prebiotic conditions, formaldehyde adds to uracil at the C-5 position to produce 5-hydroxymethyluracil with favorable rates and equilibria. Hydroxymethyluracil adds a variety of nucleophiles, such as ammonia, glycine, guanidine, hydrogen sulfide, hydrogen cyanide, imidazole, indole, and phenol, to give 5-substituted uracils with the side chains of most of the 20 amino acids in proteins. These reactions are sufficiently robust that, if uracil had been present on the primitive Earth, then these substituted uracils would also have been present. The ribozymes of the RNA world would have included many of the functional groups found in proteins today, and their catalytic activities may have been considerably greater than presently assumed.

  15. Prebiotic synthesis of 5-substituted uracils: a bridge between the RNA world and the DNA-protein world

    NASA Technical Reports Server (NTRS)

    Robertson, M. P.; Miller, S. L.

    1995-01-01

    Under prebiotic conditions, formaldehyde adds to uracil at the C-5 position to produce 5-hydroxymethyluracil with favorable rates and equilibria. Hydroxymethyluracil adds a variety of nucleophiles, such as ammonia, glycine, guanidine, hydrogen sulfide, hydrogen cyanide, imidazole, indole, and phenol, to give 5-substituted uracils with the side chains of most of the 20 amino acids in proteins. These reactions are sufficiently robust that, if uracil had been present on the primitive Earth, then these substituted uracils would also have been present. The ribozymes of the RNA world would have included many of the functional groups found in proteins today, and their catalytic activities may have been considerably greater than presently assumed.

  16. Hydrogen-bonding effects on infrared spectra from anharmonic computations: uracil-water complexes and uracil dimers.

    PubMed

    Fornaro, Teresa; Burini, Diletta; Biczysko, Malgorzata; Barone, Vincenzo

    2015-05-07

    Hydrogen-bonding interactions lead to significant changes in the infrared (IR) spectrum, like frequency shifts of the order of magnitude of hundreds of cm(-1) and increases of IR intensity for bands related to vibrational modes of functional groups directly involved in the hydrogen-bonded bridges. We are actively developing a comprehensive and robust computational protocol aimed at the quantitative reproduction of the spectra of bio-organic and hybrid organic/inorganic molecular systems with a proper account of the variety of intra- and intermolecular interactions. We have resorted to fully anharmonic quantum mechanical computations within the generalized second-order vibrational perturbation theory (GVPT2) approach, combined with the B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such an approach has been validated in a previous work ( Phys. Chem. Chem. Phys. 2014 , 16 , 10112 - 10128 ) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended our computational protocol toward hybrid models, with the harmonic part computed at the B2PLYP level, in conjunction with the maug-cc-pVTZ basis set, or by a cost-effective ONIOM B2PLYP:B3LYP focused model, where only part of the molecular system forming the hydrogen bonds is treated at the B2PLYP level of theory. In this work experimental frequencies available for a set of four uracil-water complexes have been considered as references for the computational methodologies applied to the simulation of hydrogen-bonding effects on the infrared spectrum, obtaining average uncertainties of about 22 cm(-1) for B3LYP-D3/N07D and improved description within 10 cm(-1) by hybrid B2PLYP/B3LYP-D3 approaches. The same computational schemes have been next applied to simulate fully anharmonic IR spectra of six different hydrogen-bonded uracil dimers, providing reliable support for future experimental investigations on hydrogen

  17. Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives.

    PubMed

    Gustavsson, Thomas; Bányász, Akos; Lazzarotto, Elodie; Markovitsi, Dimitra; Scalmani, Giovanni; Frisch, Michael J; Barone, Vincenzo; Improta, Roberto

    2006-01-18

    The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy. The excited-state lifetimes were measured using femtosecond fluorescence upconversion in the UV. The absorption and emission spectra of five representative compounds have been computed at the TD-DFT level, using the PBE0 exchange-correlation functional for ground- and excited-state geometry optimization and the Polarizable Continuum Model (PCM) to simulate the aqueous solution. The calculated spectra are in good agreement with the experimental ones. Experiments show that the excited-state lifetimes of all the compounds examined are dominated by an ultrafast (<100 fs) component. Only 5-substituted compounds show more complex behavior than uracil, exhibiting longer excited-state lifetimes and biexponential fluorescence decays. The S(0)/S(1) conical intersection, located at CASSCF (8/8) level, is indeed characterized by pyramidalization and out of plane motion of the substituents on the C5 atom. A thorough analysis of the excited-state Potential Energy Surfaces, performed at the PCM/TD-DFT(PBE0) level in aqueous solution, shows that the energy barrier separating the local S(1) minimum from the conical intersection increases going from uracil through thymine to 5-fluorouracil, in agreement with the ordering of the experimental excited-state lifetime.

  18. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

    DOE PAGES

    Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; ...

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This alsomore » represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.« less

  19. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

    SciTech Connect

    Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; Chattopadhyay, Debasish

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This also represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.

  20. Physical and functional interaction of human nuclear uracil-DNA glycosylase with proliferating cell nuclear antigen☆

    PubMed Central

    Ko, Rinkei; Bennett, Samuel E.

    2011-01-01

    Uracil residues arise in DNA by the misincorporation of dUMP in place of dTMP during DNA replication or by the deamination of cytosine in DNA. Uracil-DNA glycosylase initiates DNA base excision repair of uracil residues by catalyzing the hydrolysis of the N-glycosylic bond linking the uracil base to deoxyribose. In human cells, the nuclear form of uracil-DNA glycosylase (UNG2) contains a conserved PCNA-binding motif located at the N-terminus that has been implicated experimentally in binding PCNA. Here we use purified preparations of UNG2 and PCNA to demonstrate that UNG2 physically associates with PCNA. UNG2 co-eluted with PCNA during size exclusion chromatography and bound to a PCNA affinity column. Association of UNG2 with PCNA was abolished by the addition of 100 mM NaCl, and significantly decreased in the presence of 10 mM MgCl2. The functional significance of the UNG2·PCNA association was demonstrated by UNG2 activity assays. Addition of PCNA (30–810 pmol) to standard uracil-DNA glycosylase reactions containing linear [uracil-3H]DNA stimulated UNG2 catalytic activity up to 2.6-fold. UNG2 activity was also stimulated by 7.5 mM MgCl2. The stimulatory effect of PCNA was increased by the addition of MgCl2; however, the dependence on PCNA concentration was the same, indicating that the effects of MgCl2 and PCNA on UNG2 activity occurred by independent mechanisms. Loading of PCNA onto the DNA substrate was required for stimulation, as the activity of UNG2 on circular DNA substrates was not affected by the addition of PCNA. Addition of replication factor C and ATP to reactions containing 90 pmol of PCNA resulted in two-fold stimulation of UNG2 activity on circular DNA. PMID:16216562

  1. 21 CFR 73.3122 - 4-[(2,4-dimethylphenyl)azo]-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 1 2011-04-01 2011-04-01 false 4- -2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one...-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one. (a) Identity. The color additive is 4- -2,4-dihydro-5-methyl-2-phenyl-3H- pyrazol-3-one (CAS Reg. No. 6407-78-9). (b) Uses and restrictions. (1) The substances listed...

  2. Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors.

    PubMed

    Banyasz, Akos; Esposito, Luciana; Douki, Thierry; Perron, Marion; Lepori, Clément; Improta, Roberto; Markovitsi, Dimitra

    2016-05-12

    C5-methylation of cytosines is strongly correlated with UV-induced mutations detected in skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of pyrimidine cyclobutane dimers (CPDs). The present study, performed for the model DNA duplex (TCGTA)3·(TACGA)3 and the constitutive single strands, examines the factors underlying the effect of C5-methylation on pyrimidine dimerization at TCG sites. This effect is quantified for the first time by quantum yields ϕ. They were determined following irradiation at 255, 267, and 282 nm and subsequent photoproduct analysis using HPLC coupled to mass spectrometry. C5-methylation leads to an increase of the CPD quantum yield up to 80% with concomitant decrease of that of pyrimidine(6-4) pyrimidone adducts (64PPs) by at least a factor of 3. The obtained ϕ values cannot be explained only by the change of the cytosine absorption spectrum upon C5-methylation. The conformational and electronic factors that may affect the dimerization reaction are discussed in light of results obtained by fluorescence spectroscopy, molecular dynamics simulations, and quantum mechanical calculations. Thus, it appears that the presence of an extra methyl on cytosine affects the sugar puckering, thereby enhancing conformations of the TC step that are prone to CPD formation but less favorable to 64PPs. In addition, C5-methylation diminishes the amplitude of conformational motions in duplexes; in the resulting stiffer structure, ππ* excitations may be transferred from initially populated exciton states to reactive pyrimidines giving rise to CPDs.

  3. Fluorescence of 5-arylvinyl-5'-methyl-2,2'-bipyridyl ligands and their zinc complexes.

    PubMed

    Younes, Ali H; Zhang, Lu; Clark, Ronald J; Zhu, Lei

    2009-11-20

    The photophysical properties of 5-arylvinyl-5'-methyl-2,2'-bipyridyls (AVMBs, 1-9, 11) and their zinc complexes were studied. Similar 2,2'-bipyridyl-based ligands have been applied as optical sensors for metal ions and sensitizers for solar energy conversion. The goal of this investigation is to reveal the factors that determine the emission band shift and fluorescence quantum yield change of the title ligand system upon zinc binding. The outcome of this study will not only advance the fundamental understanding of the coordination-driven photophysical processes embodied in the AVMB platform but facilitate the rational design of fluorescent probes for metal ions, particularly zinc. The AVMB ligands were synthesized using the Horner-Wadsworth-Emmons reaction. AVMBs containing electron-donating aryl groups show absorption and emission in the visible region, which can be assigned to charge-transfer transitions as supported by solvent-dependency and computational studies. The binding between AVMB ligands and zinc ion in acetonitrile was studied using isothermal titration calorimetry (ITC). A multicomponent equilibrium model is suggested that explains the multiple transitions evidenced in fluorescence titration isotherms. Coordination to zinc ion stabilizes the charge-transfer excited state of an AVMB ligand with an electron-donating aryl substituent, consequently results in bathochromic shifts in both absorption and emission. However, unlike the emission band shift, the fluorescence quantum yield change upon zinc complex formation does not have an intuitive correlation with the electronic nature of the aryl group. Lifetime measurements using the Time-Correlated Single Photon Counting method enabled the determination of nonradiative and radiative decay rate constants. Both rates of an AVMB ligand decrease upon zinc binding. The collective effect gives rise to the change in fluorescence quantum yield with the apparent lack of correlation with the electronic property of

  4. Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily

    PubMed Central

    Xia, Bo; Liu, Yinling; Guevara, Jose; Li, Jing; Jilich, Celeste; Yang, Ye; Wang, Liangjiang; Dominy, Brian N.; Cao, Weiguo

    2017-01-01

    Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG doublet in family 4 Thermus thermophilus UDGa to QD doublet increases the catalytic efficiency by over one hundred-fold and seventeen-fold over the E41Q and G42D single mutation, respectively, rectifying the strong correlation in the doublet. Molecular dynamics simulations suggest that the correlated mutations in the doublet in motif 1 position the catalytic H155 in motif 2 to stabilize the leaving uracilate anion. The integrated approach has important implications in studying enzyme evolution and protein structure and function. PMID:28397787

  5. Enzymatic Capture of an Extrahelical Thymine in the Search for Uracil in DNA

    SciTech Connect

    Parker,J.; Bianchet, M.; Krosky, D.; Friedman, J.; Amzel, L.; Stivers, J.

    2007-01-01

    The enzyme uracil DNA glycosylase (UNG) excises unwanted uracil bases in the genome using an extrahelical base recognition mechanism. Efficient removal of uracil is essential for prevention of C-to-T transition mutations arising from cytosine deamination, cytotoxic U{single_bond}A pairs arising from incorporation of dUTP in DNA, and for increasing immunoglobulin gene diversity during the acquired immune response. A central event in all of these UNG-mediated processes is the singling out of rare U{single_bond}A or U{single_bond}G base pairs in a background of approximately 109 T{single_bond}A or C{single_bond}G base pairs in the human genome. Here we establish for the human and Escherichia coli enzymes that discrimination of thymine and uracil is initiated by thermally induced opening of T{single_bond}A and U{single_bond}A base pairs and not by active participation of the enzyme. Thus, base-pair dynamics has a critical role in the genome-wide search for uracil, and may be involved in initial damage recognition by other DNA repair glycosylases.

  6. Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily.

    PubMed

    Xia, Bo; Liu, Yinling; Guevara, Jose; Li, Jing; Jilich, Celeste; Yang, Ye; Wang, Liangjiang; Dominy, Brian N; Cao, Weiguo

    2017-04-11

    Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG doublet in family 4 Thermus thermophilus UDGa to QD doublet increases the catalytic efficiency by over one hundred-fold and seventeen-fold over the E41Q and G42D single mutation, respectively, rectifying the strong correlation in the doublet. Molecular dynamics simulations suggest that the correlated mutations in the doublet in motif 1 position the catalytic H155 in motif 2 to stabilize the leaving uracilate anion. The integrated approach has important implications in studying enzyme evolution and protein structure and function.

  7. Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily

    NASA Astrophysics Data System (ADS)

    Xia, Bo; Liu, Yinling; Guevara, Jose; Li, Jing; Jilich, Celeste; Yang, Ye; Wang, Liangjiang; Dominy, Brian N.; Cao, Weiguo

    2017-04-01

    Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG doublet in family 4 Thermus thermophilus UDGa to QD doublet increases the catalytic efficiency by over one hundred-fold and seventeen-fold over the E41Q and G42D single mutation, respectively, rectifying the strong correlation in the doublet. Molecular dynamics simulations suggest that the correlated mutations in the doublet in motif 1 position the catalytic H155 in motif 2 to stabilize the leaving uracilate anion. The integrated approach has important implications in studying enzyme evolution and protein structure and function.

  8. Uracil misincorporation into DNA and folic acid supplementation.

    PubMed

    Hazra, Aditi; Selhub, Jacob; Chao, Wei-Hsun; Ueland, Per Magne; Hunter, David J; Baron, John A

    2010-01-01

    Folate deficiency decreases thymidylate synthesis from deoxyuridylate, which results in an imbalance of deoxyribonucleotide that may lead to excessive uracil misincorporation (UrMis) into DNA during replication and repair. We evaluated the relation between UrMis in different tissues and the effect of folate supplementation on UrMis. We analyzed UrMis concentrations in rectal mucosa (n = 92) and white blood cells (WBCs; n = 60) among individuals randomly assigned to receive supplementation with 1 mg folate/d or placebo, who were then evaluated for colorectal adenoma recurrence. As expected, total homocysteine was significantly lower among the study participants who received active folate treatment (Wilcoxon's P = 0.003) than among those in the placebo group. The median UrMis concentration in rectal mucosa and WBCs among individuals treated with folate was not significantly lower than that in those who received placebo (Wilcoxon's P = 0.17). UrMis concentrations in both rectal mucosa and WBCs did not correlate significantly with folate measured in plasma and red blood cells. UrMis in rectal mucosa was marginally associated with an increased risk of adenoma recurrence (odds ratio per SD: 1.43; 95% CI: 0.91, 2.25). UrMis measurements in WBCs are not a robust surrogate for UrMis measurements in the rectal mucosa (Spearman correlation coefficient = 0.23, P = 0.08). Furthermore, folate supplementation in an already replete population (half treated with folic acid supplements and all exposed to folic acid fortification of the food supply) was not significantly associated with reduced UrMis in rectal mucosa cells or WBCs. Large-scale studies are needed to evaluate whether excessive UrMis concentrations are an important risk factor for colorectal neoplasia. This trial was registered at clinicaltrials.gov as NCT00272324.

  9. Dissociative Electron Attachment Dynamics in the Nucleobase Uracil and Related Molecules

    NASA Astrophysics Data System (ADS)

    Slaughter, Daniel; Kuriyama, Yosuke; Kawarai, Yu; Azuma, Yoshiro; Winstead, Carl; McKoy, Vincent; Weber, Thorsten; Belkacem, Ali

    2015-05-01

    We report the dynamics of dissociative electron attachment (DEA) in the biologically-relevant molecule uracil and the diazines pyrazine and pyrimidine. Our DEA reaction microscope consists of a 3D momentum-imaging spectrometer, a pulsed low-energy electron gun and an effusive gas target. The experimental approach allows the measurement of kinetic energy and angular distributions of ionic fragments produced by DEA, in some cases elucidating the total kinetic energy release following two-body breakup. By comparison of calculations of the electron attachment probability in the molecular frame with measured ion angular distributions, we determine that one of the uracil anion resonances could be a Feshbach resonance and we compare the dynamics of the dissociation of the uracil anion with the diazines. Work supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE

  10. Single nucleotide polymorphisms in uracil-processing genes, intake of one-carbon nutrients and breast cancer risk

    USDA-ARS?s Scientific Manuscript database

    Background/Objectives: The misincorporation of uracil into DNA leads to genomic instability. In a previous study, some of us identified four common single nucleotide polymorphisms (SNPs) in uracil-processing genes (rs2029166 and rs7296239 in SMUG1, rs34259 in UNG and rs4775748 in DUT) that were asso...

  11. Barrier-free intermolecular proton transfer in the uracil-glycine complex induced by excess electron attachment

    NASA Astrophysics Data System (ADS)

    Gutowski, M.; Dąbkowska, I.; Rak, J.; Xu, S.; Nilles, J. M.; Radisic, D.; Bowen, K. H., Jr.

    2002-09-01

    The photoelectron spectra (PES) of anions of uracil-glycine and uracil-phenylalanine complexes reveal broad features with maxima at 1.8 and 2.0 eV. The results of ab initio density functional B3LYP and second order Møller-Plesset theory calculations indicate that the excess electron occupies a π^* orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of glycine to the O8 atom of uracil. As a result, the four most stable structures of the anion of uracil-glycine complex can be characterized as the neutral radical of hydrogenated uracil solvated by the anion of deprotonated glycine. The similarity between the PES spectra for the uracil complexes with glycine and phenylalanine suggests that the BFPT is also operative in the case of the latter anionic species. The BFPT to the O8 atom of uracil may be related to the damage of nucleic acid bases by low energy electrons because the O8 atom is involved in a hydrogen bond with adenine in the standard Watson-Crick pairing scheme.

  12. Ferrocene-bis(thymine/uracil) conjugates: base pairing directed, spacer dependent self-assembly and supramolecular packing.

    PubMed

    Patwa, Amit N; Gonnade, Rajesh G; Kumar, Vaijayanti A; Bhadbhade, Mohan M; Ganesh, Krishna N

    2010-12-17

    X-ray crystallographic studies of methylene linked Ferrocene-bis(thymine/uracil) conjugates Fc(T:T)(M) and Fc(U:U)(M) reveal base dependent 2-D supramolecular assemblies generated via wobble self-pairing for bis-thymine and reverse wobble self-pairing for bis-uracil conjugates, differing in architecture from the corresponding butylene spacer linked conjugates.

  13. Pulsed field ionization electron spectroscopy and molecular structure of aluminum uracil.

    PubMed

    Krasnokutski, Serge A; Yang, Dong-Sheng

    2007-10-25

    Al-uracil (Al-C4H4N2O2) was synthesized in a laser-vaporization supersonic molecular beam source and studied with pulsed field ionization-zero electron kinetic energy (ZEKE) photoelectron spectroscopy and density functional theory (DFT). The DFT calculations predicted several low-energy Al-uracil isomers with Al binding to the diketo, keto-enol, and dienol tautomers of uracil. The ZEKE spectroscopic measurements of Al-uracil determined the ionization energy of 43 064(5) cm-1 [or 5.340(6) eV] and a vibrational mode of 51 cm-1 for the neutral complex and several vibrational modes of 51, 303, 614, and 739 cm-1 for the ionized species. Combination of the ZEEK spectrum with the DFT and Franck-Condon factor calculations determined the preferred isomeric structure and electronic states of the Al-uracil complex. This isomer is formed by Al binding to the O4 atom of the diketo tautomer of uracil and has a planar Cs symmetry. The ground electronic states of the neutral and ionized species are 2A' ' and 1A', respectively. The 2A' ' neutral state has a slightly shorter Al-O4 distance than the 1A' ion state. However, the 1A' ion state has stronger metal-ligand binding compared to the 2A' ' state. The increased Al-O4 distance from the 2A' ' state to the 1A' state is attributed to the loss of the pi binding interaction between Al and O4 in the singlet ion state, whereas the increased metal-ligand binding strength is due to the additional charge-dipole interaction in the ion that surpasses the loss of the pi orbital interaction.

  14. Synthesis and crystal structure of new heterocyles derived from saccharin and uracil carrying 1,2,4-oxadiazolylmethyl group.

    PubMed

    Dürüst, Yaşar; Özer, Besra; Kariuki, Benson M; Cariuki, Benson M

    2015-05-01

    Saccharin, uracil, and 1,2,4-oxadiazole heterocyles are important in terms of exhibiting various biological acitivities. In this work, four series of 1,2,4-oxadiazolylmethyl-substituted saccharin, and uracil derivatives are synthesized and their structures are identified by means of spectral/physical characteristics. The first series are oxadiazolylmethyl-substituted saccharins. The second one is oxadiazole-substituted uracils which are obtained as a separable mixture of both mono- and bis-substituted end products. Third series is obtained from 5-amino uracil and chloromethyl oxadiazoles. The fourth group is oxadiazolyl methyl-substituted imino uracils. The structures of some title compounds are also confirmed by X-ray diffraction data.

  15. Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

    NASA Astrophysics Data System (ADS)

    López-Tarifa, Pablo; Hervé du Penhoat, Marie-Anne; Vuilleumier, Rodophe; Gaigeot, Marie-Pierre; Rothlisberger, Ursula; Tavernelli, Ivano; Le Padellec, Arnaud; Champeaux, Jean-Philippe; Alcamí, Manuel; Moretto-Capelle, Patrick; Martín, Fernando; Politis, Marie-Françoise

    2014-02-01

    We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons.

  16. Synthesis, photophysical and electroluminescent properties of novel iridium (III) complexes based on 5-methyl-2-phenylbenzo[d]oxazole derivatives

    NASA Astrophysics Data System (ADS)

    Li, Xiao; Chi, Hai-Jun; Dong, Yan; Xiao, Guo-Yong; Lei, Peng; Zhang, Dong-Yu; Cui, Zheng

    2013-12-01

    A new series of phosphorescent iridium (III) complexes based on 5-methyl-2-phenylbenzo[d]oxazole derivatives as main ligands, i.e. bis(5-methyl-2- phenylbenzo[d]oxazole-N,C2‧)iridium(acetylacetonate) [(mpbo)2Ir(acac)], bis(2-(4-fluorophenyl)-5-methylbenzo[d]oxazole-N,C2‧)iridium(acetylacetonate) [(fmbo)2Ir(acac)] and bis(5-methyl-2-p-tolylbenzo[d]oxazole-N,C2‧) iridium(acetylacetonate) [(mtbo)2Ir(acac)], were synthesized for organic light-emitting diodes (OLEDs), and their photophysical, electroluminescent properties were investigated. All complexes have high thermal stability and emit intense phosphorescence from green to yellow at room temperature with high quantum efficiencies and relatively short lifetimes. The OLED based on (fmbo)2Ir(acac) as dopant emitter showed very high luminance of 26,004 cd m-2 and luminance efficiency of 18.5 cd A-1. The evidences indicated that this series of iridium (III) complexes were potential candidates for applications in organic electroluminescent devices.

  17. Excited-state deactivation pathways in uracil versus hydrated uracil: solvatochromatic shift in the (1)nπ* state is the key.

    PubMed

    Zhang, Xing; Herbert, John M

    2014-07-17

    Excited-state deactivation mechanisms of uracil are investigated using spin-flip time-dependent density functional theory. Two important minimum-energy crossing points are located, for both gas-phase and hydrated uracil, and optimized relaxation pathways connecting the most important critical points on the (1)nπ* and (1)ππ* potential energy surfaces are determined. An ultrafast decay time constant, measured via femtosecond spectroscopy, is assigned to direct (1)ππ* → S0 deactivation, while a slower decay component is assigned to indirect (1)ππ* → (1)nπ* → S0 deactivation. The shorter lifetime of the dark (1)nπ* state in aqueous solution is attributed to a decrease in the energy barrier along the pathway connecting the (1)nπ* minimum to a (1)ππ*/S0 conical intersection. This barrier arises due to hydrogen bonding between uracil and water, leading to a blue-shift in the S0 → (1)nπ* excitation energy and considerable modification of energy barriers on the (1)nπ* potential surface. These results illustrate how hydrogen bonding to the chromophore can significantly impact excited-state dynamics and also highlight that relaxation pathways can be elucidated using low-cost methods based on density functional theory.

  18. B cells from hyper-IgM patients carrying UNG mutations lack ability to remove uracil from ssDNA and have elevated genomic uracil.

    PubMed

    Kavli, Bodil; Andersen, Sonja; Otterlei, Marit; Liabakk, Nina B; Imai, Kohsuke; Fischer, Alain; Durandy, Anne; Krokan, Hans E; Slupphaug, Geir

    2005-06-20

    The generation of high-affinity antibodies requires somatic hypermutation (SHM) and class switch recombination (CSR) at the immunoglobulin (Ig) locus. Both processes are triggered by activation-induced cytidine deaminase (AID) and require UNG-encoded uracil-DNA glycosylase. AID has been suggested to function as an mRNA editing deaminase or as a single-strand DNA deaminase. In the latter model, SHM may result from replicative incorporation of dAMP opposite U or from error-prone repair of U, whereas CSR may be triggered by strand breaks at abasic sites. Here, we demonstrate that extracts of UNG-proficient human B cell lines efficiently remove U from single-stranded DNA. In B cell lines from hyper-IgM patients carrying UNG mutations, the single-strand-specific uracil-DNA glycosylase, SMUG1, cannot complement this function. Moreover, the UNG mutations lead to increased accumulation of genomic uracil. One mutation results in an F251S substitution in the UNG catalytic domain. Although this UNG form was fully active and stable when expressed in Escherichia coli, it was mistargeted to mitochondria and degraded in mammalian cells. Our results may explain why SMUG1 cannot compensate the UNG2 deficiency in human B cells, and are fully consistent with the DNA deamination model that requires active nuclear UNG2. Based on our findings and recent information in the literature, we present an integrated model for the initiating steps in CSR.

  19. Folate supplementation differently affects uracil content in DNA in the mouse colon and liver

    USDA-ARS?s Scientific Manuscript database

    High folate intake may increase the risk of cancer, especially in the elderly. The present study examined the effects of ageing and dietary folate on uracil misincorporation into DNA, which has a mutagenic effect, in the mouse colon and liver. Old (18 months; n 42) and young (4 months; n 42) male C5...

  20. The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates

    PubMed Central

    Aravind, L; Koonin, Eugene V

    2000-01-01

    Background: Uracil DNA glycosylases (UDGs) are major repair enzymes that protect DNA from mutational damage caused by uracil incorporated as a result of a polymerase error or deamination of cytosine. Four distinct families of UDGs have been identified, which show very limited sequence similarity to each other, although two of them have been shown to possess the same structural fold. The structural and evolutionary relationships between the rest of the UDGs remain uncertain. Results: Using sequence profile searches, multiple alignment analysis and protein structure comparisons, we show here that all known UDGs possess the same fold and must have evolved from a common ancestor. Although all UDGs catalyze essentially the same reaction, significant changes in the configuration of the catalytic residues were detected within their common fold, which probably results in differences in the biochemistry of these enzymes. The extreme sequence divergence of the UDGs, which is unusual for enzymes with the same principal activity, is probably due to the major role of the uracil-flipping caused by the conformational strain enacted by the enzyme on uracil-containing DNA, as compared with the catalytic action of individual polar residues. We predict two previously undetected families of UDGs and delineate a hypothetical scenario for their evolution. Conclusions: UDGs form a single protein superfamily with a distinct structural fold and a common evolutionary origin. Differences in the catalytic mechanism of the different families combined with the construction of the catalytic pocket have, however, resulted in extreme sequence divergence of these enzymes. PMID:11178247

  1. DNA base excision repair of uracil residues in reconstituted nucleosome core particles

    PubMed Central

    Nilsen, Hilde; Lindahl, Tomas; Verreault, Alain

    2002-01-01

    The human base excision repair machinery must locate and repair DNA base damage present in chromatin, of which the nucleosome core particle is the basic repeating unit. Here, we have utilized fragments of the Lytechinus variegatus 5S rRNA gene containing site-specific U:A base pairs to investigate the base excision repair pathway in reconstituted nucleosome core particles in vitro. The human uracil-DNA glycosylases, UNG2 and SMUG1, were able to remove uracil from nucleosomes. Efficiency of uracil excision from nucleosomes was reduced 3- to 9-fold when compared with naked DNA, and was essentially uniform along the length of the DNA substrate irrespective of rotational position on the core particle. Furthermore, we demonstrate that the excision repair pathway of an abasic site can be reconstituted on core particles using the known repair enzymes, AP-endonuclease 1, DNA polymerase β and DNA ligase III. Thus, base excision repair can proceed in nucleosome core particles in vitro, but the repair efficiency is limited by the reduced activity of the uracil-DNA glycosylases and DNA polymerase β on nucleosome cores. PMID:12411511

  2. Enhancement of infrared absorption of low-temperature uracil thin films by a nanostructured silver surface

    NASA Astrophysics Data System (ADS)

    Ivanov, A. Yu.; Stepanian, S. G.; Adamowicz, L.; Karachevtsev, V. A.

    2016-02-01

    Enhancement of infrared absorption (SEIRA) of adsorbed biological molecules by a nanostructured metal surface is one of the main routes to increasing the sensitivity of modern optical biosensors. The FTIR absorption spectra of thin films of the RNA base uracil deposited on low-temperature substrate (T = 6 K) with nanoscale silver structures were investigated in the spectral range 2700-600 cm-1. It was shown that the intensity of the absorption bands corresponding to νCO stretching vibrations (range 1800-1600 cm-1) of uracil (Ur) thin films increases 3-4 fold. For multilayer films, the influence of the nanostructures on the vibrational spectra weakens, and for the film layers more than 15 nm away from the surface, the enhancement is essentially absent. The energies and the vibrational spectra of the complexes of uracil monomers and dimers with 20-atom tetrahedral silver nanoclusters were calculated by the quantum-mechanical method DFT/B3LYP. The most stable complexes have the coordination bond between the top of the silver tetrahedron and the oxygen of the carbonyl group C4O. It was found that the formation of such complexes significantly (3-5 fold) enhances the intensity of the νC4O stretching vibration of uracil, while the intensities of the βNH, βCH and ring bending vibrations do not increase significantly.

  3. Characterizing the dark state in thymine and uracil by double resonant spectroscopy and quantum computation.

    PubMed

    Ligare, M; Siouri, F; Bludsky, O; Nachtigallová, D; de Vries, M S

    2015-10-07

    We report on gas phase double resonant spectroscopy of both the ground state and the dark excited state in isolated uracil and thymine. We also report lifetimes of the dark state for different excitation wavelengths. In combination with ab initio calculations the results suggest that the dark state is of triplet ((3)ππ*) character.

  4. Why are selenouracils as basic as but stronger acids than uracil in the gas phase?

    PubMed

    Trujillo, Cristina; Mó, Otilia; Yáñez, Manuel

    2008-08-25

    The gas-phase basicity and acidity of 2-selenouracil (2SU), 4-selenouracil (4SU), and 2,4-diselenouracil (24SU) have been calculated at the B3LYP/6-311+G(3df,2p) level of theory. Our results showed that all these compounds behave as bases of moderate strength in the gas phase. As was found for uracil and for the thiouracil analogues, the most basic site is the heteroatom at position 4, and only for 2SU is there a certain ambiguity in assigning the basic site. More importantly, with the only exception of 2SU, selenouracils are as basic as or slightly less basic than uracil, because the replacement of the oxygen atom at position 2 by a selenium atom leads to an increase of the electron delocalization inside the six-membered ring, which decreases the intrinsic basicity of the heteroatom at position 4. As already reported for uracil and thiouracils, for selenouracils N1 is the most acidic site. However, selenouracils are predicted to be stronger acids than uracil. This acidity enhancement is essentially due to a specific stabilization of the anion when O is replaced by Se. Two factors are responsible for this stabilization: a significant aromatization of the ring upon deprotonation and a better dispersion of the excess electron density when the system contains third-row atoms.

  5. Inhibition of uracil-DNA glycosylase increases SCEs in BrdU-treated and visible light-irradiated cells

    SciTech Connect

    Maldonado, A.; Hernandez, P.; Gutierrez, C.

    1985-11-01

    The authors have approached the study of the ability of different types of lesions produced by DNA-damaging agents to develop sister-chromatid exchanges (SCEs) by analyzing SCE levels observed in Allium cepa L cells with BrdU-substituted DNA and exposed to visible light (VL), an irradiation which produces uracil residues in DNA after debromination of bromouracil and enhances SCE levels but only above a certain dose. They have partially purified an uracil-DNA glycosylase activity from A. cepa L root meristem cells, which removes uracil from DNA, the first step in the excision repair of this lesion. This enzyme was inhibited in vitro by 6-amino-uracil and uracil but not by thymine. When cells exposed to VL, at a dose that did not produce per se an SCE increase, were immediately post-treated with these inhibitors of uracil-DNA glycosylase, a significant increase in SCE levels was obtained. Moreover, SCE levels in irradiated cells dropped to control level when a short holding time elapsed between exposure to VL and the beginning of post-treatment with the inhibitor. Thus, our results showed that inhibitors of uracil-DNA glycosylase enhanced SCE levels in cells with unifilarly BrdU-substituted DNA exposed to visible light; and indicated the existence of a very rapid repair of SCE-inducing lesions produced by visible light irradiation of cells with unifilarly BrdU-containing DNA.

  6. Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil.

    PubMed

    Richardson, Tomas T; Wu, Xiaohua; Keith, Brian J; Heslop, Pauline; Jones, Anita C; Connolly, Bernard A

    2013-02-01

    Archaeal family-B DNA polymerases bind tightly to deaminated bases and stall replication on encountering uracil in template strands, four bases ahead of the primer-template junction. Should the polymerase progress further towards the uracil, for example, to position uracil only two bases in front of the junction, 3'-5' proof-reading exonuclease activity becomes stimulated, trimming the primer and re-setting uracil to the +4 position. Uracil sensing prevents copying of the deaminated base and permanent mutation in 50% of the progeny. This publication uses both steady-state and time-resolved 2-aminopurine fluorescence to show pronounced unwinding of primer-templates with Pyrococcus furiosus (Pfu) polymerase-DNA complexes containing uracil at +2; much less strand separation is seen with uracil at +4. DNA unwinding has long been recognized as necessary for proof-reading exonuclease activity. The roles of M247 and Y261, amino acids suggested by structural studies to play a role in primer-template unwinding, have been probed. M247 appears to be unimportant, but 2-aminopurine fluorescence measurements show that Y261 plays a role in primer-template strand separation. Y261 is also required for full exonuclease activity and contributes to the fidelity of the polymerase.

  7. Compartmentalized self-replication (CSR) selection of Thermococcus litoralis Sh1B DNA polymerase for diminished uracil binding.

    PubMed

    Tubeleviciute, Agne; Skirgaila, Remigijus

    2010-08-01

    The thermostable archaeal DNA polymerase Sh1B from Thermococcus litoralis has a typical uracil-binding pocket, which in nature plays an essential role in preventing the accumulation of mutations caused by cytosine deamination to uracil and subsequent G-C base pair transition to A-T during the genomic DNA replication. The uracil-binding pocket recognizes and binds uracil base in a template strand trapping the polymerase. Since DNA replication stops, the repair systems have a chance to correct the promutagenic event. Archaeal family B DNA polymerases are employed in various PCR applications. Contrary to nature, in PCR the uracil-binding property of archaeal polymerases is disadvantageous and results in decreased DNA amplification yields and lowered sensitivity. Furthermore, in diagnostics qPCR, RT-qPCR and end-point PCR are performed using dNTP mixtures, where dTTP is partially or fully replaced by dUTP. Uracil-DNA glycosylase treatment and subsequent heating of the samples is used to degrade the DNA containing uracil and prevent carryover contamination, which is the main concern in diagnostic laboratories. A thermostable archaeal DNA polymerase with the abolished uracil binding would be a highly desirable and commercially interesting product. An attempt to disable uracil binding in DNA polymerase Sh1B from T. litoralis by generating site-specific mutants did not yield satisfactory results. However, a combination of random mutagenesis of the whole polymerase gene and compartmentalized self-replication was successfully used to select variants of thermostable Sh1B polymerase capable of performing PCR with dUTP instead of dTTP.

  8. Effects of protonation and C5 methylation on the electrophilic addition reaction of cytosine: a computational study.

    PubMed

    Jin, Lingxia; Wang, Wenliang; Hu, Daodao; Min, Suotian

    2013-01-10

    The mechanism for the effects of protonation and C5 methylation on the electrophilic addition reaction of Cyt has been explored by means of CBS-QB3 and CBS-QB3/PCM methods. In the gas phase, three paths, two protonated paths (N3 and O2 protonated paths B and C) as well as one neutral path (path A), were mainly discussed, and the calculated results indicate that the reaction of the HSO(3)(-) group with neutral Cyt is unlikely because of its high activation free energy, whereas O2-protonated path (path C) is the most likely to occur. In the aqueous phase, path B is the most feasible mechanism to account for the fact that the activation free energy of path B decreases compared with the corresponding path in the gas phase, whereas those of paths A and C increase. The main striking results are that the HSO(3)(-) group directly interacts with the C5═C6 bond rather than the N3═C4 bond and that the C5 methylation, compared with Cyt, by decreasing values of global electrophilicity index manifests that C5 methylation forms are less electrophilic power as well as by decreasing values of NPA charges on C5 site of the intermediates make the trend of addition reaction weaken, which is in agreement with the experimental observation that the rate of 5-MeCyt reaction is approximately 2 orders of magnitude slower than that of Cyt in the presence of bisulfite. Apart from cis and trans isomers, the rare third isomer where both the CH(3) and SO(3) occupy axial positions has been first found in the reactions of neutral and protonated 5-MeCyt with the HSO(3)(-) group. Furthermore, the transformation of the third isomer from the cis isomer can occur easily.

  9. 3-Cyano-6-(5-methyl-3-pyrazoloamino) pyridines (Part 2): A dual inhibitor of Aurora kinase and tubulin polymerization.

    PubMed

    Morioka, Masahiko

    2016-12-15

    A new class of a dual inhibitor of Aurora kinase and tubulin polymerization was created by introducing various substituted phenoxyethylamino or pyridyloxyethylamino groups to the 2-position of 3-cyano-4-methyl-6-(5-methyl-3-pyrazoloamino)-pyridine. Compound 3g exhibited Aurora kinase inhibition, excellent protein kinase selectivity to Aurora kinase in comparison with 66 other kinases, inhibition of phosphorylation of Ser10 of histone H3 as an Aurora kinase inhibitor, inhibition of tubulin polymerization in vitro, good cell membrane permeability, and a good PK profile. Therefore compound 3g was effective in some antitumor mouse models at a dose of 30mg/kgpoqd.

  10. Crystal thickness dependence of the photoinduced crystal bending of 1-(5-methyl-2-(4-(p-vinylbenzoyloxymethyl)phenyl)-4-thiazolyl)-2-(5-methyl-2-phenyl-4-thiazolyl)perfluorocyclopentene.

    PubMed

    Kitagawa, Daichi; Kobatake, Seiya

    2014-05-01

    Rod-like crystals of 1-(5-methyl-2-(4-(p-vinylbenzoyloxymethyl)phenyl)-4-thiazolyl)-2-(5-methyl-2-phenyl-4-thiazolyl)perfluorocyclopentene with lengths of over 1 mm showed photoreversible bending over 100 cycles upon irradiation with alternating ultraviolet (UV) and visible light. The crystals bent toward the incident light due to a contraction of the crystal length and a gradient of the crystal thickness, which depend on the extent of photoisomerization. It was observed that the bending speed depends on the crystal thickness, and the curvature change on changing the crystal thickness agrees well with Timoshenko's bimetal model, as well as with the observation that crystals of 1,2-bis(2-methyl-5-(4-(1-naphthoyloxymethyl)phenyl)-3-thienyl)perfluorocyclopentene bend away from the incident light due to an expansion of the crystal length and a gradient of the crystal thickness, which depend on the extent of photoisomerization. It was revealed that Timoshenko's bimetal model can be applied to photoinduced crystal bending behaviors caused by both contraction and expansion. These findings are very useful for evaluating and designing photomechanical actuators.

  11. Formation of 5-methyl-4-hydroxy-3[2H]-furanone in cytosolic extracts obtained from Zygosaccharomyces rouxii.

    PubMed

    Hauck, Tobias; Landmann, Christian; Brühlmann, Fredi; Schwab, Wilfried

    2003-02-26

    Formation of the flavor compound and precursor 4-hydroxy-5-methyl-3[2H]-furanone (HMF, norfuraneol) was demonstrated in cytosolic protein extracts obtained from Zygosaccharomyces rouxii after incubation with a number of carbohydrate phosphates. 4-Hydroxy-5-methyl-3[2H]-furanone was produced from d-fructose-1,6-diphosphate, d-fructose-6-phosphate, d-glucose-6-phosphate, 6-phosphogluconate, d-ribose-5-phosphate, and d-ribulose-1,5-diphosphate. Enzyme assays revealed d-fructose-1,6-diphosphatase, phosphohexose isomerase, d-glucose-6-phosphate dehydrogenase, and 6-phosphogluconate dehydrogenase activity in the cytosolic extracts. Model studies showed the spontaneous formation of HMF from d-ribulose-5-phosphate. It is assumed that d-ribulose-5-phosphate is generated in cytosolic extracts by the action of the investigated enzymes from the carbohydrate phosphates and is then chemically transformed to HMF. The hypothesis was proven by the production of HMF in solutions containing commercially available enzymes and [6-(13)C]-d-glucose-6-phosphate.

  12. 21 CFR 73.3122 - 4-[(2,4-dimethylphenyl)azo]-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...-phenyl-3H-pyrazol-3-one. 73.3122 Section 73.3122 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT... Devices § 73.3122 4-[(2,4-dimethylphenyl)azo]-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one. (a) Identity. The color additive is 4-[(2,4-dimethylphenyl)azo]-2,4-dihydro-5-methyl-2-phenyl-3H- pyrazol-3-one (CAS...

  13. Platinum(IV) complexes with some derivatives of 5-methyl-5-(4-pyridyl) hydantoin. Synthesis, study and comparative pharmacological investigation.

    PubMed

    Bakalova, A; Buyukliev, R; Ivanova, Z; Momekov, G; Ivanov, D

    2013-08-01

    3 Pt(IV) complexes with 3-ethyl-5-methyl-5-(4-pyridyl)hydantoin (4), 3-propyl-5-methyl-5-(4-pyridyl)hydantoin (5) and 3-benzyl-5-methyl-5-(4-pyridyl)hydantoin (6) with general formulae cis-[Pt(L)2Cl4] were synthesized. The novel compounds were characterized by elemental analysis, IR, 1H, 13C, NMR spectra in solid state and in solution. The studies showed that the ligands coordinate to the platinum ions in a monodentate manner through the nitrogen atom from the pyridine ring. The cytotoxic activity in vitro of newly synthesized complexes as well as their previously prepared analogous of Pt(IV) with other derivatives like 3-amino-5-methyl-5-(4-pyridyl)hydantoin (1), 5-methyl-5-(4-pyridyl)hydantoin (2), 3,5-dimethyl-5-(4-pyridyl)hydantoin (3) was screened against a panel of human tumor cell lines. The tested compounds displayed cytotoxic activity which was invariably superior with the Pt(IV) complex with 3-benzyl-5-methyl-5-(4-pyridyl)hydantoin (6) causing 50% inhibition of cellular viability at micromolar concentration, though the activity of the other studied Pt(IV) complexes proved to greatly decrease in the order 5-4-3-2-1. © Georg Thieme Verlag KG Stuttgart · New York.

  14. The Photochemistry of Pyrimidine in Pure H2O Ice Subjected to Different Radiation Environments and the Formation of Uracil

    NASA Technical Reports Server (NTRS)

    Nuevo, M.; Chen, Y.-J.; Materese. C. K..; Hu, W.-J.; Qiu, J.-M.; Wu, S.-R.; Fung, H.-S.; Sandford, S. A.; Chu, C.-C.; Yih, T.-S.; hide

    2013-01-01

    Nucleobases are N-heterocycles which are the informational subunits of DNA and RNA. They include pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in several meteorites, although no Nheterocycles have been observed in space to data. Laboratory experiments showed that the ultraviolet (UV) irradiation of pyrimidine in pure H2O ice at low temperature (<=20 K) leads to the formation of pyrimidine derivatives including the nucleobase uracil and its precursor 4(3H)-pyrimidone. These results were confirmed by quantum chemical calculations. When pyrimidine is mixed with combinations of H2O, NH3, CH3OH, and CH4 ices under similar conditions, uracil and cytosine are formed. In the present work we study the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in H2O ice with high-energy UV photons (Lyman , He I, and He II lines) provided by a synchrotron source. The photo-destruction of pyrimidine in these H2O ices as well as the formation yields for 4(3H)-pyrimidone and uracil are compared with our previous results in order to study the photo-stability of pyrimidine and the production efficiency of uracil as a function of the photon energy.

  15. Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.

    PubMed Central

    Schumacher, M A; Carter, D; Scott, D M; Roos, D S; Ullman, B; Brennan, R G

    1998-01-01

    Uracil phosphoribosyltransferase (UPRTase) catalyzes the transfer of a ribosyl phosphate group from alpha-D-5-phosphoribosyl-1-pyrophosphate to the N1 nitrogen of uracil. The UPRTase from the opportunistic pathogen Toxoplasma gondii is a rational target for antiparasitic drug design. To aid in structure-based drug design studies against toxoplasmosis, the crystal structures of the T.gondii apo UPRTase (1.93 A resolution), the UPRTase bound to its substrate, uracil (2.2 A resolution), its product, UMP (2.5 A resolution), and the prodrug, 5-fluorouracil (2.3 A resolution), have been determined. These structures reveal that UPRTase recognizes uracil through polypeptide backbone hydrogen bonds to the uracil exocyclic O2 and endocyclic N3 atoms and a backbone-water-exocyclic O4 oxygen hydrogen bond. This stereochemical arrangement and the architecture of the uracil-binding pocket reveal why cytosine and pyrimidines with exocyclic substituents at ring position 5 larger than fluorine, including thymine, cannot bind to the enzyme. Strikingly, the T. gondii UPRTase contains a 22 residue insertion within the conserved PRTase fold that forms an extended antiparallel beta-arm. Leu92, at the tip of this arm, functions to cap the active site of its dimer mate, thereby inhibiting the escape of the substrate-binding water molecule. PMID:9628859

  16. Sorption of organic molecules on surfaces of a microporous polymer adsorbent modified with different quantities of uracil

    NASA Astrophysics Data System (ADS)

    Gus'kov, V. Yu.; Ganieva, A. G.; Kudasheva, F. Kh.

    2016-11-01

    The sorption of organic molecules on the surfaces of a number of adsorbents based on a microporous copolymer of styrene and divinylbenzene modified with different quantities of uracil is studied by means of inverse gas chromatography at infinite dilution. Samples containing 10-6, 10-5, 10-4, 10-3, 10-2, and 0.5 × 10‒1 weight parts of uracil (the pC of uracil ranges from 1.3 to 6) are studied. The contributions from different intermolecular interactions to the Helmholtz energy of sorption are calculated via the linear free energy relationship. It is found that as the concentration of uracil on the surface of the polymer adsorbent grows, the contributions from different intermolecular interactions and the conventional polarity of the surface have a bend at pC = 3, due probably to the formation of a supramolecular structure of uracil. Based on the obtained results, it is concluded that the formation of the supramolecular structure of uracil on the surface of the polymer adsorbent starts when pC < 3.

  17. Electron-induced hydrogen loss in uracil in a water cluster environment

    SciTech Connect

    Smyth, M.; Kohanoff, J.; Fabrikant, I. I.

    2014-05-14

    Low-energy electron-impact hydrogen loss due to dissociative electron attachment (DEA) to the uracil and thymine molecules in a water cluster environment is investigated theoretically. Only the A{sup ′}-resonance contribution, describing the near-threshold behavior of DEA, is incorporated. Calculations are based on the nonlocal complex potential theory and the multiple scattering theory, and are performed for a model target with basic properties of uracil and thymine, surrounded by five water molecules. The DEA cross section is strongly enhanced when the attaching molecule is embedded in a water cluster. This growth is due to two effects: the increase of the resonance lifetime and the negative shift in the resonance position due to interaction of the intermediate negative ion with the surrounding water molecules. A similar effect was earlier found in DEA to chlorofluorocarbons.

  18. The study of interaction between PFOA/PFOS and uracil by topology quality and spectroscopic analysis

    NASA Astrophysics Data System (ADS)

    Xu, Hui-Ying; Zhu, Jian-Qing; Wang, Wei; Xu, Xiao-Lu; Lu, Yin

    2014-02-01

    It has been established that perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) can be considered as emerging persistent organic pollutants. In recent years, there was increasing distribution of PFOA/PFOS in environmental systems, and accumulation and toxic effects of PFOA/PFOS in human body. In this paper, quantum chemistry methods were employed to study the interaction between perfluorinated organic pollutants and base (uracil). The results showed that there were four stable binding modes between the two perfluorinated compounds with uracil, especially the second mode which caused the most detrimental physiological functional response. NBO analysis showed that reactive hydrogen in the two perfluorinated compounds had the greatest effect on the hydrogen bond. The nature of the hydrogen bond formed between the two perfluorinated compounds and base was investigated using the AIM theory. The changes of spectroscopic properties in complexes were analyzed by IR and NMR spectra.

  19. Human uracil DNA N-glycosidase: studies in normal and repair defective cultured fibroblasts.

    PubMed Central

    Kuhnlein, U; Lee, B; Linn, S

    1978-01-01

    Uracil DNA N-glycosidase, an enzyme which participates in the excision of uracil from DNA, was measured in extracts from fibroblasts lines cultured from normal subjects, from several subjects with the genetic disease xeroderma pigmentosum, and from a subject with ataxia telangiectasia. The cell lines representative of complementation groups A and D of xeroderma pigmentosum and of ataxia telangiectasia had roughly the same level of activity as did the normal cells. On the other hand, cells from two xeroderma pigmentosum variants (XP4BE and XP13BE) had roughly half the normal level of activity, and cells from the heterozygous mother of XP4BE had an intermediate level of activity. In spite of these quantitative differences, no systematic alterations in reaction characteristics, apparent Km for substrate, or purification characteristics were noted for enzyme from any of the lines. Thus a causal relationship, if any, between levels of activity and the disease symptoms is equivocal. PMID:643602

  20. Excitation-dependent fluorescence from atomic/molecular layer deposited sodium-uracil thin films.

    PubMed

    Pale, Ville; Giedraityte, Zivile; Chen, Xi; Lopez-Acevedo, Olga; Tittonen, Ilkka; Karppinen, Maarit

    2017-08-01

    Atomic/molecular layer deposition (ALD/MLD) offers unique possibilities in the fabrication of inorganic-organic thin films with novel functionalities. Especially, incorporating nucleobases in the thin-film structures could open new avenues in the development of bio-electronic and photonic devices. Here we report an intense blue and widely excitation-dependent fluorescence in the visible region for ALD/MLD fabricated sodium-uracil thin films, where the crystalline network is formed from hydrogen-bonded uracil molecules linked via Na atoms. The excitation-dependent fluorescence is caused by the red-edge excitation shift (REES) effect taking place in the red-edge of the absorption spectrum, where the spectral relaxation occurs in continuous manner as demonstrated by the time-resolved measurements.

  1. Threshold behavior in metastable dissociation of multi-photon ionized thymine and uracil

    NASA Astrophysics Data System (ADS)

    Pandey, R.; Ryszka, M.; da Fonseca Cunha, T.; Lalande, M.; Dampc, M.; Limão-Vieira, P.; Mason, N. J.; Poully, J. C.; Eden, S.

    2017-09-01

    Microsecond-timescale HNCO loss has been observed from single-color multi-photon ionized pyrimidine nucleobases in the gas phase. Photon energy thresholds for the metastable channels have been measured at 5.55 ± 0.02 eV for thymine and 5.57 ± 0.02 eV for uracil. We argue that these results can be attributed to accessing the molecules' S1 states with additional vibrational energy matching the threshold energy for HNCO loss from the radical cation. Combined with previous photoionization energies, this enables the S1 adiabatic energies to be deduced: 3.67 ± 0.07 eV for thymine and 3.77 ± 0.07 eV for uracil. These values are consistent with recent calculations.

  2. Quantum chemical predictions of the vibrational spectra of polyatomic molecules. The uracil molecule and two derivatives.

    PubMed

    Palafox, Mauricio Alcolea; Rastogi, V K

    2002-02-01

    This work describes the different scaling procedures used to correct the quantum-chemical theoretical predictions of the IR and Raman vibrational wavenumbers. Examples of each case are shown, with special attention to the uracil molecule and some derivatives. The results obtained with different semiempirical and ab initio methods, and basis sets, are compared and discussed. A comprehensive compendium of the main scale factors and scaling equations available to obtain the scaled wavenumbers is also shown.

  3. Functional changes in a novel uracil-DNA glycosylase determined by mutational analyses.

    PubMed

    Im, E K; Han, Y S; Chung, J H

    2008-01-01

    Uracil-DNA glycosylase (UDG) is a ubiquitous enzyme found in bacteria and eukaryotes, which removes uracil residues from DNA strands. Methanococcus jannaschii UDG (MjUDG), a novel monofunctional glycosylase, contains a helix-hairpin-helix (HhH) motif and Gly/Pro rich loop (GPD region), which is important for catalytic activity; it shares these features with other glycosylases such as endonuclease III. First, to examine the role of two conserved amino acid residues (Asp150 and Tyr152) in the HhH-GPD region of MjUDG, mutant MjUDG proteins were constructed, in which Asp 150 was replaced with either Glu or Trp (D150E and D150W), Tyr152 was replaced with either Glu or Asn (Y152E and Y152N). Mutant D150W completely lacked DNA glycosylase activity, whereas D150E displayed reduced activity of about 70% of the wild type value. However, the mutants Y152E and Y152N retained unchanged levels of UDG activity. We also replaced Glu132 in the HhH motif with a lysine residue equivalent to Lys120 in endonuclease III. This mutation converted the enzyme into a bifunctional glycosylase/AP lyase capable of both removing uracil at a glycosylic bond and cleaving the phosphodiester backbone at an AP site. Mutant E132K catalyzes a beta-elimination reaction at the AP site via uracil excision and forms a Schiff base intermediate in the form of a protein-DNA complex.

  4. Single-nucleotide patch base excision repair of uracil in DNA by mitochondrial protein extracts.

    PubMed

    Stierum, R H; Dianov, G L; Bohr, V A

    1999-09-15

    Mammalian mitochondria contain several 16.5 kb circular DNAs (mtDNA) encoding electron transport chain proteins. Reactive oxygen species formed as byproducts from oxidative phosphorylation in these organelles can cause oxidative deamination of cytosine and lead to uracil in mtDNA. Upon mtDNA replication, these lesions, if unrepaired, can lead to mutations. Until recently, it was thought that there was no DNA repair in mitochondria, but lately there is evidence that some lesions are efficiently repaired in these organelles. In the study of nuclear DNA repair, the in vitro repair measurements in cell extracts have provided major insights into the mechanisms. The use of whole-cell extract based DNA repair methods has revealed that mammalian nuclear base excision repair (BER) diverges into two pathways: the single-nucleotide replacement and long patch repair mechanisms. Similar in vitro methods have not been available for the study of mitochondrial BER. We have established an in vitro DNA repair system supported by rat liver mitochondrial protein extract and DNA substrates containing a single uracil opposite to a guanine. Using this approach, we examined the repair pathways and the identity of the DNA polymerase involved in mitochondrial BER (mtBER). Employing restriction analysis of in vitro repaired DNA to map the repair patch size, we demonstrate that only one nucleotide is incorporated during the repair process. Thus, in contrast to BER in the nucleus, mtBER of uracil in DNA is solely accomplished by single-nucleotide replacement.

  5. Analogues of uracil nucleosides with intrinsic fluorescence (NIF-analogues): synthesis and photophysical properties.

    PubMed

    Segal, Meirav; Fischer, Bilha

    2012-02-28

    Uridine cannot be utilized as fluorescent probe due to its extremely low quantum yield. For improving the uracil fluorescence characteristics we extended the natural chromophore at the C5 position by coupling substituted aromatic rings directly or via an alkenyl or alkynyl linker to create fluorophores. Extension of the uracil base was achieved by treating 5-I-uridine with the appropriate boronic acid under the Suzuki coupling conditions. Analogues containing an alkynyl linker were obtained from 5-I-uridine and the suitable boronic acid in a Sonogashira coupling reaction. The uracil fluorescent analogues proposed here were designed to satisfy the following requirements: a minimal chemical modification at a position not involved in base-pairing, resulting in relatively long absorption and emission wavelengths and high quantum yield. 5-((4-Methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6b, was found to be a promising fluorescent probe. Probe 6b exhibits a quantum yield that is 3000-fold larger than that of the natural chromophore (Φ 0.12), maximum emission (478 nm) which is 170 nm red shifted as compared to uridine, and a Stokes shift of 143 nm. In addition, since probe 6b adopts the anti conformation and S sugar puckering favored by B-DNA, it makes a promising nucleoside analogue to be incorporated in an oligonucleotide probe for detection of genetic material.

  6. Folate deficiency induces neurodegeneration and brain dysfunction in mice lacking uracil DNA glycosylase.

    PubMed

    Kronenberg, Golo; Harms, Christoph; Sobol, Robert W; Cardozo-Pelaez, Fernando; Linhart, Heinz; Winter, Benjamin; Balkaya, Mustafa; Gertz, Karen; Gay, Shanna B; Cox, David; Eckart, Sarah; Ahmadi, Michael; Juckel, Georg; Kempermann, Gerd; Hellweg, Rainer; Sohr, Reinhard; Hörtnagl, Heide; Wilson, Samuel H; Jaenisch, Rudolf; Endres, Matthias

    2008-07-09

    Folate deficiency and resultant increased homocysteine levels have been linked experimentally and epidemiologically with neurodegenerative conditions like stroke and dementia. Moreover, folate deficiency has been implicated in the pathogenesis of psychiatric disorders, most notably depression. We hypothesized that the pathogenic mechanisms include uracil misincorporation and, therefore, analyzed the effects of folate deficiency in mice lacking uracil DNA glycosylase (Ung-/-) versus wild-type controls. Folate depletion increased nuclear mutation rates in Ung-/- embryonic fibroblasts, and conferred death of cultured Ung-/- hippocampal neurons. Feeding animals a folate-deficient diet (FD) for 3 months induced degeneration of CA3 pyramidal neurons in Ung-/- but not Ung+/+ mice along with decreased hippocampal expression of brain-derived neurotrophic factor protein and decreased brain levels of antioxidant glutathione. Furthermore, FD induced cognitive deficits and mood alterations such as anxious and despair-like behaviors that were aggravated in Ung-/- mice. Independent of Ung genotype, FD increased plasma homocysteine levels, altered brain monoamine metabolism, and inhibited adult hippocampal neurogenesis. These results indicate that impaired uracil repair is involved in neurodegeneration and neuropsychiatric dysfunction induced by experimental folate deficiency.

  7. Mechanism of translocation of uracil-DNA glycosylase from Escherichia coli between distributed lesions.

    PubMed

    Mechetin, Grigory V; Zharkov, Dmitry O

    2011-10-22

    Uracil-DNA glycosylase (Ung) is a DNA repair enzyme that excises uracil bases from DNA, where they appear through deamination of cytosine or incorporation from a cellular dUTP pool. DNA repair enzymes often use one-dimensional diffusion along DNA to accelerate target search; however, this mechanism remains poorly investigated mechanistically. We used oligonucleotide substrates containing two uracil residues in defined positions to characterize one-dimensional search of DNA by Escherichia coli Ung. Mg(2+) ions suppressed the search in double-stranded DNA to a higher extent than K(+) likely due to tight binding of Mg(2+) to DNA phosphates. Ung was able to efficiently overcome short single-stranded gaps within double-stranded DNA. Varying the distance between the lesions and fitting the data to a theoretical model of DNA random walk, we estimated the characteristic one-dimensional search distance of ~100 nucleotides and translocation rate constant of ~2×10(6) s(-1). Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Diaqua-(5-methyl-1H-pyrazole-3-carboxyl-ato)(4-nitro-benzoato)copper(II).

    PubMed

    Hu, Fei-Long; Yin, Xian-Hong; Feng, Yu; Mi, Yan; Zhang, Shan-Shan

    2009-01-23

    In the title complex, [Cu(C(7)H(4)NO(4))(C(5)H(5)N(2)O(2))(H(2)O)(2)], the Cu(II) ion is coordinated in a slightly distorted square-pyramidal enviroment. The basal plane is formed by an N atom and an O atom from a 5-methyl-1H-pyrazole-3-carboxyl-ate ligand and by two O atoms from two water ligands. The apical position is occupied by a carboxylate O atom from a 4-nitro-benzoate ligand. In the crystal structure, inter-molecular O-H⋯O and N-H⋯O hydrogen bonds link complex moleclues, forming extended chains parallel to the a axis.

  9. Structural and vibrational studies on 1-(5-methyl-[1,3,4] thiadiazol-2-yl)-pyrolidin-2-ol

    NASA Astrophysics Data System (ADS)

    Ramesh Babu, N.; Saleem, H.; Subashchandrabose, S.; Padusha, M. Syed Ali; Bharanidharan, S.

    2016-01-01

    FT-Raman and FT-IR spectra were recorded for1-(5-methyl-[1,3,4]thiadiazol-2-yl)-pyrolidin-2-ol (MTPN) sample in solid state. The equilibrium geometries, harmonic vibrational frequencies, IR and the Raman scattering intensities were computed using DFT/6-311++G (d,p) level. Results obtained at this level of theory were used for a detailed interpretation of the IR and Raman spectra, based on the TED of the normal modes. Molecular parameters such as bond lengths, bond angles and dihedral angles were calculated. The intra-molecular charge transfer was calculated by means of NBO. Hyperconjugative interaction energy was more during the π-π∗ transition. Energy gap of the molecule has been found using HOMO and LUMO calculation, hence the less band gap, which seems to be more stable.

  10. Isomeric luminescent Zn(II) coordination polymers based on pyridinecarboxylate and 5-methyl-1H-tetrazole ligands

    NASA Astrophysics Data System (ADS)

    An, Zhe; Gao, Jing; Zhu, Ling

    2013-12-01

    Two new metal-organic frameworks, namely [Zn(nic)(mtz)]n (1) and [Zn(isonic)(mtz)]n (2) (Hnic = nicotinic acid, Hisonic = isonicotinic acid, Hmtz = 5-methyl-1H-tetrazole), have been obtained through the solvothermal reactions of Zn(NO3)2, Htmz and Hnic or Hisonic. Single crystal X-ray diffraction analysis reveals that compound 1 features a 2D layered structure with sql topology, which is further extended into a 3D supramolecular framework via weak CH…π interactions, and compound 2 is 2-fold interpenetrated 3D framework with dia topology. Luminescent investigation shows that both of them emit blue luminescence at room temperature.

  11. The thermodynamic contribution of the 5-methyl group of thymine in the two- and three-stranded complexes formed by poly(dU) and poly(dT) with poly(dA).

    PubMed

    Ross, Philip D; Howard, Frank B

    2003-02-01

    To assess the thermodynamic contribution of the 5-methyl group of thymine, we have studied the two-stranded helical complexes poly(dA).poly(dU) and poly(dA).poly(dT) and the three-stranded complexes--poly(dA).2poly(dU), poly(dA).poly(dT).poly(dU) and poly(dA).2poly(dT)--by differential scanning calorimetry, and uv optical melting experiments. The thermodynamic quantities associated with the 3 --> 2, 2 --> 1, and 3 --> 1 melting transitions are found to vary with salt concentration and temperature in a more complex manner than commonly believed. The transition temperatures, T(m), are generally not linear in the logarithm of concentration or activity of NaCl. The change in enthalpy and in entropy upon melting varies with salt concentration and temperature, and a change in heat capacity accompanies each transition. The poly(dA).2poly(dU) triple helix is markedly different from poly(dA).2poly(dT) in both its CD spectrum and thermodynamic behavior, while the poly(dA).poly(dT).poly(dU) triple helix resembles poly(dA).2poly(dT) in these properties. In comparing poly(dA).2poly(dT) with either the poly(dA).poly(dT).poly(dU) or the poly(dA).2poly(dU) triplexes, the substitution of thymine for uracil in the third strand results in an enhancement of stability against the 3 --> 2 dissociation of deltadeltaG degrees = -135 +/- 85 cal (mol A)(-1) at 37 degrees C. This represents a doubling of the absolute stability toward dissociation compared to the triplexes with poly(dU) as the third strand. The poly (dA).poly (dT) duplex is more stable than poly(dA).poly(dU) by deltadeltaG degrees = -350 +/- 60 cal (mol base pair)(-1) at 37 degrees C. Poly(dA).poly(dT) has 50% greater stability than poly(dA).poly(dU) as a result of the dT for dU substitution in the duplex.

  12. Generation of a Uracil Auxotroph Strain of the Probiotic Yeast Saccharomyces boulardii as a Host for the Recombinant Protein Production

    PubMed Central

    Hamedi, Hassan; Misaghi, Ali; Modarressi, Mohammad Hossein; Salehi, Taghi Zahraei; Khorasanizadeh, Dorsa; Khalaj, Vahid

    2013-01-01

    Background Saccharomyces boulardii (S. boulardii) is the best known probiotic yeast. The genetic engineering of this probiotic strain requires the availability of appropriate mutants to accept various gene constructs carrying different selection markers. As the auxotrophy selection markers are under focus, we have generated a ura3 auxotroph mutant of S. boulardii for use in further genetic manipulations. Methods Classical UV mutagenesis was used for the generation of auxotroph mutants. The mutants were selected in the presence of 5-FOA (5-Fluoroorotic acid), uracil and uridine. Uracil auxotrophy phenotype was confirmed by the ability of mutants to grow in the presence of uracil and the lack of growth in the absence of this compound. To test whether the uracil auxotrophy phenotype is due to the inactivation of URA3, the mutants were transformed with a plasmid carrying the gene. An in vitro assay was used for the analysis of acid and bile resistance capacity of these mutants. Results Three mutants were found to be ura3 auxotroph as they were able to grow only in the presence of uracil. When the URA3 gene was added, these mutants were able to grow normally in the absence of uracil. Further in vitro analysis showed that the acid and bile resistance capacity of one of these mutants is intact and similar to the wild type. Conclusion A uracil auxotroph mutant of the probiotic yeast, S. boulardii, was generated and characterized. This auxotroph strain may have potential applications in the production and delivery of the recombinant pharmacuetics into the intestinal lumen. PMID:23626874

  13. Development of a stable isotope dilution assay for the quantification of 5-methyl-(E)-2-hepten-4-one: application to hazelnut oils and hazelnuts.

    PubMed

    Pfnuer, P; Matsui, T; Grosch, W; Guth, H; Hofmann, T; Schieberle, P

    1999-05-01

    A stable isotope dilution assay was developed for the quantitation of the hazelnut odorant 5-methyl-(E)-2-hepten-4-one by mass chromatography using synthesized [(2)H](2)-5-methyl-(E)-2-hepten-4-one as the internal standard. Application of the method on two batches of commercial hazelnut oils, processed from either roasted or unroasted nuts, revealed 6.4 microg 5-methyl-(E)-2-hepten-4-one per kg of unroasted oil whereas 315.8 microg per kg was determined in the roasted nut oil. The about 50-fold higher amount of 5-methyl-(E)-2-hepten-4-one in roasted hazelnut oil suggested the necessity of a thermal treatment to generate the flavor compound. Pan frying of raw hazelnuts (9 to 15 min) or boiling of the crushed nut material for 1 h in water led to an increase of 5-methyl-(E)-2-hepten-4-one by factors of 600 and 800, respectively, thereby corroborating that the major part of the nut flavorant is formed during heat treatment from a yet unknown precursor in hazelnuts.

  14. Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity

    PubMed Central

    Chembazhi, Ullas Valiya; Patil, Vinod Vikas; Sah, Shivjee; Reeve, Wayne; Tiwari, Ravi P.

    2017-01-01

    Abstract Repair of uracils in DNA is initiated by uracil DNA glycosylases (UDGs). Family 1 UDGs (Ung) are the most efficient and ubiquitous proteins having an exquisite specificity for uracils in DNA. Ung are characterized by motifs A (GQDPY) and B (HPSPLS) sequences. We report a novel dimeric UDG, Blr0248 (BdiUng) from Bradyrhizobium diazoefficiens. Although BdiUng contains the motif A (GQDPA), it has low sequence identity to known UDGs. BdiUng prefers single stranded DNA and excises uracil, 5-hydroxymethyl-uracil or xanthine from it. BdiUng is impervious to inhibition by AP DNA, and Ugi protein that specifically inhibits family 1 UDGs. Crystal structure of BdiUng shows similarity with the family 4 UDGs in its overall fold but with family 1 UDGs in key active site residues. However, instead of a classical motif B, BdiUng has a uniquely extended protrusion explaining the lack of Ugi inhibition. Structural and mutational analyses of BdiUng have revealed the basis for the accommodation of diverse substrates into its substrate binding pocket. Phylogenetically, BdiUng belongs to a new UDG family. Bradyrhizobium diazoefficiens presents a unique scenario where the presence of at least four families of UDGs may compensate for the absence of an efficient family 1 homologue. PMID:28369586

  15. A multiancestry study identifies novel genetic associations with CHRNA5 methylation in human brain and risk of nicotine dependence

    PubMed Central

    Hancock, Dana B.; Wang, Jen-Chyong; Gaddis, Nathan C.; Levy, Joshua L.; Saccone, Nancy L.; Stitzel, Jerry A.; Goate, Alison; Bierut, Laura J.; Johnson, Eric O.

    2015-01-01

    Nicotine dependence is influenced by chromosome 15q25.1 single nucleotide polymorphisms (SNPs), including the missense SNP rs16969968 that alters function of the α5 nicotinic acetylcholine receptor (CHRNA5) and noncoding SNPs that regulate CHRNA5 mRNA expression. We tested for cis-methylation quantitative trait loci (cis-meQTLs) using SNP genotypes and DNA methylation levels measured across the IREB2-HYKK-PSMA4-CHRNA5-CHRNA3-CHRNB4 genes on chromosome 15q25.1 in the BrainCloud and Brain QTL cohorts [total N = 175 European-Americans and 65 African-Americans (AAs)]. We identified eight SNPs that were significantly associated with CHRNA5 methylation in prefrontal cortex: P ranging from 6.0 × 10−10 to 5.6 × 10−5. These SNP–methylation associations were also significant in frontal cortex, temporal cortex and pons: P ranging from 4.8 × 10−12 to 3.4 × 10−3. Of the eight cis-meQTL SNPs, only the intronic CHRNB4 SNP rs11636753 was associated with CHRNA5 methylation independently of the known SNP effects in prefrontal cortex, and it was the most significantly associated SNP with nicotine dependence across five independent cohorts (total N = 7858 European ancestry and 3238 AA participants): P = 6.7 × 10−4, odds ratio (OR) [95% confidence interval (CI)] = 1.11 (1.05–1.18). The rs11636753 major allele (G) was associated with lower CHRNA5 DNA methylation, lower CHRNA5 mRNA expression and increased nicotine dependence risk. Haplotype analyses showed that rs11636753-G and the functional rs16969968-A alleles together increased risk of nicotine dependence more than each variant alone: P = 3.1 × 10−12, OR (95% CI) = 1.32 (1.22–1.43). Our findings identify a novel regulatory SNP association with nicotine dependence and connect, for the first time, previously observed differences in CHRNA5 mRNA expression and nicotine dependence risk to underlying DNA methylation differences. PMID:26220977

  16. Analysis of the tet repressor-operator interactions using the uracil-DNA glycosylase footprinting system

    SciTech Connect

    Devchand, P.R.; McGhee, J.D.; Sande, J.H. Van De

    1994-12-31

    The tet repressor regulated expression of the Tn-10-encoded tetracycline resistance determinant in a tetracycline-dependent manner. In the absence of tetracycline, the tet repressor binds as a dimer to the 19-base-pair palindromic tet operator sequence. Amino acid homologies and genetic studies with trans-dominant mutants suggest that sequence-specific recognition of the tet operator involves the extensively studied helix-turn-helix motif. We have used the uracil-DNA glycosylase (UDG) footprinting systems to identify thymine contacts in the tet operator that are essential for the formation of tet repressor-operator complexes.

  17. VizieR Online Data Catalog: Line Frequencies for Uracil (Bruenken+, 2006)

    NASA Astrophysics Data System (ADS)

    Bruenken, S.; McCarthy, M. C.; Thaddeus, P.; Godfrey, P. D.; Brown, R. D.

    2006-08-01

    We report new laboratory spectroscopic data on the nucleic acid uracil. The dataset has been extended both into the microwave and towards mm-wavelengths with the aim to provide accurate transition rest frequencies for astrophysical searches. The complete experimental linelist used for the analysis of the data is compiled in Table 2. Lines marked with an asterisk are taken from Brown et al. (1988, J. Mol. Struct. 190, 185 and J. Am. Chem. Soc. 110, 2329), all other lines have been measured in this work. (1 data file).

  18. Biological evaluation of some uracil derivatives as potent glutathione reductase inhibitors

    NASA Astrophysics Data System (ADS)

    Güney, Murat; Ekinci, Deniz; Ćavdar, Huseyin; Şentürk, Murat; Zilbeyaz, Kani

    2016-04-01

    Discovery of glutathione reductase (GR) inhibitors has become very popular recently due to antimalarial and anticancer activities. In this study, GR inhibitory capacities of some uracil derivatives (UDCs) (1-4) were reported. Some commercially available molecules (5-6) were also tested for comparison reasons. The novel UDCs were obtained in high yields using simple chemical procedures and exhibited much potent inhibitory activities against GR at low nanomolar concentrations with IC50 values ranging from 2.68 to 166.6 nM as compared with well-known agents.

  19. Uptake and Incorporation of Thymine, Thymidine, Uracil, Uridine, and 5-Fluorouracil into the Nucleic Acids of Bacillus subtilis

    PubMed Central

    Bodmer, Walter F.; Grether, Susan

    1965-01-01

    Bodmer, Walter F. (Stanford University School of Medicine, Palo Alto, Calif.), and Susan Grether. Uptake and incorporation of thymine, thymidine, uracil, uridine, and 5-fluorouracil into the nucleic acids of Bacillus subtilis. J. Bacteriol. 89:1011–1014. 1965.—From 55 to 95% of uracil, uridine, or 5-fluorouracil (FU) added to the culture medium is incorporated into the acid-insoluble fraction of cells of Bacillus subtilis strains SB 19 (prototroph) and SB 503 (FU-resistant). Thymine is poorly incorporated (less than 1%); thus, the incorporation of thymidine is limited (less than 12%) by the rapid degradation of the nucleoside to thymine, probably by the enzyme thymidine phosphorylase. Uracil, uridine, and FU were not incorporated into the deoxyribonucleic acid (DNA) of either strain, whereas all the incorporated thymidine was found in the DNA. PMID:14276087

  20. Uracil-DNA glycosylases—Structural and functional perspectives on an essential family of DNA repair enzymes

    PubMed Central

    Schormann, N; Ricciardi, R; Chattopadhyay, D

    2014-01-01

    Uracil-DNA glycosylases (UDGs) are evolutionarily conserved DNA repair enzymes that initiate the base excision repair pathway and remove uracil from DNA. The UDG superfamily is classified into six families based on their substrate specificity. This review focuses on the family I enzymes since these are the most extensively studied members of the superfamily. The structural basis for substrate specificity and base recognition as well as for DNA binding, nucleotide flipping and catalytic mechanism is discussed in detail. Other topics include the mechanism of lesion search and molecular mimicry through interaction with uracil-DNA glycosylase inhibitors. The latest studies and findings detailing structure and function in the UDG superfamily are presented. PMID:25252105

  1. DNA uracil repair initiated by the archaeal ExoIII homologue Mth212 via direct strand incision

    PubMed Central

    Schomacher, Lars; Chong, James P. J.; McDermott, Paul; Kramer, Wilfried; Fritz, Hans-Joachim

    2009-01-01

    No genes for any of the known uracil DNA glycosylases of the UDG superfamily are present in the genome of Methanothermobacter thermautotrophicus ΔH, making it difficult to imagine how DNA-U repair might be initiated in this organism. Recently, Mth212, the ExoIII homologue of M. thermautotrophicus ΔH has been characterized as a DNA uridine endonuclease, which suggested the possibility of a novel endonucleolytic entry mechanism for DNA uracil repair. With no system of genetic experimentation available, the problem was approached biochemically. Assays of DNA uracil repair in vitro, promoted by crude cellular extracts, provide unequivocal confirmation that this mechanism does indeed operate in M. thermautotrophicus ΔH. PMID:19240141

  2. The calculated free energy effects of 5-methyl cytosine on the B to Z transition in DNA.

    PubMed

    Pearlman, D A; Kollman, P A

    We have examined the free energy effects of 5-methylation of cytosine on the B in equilibrium Z conformational equilibrium in DNA. Free energy differences were calculated using the free energy perturbation approach, which uses an easily derived equation from classical statistical mechanics to relate the free energy difference between two states to the ensemble average of the potential energy difference between the states. Calculations were carried both in explicit solvent and (for comparison) in vacuo. The free energy values obtained for the explicit solvent systems are total free energies, with contributions from all parts of the system (solvent + solute), and so are relevant to the B in equilibrium Z transitions observed under real (physiological) conditions. We calculate that in solution, methylation makes the B in equilibrium Z transition more favorable by about -0.4 kcal/mole base pair (bp) in free energy. This value compares well with approximate experimentally derived values of about -0.3 kcal/mole-bp. We also discuss a method for determining the free energy difference between conformational states poorly maintained by a potential energy model. Finally, the effects of methylation on the melting temperature of DNA are examined.

  3. 8-Hydroxyirilone 5-methyl ether and 8-hydroxyirilone, new antioxidant and α-amylase inhibitors isoflavonoids from Iris germanica rhizomes.

    PubMed

    Ibrahim, Sabrin R M; Mohamed, Gamal A; Zayed, Mohamed F; Ross, Samir A

    2017-02-01

    Iris species are well recognized as wealthy sources of isoflavonoids. In the present study, phytochemical investigation of the rhizomes of Iris germanica (Iridaceae) procure the isolation of two new isoflavonoids namely, 8-hydroxyirilone 5-methyl ether (2) and 8-hydroxyirilone (3), along with eight known isoflavonoids: irilone 4'-methyl ether (1), irilone (4), irisolidone (5), irigenin S (6), irigenin (7), irilone 4'-O-β-d-glucopyranoside (8), iridin S (9), and iridin (10). The isolated flavonoids were structurally characterized with the assist of comprehensive spectroscopic analyses (UV, IR, 1D and 2D NMR, and HRMS) and comparing with the published data. They were estimated for their antioxidant and antidaibetic capacities using DPPH and α-amylase inhibition assays, respectively. Compounds 2, 3, and 4 exhibited prominent antioxidant activities with IC50 values of 12.92, 9.23, and 10.46μM, respectively compared to propyl gallate (IC50 7.11μM). Moreover, 2-5 possessed highest α-amylase inhibitory activity with % inhibition 66.1, 78.3, 67.3, and 70.1, respectively in comparison to acarbose (reference α-amylase inhibitor). Additionally, their structure-activity relationship has been discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Chemically Modified, α-Amino-3-hydroxy-5-methyl-4-isoxazole (AMPA) Receptor RNA Aptamers Designed for in Vivo Use.

    PubMed

    Huang, Zhen; Wen, Wei; Wu, Andrew; Niu, Li

    2017-09-05

    Glutamate ion channels have three subtypes, that is, α-amino-3-hydroxy-5-methyl-4-isoxazole (AMPA), kainate, and N-methyl-d-aspartate (NMDA) receptors. Excessive activity of these receptor subtypes either individually or collectively is involved in various neurological disorders. RNA aptamers as antagonists of these receptors are potential therapeutics. For developing aptamer therapeutics, the RNA aptamers must be chemically modified to become ribonuclease-resistant or stable in biological fluids. Using systematic evolution of ligands by exponential enrichment (SELEX) and a chemically modified library, prepared enzymatically (i.e., the library contains RNAs with 2'-fluoro modified nucleoside triphosphates or ATPs, CTPs and UTPs, but regular GTPs), we have isolated an aptamer. The short aptamer (69 nucleotides) FN1040s selectively inhibits the GluA1 and GluA2Qflip AMPA receptor subunits, whereas the full-length aptamer (101 nucleotides) FN1040 additionally inhibits GluK1, but not GluK2, kainate receptor, and GluN1a/2A and GluN1a/2B, the two major native NMDA receptors. The two aptamers show similar potency (2-4 μM) and are stable with a half-life of at least 2 days in serum-containing medium or cerebrospinal fluid. Therefore, these two aptamers are amenable for in vivo use.

  5. Bis­(2-amino-5-methyl­pyridinium) fumarate–fumaric acid (1/1)

    PubMed Central

    Hemamalini, Madhukar; Fun, Hoong-Kun

    2010-01-01

    In the crystal structure of the title compound, C6H9N2 +·0.5C4H2O4 2−·0.5C4H6O4, the fumarate dianion and fumaric acid mol­ecule are located on inversion centres. The 2-amino-5-methyl­pyrimidinium cation inter­acts with the carboxyl­ate group of the fumarate anion through a pair of N—H⋯O hydrogen bonds, forming an R 2 2(8) ring motif. These motifs are centrosymmetrically paired via N—H⋯O hydrogen bonds, forming a complementary DDAA array. The carboxyl groups of the fumaric acid mol­ecules and the carboxyl­ate groups of the fumarate anions are hydrogen bonded through O—H⋯O hydrogen bonds, leading to a supra­molecular chain along [101]. The crystal structure is further stabilized by weak C—H⋯O hydrogen bonds. PMID:21588388

  6. FT-IR, Laser-Raman spectra and computational analysis of 5-Methyl-3-phenylisoxazole-4-carboxylic acid.

    PubMed

    Sert, Yusuf; Mahendra, M; Keskinoğlu, S; Chandra; Srikantamurthy, N; Umesha, K B; Çırak, Ç

    2015-03-15

    In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor, antiviral, hypoglycemic, antifungal and anti-HIV agent namely, 5-Methyl-3-phenylisoxazole-4-carboxylic acid has been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parametrized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated by using the same theoretical calculations.

  7. FT-IR, Laser-Raman spectra and computational analysis of 5-Methyl-3-phenylisoxazole-4-carboxylic acid

    NASA Astrophysics Data System (ADS)

    Sert, Yusuf; Mahendra, M.; Keskinoğlu, S.; Chandra; Srikantamurthy, N.; Umesha, K. B.; Çırak, Ç.

    2015-03-01

    In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor, antiviral, hypoglycemic, antifungal and anti-HIV agent namely, 5-Methyl-3-phenylisoxazole-4-carboxylic acid has been investigated. The experimental FT-IR (4000-400 cm-1) and Laser-Raman spectra (4000-100 cm-1) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parametrized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated by using the same theoretical calculations.

  8. Non-classical mechanism of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor channel block by fluoxetine.

    PubMed

    Barygin, Oleg I; Komarova, Margarita S; Tikhonova, Tatiana B; Tikhonov, Denis B

    2015-04-01

    Antidepressants have many targets in the central nervous system. A growing body of data demonstrates the influence of antidepressants on glutamatergic neurotransmission. In the present work, we studied the inhibition of native Ca(2+)-permeable and Ca(2+)-impermeable α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in rat brain neurons by fluoxetine. The Ca(2+)-impermeable AMPA receptors in CA1 hippocampal pyramidal neurons were weakly affected. The IC50 value for the inhibition of Ca(2+)-permeable AMPA receptors in giant striatal interneurons was 43 ± 7 μM. The inhibition of Ca(2+)-permeable AMPA receptors was voltage dependent, suggesting deep binding in the pore. However, the use dependence of fluoxetine action differed markedly from that of classical AMPA receptor open-channel blockers. Moreover, fluoxetine did not compete with other channel blockers. In contrast to fluoxetine, its membrane-impermeant quaternary analog demonstrated all of the features of channel inhibition typical for open-channel blockers. It is suggested that fluoxetine reaches the binding site through a hydrophobic access pathway. Such a mechanism of block is described for ligands of sodium and calcium channels, but was never found in AMPA receptors. Molecular modeling suggests binding of fluoxetine in the subunit interface; analogous binding was proposed for local anesthetics in closed sodium channels and for benzothiazepines in calcium channels.

  9. Determination of 5-methyl-2'-deoxycytidine in genomic DNA using high performance liquid chromatography-ultraviolet detection.

    PubMed

    Sandhu, Jatinderpal; Kaur, Balvinder; Armstrong, Christine; Talbot, Christopher J; Steward, William P; Farmer, Peter B; Singh, Rajinder

    2009-07-01

    The formation of 5-methyl-2'-deoxycytidine (5-MedC) following methylation of the C-5 position of cytosine in genomic DNA provides an epigenetic mechanism for the regulation of gene expression and cellular differentiation. We describe the development of a method using HPLC-ultraviolet (UV) detection for the accurate determination of 5-MedC in DNA. Genomic DNA was obtained from HeLa cells and rat liver tissue using an optimised anion-exchange column DNA extraction procedure incorporating a ribonuclease incubation step to remove any potential interference from RNA. Following extraction the DNA samples were enzymatically hydrolysed to 2'-deoxynucleosides using a combination of an endo-exonuclease plus 5'-exonuclease together with a 3'-nucleotidase. The hydrolysed DNA samples (10 microg on column) were analysed using narrow-bore reverse phase HPLC-UV detection. The level of 5-MedC in the DNA samples was expressed as a percentage of the level of 2'-deoxycytidine (dC) determined from calibration lines constructed using authentic standards for 5-MedC and dC. The percentage 5-MedC level determined for commercially available calf thymus DNA was 6.26%, for HeLa cell DNA was 3.02% and for rat liver DNA was 3.55%.

  10. CD spectra of 5-methyl-2-thiouridine in tRNA-Met-f from an extreme thermophile.

    PubMed Central

    Watanabe, K; Oshima, T; Nishimura, S

    1976-01-01

    5-Methyl-2-thiouridine (S) in tRNA-Met-f from an extreme thermophile is located in the TpsiC region, replacing T, and has a positive CD band centered at 310 nm. Upon heating, the profiles of the change in this band were similar to the UV melting profiles of the change monitored at 260 nm. This strongly suggests a close relation between heat denaturation of the tRNA and the conformation of the S base. Oligonucleotides containing S showed negative CD bands at 320-330 nm, like the monomer S itself, but when the 3'-2/5 fragment containing S formed a complex with the complementary 5'-3/5 fragment, a positive CD band appeared at 310 nm. These results suggest that combination of the TpsiC loop containing S with the hU loop is necessary for the positive band of S at 310 nm. S may serve to strengthen the association of the TpsiC loop with the hU loop in tRNA of the thermophile. PMID:967669

  11. Field induced changes in the ring/chain equilibrium of hydrogen bonded structures: 5-methyl-3-heptanol

    NASA Astrophysics Data System (ADS)

    Young-Gonzales, Amanda R.; Richert, Ranko

    2016-08-01

    Using non-linear dielectric techniques, we have measured the dynamics of 5-methyl-3-heptanol at a temperature at which the Kirkwood correlation factor gK indicates the coexistence of ring- and chain-like hydrogen-bonded structures. Steady state permittivity spectra recorded in the presence of a high dc bias electric field (17 MV/m) reveal that both the amplitude and the time constant are increased by about 10% relative to the low field limit. This change is attributed to the field driven conversion from ring-like to the more polar chain-like structures, and a direct observation of its time dependence shows that the ring/chain structural transition occurs on a time scale that closely matches that of the dielectric Debye peak. This lends strong support to the picture that places fluctuations of the end-to-end vector of hydrogen bonded structures at the origin of the Debye process, equivalent to fluctuations of the net dipole moment or gK. Recognizing that changes in the ring/chain equilibrium constant also impact the spectral separation between Debye and α-process may explain the difference in their temperature dependence whenever gK is sensitive to temperature, i.e., when the structural motifs of hydrogen bonding change considerably.

  12. Effects of quercetin on human α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor-mediated ion currents.

    PubMed

    Shin, Tae-Joon; Choi, Sun-Hye; Lee, Byung-Hwan; Pyo, Mi Kyung; Hwang, Sung-Hee; Kim, Bo-Ra; Lee, Sang-Mok; Han, Ye Sun; Lee, Jun-Ho; Park, Ji-Ho; Kim, Hyoung-Chun; Rhim, Hyewhon; Nah, Seung-Yeol

    2010-01-01

    Quercetin is a low molecular weight flavonoid found in dietary fruits and vegetables. Quercetin, like other flavonoids, has demonstrated neuroprotective effects in vitro and in vivo. However, relatively little is known about how quercetin achieves its neuroprotective abilities. The alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor is one of several excitatory receptors, which play an important role in postsynaptic neurotransmission. Over-stimulation of ionotropic glutamate receptor including AMPA receptors is closely associated with excitatory neurotoxicities. In the present study, we investigated the effects of quercetin on the glutamate-induced inward current (IGlu) in Xenopus oocytes that heterologously express human AMPA receptor and stargazin, an auxiliary subunit of AMPA receptor. IGlu was measured using the two-electrode voltage clamp technique. In oocytes injected with cRNAs coding AMPA receptor (GluR1) and stargazin, quercetin inhibited IGlu in a reversible and concentration-dependent manner. The IC50 was 84.9+/-15.0 microM. Quercetin action on IGlu was attenuated by increasing glutamate concentration, and was membrane holding potential-dependent. These results show a possibility that quercetin interacts with AMPA receptor, which was heterologously expressed in Xenopus oocytes and that quercetin action on IGlu of AMPA receptor could be one of contributions of quercetin-mediated neuroprotections.

  13. Inhibition of uracil DNA glycosylase sensitizes cancer cells to 5-fluorodeoxyuridine through replication fork collapse-induced DNA damage

    PubMed Central

    Yan, Yan; Han, Xiangzi; Qing, Yulan; Condie, Allison G.; Gorityala, Shashank; Yang, Shuming; Xu, Yan; Zhang, Youwei; Gerson, Stanton L.

    2016-01-01

    5-fluorodeoxyuridine (5-FdU, floxuridine) is active against multiple cancers through the inhibition of thymidylate synthase, which consequently introduces uracil and 5-FU incorporation into the genome. Uracil DNA glycosylase (UDG) is one of the main enzymes responsible for the removal of uracil and 5-FU. However, how exactly UDG mediates cellular sensitivity to 5-FdU, and if so whether it is through its ability to remove uracil and 5-FU have not been well characterized. In this study, we report that UDG depletion led to incorporation of uracil and 5-FU in DNA following 5-FdU treatment and significantly enhanced 5-FdU's cytotoxicity in cancer cell lines. Co-treatment, but not post-treatment with thymidine prevented cell death of UDG depleted cells by 5-FdU, indicating that the enhanced cytotoxicity is due to the retention of uracil and 5-FU in genomic DNA in the absence of UDG. Furthermore, UDG depleted cells were arrested at late G1 and early S phase by 5-FdU, followed by accumulation of sub-G1 population indicating cell death. Mechanistically, 5-FdU dramatically reduced DNA replication speed in UDG depleted cells. UDG depletion also greatly enhanced DNA damage as shown by γH2AX foci formation. Notably, the increased γH2AX foci formation was not suppressed by caspase inhibitor treatment, suggesting that DNA damage precedes cell death induced by 5-FdU. Together, these data provide novel mechanistic insights into the roles of UDG in DNA replication, damage repair, and cell death in response to 5-FdU and suggest that UDG is a target for improving the anticancer effect of this agent. PMID:27517750

  14. Uracil DNA glycosylase initiates degradation of HIV-1 cDNA containing misincorporated dUTP and prevents viral integration

    PubMed Central

    Weil, Amy F.; Ghosh, Devlina; Zhou, Yan; Seiple, Lauren; McMahon, Moira A.; Spivak, Adam M.; Siliciano, Robert F.; Stivers, James T.

    2013-01-01

    HIV-1 reverse transcriptase discriminates poorly between dUTP and dTTP, and accordingly, viral DNA products become heavily uracilated when viruses infect host cells that contain high ratios of dUTP:dTTP. Uracilation of invading retroviral DNA is thought to be an innate immunity barrier to retroviral infection, but the mechanistic features of this immune pathway and the cellular fate of uracilated retroviral DNA products is not known. Here we developed a model system in which the cellular dUTP:dTTP ratio can be pharmacologically increased to favor dUTP incorporation, allowing dissection of this innate immunity pathway. When the virus-infected cells contained elevated dUTP levels, reverse transcription was found to proceed unperturbed, but integration and viral protein expression were largely blocked. Furthermore, successfully integrated proviruses lacked detectable uracil, suggesting that only nonuracilated viral DNA products were integration competent. Integration of the uracilated proviruses was restored using an isogenic cell line that had no detectable human uracil DNA glycosylase (hUNG2) activity, establishing that hUNG2 is a host restriction factor in cells that contain high dUTP. Biochemical studies in primary cells established that this immune pathway is not operative in CD4+ T cells, because these cells have high dUTPase activity (low dUTP), and only modest levels of hUNG activity. Although monocyte-derived macrophages have high dUTP levels, these cells have low hUNG activity, which may diminish the effectiveness of this restriction pathway. These findings establish the essential elements of this pathway and reconcile diverse observations in the literature. PMID:23341616

  15. Solvent effects on the steady-state absorption and fluorescence spectra of uracil, thymine and 5-fluorouracil.

    PubMed

    Gustavsson, Thomas; Sarkar, Nilmoni; Bányász, Akos; Markovitsi, Dimitra; Improta, Roberto

    2007-01-01

    We report a comparison of the steady-state absorption and fluorescence spectra of three representative uracil derivatives (uracil, thymine and 5-fluorouracil) in alcoholic solutions. The present results are compared with those from our previous experimental and computational studies of the same compounds in water and acetonitrile. The effects of solvent polarity and hydrogen bonding on the spectra are discussed in the light of theoretical predictions. This comparative analysis provides a more complete picture of the solvent effects on the absorption and fluorescence properties of pyrimidine nucleobases, with special emphasis on the mechanism of the excited state deactivation.

  16. Polymerase recognition of 2-thio-iso-guanine·5-methyl-4-pyrimidinone (iGs·P)--A new DD/AA base pair.

    PubMed

    Lee, Dong-Kye; Switzer, Christopher

    2016-02-15

    Polymerase specificity is reported for a previously unknown base pair with a non-standard DD/AA hydrogen bonding pattern: 2-thio-iso-guanine·5-methyl-4-pyrimidinone. Our findings suggest that atomic substitution may provide a solution for low fidelity previously associated with enzymatic copying of iso-guanine. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. N-[(E)-(5-Methyl-thio-phen-2-yl)methyl-idene]-1H-1,2,4-triazol-3-amine.

    PubMed

    Chohan, Zahid H; Hanif, Muhammad; Tahir, M Nawaz

    2008-12-13

    In the title Schiff base, C(8)H(8)N(4)S, a condensation product of 5-methyl-thio-phene-2-carboxaldehyde and 3-amino-1,2,4-triazole, the dihedral angle between the triazolyl and thienyl rings is 6.44 (14)°. The compound exists as a polymeric chain arising from inter-molecular N-H⋯N bonding.

  18. 21 CFR 73.3122 - 4-[(2,4-dimethylphenyl)azo]-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 1 2013-04-01 2013-04-01 false 4- -2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one. 73.3122 Section 73.3122 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... exceed the minimum reasonably required to accomplish the intended coloring effect. (2) Authorization...

  19. 21 CFR 73.3122 - 4-[(2,4-dimethylphenyl)azo]-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 1 2012-04-01 2012-04-01 false 4- -2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one. 73.3122 Section 73.3122 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... exceed the minimum reasonably required to accomplish the intended coloring effect. (2) Authorization...

  20. Escherichia coli-Derived Uracil Increases the Antibacterial Activity and Growth Rate of Lactobacillus plantarum.

    PubMed

    Ha, Eun-Mi

    2016-05-28

    Lactobacillus plantarum (L. plantarum) is a representative probiotic. In particular, L. plantarum is the first commensal bacterium to colonize the intestine of infants. For this reason, the initial settlement of L. plantarum can play an important role in determining an infant's health as well as their eventual health status as an adult. In addition, L. plantarum combats pathogenic infections (such as Escherichia coli (E. coli), one of the early pathogenic colonizers in an unhealthy infant gut) by secreting antimicrobial substances. The aim of this research was to determine how L. plantarum combats E. coli infection and why it is a representative probiotic in the intestine. Consequently, this research observed that E. coli releases uracil. L. plantarum specifically recognizes E. coli-derived uracil, which increases the growth rate and production of antimicrobial substance of L. plantarum. In addition, through the inhibitory activity test, this study postulates that the antimicrobial substance is a protein and can be considered a bacteriocin-like substance. Therefore, this research assumes that L. plantarum exerts its antibacterial ability by recognizing E. coli and increasing its growth rate as a result, and this phenomenon could be one of the reasons for L. plantarum settling in the intestine of infants as a beneficial bacterium.

  1. The peculiar spectral properties of amino-substituted uracils: a combined theoretical and experimental study.

    PubMed

    Bányász, Akos; Karpati, Szilvia; Mercier, Yannick; Reguero, Mar; Gustavsson, Thomas; Markovitsi, Dimitra; Improta, Roberto

    2010-10-07

    A detailed experimental and computational study of the absorption and fluorescence spectra of 5-aminouracil (5 AU) and 6-aminouracil (6 AU) in aqueous solution is reported. The lowest energy band of the steady-state absorption spectra of 5 AU is considerably red-shifted, noticeably less intense, and broader than its counterpart in uracil (U). On the contrary, the 6 AU lowest energy absorption peak is close in energy to that of U, but it is much narrower and the transition is much more intense. The emission properties of 5 AU, 6 AU, and U are also very different. Both amino-substituted compounds exhibit indeed a much larger Stokes shift as compared to U, and the emission band of 5 AU is much narrower than that of 6 AU. Those features are fully rationalized with the help of PCM/TD-PBE0 calculations in aqueous solution and MS-CASPT2/CASSCF calculations in the gas phase. A stable minimum on the potential energy surface of the lowest energy bright state is found for 5 AU, both in the gas phase and in aqueous solution. For 6 AU a barrierless path leads to the conical intersection with the ground electronic state, but a nonplanar plateau region is predicted in aqueous solution, which is responsible for the very large Stokes shift. Some general considerations on the excited-state dynamics of uracil derivatives are also reported.

  2. Optical properties of organically functionalized silicon surfaces: Uracil-like nucleobases on Si(001)

    NASA Astrophysics Data System (ADS)

    Molteni, Elena; Cappellini, Giancarlo; Onida, Giovanni; Fratesi, Guido

    2017-02-01

    We predict UV reflectance anisotropy spectra (RAS) of the organically functionalized silicon (001) surface covered by pyrimidinic uracil-like nucleobases. First-principles results based on density functional theory show characteristic spectral features appearing in the UV range between 3 and 7 eV, besides the expected quench in the well-known two-minima RAS signal of clean Si(001). Nucleobase adsorption in the energetically favored "dimer bridge" configuration gives rise to a characteristic RAS line shape, common to thymine, uracil, and 5-fluorouracil. We trace back the origin of such spectral features by singling out RAS structures induced by relaxation and passivation effects on the Si surface, and those directly associated with molecular excitations. The former turn out to be the same for the three nucleobases, and are totally unaffected by molecular tilting. The sign and position of the latter RAS peaks at higher energy exhibit a moderate nucleobase dependence, and can be fully rationalized in terms of the molecular orbitals involved. The present theoretical results call for a RAS experimental study in the UV region extending up to ≃6 -7 eV.

  3. Human immunodeficiency virus type 1 Vpr protein binds to the uracil DNA glycosylase DNA repair enzyme.

    PubMed Central

    Bouhamdan, M; Benichou, S; Rey, F; Navarro, J M; Agostini, I; Spire, B; Camonis, J; Slupphaug, G; Vigne, R; Benarous, R; Sire, J

    1996-01-01

    The role of the accessory gene product Vpr during human immunodeficiency virus type 1 infection remains unclear. We have used the yeast two-hybrid system to identify cellular proteins that interact with Vpr and could be involved in its function. A cDNA clone which encodes the human uracil DNA glycosylase (UNG), a DNA repair enzyme involved in removal of uracil in DNA, has been isolated. Interaction between Vpr and UNG has been demonstrated by in vitro protein-protein binding assays using translated, radiolabeled Vpr and UNG recombinant proteins expressed as a glutathione S-transferase fusion protein. Conversely, purified UNG has been demonstrated to interact with Vpr recombinant protein expressed as a glutathione S-transferase fusion protein. Coimmunoprecipitation experiments confirmed that Vpr and UNG are associated within cells expressing Vpr. By using a panel of C- and N-terminally deleted Vpr mutants, we have determined that the core protein of Vpr, spanning amino acids 15 to 77, is involved in the interaction with UNG. We also demonstrate by in vitro experiments that the enzymatic activity of UNG is retained upon interaction with Vpr. PMID:8551605

  4. Influence of uracil photohydrate formation on the conformational properties of heterodinucleoside monophosphates

    SciTech Connect

    Ezra, F.S.; Maccoss, M.; Danyluk, S.S.

    1980-01-01

    The structural properties of uracil photohydrates at the monomer and dimer level in aqueous solution have been examined in detail by nmr spectroscopy. Based on such evidence, the absolute configurations of the two diastereomers have been assigned, and the conformational perturbations induced by photohydration have been evaluated. In all instances, photohydration shifts the /sup 2/E reversible /sup 3/E puckering equilibrium of the sugar ring of the uridylyl fragment towards /sup 2/E (from 12 to 18%). Significant base-base interactions were observed in both hydrated dimers despite the loss of the planar ..pi..-system in the uracil fragment. In addition, the rate of photohydration for a particular dimer pair is shown to be inversely dependent on the amount of base stacking in the parent dimer. This latter parameter has also been correlated with the ratio of the two possible diastereomers formed in the reaction and is associated with a preferential attack at one face of the pyrimidine base ring. The possible biological significance of the above-mentioned conformational aspects is discussed.

  5. Tritium labelling of nucleic acids accompanied by conversion of cytosine to uracil.

    PubMed Central

    Scheinker, V S

    1976-01-01

    A new method of incorporation of tritium into nucleic acids with an accompanying conversion of cytosine to uracil is proposed. The method is based on the reaction of nucleic acids with bisulfite in the presence of 3H2O. Under certain conditions poly(C) is quantitatively converted to a radioactive poly(U), whereas similar bisulfite treatment of poly(U) does not result in any tritium incorporation. Specificity of the reaction is confirmed by the results of analysis of modified tRNA and rRNA. Incubation of tRNA with bisulfite and 3H2O does not lead to cleavage of the polynucleotide chain. Similar treatment of the denatured DNA results in tritium incorporation into DNA which is accompanied by a conversion of cytosine to uracil. There is virtually no reaction between native DNA and bisulfite. Only certain cytosone residues in yeast tRNAVal/2a interact with bisulfate providing that reaction is carried out under sufficiently mild conditions. PMID:1272798

  6. Simulation of the resonance Raman spectra for 5-halogenated (F, Cl, and Br) uracils.

    PubMed

    Sun, Shuai; Brown, Alex

    2015-04-30

    The resonance Raman spectra of the 5-halogenated (F, Cl, and Br) uracils are simulated via the Herzberg-Teller (HT) short-time dynamics formalism. The gradient of the S1 excited state is computed at the CAMB3LYP/aug-cc-pVTZ level of theory in the conductor-like polarizable continuum model for water (C-PCM, H2O), based on the equilibrium geometry determined using PBE0/aug-cc-pVTZ in H2O (C-PCM). The simulated resonance Raman spectra show good agreement with the experimental spectra in terms of both peak positions and intensities. The differences between the resonance Raman spectra of the three 5-halogenated uracils, caused by the effect of halogen substitution, are examined in terms of ground-state normal-mode eigenvectors and excited-state Cartesian gradients, according to the HT formalism. The differences in the normal-mode eigenvectors and excited-state Cartesian gradients between 5-fluorouracil and 5-chlorouracil are used to interpret the dissimilarity between their resonance Raman spectra. Meanwhile, the similarity between the spectra of 5-chlorouracil and 5-bromouracil is explained by the correspondence between their normal modes and excited-state gradients.

  7. Generation of a recombinant single-chain variable fragment (scFv) targeting 5-methyl-2'-deoxycytidine.

    PubMed

    Ohshima, Motohiro; Tadakuma, Tomomi; Hayashi, Hideki; Inoue, Kazuyuki; Itoh, Kunihiko

    2010-01-01

    We generated a single-chain variable fragment (scFv) against 5-methyl-2'-deoxycytidine (m(5)dCyd) using phage display technology. The heavy and light chain variable region genes were amplified by the polymerase chain reaction (PCR) from hybridoma cell line FMC9 and assembled as an scFv fragment with a flexible linker (Gly(4)-Ser)(3). The scFv DNA fragment was then cloned into pCANTAB-5E, and a phage displaying the scFv was produced. Antigen-positive phage clones were successfully selected by enzyme-linked immunosorbent assay (ELISA). The scFv was modified with FLAG and His tags for detection and purification. The scFv reacted strongly with m(5)dCyd and weakly with 5-methylcytidine (m(5)Cyd) but not with cytidine (Cyd) and 1-methyladenosine in a manner similar to the monoclonal antibody (MoAb). Although the specificities of scFv and MoAb were almost identical, the sensitivity of the scFv (IC(50) 0.054 microg/ml) was approximately 80 times higher than that of the parent MoAb (IC(50) 4.27 microg/ml), determined by inhibition ELISA. As a biochemical application of this scFv, we quantified the m(5)dCyd content of genomic DNA by enzymatic hydrolysis using inhibition ELISA. The cancer cell lines HeLa, HeLa S3 and MDA-MB-453 contained approximately 1% of the methylated DNA in total genomic DNA, as did peripheral blood cell genomic DNA from healthy volunteers, but HT29 and T-47D showed hypomethylation compared with the HeLa, HeLa S3 and MDA-MB-453 cell lines. The scFv generated here may be applicable to the assessment of cellular DNA methylation levels and is more sensitive than the MoAb.

  8. Cellular Plasticity Induced by Anti–α-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid (AMPA) Receptor Encephalitis Antibodies

    PubMed Central

    Peng, Xiaoyu; Hughes, Ethan G; Moscato, Emilia H; Parsons, Thomas D; Dalmau, Josep; Balice-Gordon, Rita J

    2015-01-01

    Objective Autoimmune-mediated anti–α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) encephalitis is a severe but treatment-responsive disorder with prominent short-term memory loss and seizures. The mechanisms by which patient antibodies affect synapses and neurons leading to symptoms are poorly understood. Methods The effects of patient antibodies on cultures of live rat hippocampal neurons were determined with immunostaining, Western blot, and electrophysiological analyses. Results We show that patient antibodies cause a selective decrease in the total surface amount and synaptic localization of GluA1- and GluA2-containing AMPARs, regardless of receptor subunit binding specificity, through increased internalization and degradation of surface AMPAR clusters. In contrast, patient antibodies do not alter the density of excitatory synapses, N-methyl-D-aspartate receptor (NMDAR) clusters, or cell viability. Commercially available AMPAR antibodies directed against extracellular epitopes do not result in a loss of surface and synaptic receptor clusters, suggesting specific effects of patient antibodies. Whole-cell patch clamp recordings of spontaneous miniature postsynaptic currents show that patient antibodies decrease AMPAR-mediated currents, but not NMDAR-mediated currents. Interestingly, several functional properties of neurons are also altered: inhibitory synaptic currents and vesicular γ-aminobutyric acid transporter (vGAT) staining intensity decrease, whereas the intrinsic excitability of neurons and short-interval firing increase. Interpretation These results establish that antibodies from patients with anti-AMPAR encephalitis selectively eliminate surface and synaptic AMPARs, resulting in a homeostatic decrease in inhibitory synaptic transmission and increased intrinsic excitability, which may contribute to the memory deficits and epilepsy that are prominent in patients with this disorder. PMID:25369168

  9. Time-resolved photoelectron imaging of the iodide-thymine and iodide-uracil binary cluster systems.

    PubMed

    King, Sarah B; Yandell, Margaret A; Neumark, Daniel M

    2013-01-01

    The energetics and dynamics of thymine and uracil transient negative ions were examined using femtosecond time-resolved photoelectron imaging. The vertical detachment energies (VDEs) of these systems were found to be 4.05 eV and 4.11 eV for iodide-thymine (I(-) x T) and iodide-uracil (I(-) x U) clusters, respectively. An ultraviolet pump pulse was used to promote intracluster charge transfer from iodide to the nucleobase. Subsequent electron detachment using an infrared probe pulse monitored the dynamics of the resulting transient negative ion. Photoelectron spectra reveal two primary features: a near-zero electron kinetic energy signal attributed to autodetachment and a transient feature representing photodetachment from the excited anion state. The transient state exhibits biexponential decay in both thymine and uracil complexes with short and long decay time constants ranging from 150-600 fs and 1-50 ps, respectively, depending on the excitation energy. However, both time constants are systematically shorter for I(-) x T. Vibrational autodetachment and iodine loss are identified as the primary decay mechanisms of the transient negative ions of thymine and uracil.

  10. Eimeria tenella: parasite-specific incorporation of /sup 3/H-uracil as a quantitative measure of intracellular development

    SciTech Connect

    Schmatz, D.M.; Crane, M.S.; Murray, P.K.

    1986-02-01

    An assay has been developed using parasite-specific incorporation of /sup 3/H-uracil to assess the intracellular growth of Eimeria tenella in vitro. As shown by both scintillation counts and autoradiography, /sup 3/H-uracil was incorporated specifically into intracellular parasites from the onset of infection and continued throughout development of the first generation schizonts. Mature schizonts and first generation merozoites did not continue to incorporate additional /sup 3/H-uracil, indicating that RNA synthesis had halted in these stages. Based on these findings, a semi-automated microscale uracil incorporation assay was developed to determine parasite viability. This method should be useful for biochemical studies with intracellular parasites and for screening compounds for anticoccidial activity. The ease, rapidity, and quantitative nature of this assay contrasts favorably with standard morphometric approaches of determining parasite development. In addition, parallel studies using host cell incorporation of /sup 3/H-uridine have been introduced as a method of determining whether antiparasitic activity is direct or indirect in relation to effects on the host cell.

  11. Epithelia hyperplasia in the renal papilla and pelvis but not the urinary bladder of male F344 rats associated with dietary sodium phosphates after uracil exposure.

    PubMed

    Shibata, M A; Sano, M; Shirai, T; Imaida, K; Fukushima, S

    1993-08-01

    Effects of the bladder tumor promoter Na3PO4 and the non-bladder-tumor promoter NaH2PO4 on development of hyperplastic lesions of urinary bladder and renal papilla/pelvis were investigated after exposure of male F344 rats to the nongenotoxic carcinogen uracil. Animals were administered with 3.0% uracil in the diet for 4 weeks and thereafter fed 3.0% Na3PO4 or 3.0% NaH2PO4 for 32 weeks. No enhancing effect of either phosphate salt on uracil-induced proliferative lesions of urinary bladder was observed. However, the sequential treatments gave rise to enhanced development of hyperplastic lesions in the renal papilla/pelvis compared to the case with uracil alone. In addition, a small number of renal pelvic papillomas were observed in the group given Na3PO4 after uracil. These phosphate salts also induced nephrocalcinosis in the papilla/pelvis concomitant with development of renal hyperplastic lesions in this location. A sequential study revealed calculus formation and proliferative lesions in both the urinary bladder and renal papilla/pelvis after 4 weeks dietary application of uracil. After cessation, calculi disappeared and the majority of hyperplastic lesions regressed, consistent with a decrease in DNA synthesis levels. Persistence of uracil-induced epithelial hyperplasia in renal papilla/pelvis under the influence of phosphate salts might have been directly due to chronic stimulation by nephrocalcinosis in these sites.

  12. Hydrogen-bonding and the dissolution mechanism of uracil in an acetate ionic liquid: new insights from NMR spectroscopy and quantum chemical calculations.

    PubMed

    Araújo, João M M; Pereiro, Ana B; Canongia Lopes, José N; Rebelo, Luís P N; Marrucho, Isabel M

    2013-04-18

    The dissolution of uracil-a pyrimidine nucleic acid base-in the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][CH3COO]) has been investigated by methods of (1)H and (13)C NMR spectroscopy, (1)H-(1)H NOESY NMR spectroscopy, and quantum chemical calculations. The uracil-[C2mim][CH3COO] interactions that define the dissolution mechanism comprise the hydrogen bonds between the oxygen atoms of the acetate anion and the hydrogen atoms of the N1-H and N3-H groups of uracil and also the hydrogen bonds between the most acidic aromatic hydrogen atom (H2) of the imidazolium cation and the oxygen atoms of the carbonyl groups of uracil. The bifunctional solvation nature of the ionic liquid can be inferred from the presence of interactions between both ions of the ionic liquid and the uracil molecule. The location of such interaction sites was revealed using NMR data ((1)H and (13)C chemical shifts both in the IL and in the uracil molecule), complemented by DFT calculations. NOESY experiments provided additional evidence concerning the cation-uracil interactions.

  13. The Role of Sarcosine, Uracil, and Kynurenic Acid Metabolism in Urine for Diagnosis and Progression Monitoring of Prostate Cancer.

    PubMed

    Gkotsos, Georgios; Virgiliou, Christina; Lagoudaki, Ioanna; Sardeli, Chrysanthi; Raikos, Nikolaos; Theodoridis, Georgios; Dimitriadis, Georgios

    2017-02-23

    The aim of this pilot study is to evaluate sarcosine, uracil, and kynurenic acid in urine as potential biomarkers in prostate cancer detection and progression monitoring. Sarcosine, uracil, and kynurenic acid were measured in urine samples of 32 prostate cancer patients prior to radical prostatectomy, 101 patients with increased prostate-specific antigen prior to ultrasonographically-guided prostatic biopsy collected before and after prostatic massage, and 15 healthy volunteers (controls). The results were related to histopathologic data, Gleason score, and PSA (Prostate Specific Antigen). Metabolites were measured after analysis of urine samples with Ultra-High Performance Liquid Chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) instrumentation. Multivariate, nonparametric statistical tests including receiver operating characteristics analyses, one-way analysis of variance (Kruskal-Wallis test), parametric statistical analysis, and Pearson correlation, were performed to evaluate diagnostic performance. Decreased median sarcosine and kynurenic acid and increased uracil concentrations were observed for patients with prostate cancer compared to participants without malignancy. Results showed that there was no correlation between the concentration of the studied metabolites and the cancer grade (Gleason score <7 vs. ≥7) and the age of the patients. Evaluation of biomarkers by ROC (Receiving Operating Characteristics) curve analysis showed that differentiation of prostate cancer patients from participants without malignancy was not enhanced by sarcosine or uracil levels in urine. In contrast to total PSA values, kynurenic acid was found a promising biomarker for the detection of prostate cancer particularly in cases where collection of urine samples was performed after prostatic massage. Sarcosine and uracil in urine samples of patients with prostate cancer were not found as significant biomarkers for the diagnosis of prostate cancer. None of the three

  14. The Role of Sarcosine, Uracil, and Kynurenic Acid Metabolism in Urine for Diagnosis and Progression Monitoring of Prostate Cancer

    PubMed Central

    Gkotsos, Georgios; Virgiliou, Christina; Lagoudaki, Ioanna; Sardeli, Chrysanthi; Raikos, Nikolaos; Theodoridis, Georgios; Dimitriadis, Georgios

    2017-01-01

    The aim of this pilot study is to evaluate sarcosine, uracil, and kynurenic acid in urine as potential biomarkers in prostate cancer detection and progression monitoring. Sarcosine, uracil, and kynurenic acid were measured in urine samples of 32 prostate cancer patients prior to radical prostatectomy, 101 patients with increased prostate-specific antigen prior to ultrasonographically-guided prostatic biopsy collected before and after prostatic massage, and 15 healthy volunteers (controls). The results were related to histopathologic data, Gleason score, and PSA (Prostate Specific Antigen). Metabolites were measured after analysis of urine samples with Ultra-High Performance Liquid Chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) instrumentation. Multivariate, nonparametric statistical tests including receiver operating characteristics analyses, one-way analysis of variance (Kruskal–Wallis test), parametric statistical analysis, and Pearson correlation, were performed to evaluate diagnostic performance. Decreased median sarcosine and kynurenic acid and increased uracil concentrations were observed for patients with prostate cancer compared to participants without malignancy. Results showed that there was no correlation between the concentration of the studied metabolites and the cancer grade (Gleason score <7 vs. ≥7) and the age of the patients. Evaluation of biomarkers by ROC (Receiving Operating Characteristics) curve analysis showed that differentiation of prostate cancer patients from participants without malignancy was not enhanced by sarcosine or uracil levels in urine. In contrast to total PSA values, kynurenic acid was found a promising biomarker for the detection of prostate cancer particularly in cases where collection of urine samples was performed after prostatic massage. Sarcosine and uracil in urine samples of patients with prostate cancer were not found as significant biomarkers for the diagnosis of prostate cancer. None of the

  15. Anomalous high reactivity of formyl and acetone ketyl radicals with uracil and its derivatives

    NASA Astrophysics Data System (ADS)

    Aravindakumar, C. T.; Jacob, T. A.; Mohan, H.; Mahal, H. S.; Mukherjee, T.; Mittal, J. P.

    1998-05-01

    CO2·- and ( CH3) 2·COH radicals apparently react with uracil and its derivatives, containing two carbonyl groups, with high rate constants ( k=10 10 dm 3 mol -1 s -1). Various mechanistic aspects of such reactions have been probed. The effect of pH and buffer concentration on the initial formation of absorbance points to some keto-enol tautomerism-type fast-reaction between OH - and the substrate, followed by a slower relaxation to the original equilibrium. The radical anions of these compounds react with methyl viologen mainly via an electron transfer reaction with a high rate constant value (4-9)×10 9 dm 3 mol -1 s -1.

  16. Surface-Enhanced Hyper-Raman Spectra of Adenine, Guanine, Cytosine, Thymine, and Uracil

    PubMed Central

    2016-01-01

    Using picosecond excitation at 1064 nm, surface-enhanced hyper-Raman scattering (SEHRS) spectra of the nucleobases adenine, guanine, cytosine, thymine, and uracil with two different types of silver nanoparticles were obtained. Comparing the SEHRS spectra with SERS data from the identical samples excited at 532 nm and with known infrared spectra, the major bands in the spectra are assigned. Due to the different selection rules for the one- and two-photon excited Raman scattering, we observe strong variation in relative signal strengths of many molecular vibrations obtained in SEHRS and SERS spectra. The two-photon excited spectra of the nucleobases are found to be very sensitive with respect to molecule–nanoparticle interactions. Using both the SEHRS and SERS data, a comprehensive vibrational characterization of the interaction of nucleobases with silver nanostructures can be achieved. PMID:28077982

  17. Theoretical structural and vibrational study of 5-trifluoromethyluracil. A comparison with uracil

    SciTech Connect

    Rudyk, Roxana; Ramos, María E.; Checa, María A.; Brandán, Silvia A.; Chamorro, Eduardo E.

    2014-10-06

    In the present work, a comparative study on the structural and vibrational properties of the 5-trifluoromethyluracil (TFMU) derivative with those corresponding to uracil in gas and aqueous solution phases was performed combining the available H{sup 1}-NMR, C{sup 13}-NMR, F{sup 19}-NMR and FTIR spectra with Density Functional Theory (DFT) calculations. Three stable conformers were theoretically determined in both media by using the hybrid B3LYP/6-31G* method. The solvent effects were simulated by means of the self-consistent reaction field (SCRF) method employing the integral equation formalism variant (IEFPCM). Complete assignments of the vibrational spectra in both phases were performed combining the internal coordinates analysis and the DFT calculations with the Scaled Quantum Mechanics Force Field (SQMFF) methodology. The atomic charges, bond orders, solvation energies, dipole moments, molecular electrostatic potentials and force constants parameters were calculated for the three conformers of TFMU in gas phase and aqueous solution.

  18. Sites of Adsorption of Adenine, Uracil, and Their Corresponding Derivatives on Sodium Montmorillonite

    NASA Astrophysics Data System (ADS)

    Perezgasga, L.; Serrato-Díaz, A.; Negrón-Mendoza, A.; Gal'N, L. De Pablo; Mosqueira, F. G.

    2005-04-01

    Clay minerals are considered important to chemical evolution processes due to their properties, ancient origin, and wide distribution. To extend the knowledge of their role in the prebiotic epoch, the adsorption sites of adenine, adenosine, AMP, ADP, ATP, Poly A, uracil, uridine, UMP, UDP, UTP and Poly U on sodium montmorillonite are investigated. X-ray diffraction, ultraviolet and infrared spectroscopy studies indicate that these molecules distribute into the interlamellar channel and the edge of the clay crystals. Monomers are adsorbed predominantly in the interlamellar channel, whereas polymers adsorb along the crystal edges. Such behavior is discussed mainly in terms of bulk pH, pKa of the adsorbate, and Van der Waals interactions.

  19. Ferrocene-linked thymine/uracil conjugates: base pairing directed self-assembly and supramolecular packing.

    PubMed

    Patwa, Amit N; Gupta, Susmita; Gonnade, Rajesh G; Kumar, Vaijayanti A; Bhadbhade, Mohan M; Ganesh, Krishna N

    2008-02-15

    Ferrocene-linked bis(nucleobase) (1a-c) and chimeric nucleobase (1d) conjugates have been synthesized from mono- and bis(hydroxybutyl)ferrocene 6 via Mitsunobu reaction as the key step. X-ray crystallographic studies of ferrocene bis(nucleobase) conjugates reveal two-dimensional supramolecular organizations of backbones through self-assembled Watson-Crick and reverse Watson-Crick type pairs. Ferrocene-bis(thymine) conjugate self-assembles by reverse Watson-Crick pairing, while the corresponding bis(uracil) conjugate self-assembles by alternating WC and reverse WC type pairing. Such continuous assemblies are not seen in monosubstituted ferrocene nucleobase conjugates which form only planar sheets. The results are interesting from the point of understanding and engineering supramolecular assemblies through rational design of base pairing patterns.

  20. Planar versus non-planar: The important role of weak C-H⋯O hydrogen bonds in the crystal structure of 5-methyl-salicyl-aldehyde.

    PubMed

    Baisch, Ulrich; Scicluna, Marie Christine; Näther, Christian; Vella-Zarb, Liana

    2017-02-01

    The crystal structure of 5-methyl-salicyl-aldehyde (5-MSA; systematic name 2-hy-droxy-5-methyl-benzaldehyde), C8H8O2, was discovered to be a textbook example of the drastic structural changes caused by just a few weak C-H⋯O inter-actions due to the additional methyl-ation of the aromatic ring compared to salicyl-aldehyde SA. This weak inter-molecular hydrogen bonding is observed between aromatic or methyl carbon donor atoms and hydroxyl or aldehyde acceptor oxygen atoms with d(D⋯A) = 3.4801 (18) and 3.499 (11) Å. The mol-ecule shows a distorted geometry of the aromatic ring with elongated bonds in the vicinity of substituted aldehyde and hydroxyl carbon atoms. The methyl hydrogen atoms are disordered over two sets of sites with occupancies of 0.69 (2) and 0.31 (2).

  1. Crystal structures of (S)-(+)-5-(3-bromo/chloro-4-isopropoxyphen­yl)-5-methyl­imidazolidine-2,4-dione

    PubMed Central

    Ohba, Shigeru; Koura, Minoru; Sumida, Hisashi; Shibuya, Kimiyuki

    2016-01-01

    In (S)-(+)-5-(3-bromo-4-isopropoxyphen­yl)-5-methyl­imidazolidine-2,4-dione, C13H15BrN2O3, (I), the hydantoin groups are connected via inter­molecular N—H⋯O hydrogen bonds, forming a terraced sheet structure. In the chloro analogue, (S)-(+)-5-(3-chloro-4-isopropoxyphen­yl)-5-methyl­imidazolidine-2,4-dione, C13H15ClN2O3, (II), the inter­molecular N—H⋯O hydrogen-bonding network forms a flat sheet. Comparison of the crystal structures reveals that (II) is more loosely packed than (I). PMID:26958383

  2. [An effective scheme to produce recombinant uracil-DNA glycosylase of Escherichia coli for PCR diagnostics].

    PubMed

    Dmitrochenko, A E; Turiianskaia, O M; Gilep, A A; Usanov, S A; Iantsevich, A V

    2014-01-01

    An effective scheme has been developed to produce recombinant uracil-DNA glycosylase of Escherichia coli K12 intended to be used for PCR diagnostics, making it possible to achieve a high yield of the end product using a two-stage purification. The gene encoding this enzyme was cloned into the pCWori vector within the same reading frame with six residues of histidine in the C-erminal sequence. Using this vector and the E. coli DH5alpha, a host-vector expression system has been developed and conditions for protein synthesis have been optimized. To purify the protein, metal affinity chromatography with further dialysis was used to remove imidazole. The enzyme yield was no less than 60 mg of the end protein per 1 L of the culture medium. The concordance between amino acid sequences of the recombinant and native enzymes was proved by peptide mass fingerprinting and mass spectrometry. A rapid test to determine the activity of the enzyme preparation was suggested. It was found that the activity of 1.0 mg of the recombinant protein is no less than 3 x 10(3) units. The recombinant enzyme was most stable at pH 8.0 and an ionic strength of the solution equal to 200 mM; it lost its activity completely for 10 min at 60 degrees C. Storage during 1 h at 20 degrees C resulted in the loss of no more than 30% of activity. In the enzyme preparation, the activity of DNase was absent. The free energy of the unfolding of the protein globule of the recombinant uracil-DNA glycosylase is 23.1 +/- 0.2 kJ/mol. The data obtained indicate that the recombinant enzyme may be recommended for use in PCR diagnostics to prevent the appearance of false positive results caused by pollution of the reaction mixture by products of the preceding reactions.

  3. Increased uracil insertion in DNA is cytotoxic and increases the frequency of mutation, double strand break formation and VSG switching in Trypanosoma brucei.

    PubMed

    Castillo-Acosta, Víctor M; Aguilar-Pereyra, Fernando; Bart, Jean-Mathieu; Navarro, Miguel; Ruiz-Pérez, Luis M; Vidal, Antonio E; González-Pacanowska, Dolores

    2012-12-01

    Deoxyuridine 5'-triphosphate pyrophosphatase (dUTPase) and uracil-DNA glycosylase (UNG) are key enzymes involved in the control of the presence of uracil in DNA. While dUTPase prevents uracil misincorporation by removing dUTP from the deoxynucleotide pool, UNG excises uracil from DNA as a first step of the base excision repair pathway (BER). Here, we report that strong down-regulation of dUTPase in UNG-deficient Trypanosoma brucei cells greatly impairs cell viability in both bloodstream and procyclic forms, underscoring the extreme sensitivity of trypanosomes to uracil in DNA. Depletion of dUTPase activity in the absence of UNG provoked cell cycle alterations, massive dUTP misincorporation into DNA and chromosomal fragmentation. Overall, trypanosomatid cells that lack dUTPase and UNG activities exhibited greater proliferation defects and DNA damage than cells deficient in only one of these activities. To determine the mutagenic consequences of uracil in DNA, mutation rates and spectra were analyzed in dUTPase-depleted cells in the presence of UNG activity. These cells displayed a spontaneous mutation rate 9-fold higher than the parental cell line. Base substitutions at A:T base pairs and deletion frequencies were both significantly enhanced which is consistent with the generation of mutagenic AP sites and DNA strand breaks. The increase in strand breaks conveyed a concomitant increase in VSG switching in vitro. The low tolerance of T. brucei to uracil in DNA emphasizes the importance of uracil removal and regulation of intracellular dUTP pool levels in cell viability and genetic stability and suggests potential strategies to compromise parasite survival.

  4. Microsolvation effect, hydrogen-bonding pattern, and electron affinity of the uracil-water complexes U-(H2O)n (n = 1, 2, 3).

    PubMed

    Bao, Xiaoguang; Sun, Huai; Wong, Ning-Bew; Gu, Jiande

    2006-03-30

    To achieve a systematic understanding of the influence of microsolvation on the electron accepting behaviors of nucleobases, the reliable theoretical method (B3LYP/DZP++) has been applied to a comprehensive conformational investigation on the uracil-water complexes U-(H(2)O)(n) (n = 1, 2, 3) in both neutral and anionic forms. For the neutral complexes, the conformers of hydration on the O2 of uracil are energetically favored. However, hydration on the O4 atom of uracil is more stable for the radical anions. The electron structure analysis for the H-bonding patterns reveal that the CH...OH(2) type H-bond exists only for di- and trihydrated uracil complexes in which a water dimer or trimer is involved. The electron density structure analysis and the atoms-in-molecules (AIM) analysis for U-(H(2)O)(n) suggest a threshold value of the bond critical point (BCP) density to justify the CH...OH(2) type H-bond; that is, CH...OH(2) could be considered to be a H-bond only when its BCP density value is equal to or larger than 0.010 au. The positive adiabatic electron affinity (AEA) and vertical detachment energy (VDE) values for the uracil-water complexes suggest that these hydrated uracil anions are stable. Moreover, the average AEA and VDE of U-(H(2)O)(n) increase as the number of the hydration waters increases.

  5. Helix–hairpin–helix protein MJ1434 from Methanocaldococcus jannaschii and EndoIV homologue TTC0482 from Thermus thermophilus HB27 do not process DNA uracil residues

    PubMed Central

    Schomacher, Lars; Smolorz, Sabine; Ciirdaeva, Elena; Ber, Svetlana; Kramer, Wilfried; Fritz, Hans-Joachim

    2010-01-01

    The mutagenic threat of hydrolytic DNA cytosine deamination is met mostly by uracil DNA glycosylases (UDG) initiating base excision repair. However, several sequenced genomes of archaeal organisms are devoid of genes coding for homologues of the otherwise ubiquitous UDG superfamily of proteins. Previously, two possible solutions to this problem were offered by (i) a report of a newly discovered family of uracil DNA glycosylases exemplified by MJ1434, a protein found in the hyperthermophilic archaeon Methanocaldococcus jannaschii, and (ii) the description of TTC0482, an EndoIV homologue from the hyperthermophilic bacterium Thermus thermophilus HB27, as being able to excise uracil from DNA. Sequence homologues of both proteins can be found throughout the archaeal domain of life. Three proteins orthologous to MJ1434 and the family founder itself were tested for but failed to exhibit DNA uracil glycosylase activity when produced in an Ung-deficient Escherichia coli host. Likewise, no DNA uracil processing activity could be detected to be associated with TTC0482, while the protein was fully active as an AP endonuclease. We propose that the uracil processing activities formerly found were due to contaminations with Ung enzyme. Use of Δung-strains as hosts for production of putatively DNA-U processing enzymes provides a simple safeguard. PMID:20410075

  6. Chimeras between single-stranded DNA-binding proteins from Escherichia coli and Mycobacterium tuberculosis reveal that their C-terminal domains interact with uracil DNA glycosylases.

    PubMed

    Handa, P; Acharya, N; Varshney, U

    2001-05-18

    Uracil, a promutagenic base in DNA can arise by spontaneous deamination of cytosine or incorporation of dUMP by DNA polymerase. Uracil is removed from DNA by uracil DNA glycosylase (UDG), the first enzyme in the uracil excision repair pathway. We recently reported that the Escherichia coli single-stranded DNA binding protein (SSB) facilitated uracil excision from certain structured substrates by E. coli UDG (EcoUDG) and suggested the existence of interaction between SSB and UDG. In this study, we have made use of the chimeric proteins obtained by fusion of N- and C-terminal domains of SSBs from E. coli and Mycobacterium tuberculosis to investigate interactions between SSBs and UDGs. The EcoSSB or a chimera containing its C-terminal domain interacts with EcoUDG in a binary (SSB-UDG) or a ternary (DNA-SSB-UDG) complex. However, the chimera containing the N-terminal domain from EcoSSB showed no interactions with EcoUDG. Thus, the C-terminal domain (48 amino acids) of EcoSSB is necessary and sufficient for interaction with EcoUDG. The data also suggest that the C-terminal domain (34 amino acids) of MtuSSB is a predominant determinant for mediating its interaction with MtuUDG. The mechanism of how the interactions between SSB and UDG could be important in uracil excision repair pathway has been discussed.

  7. pH effect on structural character of uracil in aqueous solution studied by single-shot CARS

    NASA Astrophysics Data System (ADS)

    Qin, Wenhong; Zhao, Dong; Guo, Chu

    1991-10-01

    A preliminary study is reported on the structure of uracil, a base residue of nucleic acid, in aqueous solutions of different pH values by coherent anti-Stokes Raman scattering (CARS). The results obtained reveal that Raman lines associated with the stretching and bending vibration modes of the uracil ring around 1000 and 1240 cm -1 are sensitive to the pH of the solutions. All thes findings, however, are difficult to observe by laser resonance Raman spectroscopy, which is used widely in practice at present. In addition, we conclude that CARS measurement seems to be a powerful tool capable of offering structural specificity associated with molecular vibrational frequencies of base residues of nucleic acids and their interactions with the surrounding media.

  8. Uracil uptake in Escherichia coli K-12: isolation of uraA mutants and cloning of the gene.

    PubMed Central

    Andersen, P S; Frees, D; Fast, R; Mygind, B

    1995-01-01

    Mutants defective in utilization of uracil at low concentrations have been isolated and characterized. The mutations in question (uraA) map close to the upp gene encoding uracil phosphoribosyltransferase. By complementation analysis, a plasmid that complements the uraA mutation has been isolated. The uraA gene was shown to be the second gene in a bicistronic operon with upp as the promoter proximal gene. The nucleotide sequence of the gene was determined, and the gene encodes a hydrophobic membrane protein with a calculated Mr of 45,030. The UraA protein has been identified in sodium dodecyl sulfate-polyacrylamide gels in the membrane fraction of minicells harboring the uraA plasmids. PMID:7721693

  9. Exploration of acetanilide derivatives of 1-(ω-phenoxyalkyl)uracils as novel inhibitors of Hepatitis C Virus replication.

    PubMed

    Magri, Andrea; Ozerov, Alexander A; Tunitskaya, Vera L; Valuev-Elliston, Vladimir T; Wahid, Ahmed; Pirisi, Mario; Simmonds, Peter; Ivanov, Alexander V; Novikov, Mikhail S; Patel, Arvind H

    2016-07-12

    Hepatitis C Virus (HCV) is a major public health problem worldwide. While highly efficacious directly-acting antiviral agents have been developed in recent years, their high costs and relative inaccessibility make their use limited. Here, we describe new 1-(ω-phenoxyalkyl)uracils bearing acetanilide fragment in 3 position of pyrimidine ring as potential antiviral drugs against HCV. Using a combination of various biochemical assays and in vitro virus infection and replication models, we show that our compounds are able to significantly reduce viral genomic replication, independently of virus genotype, with their IC50 values in the nanomolar range. We also demonstrate that our compounds can block de novo RNA synthesis and that effect is dependent on a chemical structure of the compounds. A detailed structure-activity relationship revealed that the most active compounds were the N(3)-substituted uracil derivatives containing 6-(4-bromophenoxy)hexyl or 8-(4-bromophenoxy)octyl fragment at N(1) position.

  10. Visual and light scattering spectrometric method for the detection of melamine using uracil 5'-triphosphate sodium modified gold nanoparticles.

    PubMed

    Liang, Lijiao; Zhen, Shujun; Huang, Chengzhi

    2017-02-15

    A highly selective method was presented for colorimetric determination of melamine using uracil 5'-triphosphate sodium modified gold nanoparticles (UTP-Au NPs) in this paper. Specific hydrogen-bonding interaction between uracil base (U) and melamine resulted in the aggregation of AuNPs, displaying variations of localized surface plasmon resonance (LSPR) features such as color change from red to blue and enhanced localized surface plasmon resonance light scattering (LSPR-LS) signals. Accordingly, the concentration of melamine could be quantified based on naked eye or a spectrometric method. This method was simple, inexpensive, environmental friendly and highly selective, which has been successfully used for the detection of melamine in pretreated liquid milk products with high recoveries.

  11. A DNA machine-based fluorescence amplification strategy for sensitive detection of uracil-DNA glycosylase activity.

    PubMed

    Wu, Yushu; Wang, Lei; Zhu, Jing; Jiang, Wei

    2015-06-15

    Sensitive detection of uracil-DNA glycosylase (UDG) activity is critical for function study of UDG and clinical diagnosis. Here, we developed a novel fluorescent strategy for sensitive detection of UDG activity based on the signal amplification by a label-free and enzyme-free DNA machine. A double-strand DNA (dsDNA) probe P1-P2 with uracil bases and trigger sequence was designed for UDG recognition and signal transduction. Two hairpin probes H1 and H2 which were partially complementary were employed to construct the label-free and enzyme-free DNA machine. Under the action of UDG, uracil bases were removed from the P1-P2 dsDNA probe, and then a strand P2' with abasic sites was released. Subsequently, the liberated P2' activated the DNA machine and generated numerous H1-H2 complexes containing G-quadruplex (G4) structures in the end. Finally, the G4 structures could bind with N-methylmesoporphyrin IX (NMM) to form G4-NMM complexes with the enhanced fluorescence responses. This strategy could detect UDG activity as low as 0.00044 U/mL. In addition, the strategy was also applied for the analysis of UDG activity in HeLa cells lysate with low effect of cellular components. Moreover, this strategy was successfully applied for assaying the inhibition of UDG using uracil glycosylase inhibitor (UGI). This strategy provided a potential tool for sensitive quantification of UDG activity in UDG functional study and clinical diagnosis.

  12. Crystal structure and functional insights into uracil-DNA glycosylase inhibition by phage ϕ29 DNA mimic protein p56

    PubMed Central

    Baños-Sanz, José Ignacio; Mojardín, Laura; Sanz-Aparicio, Julia; Lázaro, José M.; Villar, Laurentino; Serrano-Heras, Gemma; González, Beatriz; Salas, Margarita

    2013-01-01

    Uracil-DNA glycosylase (UDG) is a key repair enzyme responsible for removing uracil residues from DNA. Interestingly, UDG is the only enzyme known to be inhibited by two different DNA mimic proteins: p56 encoded by the Bacillus subtilis phage ϕ29 and the well-characterized protein Ugi encoded by the B. subtilis phage PBS1/PBS2. Atomic-resolution crystal structures of the B. subtilis UDG both free and in complex with p56, combined with site-directed mutagenesis analysis, allowed us to identify the key amino acid residues required for enzyme activity, DNA binding and complex formation. An important requirement for complex formation is the recognition carried out by p56 of the protruding Phe191 residue from B. subtilis UDG, whose side-chain is inserted into the DNA minor groove to replace the flipped-out uracil. A comparative analysis of both p56 and Ugi inhibitors enabled us to identify their common and distinctive features. Thereby, our results provide an insight into how two DNA mimic proteins with different structural and biochemical properties are able to specifically block the DNA-binding domain of the same enzyme. PMID:23671337

  13. Crystal structure and functional insights into uracil-DNA glycosylase inhibition by phage Φ29 DNA mimic protein p56.

    PubMed

    Baños-Sanz, José Ignacio; Mojardín, Laura; Sanz-Aparicio, Julia; Lázaro, José M; Villar, Laurentino; Serrano-Heras, Gemma; González, Beatriz; Salas, Margarita

    2013-07-01

    Uracil-DNA glycosylase (UDG) is a key repair enzyme responsible for removing uracil residues from DNA. Interestingly, UDG is the only enzyme known to be inhibited by two different DNA mimic proteins: p56 encoded by the Bacillus subtilis phage 29 and the well-characterized protein Ugi encoded by the B. subtilis phage PBS1/PBS2. Atomic-resolution crystal structures of the B. subtilis UDG both free and in complex with p56, combined with site-directed mutagenesis analysis, allowed us to identify the key amino acid residues required for enzyme activity, DNA binding and complex formation. An important requirement for complex formation is the recognition carried out by p56 of the protruding Phe191 residue from B. subtilis UDG, whose side-chain is inserted into the DNA minor groove to replace the flipped-out uracil. A comparative analysis of both p56 and Ugi inhibitors enabled us to identify their common and distinctive features. Thereby, our results provide an insight into how two DNA mimic proteins with different structural and biochemical properties are able to specifically block the DNA-binding domain of the same enzyme.

  14. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil.

    PubMed

    Puzzarini, Cristina; Barone, Vincenzo

    2011-04-21

    The equilibrium structure of uracil has been investigated using both theoretical and experimental data. With respect to the former, quantum-chemical calculations at the coupled-cluster level in conjunction with a triple-zeta basis set have been carried out. Extrapolation to the basis set limit, performed employing the second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections have also been considered. Based on the available rotational constants for various isotopic species together with corresponding computed vibrational corrections, the semi-experimental equilibrium structure of uracil has been determined for the first time. Theoretical and semi-experimental structures have been found in remarkably good agreement, thus pointing out the limitations of previous experimental determinations. Molecular and spectroscopic properties of uracil have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the revision of the dipole moment. On the whole, it has been proved that the computational procedure presented is able to provide parameters with the proper accuracy to support experimental investigations of large molecules of biological interest.

  15. Loss of Caenorhabditis elegans UNG-1 uracil-DNA glycosylase affects apoptosis in response to DNA damaging agents.

    PubMed

    Skjeldam, Hanne K; Kassahun, Henok; Fensgård, Oyvind; SenGupta, Tanima; Babaie, Eshrat; Lindvall, Jessica M; Arczewska, Katarzyna; Nilsen, Hilde

    2010-08-05

    The nematode Caenorhabditis elegans has been used extensively to study responses to DNA damage. In contrast, little is known about DNA repair in this organism. C. elegans is unusual in that it encodes few DNA glycosylases and the uracil-DNA glycosylase (UDG) encoded by the ung-1 gene is the only known UDG. C. elegans could therefore become a valuable model organism for studies of the genetic interaction networks involving base excision repair (BER). As a first step towards characterization of BER in C. elegans, we show that the UNG-1 protein is an active uracil-DNA glycosylase. We demonstrate that an ung-1 mutant has reduced ability to repair uracil-containing DNA but that an alternative Ugi-inhibited activity is present in ung-1 nuclear extracts. Finally, we demonstrate that ung-1 mutants show altered levels of apoptotic cell corpses formed in response to DNA damaging agents. Increased apoptosis in the ung-1 mutant in response to ionizing radiation (IR) suggests that UNG-1 contributes to repair of IR-induced DNA base damage in vivo. Following treatment with paraquat however, the apoptotic corpse-formation was reduced. Gene expression profiling suggests that this phenotype is a consequence of compensatory transcriptomic shifts that modulate oxidative stress responses in the mutant and not an effect of reduced DNA damage signaling. 2010 Elsevier B.V. All rights reserved.

  16. Role of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor regulation in stress-induced pain chronification

    PubMed Central

    Liu, Sufang; Tao, Feng

    2017-01-01

    Persistent postsurgical pain is a serious issue in public health, which has received increased interest in recent years. Previous studies have reported that psychological factors promote the development of chronic postsurgical pain. However, it is unclear how chronification of postsurgical pain occurs. The α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor (AMPA) phosphorylation in the central nervous system plays a critical role in synaptic plasticity and contributes to central sensitization and chronic pain development. Here, we discuss the role of AMPA receptor regulation in stress-induced pain chronification after surgery. PMID:28289513

  17. Cadmium(II) inhibition of human uracil-DNA glycosylase by catalytic water supplantation

    NASA Astrophysics Data System (ADS)

    Gokey, Trevor; Hang, Bo; Guliaev, Anton B.

    2016-12-01

    Toxic metals are known to inhibit DNA repair but the underlying mechanisms of inhibition are still not fully understood. DNA repair enzymes such as human uracil-DNA glycosylase (hUNG) perform the initial step in the base excision repair (BER) pathway. In this work, we showed that cadmium [Cd(II)], a known human carcinogen, inhibited all activity of hUNG at 100 μM. Computational analyses based on 2 μs equilibrium, 1.6 μs steered molecular dynamics (SMD), and QM/MM MD determined that Cd(II) ions entered the enzyme active site and formed close contacts with both D145 and H148, effectively replacing the catalytic water normally found in this position. Geometry refinement by density functional theory (DFT) calculations showed that Cd(II) formed a tetrahedral structure with D145, P146, H148, and one water molecule. This work for the first time reports Cd(II) inhibition of hUNG which was due to replacement of the catalytic water by binding the active site D145 and H148 residues. Comparison of the proposed metal binding site to existing structural data showed that D145:H148 followed a general metal binding motif favored by Cd(II). The identified motif offered structural insights into metal inhibition of other DNA repair enzymes and glycosylases.

  18. High-dose oral tegafur-uracil maintenance therapy in patients with uterine cervical cancer

    PubMed Central

    Motohara, Takeshi; Saito, Fumitaka; Takaishi, Kiyomi; Fukumatsu, Yukitoshi; Tohya, Toshimitsu; Shibata, Saburo; Mimori, Hiroyuki; Tashiro, Hironori; Katabuchi, Hidetaka

    2015-01-01

    Objective The aim of this study was to determine the efficacy and toxicity of oral administration of tegafur-uracil (UFT) at a high dose, 600 mg/day, based on the tegafur dose, against uterine cervical cancer. Methods This study consisted of a retrospective analysis. From April 1986 to March 1997, 309 patients with uterine cervical cancer were registered. Oral UFT was administered to 162 patients for maintenance therapy after an initial treatment (the UFT group). The other 147 patients were not treated with UFT (the control group). The survival rate was calculated for both groups and statistically analyzed using the log-rank test. Adverse events were compared between the UFT and control groups. Results In the UFT group, 103 patients (63.6%) received UFT for ≥90 days. The drug dose was 600 mg/day for 137 patients (84.6%) and 300 to 400 mg/day for the remainder. The overall survival rate was significantly higher in the UFT group than in the control group (p<0.05). The prognosis was particularly favorable in stage III cases, in cases of squamous cell carcinoma, and in cases that were treated by radiotherapy. The most frequent side effects were nausea/vomiting (12.2%), appetite loss (10.1%), and leukopenia/neutropenia (5.8%). Conclusion High-dose oral UFT maintenance treatment prolonged the disease-free survival and overall survival of patients with uterine cervical cancer, particularly of those with advanced disease. PMID:25686399

  19. Interactions of Some Divalent Metal Ions with Thymine and Uracil Thiosemicarbazide Derivatives.

    PubMed

    Hammud, Hassan H; El-Dakdouki, Mohammad H; Sonji, Nada; Sonji, Ghassan; Bouhadir, Kamal H

    2016-05-03

    The study of interactions between metal ions and nucleobases, nucleosides, nucleotides, or nucleic acids has become an active research area in chemical, biological, and therapeutic fields. In this respect, the coordination behavior of nucleobase derivatives to transition metals was studied in order to get a better understanding about DNA-metal interactions in in vitro and in vivo systems. Two nucleobase derivatives, 3-benzoyl-1-[3-(thymine-1-yl)propamido]thiourea and 3-benzoyl-1-[3-(uracil-1-yl)propamido]thiourea, were synthesized and their dissociation constants were determined at different temperatures and 0.3 ionic strength. Potentiometric studies were carried out on the interaction of the derivatives towards some divalent metals in 50% v/v ethanol-water containing 0.3 mol.dm(-3) KCl, at five different temperatures. The formation constants of the metal complexes for both ligands follow the order: Cu(2+) > Ni(2+) > Co(2+) > Zn(2+) > Pb(2+) > Cd(2+) > Mn(2+). The thermodynamic parameters were estimated; the complexation process has been found to be spontaneous, exothermic, and entropically favorable.

  20. Trading in cooperativity for specificity to maintain uracil-free DNA

    PubMed Central

    Szabó, Judit E.; Takács, Enikő; Merényi, Gábor; Vértessy, Beáta G.; Tóth, Judit

    2016-01-01

    Members of the dUTPase superfamily play an important role in the maintenance of the pyrimidine nucleotide balance and of genome integrity. dCTP deaminases and the bifunctional dCTP deaminase-dUTPases are cooperatively regulated by dTTP. However, the manifestation of allosteric behavior within the same trimeric protein architecture of dUTPases, the third member of the superfamily, has been a question of debate for decades. Therefore, we designed hybrid dUTPase trimers to access conformational states potentially mimicking the ones observed in the cooperative relatives. We studied how the interruption of different steps of the enzyme cycle affects the active site cross talk. We found that subunits work independently in dUTPase. The experimental results combined with a comparative structural analysis of dUTPase superfamily enzymes revealed that subtile structural differences within the allosteric loop and the central channel in these enzymes give rise to their dramatically different cooperative behavior. We demonstrate that the lack of allosteric regulation in dUTPase is related to the functional adaptation to more efficient dUTP hydrolysis which is advantageous in uracil-DNA prevention. PMID:27063406

  1. Identification of a prototypical single-stranded uracil DNA glycosylase from Listeria innocua.

    PubMed

    Li, Jing; Yang, Ye; Guevara, Jose; Wang, Liangjiang; Cao, Weiguo

    2017-09-01

    A recent phylogenetic study on UDG superfamily estimated a new clade of family 3 enzymes (SMUG1-like), which shares a lower homology with canonic SMUG1 enzymes. The enzymatic properties of the newly found putative DNA glycosylase are unknown. To test the potential UDG activity and evaluate phylogenetic classification, we isolated one SMUG1-like glycosylase representative from Listeria innocua (Lin). A biochemical screening of DNA glycosylase activity in vitro indicates that Lin SMUG1-like glycosylase is a single-strand selective uracil DNA glycosylase. The UDG activity on DNA bubble structures provides clue to its physiological significance in vivo. Mutagenesis and molecular modeling analyses reveal that Lin SMUG1-like glycosylase has similar functional motifs with SMUG1 enzymes; however, it contains a distinct catalytic doublet S67-S68 in motif 1 that is not found in any families in the UDG superfamily. Experimental investigation shows that the S67M-S68N double mutant is catalytically more active than either S67M or S68N single mutant. Coupled with mutual information analysis, the results indicate a high degree of correlation in the evolution of SMUG1-like enzymes. This study underscores the functional and catalytic diversity in the evolution of enzymes in UDG superfamily. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. SHMT1 knockdown induces apoptosis in lung cancer cells by causing uracil misincorporation

    PubMed Central

    Paone, A; Marani, M; Fiascarelli, A; Rinaldo, S; Giardina, G; Contestabile, R; Paiardini, A; Cutruzzolà, F

    2014-01-01

    Reprogramming of cellular metabolism towards de novo serine production fuels the growth of cancer cells, providing essential precursors such as amino acids and nucleotides and controlling the antioxidant and methylation capacities of the cell. The enzyme serine hydroxymethyltransferase (SHMT) has a key role in this metabolic shift, and directs serine carbons to one-carbon units metabolism and thymidilate synthesis. While the mitochondrial isoform of SHMT (SHMT2) has recently been identified as an important player in the control of cell proliferation in several cancer types and as a hot target for anticancer therapies, the role of the cytoplasmic isoform (SHMT1) in cancerogenesis is currently less defined. In this paper we show that SHMT1 is overexpressed in tissue samples from lung cancer patients and lung cancer cell lines, suggesting that, in this widespread type of tumor, SHMT1 plays a relevant role. We show that SHMT1 knockdown in lung cancer cells leads to cell cycle arrest and, more importantly, to p53-dependent apoptosis. Our data demonstrate that the induction of apoptosis does not depend on serine or glycine starvation, but is because of the increased uracil accumulation during DNA replication. PMID:25412303

  3. Tegafur-uracil (UFT) plus folinic acid in advanced rectal cancer.

    PubMed

    Sanchiz, F; Milla, A

    1994-12-01

    We previously reported positive results to Tegafur-Uracil (UFT) chemotherapy in a group of patients with advanced rectal cancer. We have continued the study and now report the effectiveness of UFT plus folinic acid (FA) in 52 patients with advanced rectal cancer. The therapeutic schedule was UFT, 600 mg/m2/day x 14 days p.o. + FA, 90 mg/m2/day x 14 days p.o. Fifty-two out of a total of 56 patients were evaluated for response and toxicity. A higher incidence of positive responses in patients without previous chemotherapy was appreciated. Twenty-one of the 52 evaluated patients showed a partial response (PR). Responses were strongly correlated with previous chemotherapy (14/20; 70% PR of cases without previous chemotherapy vs 7/32; 22% of cases with previous chemotherapy). All responding patients came forward with a median time to progression of 8.2 months (19.6 months for patients without previous chemotherapy vs 7.7 months for patients with previous chemotherapy, P < 0.01). We concluded that the UFT plus FA could be a treatment of choice for patients with advanced rectal cancer.

  4. Oral tegafur-uracil as metronomic therapy following intravenous FOLFOX for stage III colon cancer

    PubMed Central

    Huang, Wen-Yen; Ho, Ching-Liang; Lee, Chia-Cheng; Hsiao, Cheng-Wen; Wu, Chang-Chieh; Jao, Shu-Wen; Yang, Jen-Fu; Lo, Cheng-Hsiang; Chen, Jia-Hong

    2017-01-01

    The purpose of this study was to estimate the impact of metronomic therapy with oral tegafur-uracil (UFUR) following an intravenous FOLFOX regimen as surgical adjuvant chemotherapy on the overall survival (OS) and disease-free survival (DFS) of stage III colon cancer patients. From the retrospective database of patients who underwent a surgical resection for colorectal cancer at the Tri-Service General Hospital from October 2008 through December 2014, stage III colon carcinomas treated with radical R0 resection were reviewed. One hundred thirty two patients were treated with a FOLFOX regimen (comparison group), and 113 patients were treated with the same regimen followed by additional oral UFUR (UFUR group). The clinical characteristics and mean age of the comparison and UFUR groups were similar. Furthermore, for all study patients, DFS was not significantly different between the two groups. However, 5-year OS rates were 86.8% and 68.5% in the UFUR and comparison groups, respectively (p = 0.0107). Adding UFUR to a FOLFOX regimen was found to significantly improve the OS in patients with stage III colon cancer. UFUR as a maintenance therapy following FOLFOX regimen as an alternative therapeutic option for the treatment of stage III colon cancer patients. PMID:28328969

  5. Cadmium(II) inhibition of human uracil-DNA glycosylase by catalytic water supplantation

    PubMed Central

    Gokey, Trevor; Hang, Bo; Guliaev, Anton B.

    2016-01-01

    Toxic metals are known to inhibit DNA repair but the underlying mechanisms of inhibition are still not fully understood. DNA repair enzymes such as human uracil-DNA glycosylase (hUNG) perform the initial step in the base excision repair (BER) pathway. In this work, we showed that cadmium [Cd(II)], a known human carcinogen, inhibited all activity of hUNG at 100 μM. Computational analyses based on 2 μs equilibrium, 1.6 μs steered molecular dynamics (SMD), and QM/MM MD determined that Cd(II) ions entered the enzyme active site and formed close contacts with both D145 and H148, effectively replacing the catalytic water normally found in this position. Geometry refinement by density functional theory (DFT) calculations showed that Cd(II) formed a tetrahedral structure with D145, P146, H148, and one water molecule. This work for the first time reports Cd(II) inhibition of hUNG which was due to replacement of the catalytic water by binding the active site D145 and H148 residues. Comparison of the proposed metal binding site to existing structural data showed that D145:H148 followed a general metal binding motif favored by Cd(II). The identified motif offered structural insights into metal inhibition of other DNA repair enzymes and glycosylases. PMID:27974818

  6. Vibrational spectroscopic investigations, molecular dynamic simulations and molecular docking studies of N‧-diphenylmethylidene-5-methyl-1H-pyrazole-3-carbohydrazide

    NASA Astrophysics Data System (ADS)

    Pillai, Renjith Raveendran; Menon, Vidya V.; Mary, Y. Shyma; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan

    2017-02-01

    FT-IR and FT-Raman spectra of N‧-diphenylmethylidene-5-methyl-1H-pyrazole-3-carbohydrazide were recorded and analyzed. Due to the industrial and biological importance of pyrazole derivatives, we have carried out an extensive quantum chemical study on N‧-diphenylmethylidene-5-methyl-1H-pyrazole-3-carbohydrazide. The theoretical ground state geometry and electronic structure of the title molecule were optimized by DFT/B3LYP/6-311G++(d,p) method and compared with those of the crystal data. The wave numbers obtained are assigned by potential energy distribution. The ring breathing modes of the benzene rings are assigned theoretically at 1009 cm-1 for the mono substituted phenyl rings. The first order hyperpolarizability is comparable with that of similar derivatives and 16 times that of the standard NLO material urea. Conformational analysis was conducted in order to locate all possible conformations of the title compound, followed by investigation of local reactivity properties by MEP and ALIE surfaces. Natural bond orbital analysis has been carried out to analyse the stability of the molecule arising from hyper-conjugative interactions and charge delocalization. Further, reactive properties via autoxidation and hydrolysis mechanisms have been assessed through calculations of bond dissociation energies and radial distribution functions. Docking results confirmed that the compound was a potential inhibitor of CDK2s and were in agreement with the previous reported studies.

  7. Planar versus non-planar: The important role of weak C—H⋯O hydrogen bonds in the crystal structure of 5-methyl­salicyl­aldehyde

    PubMed Central

    Baisch, Ulrich; Scicluna, Marie Christine; Näther, Christian; Vella-Zarb, Liana

    2017-01-01

    The crystal structure of 5-methyl­salicyl­aldehyde (5-MSA; systematic name 2-hy­droxy-5-methyl­benzaldehyde), C8H8O2, was discovered to be a textbook example of the drastic structural changes caused by just a few weak C—H⋯O inter­actions due to the additional methyl­ation of the aromatic ring compared to salicyl­aldehyde SA. This weak inter­molecular hydrogen bonding is observed between aromatic or methyl carbon donor atoms and hydroxyl or aldehyde acceptor oxygen atoms with d(D⋯A) = 3.4801 (18) and 3.499 (11) Å. The mol­ecule shows a distorted geometry of the aromatic ring with elongated bonds in the vicinity of substituted aldehyde and hydroxyl carbon atoms. The methyl hydrogen atoms are disordered over two sets of sites with occupancies of 0.69 (2) and 0.31 (2). PMID:28217332

  8. Dual targeting of tumor angiogenesis and chemotherapy by endostatin-cytosine deaminase-uracil phosphoribosyltransferase.

    PubMed

    Chen, Chun-Te; Yamaguchi, Hirohito; Lee, Hong-Jen; Du, Yi; Lee, Heng-Huan; Xia, Weiya; Yu, Wen-Hsuan; Hsu, Jennifer L; Yen, Chia-Jui; Sun, Hui-Lung; Wang, Yan; Yeh, Edward T H; Hortobagyi, Gabriel N; Hung, Mien-Chie

    2011-08-01

    Several antiangiogenic drugs targeting VEGF/VEGF receptor (VEGFR) that were approved by the Food and Drug Administration for many cancer types, including colorectal and lung cancer, can effectively reduce tumor growth. However, targeting the VEGF signaling pathway will probably influence the normal function of endothelial cells in maintaining homeostasis and can cause unwanted adverse effects. Indeed, emerging experimental evidence suggests that VEGF-targeting therapy induced less tumor cell-specific cytotoxicity, allowing residual cells to become more resistant and eventually develop a more malignant phenotype. We report an antitumor therapeutic EndoCD fusion protein developed by linking endostatin (Endo) to cytosine deaminase and uracil phosphoribosyltransferase (CD). Specifically, Endo possesses tumor antiangiogenesis activity that targets tumor endothelial cells, followed by CD, which converts the nontoxic prodrug 5-fluorocytosine (5-FC) to the cytotoxic antitumor drug 5-fluorouracil (5-FU) in the local tumor area. Moreover, selective targeting of tumor sites allows an increasing local intratumoral concentration of 5-FU, thus providing high levels of cytotoxic activity. We showed that treatment with EndoCD plus 5-FC, compared with bevacizumab plus 5-FU treatment, significantly increased the 5-FU concentration around tumor sites and suppressed tumor growth and metastasis in human breast and colorectal orthotropic animal models. In addition, in contrast to treatment with bevacizumab/5-FU, EndoCD/5-FC did not induce cardiotoxicity leading to heart failure in mice after long-term treatment. Our results showed that, compared with currently used antiangiogenic drugs, EndoCD possesses potent anticancer activity with virtually no toxic effects and does not increase tumor invasion or metastasis. Together, these findings suggest that EndoCD/5-FC could become an alternative option for future antiangiogenesis therapy.

  9. Toehold-mediated strand displacement reaction-dependent fluorescent strategy for sensitive detection of uracil-DNA glycosylase activity.

    PubMed

    Wu, Yushu; Wang, Lei; Jiang, Wei

    2017-03-15

    Sensitive detection of uracil-DNA glycosylase (UDG) activity is beneficial for evaluating the repairing process of DNA lesions. Here, toehold-mediated strand displacement reaction (TSDR)-dependent fluorescent strategy was constructed for sensitive detection of UDG activity. A single-stranded DNA (ssDNA) probe with two uracil bases and a trigger sequence were designed. A hairpin probe with toehold domain was designed, and a reporter probe was also designed. Under the action of UDG, two uracil bases were removed from ssDNA probe, generating apurinic/apyrimidinic (AP) sites. Then, the AP sites could inhibit the TSDR between ssDNA probe and hairpin probe, leaving the trigger sequence in ssDNA probe still free. Subsequently, the trigger sequence was annealed with the reporter probe, initiating the polymerization and nicking amplification reaction. As a result, numerous G-quadruplex (G4) structures were formed, which could bind with N-methyl-mesoporphyrin IX (NMM) to generate enhanced fluorescent signal. In the absence of UDG, the ssDNA probe could hybridize with the toehold domain of the hairpin probe to initiate TSDR, blocking the trigger sequence, and then the subsequent amplification reaction would not occur. The proposed strategy was successfully implemented for detecting UDG activity with a detection limit of 2.7×10(-5)U/mL. Moreover, the strategy could distinguish UDG well from other interference enzymes. Furthermore, the strategy was also applied for detecting UDG activity in HeLa cells lysate with low effect of cellular components. These results indicated that the proposed strategy offered a promising tool for sensitive quantification of UDG activity in UDG-related function study and disease prognosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Crystallization and preliminary X-ray diffraction analysis of three recombinant mutants of Vaccinia virus uracil DNA glycosylase

    PubMed Central

    Sartmatova, Darika; Nash, Taishayla; Schormann, Norbert; Nuth, Manunya; Ricciardi, Robert; Banerjee, Surajit; Chattopadhyay, Debasish

    2013-01-01

    Amino-acid residues located at a highly flexible area in the uracil DNA glycosylase of Vaccinia virus were mutated. In the crystal structure of wild-type D4 these residues lie at the dimer interface. Specifically, three mutants were generated: (i) residue Arg167 was replaced with an alanine (R167AD4), (ii) residues Glu171, Ser172 and Pro173 were substituted with three glycine residues (3GD4) and (iii) residues Glu171 and Ser172 were deleted (Δ171-172D4). Mutant proteins were expressed, purified and crystallized in order to investigate the effects of these mutations on the structure of the protein. PMID:23519808

  11. Crystallization and preliminary X-ray diffraction analysis of three recombinant mutants of Vaccinia virus uracil DNA glycosylase.

    PubMed

    Sartmatova, Darika; Nash, Taishayla; Schormann, Norbert; Nuth, Manunya; Ricciardi, Robert; Banerjee, Surajit; Chattopadhyay, Debasish

    2013-03-01

    Amino-acid residues located at a highly flexible area in the uracil DNA glycosylase of Vaccinia virus were mutated. In the crystal structure of wild-type D4 these residues lie at the dimer interface. Specifically, three mutants were generated: (i) residue Arg167 was replaced with an alanine (R167AD4), (ii) residues Glu171, Ser172 and Pro173 were substituted with three glycine residues (3GD4) and (iii) residues Glu171 and Ser172 were deleted (Δ171-172D4). Mutant proteins were expressed, purified and crystallized in order to investigate the effects of these mutations on the structure of the protein.

  12. Double proton transfer mechanism in the adenine-uracil base pair and spontaneous mutation in RNA duplex

    NASA Astrophysics Data System (ADS)

    Cerón-Carrasco, José P.; Requena, Alberto; Perpète, Eric A.; Michaux, Catherine; Jacquemin, Denis

    2009-12-01

    We study the mechanism of double proton transfer (DPT) in the adenine-uracil (AU) base pair, both in gas phase and under the influence of surrounding water molecules. According to our ab initio calculations, no stable proton transfer product exists in gas phase, while in solution, the DPT process may occur only through the catalysis of water molecules. Nevertheless, a thermodynamic analysis confirms that AU does not contribute to spontaneous mutation in RNA duplex, and thus guanine-cytosine (GC) would be the only base pair contributing to spontaneous mutation.

  13. Following Ultrafast Radiationless Relaxation Dynamics With Strong Field Dissociative Ionization: A Comparison Between Adenine, Uracil, and Cytosine

    SciTech Connect

    Kotur, Marija; Weinacht, Thomas C.; Zhou, Congyi; Matsika, Spiridoula

    2011-03-22

    We present the application of ultrafast time- and mass-resolved ion yield laser spectroscopy in conjunction with ab initio electronic structure calculations to track molecular excited-state dynamics. We discuss how molecular fragment ions can be associated with conformations the molecule assumes during its relaxation, and how various features of the pump-probe signal for those fragments can be used to infer details of the excited state dynamics. We present results for radiationless relaxation in DNA and RNA bases adenine, cytosine, and uracil in the gas phase, pumped near a one-photon resonance transition to an excited state, and probed via strong-field near-IR dissociative ionization.

  14. High-performance capillary electrophoretic method for the quantification of 5-methyl 2'-deoxycytidine in genomic DNA: application to plant, animal and human cancer tissues.

    PubMed

    Fraga, Mario F; Uriol, Esther; Borja Diego, L; Berdasco, María; Esteller, Manel; Cañal, María Jesús; Rodríguez, Roberto

    2002-06-01

    A new approach to the evaluation of the relative degree of genomic DNA methylation through the quantification of 2'-deoxynucleosides is proposed. Detection and quantification of 5-methyl 2'-deoxycytidine in genomic DNA has been performed using micellar high-performance capillary electrophoresis (HPCE) with UV-Vis detection. This approach has been demonstrated to be more sensitive and specific than other HPCE methods for the quantification of DNA methylation degree and also to be faster than other HPLC-based methods. The detection and quantification of nucleosides through enzymatic hydrolyses notably increases the specificity of the technique and allows its exploitation in the analysis of poorly purified and/or concentrated DNA samples such as those obtained from meristematic plant regions and paraffin-embedded tissues.

  15. 5-Methylation of Cytosine in CG:CG Base-Pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics

    NASA Astrophysics Data System (ADS)

    Yusufaly, Tahir; Olson, Wilma; Li, Yun

    2014-03-01

    Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile ``opening'' mode and two shear ``sliding'' and ``tearing'' modes in the orthogonal plane. The stacking interactions of the methyl groups are observed to globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. The results have implications for the epigenetic control of DNA mechanics.

  16. Synthesis, HPLC Enantioresolution, and X-ray Analysis of a New Series of C5-methyl Pyridazines as N-Formyl Peptide Receptor (FPR) Agonists

    PubMed Central

    Cilibrizzi, Agostino; Crocetti, Letizia; Giovannoni, Maria Paola; Graziano, Alessia; Vergelli, Claudia; Bartolucci, Gianluca; Soldani, Giacomo; Quinn, Mark T.; Schepetkin, Igor A.; Faggi, Cristina

    2015-01-01

    The synthesis of three racemates and the corresponding non chiral analogues of a C5-methyl pyridazine series is described here, as well as the isolation of pure enantiomers and their absolute configuration assignment. In order to obtain optically active compounds, direct chromatographic methods of separation by HPLC-UV were investigated using four chiral stationary phases (CSPs: Lux Amylose-2®, Lux Cellulose-1®, Lux Cellulose-2® and Lux Cellulose-3®). The best resolution was achieved using amylose tris(5-chloro-2-methylphenylcarbamate) (Lux Amylose-2®), and single enantiomers were isolated on a semipreparative scale with high enantiomeric excess, suitable for biological assays. The absolute configuration of optically active compounds was unequivocally established by X-ray crystallographic analysis and comparative chiral HPLC-UV profile. All compounds of the series were tested for formyl peptide receptor (FPR) agonist activity, and four were found to be active, with EC50 values in the micromolar range. PMID:23744588

  17. Crystal structure of (Z)-ethyl 3-[2-(5-methyl-7-nitro-1H-indole-2-carbon-yl)hydrazinyl-idene]butano-ate.

    PubMed

    Errossafi, Amal; El Kihel, Abdellatif; Guesmi, Salaheddine; Saadi, Mohamed; El Ammari, Lahcen

    2015-09-01

    The reaction of 5-methyl-7-nitro-1H-indole-2-carbohydrazide with ethyl aceto-acetate yielded the title mol-ecule, C16H18N4O5, in which the indole ring is almost planar, with the greatest deviation from the mean plane being 0.006 (2) Å. The nine atoms of the indole ring are almost perpendicular to the mean plane through the ethyl acetate group, as indicated by the dihedral angle of 87.02 (4)° between them. In the crystal, centrosymmetric supra-molecular dimers are formed via N-H⋯O hydrogen bonds and eight-membered amide {⋯HNCO}2 synthons. These are consolidated into a three-dimensional architecture by C-H⋯O contacts, and by π-π inter-actions between six-membered rings [inter-centroid distance = 3.499 (2) Å].

  18. Synthesis and crystal structure of copper complex of 7,16-bis(2-hydroxy-5-methyl-3-nitrobenzyl)-1,4,10,13-tetraoxa-7,16-diazacyclooctadecane

    NASA Astrophysics Data System (ADS)

    Ma, Shu-lan; Zhu, Wen-xiang

    2002-12-01

    A lariat crown ether compound 7,16-bis(2-hydroxy-5-methylbenzyl)-1,4,10,13-tetraoxa-7,16-diazacyclooctadecane has been prepared via one-pot Mannich reaction. A copper(II) complex with the ligand 7,16-bis(2-hydroxy-5-methyl-3-nitrobenzyl)-1,4,10,13-tetraoxa-7,16-diazacyclooctadecane was unexpectedly synthesized and characterized by elemental analysis, IR and UV spectra. The crystal structure of the complex has been determined by X-ray diffraction. Both crystal structure analysis and spectroscopy study indicated that the side-arm phenols of lariat crown ether are nitrated while complexing with Cu(NO 3) 2. Structure shows that the copper(II) ion is coordinated to two nitrogen and four oxygen atoms, two from the crown ether and other two from the deprotonated phenolate groups. The coordination polyhedron is a distorted octahedron.

  19. 5-Methyl-1-[(4-methyl-phen-yl)sulfon-yl]-1H-pyrazol-3-yl 4-methyl-benzene-sulfonate.

    PubMed

    Murtaza, Shahzad; Kausar, Naghmana; Tahir, M Nawaz; Tariq, Javaria; Bibi, Samaira

    2012-07-01

    In the title compound, C(18)H(18)N(2)O(5)S(2), the tolyl rings are oriented at a dihedral angle of 16.15 (11)° with respect to one another. The 5-methyl-1H-pyrazol-3-ol ring is roughly planar (r.m.s. deviation = 0.0231 Å) and subtends angles of 73.82 (8) and 89.85 (8)° with the tolyl rings. In the crystal, very weak π-π inter-actions between tolyl groups, with centroid-centroid distances of 4.1364 (19) and 4.0630 (16) Å, together with a C-H⋯π contact generate a three-dimensional network.

  20. 5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics.

    PubMed

    Yusufaly, Tahir I; Li, Yun; Olson, Wilma K

    2013-12-27

    van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile "opening" mode and two shear "sliding" and "tearing" modes in the orthogonal plane. The stacking interactions of the methyl groups globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. Additionally, the indirect effects of the methyl groups on possible base-pair steps neighboring CG:CG are observed to be of comparable importance to their direct effects on CG:CG. The results have implications for the epigenetic control of DNA mechanics.

  1. Altered trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-type glutamate receptors (AMPARs) in the striatum leads to behavioral changes in emotional responses.

    PubMed

    Lee, Young; Lee, Hojin; Kim, Hyung-Wook; Yoon, Bong-June

    2015-01-01

    The striatum receives and integrates multiple inputs from diverse areas in the brain and plays a critical role in the regulation of motor activity. However, whether the striatum is involved in the alteration of behavior in the presence of emotional challenges is unknown. Here, we examined whether alterations in the surface expression of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-type glutamate receptors (AMPARs) in the dorsal striatum would affect anxiety-related behaviors. We found that the transient expression of G1CT or G2CT, AMPAR-derived peptides, in the dorsomedial striatum led to decreased mobility in high-anxiety circumstances; however, the expression of these peptides in the dorsolateral striatum did not affect anxiety-related behavior. These data suggest that excitatory connections within the dorsomedial striatum play important roles in the control of motor actions in the presence of emotional challenges. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  2. Gas-phase reactions of nopinone, 3-isopropenyl-6-oxo-heptanal, and 5-methyl-5-vinyltetrahydrofuran-2-ol with OH, NO{sub 3}, and ozone

    SciTech Connect

    Calogirou, A.; Jensen, N.R.; Nielsen, C.J.; Kotzias, D.; Hjorth, J.

    1999-02-01

    In the troposphere, {alpha}-pinene, {beta}-pinene, limonene, and linalool are mainly oxidized to pinonaldehyde, nopinone, 3-isopropenyl-6-oxoheptanal (IPOH), and 5-methyl-5-vinyltetrahydrofuran-2-ol (MVT), respectively. The rate constant of the reactions of nopinone, IPOH, and MVT with OH, NO{sub 3}, and O{sub 3} were determined by long path FT-IR spectroscopy, and the oxidation products from the reactions between the OH radical and pinonaldehyde, nopinone, IPOH, and MVT were investigated using GC-MS and HPLC. The reaction rate constants (k) for the reactions have been determined at 740 {+-} 5 Torr and 298 {+-} 5 K, and a number of reaction products were identified. From the results obtained in this investigation and previous studies, it was concluded that a typical atmospheric lifetime with respect to chemical reactions was only a few hours for pinonaldehyde, IPOH, and MVT but was much longer for nopinone with a lifetime of about 10 h.

  3. Comparison of the redox chemistry of sulfur- and selenium-containing analogs of uracil.

    PubMed

    Payne, N Connor; Geissler, Andrew; Button, Aileen; Sasuclark, Alexandru R; Schroll, Alayne L; Ruggles, Erik L; Gladyshev, Vadim N; Hondal, Robert J

    2017-03-01

    Selenium is present in proteins in the form of selenocysteine, where this amino acid serves catalytic oxidoreductase functions. The use of selenocysteine in nature is strongly associated with redox catalysis. However, selenium is also found in a 2-selenouridine moiety at the wobble position of tRNA(Glu), tRNA(Gln) and tRNA(Lys). It is thought that the modifications of the wobble position of the tRNA improves the selectivity of the codon-anticodon pair as a result of the physico-chemical changes that result from substitution of sulfur and selenium for oxygen. Both selenocysteine and 2-selenouridine have widespread analogs, cysteine and thiouridine, where sulfur is used instead. To examine the role of selenium in 2-selenouridine, we comparatively analyzed the oxidation reactions of sulfur-containing 2-thiouracil-5-carboxylic acid (s(2)c(5)Ura) and its selenium analog 2-selenouracil-5-carboxylic acid (se(2)c(5)Ura) using (1)H-NMR spectroscopy, (77)Se-NMR spectroscopy, and liquid chromatography-mass spectrometry. Treatment of s(2)c(5)Ura with hydrogen peroxide led to oxidized intermediates, followed by irreversible desulfurization to form uracil-5-carboxylic acid (c(5)Ura). In contrast, se(2)c(5)Ura oxidation resulted in a diselenide intermediate, followed by conversion to the seleninic acid, both of which could be readily reduced by ascorbate and glutathione. Glutathione and ascorbate only minimally prevented desulfurization of s(2)c(5)Ura, whereas very little deselenization of se(2)c(5)Ura occurred in the presence of the same antioxidants. In addition, se(2)c(5)Ura but not s(2)c(5)Ura showed glutathione peroxidase activity, further suggesting that oxidation of se(2)c(5)Ura is readily reversible, while oxidation of s(2)c(5)Ura is not. The results of the study of these model nucleobases suggest that the use of 2-selenouridine is related to resistance to oxidative inactivation that otherwise characterizes 2-thiouridine. As the use of selenocysteine in proteins also

  4. Adjuvant Oral Uracil-Tegafur with Leucovorin for Colorectal Cancer Liver Metastases: A Randomized Controlled Trial

    PubMed Central

    Takayama, Tadatoshi; Miyagawa, Shinichi; Yamamoto, Junji; Ijichi, Masayoshi; Teruya, Masanori; Yoshimi, Fuyo; Kawasaki, Seiji; Koyama, Hiroto; Oba, Masaru; Takahashi, Michiro; Mizunuma, Nobuyuki; Watanabe, Toshiaki

    2016-01-01

    Background The high recurrence rate after surgery for colorectal cancer liver metastasis (CLM) remains a crucial problem. The aim of this trial was to evaluate the efficacy of adjuvant therapy with uracil-tegafur and leucovorin (UFT/LV). Methods In the multicenter, open-label, phase III trial, patients undergoing curative resection of CLM were randomly assigned in a 1:1 ratio to either the UFT/LV group or surgery alone group. The UFT/LV group orally received 5 cycles of adjuvant UFT/LV (UFT 300mg/m2 and LV 75mg/day for 28 days followed by a 7-day rest per cycle). The primary endpoint was recurrence-free survival (RFS). Secondary endpoints included overall survival (OS). Results Between February 2004 and December 2010, 180 patients (90 in each group) were enrolled into the study. Of these, 3 patients (2 in the UFT/LV group and 1 in the surgery alone group) were excluded from the efficacy analysis. Median follow-up was 4.76 (range, 0.15–9.84) years. The RFS rate at 3 years was higher in the UFT/LV group (38.6%, n = 88) than in the surgery alone group (32.3%, n = 89). The median RFS in the UFT/LV and surgery alone groups were 1.45 years and 0.70 years, respectively. UFT/LV significantly prolonged the RFS compared with surgery alone with the hazard ratio of 0.56 (95% confidence interval, 0.38–0.83; P = 0.003). The hazard ratio for death of the UFT/LV group against the surgery alone group was not significant (0.80; 95% confidence interval, 0.48–1.35; P = 0.409). Conclusion Adjuvant therapy with UFT/LV effectively prolongs RFS after hepatic resection for CLM and can be recommended as an alternative choice. Trial Registration UMIN Clinical Trials Registry C000000013 PMID:27588959

  5. 1-Benzyl derivatives of 5-(arylamino)uracils as anti-HIV-1 and anti-EBV agents.

    PubMed

    Novikov, Mikhail S; Buckheit, Robert W; Temburnikar, Kartik; Khandazhinskaya, Anastasia L; Ivanov, Alexander V; Seley-Radtke, Katherine L

    2010-12-01

    Pyrimidine analogs have long found use over a broad chemotherapeutic spectrum. In an effort to further explore the antiviral potential of several uracil derivatives previously synthesized in our laboratories, a series of benzylated pyrimidines were designed and synthesized. Introduction of the benzyl residue onto the 5-phenylaminouracil scaffold was carried out using 2,4-bis(trimethylsilyloxy)pyrimidine with the corresponding benzyl bromides. Similarly, 1-benzyl-5-(benzylamino)- and 1-benzyl-5-(phenethylamino)uracils were obtained via amination of 1-benzyl-5-bromouracils with benzylamine or phenylethylamine. The results of the broad screen antiviral studies revealed that compounds 5 and 11 exhibit promising inhibitory activity against HIV-1 in CEM-SS culture. A 50% protective effect was observed at concentrations of 11.9 and 9.5 μМ, respectively. Moreover, compounds 8 and 3 exhibited good inhibitory effects against EBV in АKАТА cell culture with EC₅₀ values of 2.3 and 12 μM, respectively. The synthesis and biological studies are detailed herein. Copyright © 2010 Elsevier Ltd. All rights reserved.

  6. Molecular recognition and interaction between uracil and urea in solid-state studied by terahertz time-domain spectroscopy.

    PubMed

    Yang, Jingqi; Li, Shaoxian; Zhao, Hongwei; Song, Bo; Zhang, Guoxin; Zhang, Jianbing; Zhu, Yiming; Han, Jiaguang

    2014-11-20

    Using terahertz time-domain spectroscopy characterization, we observe that urea is able to recognize and interact with uracil efficiently even in the solid phase without involving water or solvents. A cocrystal configuration linked by a pair of hydrogen bonds between uracil and urea was formed. The terahertz absorption spectrum of the cocrystal shows a distinct new absorption at 0.8 THz (26.7 cm(-1)), which originates from the intermolecular hydrogen bonding. Both mechanical milling and heating can accelerate the reaction efficiently. Density functional theory was adopted to simulate the vibrational modes of the cocrystal, and the results agree well with the experimental observation. Multiple techniques, including powder X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy, were performed to investigate the reaction process, and they presented supportive evidence. This work enables in-depth understanding of recognition and interaction of urea with nucleobases and comprehension of the denaturation related to RNA. We also demonstrate that terahertz spectroscopy is an effective and alternative tool for online measurement and quality control in pharmaceutical and chemical industries.

  7. Exploration of acetanilide derivatives of 1-(ω-phenoxyalkyl)uracils as novel inhibitors of Hepatitis C Virus replication

    PubMed Central

    Magri, Andrea; Ozerov, Alexander A.; Tunitskaya, Vera L.; Valuev-Elliston, Vladimir T.; Wahid, Ahmed; Pirisi, Mario; Simmonds, Peter; Ivanov, Alexander V.; Novikov, Mikhail S.; Patel, Arvind H.

    2016-01-01

    Hepatitis C Virus (HCV) is a major public health problem worldwide. While highly efficacious directly-acting antiviral agents have been developed in recent years, their high costs and relative inaccessibility make their use limited. Here, we describe new 1-(ω-phenoxyalkyl)uracils bearing acetanilide fragment in 3 position of pyrimidine ring as potential antiviral drugs against HCV. Using a combination of various biochemical assays and in vitro virus infection and replication models, we show that our compounds are able to significantly reduce viral genomic replication, independently of virus genotype, with their IC50 values in the nanomolar range. We also demonstrate that our compounds can block de novo RNA synthesis and that effect is dependent on a chemical structure of the compounds. A detailed structure-activity relationship revealed that the most active compounds were the N3-substituted uracil derivatives containing 6-(4-bromophenoxy)hexyl or 8-(4-bromophenoxy)octyl fragment at N1 position. PMID:27406141

  8. Antihypertensive Effect of a Combination of Uracil and Glycerol Derived from Lactobacillus plantarum Strain TWK10-Fermented Soy Milk.

    PubMed

    Liu, Yi-Yen; Zeng, Shih-Yu; Leu, Yann-Lii; Tsai, Tsung-Yu

    2015-08-26

    We previously demonstrated that angiotensin-converting enzyme (ACE) could be inhibited by soy milk that had been fermented with the Lactobacillus plantarum strain TWK10, suggesting great potential for the development of antihypertensive products. In this work, the bioactive ACE inhibitors in TWK10-fermented soy milk water extracts were isolated, and a combination of uracil and glycerol (CUG) was identified as one of the ACE inhibitors. We then examined the physiological effects of CUG treatment in short-term and long-term studies using spontaneously hypertensive rats (SHRs) as an experimental model. The results revealed that the fermented soy milk extracts and CUG decreased blood pressure by 11.97 ± 3.71 to 19.54 ± 9.54 mmHg, 8 h after oral administration, and exhibited antihypertensive effects in SHRs in a long-term study. In addition, CUG was shown to decrease blood pressure by suppressing either the renin activity or the ACE activity and, thus, decreasing the downstream vasoconstricting peptide angiotensin II and the hormone aldosterone. CUG also promoted nitric oxide production, resulting in vasodilation and further improvement to hypertension. This important finding suggests that TWK10-fermented soy milk and its functional ingredients, uracil and glycerol, exhibit antihypertensive effects via multiple pathways and provide a healthier and more natural antihypertensive functional food.

  9. Model Uracil-Rich RNAs and Membrane Protein mRNAs Interact Specifically with Cold Shock Proteins in Escherichia coli.

    PubMed

    Benhalevy, Daniel; Bochkareva, Elena S; Biran, Ido; Bibi, Eitan

    2015-01-01

    Are integral membrane protein-encoding mRNAs (MPRs) different from other mRNAs such as those encoding cytosolic mRNAs (CPRs)? This is implied from the emerging concept that MPRs are specifically recognized and delivered to membrane-bound ribosomes in a translation-independent manner. MPRs might be recognized through uracil-rich segments that encode hydrophobic transmembrane helices. To investigate this hypothesis, we designed DNA sequences encoding model untranslatable transcripts that mimic MPRs or CPRs. By utilizing in vitro-synthesized biotinylated RNAs mixed with Escherichia coli extracts, we identified a highly specific interaction that takes place between transcripts that mimic MPRs and the cold shock proteins CspE and CspC, which are normally expressed under physiological conditions. Co-purification studies with E. coli expressing 6His-tagged CspE or CspC confirmed that the specific interaction occurs in vivo not only with the model uracil-rich untranslatable transcripts but also with endogenous MPRs. Our results suggest that the evolutionarily conserved cold shock proteins may have a role, possibly as promiscuous chaperons, in the biogenesis of MPRs.

  10. Rational design of a solvatochromic fluorescent uracil analogue with a dual-band ratiometric response based on 3-hydroxychromone.

    PubMed

    Dziuba, Dmytro; Karpenko, Iuliia A; Barthes, Nicolas P F; Michel, Benoît Y; Klymchenko, Andrey S; Benhida, Rachid; Demchenko, Alexander P; Mély, Yves; Burger, Alain

    2014-02-10

    Fluorescent nucleoside analogues with strong and informative responses to their local environment are in urgent need for DNA research. In this work, the design, synthesis and investigation of a new solvatochromic ratiometric fluorophore compiled from 3-hydroxychromones (3HCs) and uracil fragments are reported. 3HC dyes are a class of multi-parametric, environment-sensitive fluorophores providing a ratiometric response due to the presence of two well-resolved bands in their emission spectra. The synthesized conjugate demonstrates not only the preservation but also the improvement of these properties. The absorption and fluorescence spectra are shifted to longer wavelengths together with an increase of brightness. Moreover, the two fluorescence bands are better resolved and provide ratiometric responses across a broader range of solvent polarities. To understand the photophysical properties of this new fluorophore, a series of model compounds were synthesized and comparatively investigated. The obtained data indicate that uracil and 3HC fragments of this derivative are coupled into an electronic conjugated system, which on excitation attains strong charge-transfer character. The developed fluorophore is a prospective label for nucleic acids. Abstract in Ukrainian: . Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations.

    PubMed

    Aranda, Juan; Francés-Monerris, Antonio; Tuñón, Iñaki; Roca-Sanjuán, Daniel

    2017-09-28

    Oxidation of nucleic acids is ubiquitous in living beings under metabolic impairments and/or exposed to external agents such as radiation, pollutants, or drugs, playing a central role in the development of many diseases mediated by DNA/RNA degeneration. Great efforts have been devoted to unveil the molecular mechanisms behind the OH radical additions to the double bonds of nucleobases; however, the specific role of the biological environment remains relatively unexplored. The present contribution tackles the study of the OH radical addition to uracil from the gas phase to a full RNA macromolecule by means of quantum-chemistry methods combined with molecular dynamics simulations. It is shown that, in addition to the intrinsic reactivity of each position driven by the electronic effects, the presence of bridge water molecules intercalated into the RNA structure favors the addition to the C5 position of uracil in biological conditions. The results also suggest that diffusion of the OH radical does not play a relevant role in the regioselectivity of the reaction, which is mainly controlled at the chemical stage of the addition process.

  12. Cell cycle regulation as a mechanism for functional separation of the apparently redundant uracil DNA glycosylases TDG and UNG2

    PubMed Central

    Hardeland, Ulrike; Kunz, Christophe; Focke, Frauke; Szadkowski, Marta; Schär, Primo

    2007-01-01

    Human Thymine-DNA Glycosylase (TDG) is a member of the uracil DNA glycosylase (UDG) superfamily. It excises uracil, thymine and a number of chemical base lesions when mispaired with guanine in double-stranded DNA. These activities are not unique to TDG; at least three additional proteins with similar enzymatic properties are present in mammalian cells. The successful co-evolution of these enzymes implies the existence of non-redundant biological functions that must be coordinated. Here, we report cell cycle regulation as a mechanism for the functional separation of apparently redundant DNA glycosylases. We show that cells entering S-phase eliminate TDG through the ubiquitin–proteasome system and then maintain a TDG-free condition until G2. Incomplete degradation of ectopically expressed TDG impedes S-phase progression and cell proliferation. The mode of cell cycle regulation of TDG is strictly inverse to that of UNG2, which peaks in and throughout S-phase and then declines to undetectable levels until it appears again just before the next S-phase. Thus, TDG- and UNG2-dependent base excision repair alternates throughout the cell cycle, and the ubiquitin–proteasome pathway constitutes the underlying regulatory system. PMID:17526518

  13. A DFT analysis of the molecular structure, vibrational spectra and other molecular properties of 5-nitrouracil and comparison with uracil

    NASA Astrophysics Data System (ADS)

    Kattan, D.; Alcolea Palafox, M.; Rathor, S. K.; Rastogi, V. K.

    2016-02-01

    The four unit cells found in the crystals of the biomolecule 5-Nitrouracil were simulated as tetramer forms by density functional calculations. Four tetramer forms were fully optimized. Specific scale factors and scaling equations deduced from uracil molecule were employed in the predicted wavenumbers of 5-nitrouracil. The experimental FT-Raman and FT-IR spectra were recorded in the solid state. Comprehensive interpretation of the experimental FT-IR and FT-Raman spectra of the compound under study in the solid state is based on potential energy distribution. A good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. A complete vibrational assignment in the isolated state was also carried out aided by the theoretical harmonic frequency analysis and the results compared with those reported in Ar matrix. The scaled wavenumbers were used in the reassignment of several experimental bands. A comparison between the molecular structure and charge distribution of 5-Nitrouracil with related 5-uracil derivatives was presented. The effect of the nitro substitution in the 5th position of the pyrimidine ring was evaluated.

  14. Antiviral and Cytostatic Evaluation of 5-(1-Halo-2-sulfonylvinyl)- and 5-(2-Furyl)uracil Nucleosides.

    PubMed

    Wen, Zhiwei; Suzol, Sazzad H; Peng, Jufang; Liang, Yong; Snoeck, Robert; Andrei, Graciela; Liekens, Sandra; Wnuk, Stanislaw F

    2017-04-01

    Transition metal-catalyzed halosulfonylation of 5-ethynyl uracil nucleosides provided (E)-5-(1-chloro-2-tosylvinyl)uridines. Tetrabutylammonium fluoride-mediated direct CH arylation of 5-iodouracil nucleosides with furan or 2-heptylfuran gave 5-furyl-substituted nucleosides without the necessity of using the organometallic substrates. These two classes of 5-substituted uracil nucleosides as well their corresponding ester derivatives were tested against a broad range of DNA and RNA viruses and the human immunodeficiency virus (HIV). The 3',5'-di-O-acetyl-5-(E)-(1-chloro-2-tosylvinyl)-2'-deoxyuridine (24) inhibited the growth of L1210, CEM and HeLa cancer cells in the lower micromolar range. The (β-chloro)vinyl sulfone 24 and 5-(5-heptylfur-2-yl)-2'-deoxyuridine (10) displayed micromolar activity against varicella zoster virus (VZV). The 5-(5-heptylfur-2-yl) analog 10 and its 3',5'-di-O-acetyl-protected derivative showed similar activity against the cytomegalovirus (CMV). The 5-(fur-2-yl) derivatives of 2'-deoxyuridine and arabino-uridine inhibited the replication of herpes simplex virus (HSV) TK(+) strains while the 5-(5-heptylfur-2-yl) derivative 10 displayed antiviral activity against the parainfluenza virus. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Comparison of the effects of UV irradiation on 5-methyl-substituted and unsubstituted pyrimidines in alternating pyrimidine-purine sequences in DNA.

    PubMed

    Zuo, S; Boorstein, R J; Cunningham, R P; Teebor, G W

    1995-09-12

    We previously demonstrated the UV-induced formation of cytosine hydrate in DNA and its deamination product, uracil hydrate, via their release from the DNA backbone by the DNA glycosylase activity of Escherichia coli endonuclease III. Subsequently, endonuclease III-mediated release of thymine hydrate from UV-irradiated poly(dA-dT) was reported. Therefore, we asked whether 5-methylcytosine residues in DNA underwent photohydration and deamination to thymine hydrate in analogy to UV-induced deamination of cytosine. An alternating DNA copolymer containing 5-methylcytosine was irradiated with UVC and incubated with endonuclease III. No 5-methylcytosine hydrate was released. Instead, UV-induced nonenzymatic release of 5-methylcytosine occurred. Similarly, incubation of UV-irradiated poly(dA-dT) with endonuclease III did not release thymine hydrate; nonenzymatic release of thymine occurred. Nonenzymatic release of 5-methylpyrimidines was oxygen dependent, enhanced by ferric ion and inhibited by free radical scavengers. In contrast, photohydration of cytosine was oxygen independent, and only small amounts of cytosine were nonenzymatically released. Thus, 5-methylpyrimidine residues within alternating Pu-Py sequences in DNA do not undergo photohydration, but instead undergo cleavage of their N-glycosyl bonds yielding abasic (AP) sites. The inability to repair such AP sites may explain the UV sensitivity of E. coli xthnfo mutants, which lack AP endonuclease activity. We suggest that N-glycosyl bond cleavage is mediated by radical species formed via transfer of an electron from UV-excited triplet 5-methylpyrimidines to ground state oxygen and/or ferric ions.

  16. The impact of solvent polarity on intramolecular proton and electron transfer in 2-alkylamino-4-nitro-5-methyl pyridine N-oxides.

    PubMed

    Szemik-Hojniak, A; Wiśniewski, Łukasz; Deperasińska, Irena; Makarewicz, Artur; Jerzykiewicz, Lucjan; Puszko, Aniela; Erez, Yuval; Huppert, Dan

    2012-06-14

    The crystal structure of 2-butylamino-4-nitro-5-methyl pyridine N-oxide (2B5M) and solution studies of both 2B5M and 2-methylamino-4-nitro-5-methyl pyridine (2M5M) N-oxide are presented. Steady-state absorption and emission measurements were employed for both molecules while a picosecond fluorescence up-conversion technique was used to follow the dynamic behavior of the 2M5M system. The experimental methods were complemented by DFT and TD DFT B3LYP/6-31G(d,p) calculations involving ground and excited-state optimization which in the case of the smaller 2M5M molecule were extended to the CAM-B3LYP/6-31G(d,p) method. The solvent effect is incorporated by applying the polarizable continuum (PCM) model. The data reveal that the 2B5M molecule crystallizes in the monoclinic space group P2(1)/c and its crystal lattice is composed of monomers with intramolecular N-H···O [2.572(3) Å] hydrogen bonds, connected into a polymer network by weak intermolecular C-H…O [3.2-3.4 Å]-type interactions. Quantum-chemical calculations show that the aminoalkyl substitutent in aminoalkyl-pyridine N-oxides is a specific determinant of the CT nature of the lowest-lying excited electronic ππ* state, distinguishing them from other nitroaromatic compounds. The results of both picosecond fluorescence up-conversion experiments in different solvents and quantum-chemical calculations suggest that in nonpolar media the ESIPT process in 2M5M is favored, while in polar acetonitrile, the N* → PT* transition demands barrier-crossing and thus unfavorable thermodynamic conditions do not allow the ESIPT to occur. The signals of picosecond fluorescence up-conversion of 2M5M are solvent- and emission-wavelength dependent. The three time components found in a weakly polar isooctane-dioxane mixture have been attributed to solvation dynamics (∼500 fs), and to relaxation of N* and PT* forms while in acetonitrile, a very rapid fluorescence decay with a time constant (2.3-4.0 ps) indicative of the

  17. Poly[[di-aqua-deca-μ2-cyanido-κ(20) C:N-hexa-cyanido-κ(6) C-bis-(μ2-5-methyl-pyrimidine-κ(2) N:N')bis-(5-methyl-pyrimidine-κN)tricopper(II)ditungstate(V)] dihydrate].

    PubMed

    Tsunobuchi, Yoshihide; Kaneko, Souhei; Nakabayashi, Koji; Ohkoshi, Shin-Ichi

    2014-02-01

    In the title complex, {[Cu3[W(CN)8]2(C5H6N2)4(H2O)2]·2H2O} n , the coordination polyhedron of the eight-coordinated W(V) atom is a bicapped trigonal prism, in which five CN groups are bridged to Cu(II) ions, and the other three CN groups are terminally bound. Two of the Cu(II) ions lie on a centre of inversion and each of the three independent Cu(II) cations is pseudo-octahedrally coordinated. In the crystal structure, cyanido-bridged-Cu-W-Cu layers are linked by pillars involving the third independent Cu(II) ion, generating a three-dimensional network with non-coordinating water mol-ecules and 5-methyl-pyrimidine mol-ecules. O-H⋯O and O-H⋯N hydrogen bonds involve the coordinating and non-coordin-ating water mol-ecules, the CN groups and the 5-methyl-pyrimidine mol-ecules.

  18. Non-canonical uracil processing in DNA gives rise to double-strand breaks and deletions: relevance to class switch recombination

    PubMed Central

    Bregenhorn, Stephanie; Kallenberger, Lia; Artola-Borán, Mariela; Peña-Diaz, Javier; Jiricny, Josef

    2016-01-01

    During class switch recombination (CSR), antigen-stimulated B-cells rearrange their immunoglobulin constant heavy chain (CH) loci to generate antibodies with different effector functions. CSR is initiated by activation-induced deaminase (AID), which converts cytosines in switch (S) regions, repetitive sequences flanking the CH loci, to uracils. Although U/G mispairs arising in this way are generally efficiently repaired to C/Gs by uracil DNA glycosylase (UNG)-initiated base excision repair (BER), uracil processing in S-regions of activated B-cells occasionally gives rise to double strand breaks (DSBs), which trigger CSR. Surprisingly, genetic experiments revealed that CSR is dependent not only on AID and UNG, but also on mismatch repair (MMR). To elucidate the role of MMR in CSR, we studied the processing of uracil-containing DNA substrates in extracts of MMR-proficient and –deficient human cells, as well as in a system reconstituted from recombinant BER and MMR proteins. Here, we show that the interplay of these repair systems gives rise to DSBs in vitro and to genomic deletions and mutations in vivo, particularly in an S-region sequence. Our findings further suggest that MMR affects pathway choice in DSB repair. Given its amenability to manipulation, our system represents a powerful tool for the molecular dissection of CSR. PMID:26743004

  19. Synthesis and Potency of Novel Uracil Nucleotides and Derivatives as P2Y2 and P2Y6 Receptor Agonists

    PubMed Central

    Ko, Hyojin; Carter, Rhonda L.; Cosyn, Liesbet; Petrelli, Riccardo; de Castro, Sonia; Besada, Pedro; Zhou, Yixing; Cappellacci, Loredana; Franchetti, Palmarisa; Grifantini, Mario; Van Calenbergh, Serge; Harden, T. Kendall; Jacobson, Kenneth A.

    2008-01-01

    The phosphate, uracil, and ribose moieties of uracil nucleotides were varied structurally for evaluation of agonist activity at the human P2Y2, P2Y4, and P2Y6 receptors. The 2-thio modification, found previously to enhance P2Y2 receptor potency, could be combined with other favorable modifications to produce novel molecules that exhibit high potencies and receptor selectivities. Phosphonomethylene bridges introduced for stability in analogues of UDP, UTP and uracil dinucleotides markedly reduced potency. Truncation of dinucleotide agonists of the P2Y2 receptor, in the form of Up4-sugars, indicated that a terminal uracil ring is not essential for moderate potency at this receptor and that specific SAR patterns are observed at this distal end of the molecule. Key compounds reported in this study include: 9, α,β-methylene-UDP, a P2Y6 receptor agonist; 30, Up4-phenyl ester and 34, Up4-[1]glucose, selective P2Y2 receptor agonists; 43, the 2-thio analogue of INS37217 (P1-(uridine 5′)-P4- (2′-deoxycytidine 5′) tetraphosphate), a potent and selective P2Y2 receptor agonist. PMID:18514530

  20. Analysis of the impact of a uracil DNA glycosylase attenuated in AP-DNA binding in maintenance of the genomic integrity in Escherichia coli

    PubMed Central

    Bharti, Sanjay Kumar; Varshney, Umesh

    2010-01-01

    Uracil DNA glycosylase (Ung) initiates the uracil excision repair pathway. We have earlier characterized the Y66W and Y66H mutants of Ung and shown that they are compromised by ∼7- and ∼170-fold, respectively in their uracil excision activities. In this study, fluorescence anisotropy measurements show that compared with the wild-type, the Y66W protein is moderately compromised and attenuated in binding to AP-DNA. Allelic exchange of ung in Escherichia coli with ung::kan, ungY66H:amp or ungY66W:amp alleles showed ∼5-, ∼3.0- and ∼2.0-fold, respectively increase in mutation frequencies. Analysis of mutations in the rifampicin resistance determining region of rpoB revealed that the Y66W allele resulted in an increase in A to G (or T to C) mutations. However, the increase in A to G mutations was mitigated upon expression of wild-type Ung from a plasmid borne gene. Biochemical and computational analyses showed that the Y66W mutant maintains strict specificity for uracil excision from DNA. Interestingly, a strain deficient in AP-endonucleases also showed an increase in A to G mutations. We discuss these findings in the context of a proposal that the residency of DNA glycosylase(s) onto the AP-sites they generate shields them until recruitment of AP-endonucleases for further repair. PMID:20056657

  1. Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase

    PubMed Central

    Roberts, Victoria A.; Pique, Michael E.; Hsu, Simon; Li, Sheng; Slupphaug, Geir; Rambo, Robert P.; Jamison, Jonathan W.; Liu, Tong; Lee, Jun H.; Tainer, John A.; Ten Eyck, Lynn F.; Woods, Virgil L.

    2012-01-01

    X-ray crystallography provides excellent structural data on protein–DNA interfaces, but crystallographic complexes typically contain only small fragments of large DNA molecules. We present a new approach that can use longer DNA substrates and reveal new protein–DNA interactions even in extensively studied systems. Our approach combines rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). DXMS identifies solvent-exposed protein surfaces; docking is used to create a 3-dimensional model of the protein–DNA interaction. We investigated the enzyme uracil-DNA glycosylase (UNG), which detects and cleaves uracil from DNA. UNG was incubated with a 30 bp DNA fragment containing a single uracil, giving the complex with the abasic DNA product. Compared with free UNG, the UNG–DNA complex showed increased solvent protection at the UNG active site and at two regions outside the active site: residues 210–220 and 251–264. Computational docking also identified these two DNA-binding surfaces, but neither shows DNA contact in UNG–DNA crystallographic structures. Our results can be explained by separation of the two DNA strands on one side of the active site. These non-sequence-specific DNA-binding surfaces may aid local uracil search, contribute to binding the abasic DNA product and help present the DNA product to APE-1, the next enzyme on the DNA-repair pathway. PMID:22492624

  2. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-methyluracil (thymine).

    PubMed

    Singh, J S

    2015-02-25

    FT-IR (400-4000 cm(-1)) and Raman spectra (200-4000 cm(-1)) of uracil and 5-methyluracil (thymine) have been recorded and analyzed. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-methyluracil (thymine) by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, most of the B3LYP/6-311++G(∗∗) vibrational frequencies are in excellent agreement with the available experimental assignments and helped to propose in the reassignments of some missing frequencies in experimental study. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a') and non-planar (a″) for all 39 normal vibrational modes of 5-methyluracil are given by 26a'+13a″, of which 30 modes (21a'+9a″) correspond to the uracil moiety and 9 modes (5a'+4a″) to the CH3 group. Consistent assignments have been made for the internal modes of CH3 group, especially for the anti-symmetric CH3 stretching and bending modes. A possible explanation could be the planarity of pyrimidine ring and non-planarity at carbon site of methyl group which might cause the splitting of frequencies including three components due to the substitution of CH3 group at the site of C5 atom on pyrimidine ring of uracil. The three non-equivalent CH bonds of CH3 group are

  3. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-methyluracil (thymine)

    NASA Astrophysics Data System (ADS)

    Singh, J. S.

    2015-02-01

    FT-IR (400-4000 cm-1) and Raman spectra (200-4000 cm-1) of uracil and 5-methyluracil (thymine) have been recorded and analyzed. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-methyluracil (thymine) by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, most of the B3LYP/6-311++G∗∗ vibrational frequencies are in excellent agreement with the available experimental assignments and helped to propose in the reassignments of some missing frequencies in experimental study. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a‧) and non-planar (a″) for all 39 normal vibrational modes of 5-methyluracil are given by 26a‧ + 13a″, of which 30 modes (21a‧ + 9a″) correspond to the uracil moiety and 9 modes (5a‧ + 4a″) to the CH3 group. Consistent assignments have been made for the internal modes of CH3 group, especially for the anti-symmetric CH3 stretching and bending modes. A possible explanation could be the planarity of pyrimidine ring and non-planarity at carbon site of methyl group which might cause the splitting of frequencies including three components due to the substitution of CH3 group at the site of C5 atom on pyrimidine ring of uracil. The three non-equivalent CH bonds of CH3

  4. Photoelectron spectrum of valence anions of uracil and first-principles calculations of excess electron binding energies

    NASA Astrophysics Data System (ADS)

    Bachorz, Rafał A.; Klopper, Wim; Gutowski, Maciej; Li, Xiang; Bowen, Kit H.

    2008-08-01

    The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree-Fock and second-order Møller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within +/-1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of ~-0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.

  5. Photoelectron spectrum of valence anions of uracil and first-principles calculations of excess electron binding energies.

    PubMed

    Bachorz, Rafał A; Klopper, Wim; Gutowski, Maciej; Li, Xiang; Bowen, Kit H

    2008-08-07

    The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree-Fock and second-order Moller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within +/-1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of approximately -0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.

  6. Photoelectron Spectrum of Valence Anions of Uracil and First-principles Calculations of Excess Electron Binding Energies

    SciTech Connect

    Bachorz, Rafal A.; Klopper, Willem M.; Gutowski, Maciej S.; Li, Xiang; Bowen, Kit H.

    2008-08-05

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree–Fock and second-order Møller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within ±1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of ≈-0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics

  7. Synthesis and properties of oligonucleotides containing 4-thiothymidine, 5-methyl-2-pyrimidinone-1-beta-D(2'-deoxyriboside) and 2-thiothymidine.

    PubMed Central

    Connolly, B A; Newman, P C

    1989-01-01

    Methods are given for the synthesis of derivatives of 4-thiothymidine (4ST), 5-methyl-2-pyrimidinone-1-beta-D(2'-deoxyriboside) (4HT) and 2-thiothymidine (2ST) suitable for incorporation into oligodeoxynucleotides by the cyanoethyl phosphoramidite method. 4HT and 2ST are incorporated with no base protection but the sulphur atom in 4ST is protected with an S-sulphenylmethyl (-SCH3) function. This can be removed with dithiothreitol after synthesis. These T analogues have been incorporated into GACGATATCGTC, a self-complementary dodecamer containing the Eco RV recognition site (underlined), in place of the two T residues within this site. Although pure dodecamers are obtained in each case the syntheses are not as efficient as those seen when normal unmodified bases are used mainly due to the chemical reactivity of 4ST, 4HT and 2ST. Some of the chemical properties of oligonucleotides containing these bases (reactivity towards NH3) as well as their physical properties (melting temperatures, U.V., fluorescence and circular dichroism spectra) have been determined and are discussed. PMID:2762115

  8. The chemokine growth-related gene product β protects rat cerebellar granule cells from apoptotic cell death through α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptors

    PubMed Central

    Limatola, Cristina; Ciotti, Maria Teresa; Mercanti, Delio; Vacca, Fabrizio; Ragozzino, Davide; Giovannelli, Aldo; Santoni, Angela; Eusebi, Fabrizio; Miledi, Ricardo

    2000-01-01

    Cultured cerebellar granule neurons are widely used as a cellular model to study mechanisms of neuronal cell death because they undergo programmed cell death when switched from a culture medium containing 25 mM to one containing 5 mM K+. We have found that the growth-related gene product β (GROβ) partially prevents the K+-depletion-induced cell death, and that the neuroprotective action of GROβ on granule cells is mediated through the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) type of ionotropic glutamate receptors. GROβ-induced survival was suppressed by 6-cyano-7-nitroquinoxaline-2,3-dione, which is a specific antagonist of AMPA/kainate receptors; it was not affected by the inhibitor of N-methyl-d-aspartate receptors, 2-amino-5-phosphonopentanoic acid, and was comparable to the survival of granule cells induced by AMPA (10 μM) treatment. Moreover, GROβ-induced neuroprotection was abolished when granule cells were treated with antisense oligonucleotides specific for the AMPA receptor subunits, which significantly reduced receptor expression, as verified by Western blot analysis with subunit-specific antibodies and by granule cell electrophysiological sensitivity to AMPA. Our data demonstrate that GROβ is neurotrophic for cerebellar granule cells, and that this activity depends on AMPA receptors. PMID:10811878

  9. Mercury(II) complexes with 5-methyl-5-(4-pyridyl)-2,4-imidazolidenedione: Synthesis, structural characterization, and theoretical studies

    NASA Astrophysics Data System (ADS)

    Sabounchei, Seyyed Javad; Shahriary, Parisa; Salehzadeh, Sadegh; Gholiee, Yasin; Khavasi, Hamid Reza

    2013-11-01

    New Hg(II) complexes with 5-methyl-5-(4-pyridyl)-2,4-imidazolidenedione (L) and various halogen ions were synthesized. Based on elemental analysis and flame atomic absorption spectroscopy, complexes have general formula HgL2X2 (X = Cl- (1), Br- (2), and I- (3)). These compounds have been studied by IR, 1H and 13C NMR spectroscopy at room temperature. According to X-ray diffraction analysis, complex 2 crystallizes in monoclinic system. Hg(II) ion has been surrounded by a distorted tetrahedral arrangement of two monodentate ligands (each one coordinating by a Npyridine ring atom) and two bromine atoms. Based on crystal packing findings, intermolecular classical H-bonds of the type Nsbnd H⋯O and non-classical H-bonds of the type Csbnd H⋯O and Csbnd H⋯Br, as an important member of noncovalent interaction family, are driving forces for the formation of a very distorted structure. Theoretical studies showed that neither the size of the halide anion nor the intramolecular interactions between two ligands are the reason for the very small Nsbnd Hgsbnd N bond angle, observed in complex 2.

  10. Modulation of DL-. alpha. -amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid/quisqualate receptors by phospholipase A sub 2 : A necessary step in long-term potentiation

    SciTech Connect

    Massicotte, G.; Baudry, M. ); Vanderklish, P.; Lynch, G. )

    1991-03-01

    The effects of kainate (KA)-induced epileptic seizures on the binding properites of hippocampal glutamate receptors, on the modulation of DL-{alpha}-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)/quisqualate receptor by phospholipase A{sub 2} (PLA{sub 2}), and on the formation of long-term potentiation (LTP) were studied in hippocampal membranes and hippocampal slices. Systemic administration of KA produced specific changes in the binding properties of the AMPA/quisqualate receptors and its regulation. Whereas the binding of various ligands to the N-methyl-D-aspartate receptors was not modified by KA treatment, there was a singificant decrease in the maximal number of binding sites for ({sup 3}H)AMPA. The loss of LTP was not due to changes in postsynaptic responses elicited by the bursts that trigger the potentiation effect, thus suggesting that KA treatment disrupts processes that follow N-methyl-D-aspartate receptor activation. Systemic administration of KA was associated with calpain activation as the amount of spectrin breakdown products was increased severalfold in hippocampus but not in cerebellum. Pretreatment of telencephalic membranes with calpain greatly reduced the PLA{sub 2}-induced increase in ({sup 3}H)AMPA binding. The results provide evidence in favor of an essential role of PLA{sub 2} in the development of LTP and suggest that the order of activation of different calcium-dependent processes is critical for producing the final changes underlying LTP.

  11. The role of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in depression: central mediators of pathophysiology and antidepressant activity?

    PubMed

    Freudenberg, Florian; Celikel, Tansu; Reif, Andreas

    2015-05-01

    Depression is a major psychiatric disorder affecting more than 120 million people worldwide every year. Changes in monoaminergic transmitter release are suggested to take part in the pathophysiology of depression. However, more recent experimental evidence suggests that glutamatergic mechanisms might play a more central role in the development of this disorder. The importance of the glutamatergic system in depression was particularly highlighted by the discovery that N-methyl-D-aspartate (NMDA) receptor antagonists (particularly ketamine) exert relatively long-lasting antidepressant like effects with rapid onset. Importantly, the antidepressant-like effects of NMDA receptor antagonists, but also other antidepressants (both classical and novel), require activation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Additionally, expression of AMPA receptors is altered in patients with depression. Moreover, preclinical evidence supports an important involvement of AMPA receptor-dependent signaling and plasticity in the pathophysiology and treatment of depression. Here we summarize work published on the involvement of AMPA receptors in depression and discuss a possible central role for AMPA receptors in the pathophysiology, course and treatment of depression.

  12. Induction of tolerance to poison ivy urushiol in the guinea pig by epicutaneous application of the structural analog 5-methyl-3-n-pentadecylcatechol.

    PubMed

    Stampf, J L; Benezra, C; Byers, V; Castagnoli, N

    1986-05-01

    Previous studies have established that epicutaneous application of 5-methyl-3-n-pentadecylcatechol (5-Me-PDC), a synthetic analog of a poison ivy urushiol component, leads to immune tolerance to 3-n-pentadecylcatechol (PDC) in mice. The induction of tolerance by 5-Me-PDC may be mediated by a protein conjugate formed via selective reaction of thiol nucleophiles present on the carrier macromolecule with the corresponding o-quinone derived from the parent catechol. In order to examine further the tolerogenic properties of 5-Me-PDC, we have extended our studies to the guinea pig, the generally accepted experimental species for the study of contact allergy. The results have established that specific immune tolerance to poison ivy urushiol is induced following 2 epicutaneous applications of the PDC analog. Furthermore, we were able to show that the treated animals remained tolerant for at least 6 weeks, a period of time comparable to that observed following the intravenous administration of the O,O-bis-acetyl derivative of PDC. The data point to the possibility of developing a therapeutically effective topical tolerogen for poison ivy contact dermatitis.

  13. Crystal structure of (Z)-ethyl 3-[2-(5-methyl-7-nitro-1H-indole-2-carbon­yl)hydrazinyl­idene]butano­ate

    PubMed Central

    Errossafi, Amal; El Kihel, Abdellatif; Guesmi, Salaheddine; Saadi, Mohamed; El Ammari, Lahcen

    2015-01-01

    The reaction of 5-methyl-7-nitro-1H-indole-2-carbohydrazide with ethyl aceto­acetate yielded the title mol­ecule, C16H18N4O5, in which the indole ring is almost planar, with the greatest deviation from the mean plane being 0.006 (2) Å. The nine atoms of the indole ring are almost perpendicular to the mean plane through the ethyl acetate group, as indicated by the dihedral angle of 87.02 (4)° between them. In the crystal, centrosymmetric supra­molecular dimers are formed via N—H⋯O hydrogen bonds and eight-membered amide {⋯HNCO}2 synthons. These are consolidated into a three-dimensional architecture by C—H⋯O contacts, and by π–π inter­actions between six-membered rings [inter-centroid distance = 3.499 (2) Å]. PMID:26396904

  14. Photoaffinity labeling by ( sup 3 H)-N5-methyl-N5-isobutylamiloride of proteins which cofractionate with Na+/H+ antiport activity

    SciTech Connect

    Wu, J.S.; Lever, J.E. )

    1989-04-04

    N5-Methyl-N5-isobutylamiloride (MIA) is one of a series of 5-N-substituted amiloride analogues which exhibit high affinity and specificity for inhibition of Na+/H+ antiport. Amiloride-sensitive ({sup 3}H)MIA binding to renal brush border membranes exhibited a Kd of 250 nM and a Bmax of 8.6 pmol/mg of protein. Specific binding was optimal at pH 7.5 and inhibited in the presence of Na+ and Li+. Inhibition by amiloride exhibited biphasic kinetics. After resolution of solubilized membranes by high-pressure liquid chromatography, MIA binding activity cofractionated together with Na+/H+ antiport activity, measured after reconstitution in asolectin vesicles, into a major and a minor peak. When fractions containing the major peak of Na+/H+ antiport activity were incubated with ({sup 3}H)MIA and then photolyzed with a mercury arc lamp, covalent incorporation of label into polypeptides of apparent molecular mass 81 and 107 kDa was observed. These photolabeled bands were also observed in intact brush border membranes in addition to labeled polypeptides of apparent molecular mass 60 and 46 kDa, respectively. Labeling was inhibited by amiloride, reduced in the presence of Na+, and not observed in the absence of photolysis. These data point to the 81- and 107-kDa polypeptides as candidates for identification as components of a Na+/H+ antiport system in renal brush border membranes.

  15. Purification and biochemical characterization of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid/kainate-sensitive L-glutamate receptors of pig brain.

    PubMed Central

    Chang, Y C; Wu, T Y; Li, B F; Gao, L H; Liu, C I; Wu, C L

    1996-01-01

    Two preparations of glutamate receptors were purified from the synaptic junctions of pig brain by a combination of detergent solubilization, anion-exchange chromatography, wheat-germ agglutinin affinity chromatography and sedimentation through sucrose gradients. These preparations were enriched in specific L-[3H]glutamate binding activity (> 5000 pmol of glutamate binding sites/mg of protein), and the rank order of ligand affinity for binding to these preparations was: quisqualate > 6-cyano-7- nitroquinoxaline-2,3-dione > alpha-amino-3-hydroxy-5-methyl-4- isoxazolepropionic acid (AMPA) > L-glutamate > kainate > > N-methyl-D-aspartate approximately L-2-amino-4-phosphonobutyrate. SDS/PAGE analysis revealed that more than 80% of the protein in either of these preparations appeared as a single protein band of 106 kDa. Two-dimensional gel electrophoresis further revealed that these 106 kDa proteins consisted of a series of acidic proteins which were recognized by antibodies against rat AMPA receptor subunits. These 106 kDa proteins were also recognized by wheatgerm agglutinin and concanavalin A; in addition, peptide N-glycosidase F treatment of these preparations decreased their size to 99 kDa. Our results suggest that the putative glutamate receptors isolated here are likely to belong to the AMPA subtype of glutamate receptors in pig brain. Using the purification procedure reported here, 5 micrograms of AMPA receptor proteins can be isolated from 250 g of pig brain tissue. PMID:8870648

  16. DNA synthesis past a 5-methylC-containing cis-syn-cyclobutane pyrimidine dimer by yeast pol eta is highly nonmutagenic.

    PubMed

    Vu, Bich; Cannistraro, Vincent J; Sun, Liping; Taylor, John Stephen

    2006-08-01

    Cyclobutane pyrimidine dimers (CPDs) are responsible for a considerable fraction of sunlight-induced C to T and 5-methycytosine (mC) to T mutations in mammalian cells, though the precise mechanism is unknown. One possibility is that the C or mC of a CPD is not mutagenic and must first deaminate to U or T, respectively, for A to be inserted by a DNA polymerase. Alternatively, A might be directly inserted opposite the C or mC prior to deamination via an E-imino tautomer of the C or mC or by a nontemplated mechanism in which the photoproduct is sterically excluded from the active site. We have taken advantage of the retarding effect of C5 methylation on the deamination rate of cis-syn-cyclobutane dimers to prepare a template containing the cis-syn-cyclobutane dimer of mCT. Through the use of single-hit and multiple-hit competition assays, the catalytic core of pol eta was found to insert dGMP opposite the mC of the CPD with about a 120:1 selectivity relative to dAMP. No significant insertion of dTTP or dCMP was detected. The high fidelity of nonmutagenic insertion opposite the mC of the CPD provides strong support for the deamination-bypass mechanism for the origin of sunlight induced C --> T mutations.

  17. Pd(II) and Pd(IV) complexes with 5-methyl-5-(4-pyridyl)hydantoin: Synthesis, physicochemical, theoretical, and pharmacological investigation

    NASA Astrophysics Data System (ADS)

    Sabounchei, Seyyed Javad; Shahriary, Parisa; Salehzadeh, Sadegh; Gholiee, Yasin; Nematollahi, Davood; Chehregani, Abdolkarim; Amani, Ameneh; Afsartala, Zohreh

    2015-01-01

    The reaction of K2[PdCl4] and PdCl2 with 5-methyl-5-(4-pyridyl)-2,4-imidazolidenedione (L) proceeded with the formation of two different Pd complexes, PdL2Cl2 (1) and PdL2Cl4 (2c), corresponded to a substitution reaction and a substitution reaction along with unanticipated oxidation, respectively. The nature of the oxidizing agent is unknown. These compounds have been studied by elemental analysis, IR, 1H and 13CNMR, molar conductivity, and cyclic voltammetry. In addition, structural optimization by DFT calculations and simulation of NMR spectra have been performed and compared with the experimental data. NBO analysis, HOMO and LUMO, have been used to elucidate the information regarding charge transfer within the molecules. Theoretical studies confirmed that in 1 and 2c the trans structures are about 41 and 33 kJ mol-1 more stable than cis ones. Antibacterial activity and in vitro cytotoxicity of these compounds, as respectively assessed in six bacterial strains and two human tumor cell lines, have been investigated. Results showed the title complexes have the capacity of inhibiting the metabolic growth of bacteria and tumor cells to different extents.

  18. In vitro and in vivo antiherpetic effects of (1R,2R)-1-(5'-methylful-3'-yl)propane-1,2,3-triol.

    PubMed

    Sasaki, Kohei; Hayashi, Kyoko; Matsuya, Yuji; Sugimoto, Kenji; Lee, Jung-Bum; Kurosaki, Fumiya; Hayashi, Toshimitsu

    2016-04-01

    In this study, we demonstrated the in vitro and in vivo antiherpetic activities of a stable furan derivative, (1R,2R)-1-(5'-methylful-3'-yl)propane-1,2,3-triol (MFPT), which had originally been isolated from Streptomyces sp. strain FV60. In the present study, we synthesized MFPT from (5-methylfuran-3-yl)methanol in 6 steps for use in the experiments. MFPT showed potent in vitro antiviral activities against two acyclovir (ACV)-sensitive (KOS and HF) strains and an ACV-resistant (A4-3) strain of herpes simplex virus type 1 (HSV-1) and an ACV-sensitive HSV type 2 (HSV-2) UW 268 strain, their selectivity indices ranging from 310 to 530. By intravaginal application of MFPT to mice, the virus yields decreased dose-dependently against the three strains of HSV-1 and HSV-2. When MFPT was applied at a dose of 1.0 mg/day, the lesion scores, as clinical signs manifested by viral infection, were extensively suppressed in HSV-1-infected mice, whereas the lesion scores in HSV-2-infected mice were not markedly decreased. Interestingly, MFPT exerted an inhibitory effect against ACV-resistant HSV-1 in mice to a similar degree as in ACV-sensitive HSV-1-infected mice. Therefore, the compound might have potential for developing a topical antiviral agent that could be also applied to the infections caused by ACV-resistant viruses.

  19. IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-aminouracil.

    PubMed

    Singh, J S

    2014-09-15

    Infrared (IR) and Raman spectra of uracil and 5-aminouracil have been recorded and analyzed between the region 200-4000 cm(-1). The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-aminouracil by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, the most of B3LYP/6-311++G** vibrational frequencies are in the excellent agreement with available experimental assignments and helped in the reassignments of some fundamental vibrational modes. On the basis of calculated results, the assignments of some missing frequencies in the experimental study are proposed. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a') and non-planar (a″) are given by 25a'+11a″, of which 30 modes (21a'+9a″) correspond to the uracil moiety and 6 modes (4a'+2a″) to the NH2 group. Kekule ring stretching mode is found to be comparatively higher frequency magnitude than the mode of uracil due to the involvement of hydrogen bonding of amino group. But, the ring breathing is found to be lower frequency magnitude compared to those for uracil which could be due to mass effect of the NH2 group in place of the hydrogen atom. All other bands have also been assigned different fundamentals/overtones/combinations. Copyright © 2014

  20. IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-aminouracil

    NASA Astrophysics Data System (ADS)

    Singh, J. S.

    2014-09-01

    Infrared (IR) and Raman spectra of uracil and 5-aminouracil have been recorded and analyzed between the region 200-4000 cm-1. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke’s exchange in conjunction with Lee-Yang-Parr’s correlation functional and Becke’s three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-aminouracil by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, the most of B3LYP/6-311++G** vibrational frequencies are in the excellent agreement with available experimental assignments and helped in the reassignments of some fundamental vibrational modes. On the basis of calculated results, the assignments of some missing frequencies in the experimental study are proposed. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a‧) and non-planar (a″) are given by 25a‧ + 11a″, of which 30 modes (21a‧ + 9a″) correspond to the uracil moiety and 6 modes (4a‧ + 2a″) to the NH2 group. Kekule ring stretching mode is found to be comparatively higher frequency magnitude than the mode of uracil due to the involvement of hydrogen bonding of amino group. But, the ring breathing is found to be lower frequency magnitude compared to those for uracil which could be due to mass effect of the NH2 group in place of the hydrogen atom. All other bands have also been assigned different fundamentals/overtones/combinations.

  1. Opinion: uracil DNA glycosylase (UNG) plays distinct and non-canonical roles in somatic hypermutation and class switch recombination.

    PubMed

    Yousif, Ashraf S; Stanlie, Andre; Begum, Nasim A; Honjo, Tasuku

    2014-10-01

    Activation-induced cytidine deaminase (AID) is essential to class switch recombination (CSR) and somatic hypermutation (SHM). Uracil DNA glycosylase (UNG), a member of the base excision repair complex, is required for CSR. The role of UNG in CSR and SHM is extremely controversial. AID deficiency in mice abolishes both CSR and SHM, while UNG-deficient mice have drastically reduced CSR but augmented SHM raising a possibility of differential functions of UNG in CSR and SHM. Interestingly, UNG has been associated with a CSR-specific repair adapter protein Brd4, which interacts with acetyl histone 4, γH2AX and 53BP1 to promote non-homologous end joining during CSR. A non-canonical scaffold function of UNG, but not the catalytic activity, can be attributed to the recruitment of essential repair proteins associated with the error-free repair during SHM, and the end joining during CSR.

  2. Monitoring Non-Adiabatic Dynamics of the RNA Base Uracil by UV-Pump-IR-Probe Spectroscopy

    PubMed Central

    Fingerhut, Benjamin P.; Dorfman, Konstantin E.; Mukamel, Shaul

    2013-01-01

    Resolving the excited state dynamics of DNA- and RNA- nucleobases has attracted considerably attention. UV irradiation of the isolated nucleobases leads to the population of an electronic excited state which is quenched by internal conversion mediated by conical intersections on an ultrafast timescale. We present non-adiabatic on-the-fly molecular dynamics simulations of the UV-pump-IR-probe signal of the pyrimidine nucleobase uracil using a novel semiclassical protocol which takes into account the path integral over the excited state vibrational dynamics and properly describes the joint temporal and spectral resolution of the technique. Simulations of vibrational motions of carbonyl fingerprint modes in the electronically excited states reveal clear signatures of different relaxation pathways on a timescale of hundreds of femtoseconds which arise from an ultrafast branching in the excited state. We show that the inherent temporal and spectral resolution of the technique is not purely instrumental but also depends on the vibrational fluctuation timescale. PMID:23914288

  3. Adsorption induced formation of 5-5'-diuracil from 5-I-uracil: a surface X-ray structure analysis

    NASA Astrophysics Data System (ADS)

    Meyerheim, H. L.; Gloege, Th.

    2000-08-01

    An X-ray diffraction analysis of a two-dimensional organic structure is presented. Direct evidence for the singly bonded 5-5'-diuracil-dimer is given which is the object of intense discussion in biochemistry. It is formed in ultra-high-vacuum by deposition of 5-I-uracil on a clean Ag(111) surface kept at 390 K. The dimers are arranged in an uniaxial incommensurate superstructure with two molecules per unit cell whereas the released I-atoms form a (√3×√3) superstructure. The molecular structure is characterized by parallel chains of hydrogen bonded dimers. The individual pyrimidine rings of the dimers are inclined by about 30-40° to each other.

  4. Internal conversion and intersystem crossing pathways in UV excited, isolated uracils and their implications in prebiotic chemistry.

    PubMed

    Yu, Hui; Sanchez-Rodriguez, Jose A; Pollum, Marvin; Crespo-Hernández, Carlos E; Mai, Sebastian; Marquetand, Philipp; González, Leticia; Ullrich, Susanne

    2016-07-27

    The photodynamic properties of molecules determine their ability to survive in harsh radiation environments. As such, the photostability of heterocyclic aromatic compounds to electromagnetic radiation is expected to have been one of the selection pressures influencing the prebiotic chemistry on early Earth. In the present study, the gas-phase photodynamics of uracil, 5-methyluracil (thymine) and 2-thiouracil-three heterocyclic compounds thought to be present during this era-are assessed in the context of their recently proposed intersystem crossing pathways that compete with internal conversion to the ground state. Specifically, time-resolved photoelectron spectroscopy measurements evidence femtosecond to picosecond timescales for relaxation of the singlet (1)ππ* and (1)nπ* states as well as for intersystem crossing to the triplet manifold. Trapping in the excited triplet state and intersystem crossing back to the ground state are investigated as potential factors contributing to the susceptibility of these molecules to ultraviolet photodamage.

  5. Imaging [18F]FAU [1-(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl) uracil] in dogs.

    PubMed

    Sun, Haihao; Collins, Jerry M; Mangner, Thomas J; Muzik, Otto; Shields, Anthony F

    2003-01-01

    We have studied the biodistribution of [(18)F]FAU [(1-(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)uracil], which previous work has shown is incorporated into DNA and functions as an inhibitor of DNA synthesis. It is being tested as a potential antineoplastic agent and imaging agent for PET. We have produced [(18)F]FAU and injected the tracer into 3 normal dogs and imaged them for up to 4 hours and removed tissues along with blood and urine samples for HPLC and activity analysis. The results showed that [(18)F]FAU evenly distributed to most of organs. In sharp contrast to our prior experience with thymidine and its analogs, marrow had less retention of [(18)F]FAU than the non-proliferating tissues. Copyright 2002 Elsevier Science Inc.

  6. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine.

    PubMed

    Grimme, Stefan; Bauer, Christopher Alexander

    2015-01-01

    The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.

  7. A facile route to 5-methyl-5H-indeno[1,2-c]quinolones via palladium-catalyzed cyclization of 2-alkynylbromobenzenes with N,N-dimethyl-2-alkynylanilines.

    PubMed

    Pan, Xiaolin; Luo, Yong; Kuang, Yunyan; Li, Guangming

    2014-08-21

    A tandem reaction catalyzed by palladium is developed to provide a facile and simple route for the synthesis of 5-methyl-5H-indeno[1,2-c]quinolones, which can introduce diversity and complexity into the products from readily available starting materials. This transformation proceeds well with good functional group tolerance.

  8. Secretion of Rhoptry and Dense Granule Effector Proteins by Nonreplicating Toxoplasma gondii Uracil Auxotrophs Controls the Development of Antitumor Immunity.

    PubMed

    Fox, Barbara A; Sanders, Kiah L; Rommereim, Leah M; Guevara, Rebekah B; Bzik, David J

    2016-07-01

    Nonreplicating type I uracil auxotrophic mutants of Toxoplasma gondii possess a potent ability to activate therapeutic immunity to established solid tumors by reversing immune suppression in the tumor microenvironment. Here we engineered targeted deletions of parasite secreted effector proteins using a genetically tractable Δku80 vaccine strain to show that the secretion of specific rhoptry (ROP) and dense granule (GRA) proteins by uracil auxotrophic mutants of T. gondii in conjunction with host cell invasion activates antitumor immunity through host responses involving CD8α+ dendritic cells, the IL-12/interferon-gamma (IFN-γ) TH1 axis, as well as CD4+ and CD8+ T cells. Deletion of parasitophorous vacuole membrane (PVM) associated proteins ROP5, ROP17, ROP18, ROP35 or ROP38, intravacuolar network associated dense granule proteins GRA2 or GRA12, and GRA24 which traffics past the PVM to the host cell nucleus severely abrogated the antitumor response. In contrast, deletion of other secreted effector molecules such as GRA15, GRA16, or ROP16 that manipulate host cell signaling and transcriptional pathways, or deletion of PVM associated ROP21 or GRA3 molecules did not affect the antitumor activity. Association of ROP18 with the PVM was found to be essential for the development of the antitumor responses. Surprisingly, the ROP18 kinase activity required for resistance to IFN-γ activated host innate immunity related GTPases and virulence was not essential for the antitumor response. These data show that PVM functions of parasite secreted effector molecules, including ROP18, manipulate host cell responses through ROP18 kinase virulence independent mechanisms to activate potent antitumor responses. Our results demonstrate that PVM associated rhoptry effector proteins secreted prior to host cell invasion and dense granule effector proteins localized to the intravacuolar network and host nucleus that are secreted after host cell invasion coordinately control the

  9. Multiple Decay Mechanisms and 2D‐UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine‐Uracil Monophosphate

    PubMed Central

    Li, Quansong; Giussani, Angelo; Segarra‐Martí, Javier; Nenov, Artur; Rivalta, Ivan; Voityuk, Alexander A.; Mukamel, Shaul; Roca‐Sanjuán, Daniel

    2016-01-01

    Abstract The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D‐UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine 1La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine 1Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter‐base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long‐lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the 1Lb, S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D‐UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm−1 in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D‐UV spectroscopy to disentangle the photophysics of multichromophoric systems. PMID:27113273

  10. Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex.

    PubMed

    Schneider, C; Brandl, M; Sühnel, J

    2001-01-26

    A 4 ns molecular dynamics simulation of an RNA duplex (r-GGACUUCGGUCC)(2 )in solution with Na+ and Cl- as counterions was performed. The X-ray structure of this duplex includes two water-mediated uracil-cytosine pairs. In contrast to the other base-pairs in the duplex the water-mediated pairs switch between different conformations. One conformation corresponds to the geometry of the water-mediated UC pairs in the duplex X-ray structure with water acting both as hydrogen-bond donor and acceptor. Another conformation is close to that of a water-mediated UC base-pair found in the X-ray structure of the 23 S rRNA sarcin/ricin domain. In this case the oxygen of the water molecule is linked to two-base donor sites. For a very short time also a direct UC base-pair and a further conformation that is similar to the one found in the RNA duplex structure but exhibits an increased H3(U)...N3(C) distance is observed. Water molecules with unusually long residence times are involved in the water-mediated conformations. These results indicate that the dynamic behaviour of the water-mediated UC base-pairs differs from that of the duplex Watson-Crick and non-canonical guanine-uracil pairs with two or three direct hydrogen bonds. The conformational variability and increased flexibility has to be taken into account when considering these base-pairs as RNA building blocks and as recognition motifs. Copyright 2001 Academic Press.

  11. Secretion of Rhoptry and Dense Granule Effector Proteins by Nonreplicating Toxoplasma gondii Uracil Auxotrophs Controls the Development of Antitumor Immunity

    PubMed Central

    Fox, Barbara A.; Sanders, Kiah L.; Rommereim, Leah M.; Bzik, David J.

    2016-01-01

    Nonreplicating type I uracil auxotrophic mutants of Toxoplasma gondii possess a potent ability to activate therapeutic immunity to established solid tumors by reversing immune suppression in the tumor microenvironment. Here we engineered targeted deletions of parasite secreted effector proteins using a genetically tractable Δku80 vaccine strain to show that the secretion of specific rhoptry (ROP) and dense granule (GRA) proteins by uracil auxotrophic mutants of T. gondii in conjunction with host cell invasion activates antitumor immunity through host responses involving CD8α+ dendritic cells, the IL-12/interferon-gamma (IFN-γ) TH1 axis, as well as CD4+ and CD8+ T cells. Deletion of parasitophorous vacuole membrane (PVM) associated proteins ROP5, ROP17, ROP18, ROP35 or ROP38, intravacuolar network associated dense granule proteins GRA2 or GRA12, and GRA24 which traffics past the PVM to the host cell nucleus severely abrogated the antitumor response. In contrast, deletion of other secreted effector molecules such as GRA15, GRA16, or ROP16 that manipulate host cell signaling and transcriptional pathways, or deletion of PVM associated ROP21 or GRA3 molecules did not affect the antitumor activity. Association of ROP18 with the PVM was found to be essential for the development of the antitumor responses. Surprisingly, the ROP18 kinase activity required for resistance to IFN-γ activated host innate immunity related GTPases and virulence was not essential for the antitumor response. These data show that PVM functions of parasite secreted effector molecules, including ROP18, manipulate host cell responses through ROP18 kinase virulence independent mechanisms to activate potent antitumor responses. Our results demonstrate that PVM associated rhoptry effector proteins secreted prior to host cell invasion and dense granule effector proteins localized to the intravacuolar network and host nucleus that are secreted after host cell invasion coordinately control the

  12. Reactions of 5-methylcytosine cation radicals in DNA and model systems: thermal deprotonation from the 5-methyl group vs. excited state deprotonation from sugar

    PubMed Central

    Adhikary, Amitava; Kumar, Anil; Palmer, Brian J.; Todd, Andrew D.; Heizer, Alicia N.; Sevilla, Michael D.

    2014-01-01

    Purpose To study the formation and subsequent reactions of the 5-methyl-2′-deoxycytidine cation radical (5-Me-2′-dC•+) in nucleosides and DNA-oligomers and compare to one electron oxidized thymidine. Materials and methods Employing electron spin resonance (ESR), cation radical formation and its reactions were investigated in 5-Me-2′-dC, thymidine (Thd) and their derivatives, in fully double stranded (ds) d[GC*GC*GC*GC*]2 and in the 5-Me-C/A mismatched, d[GGAC*AAGC:CCTAATCG], where C* = 5-Me-C. Results We report 5-Me-2′-dC•+ production by one-electron oxidation of 5-Me-2′-dC by Cl2•− via annealing in the dark at 155 K. Progressive annealing of 5-Me-2′-dC•+ at 155 K produces the allylic radical (C-CH2•). However, photoexcitation of 5-Me-2′-dC•+ by 405 nm laser or by photoflood lamp leads to only C3′• formation. Photoexcitation of N3-deprotonated thyminyl radical in Thd and its 5′-nucleotides leads to C3′• formation but not in 3′-TMP which resulted in the allylic radical (U-CH2•) and C5′• production. For excited 5-Me-2′,3′-ddC•+, absence of the 3′-OH group does not prevent C3′• formation. For d[GC*GC*GC*GC*]2 and d[GGAC*AAGC:CCTAATCG], intra-base paired proton transferred form of G cation radical (G(N1-H)•:C(+H+)) is found with no observable 5-Me-2′-dC•+ formation. Photoexcitation of (G(N1-H)•:C(+H+)) in d[GC*GC*GC*GC*]2 produced only C1′• and not the expected photoproducts from 5-Me-2′-dC•+. However, photoexcitation of (G(N1-H)•:C(+H+)) in d[GGAC*AAGC:CCTAATCG] led to C5′• and C1′• formation. Conclusions C-CH2• formation from 5-Me-2′-dC•+ occurs via ground state deprotonation from C5-methyl group on the base. In the excited 5-Me-2′-dC•+ and 5-Me-2′,3′-ddC•+, spin and charge localization at C3′ followed by deprotonation leads to C3′• formation. Thus, deprotonation from C3′ in the excited cation radical is kinetically controlled and sugar C-H bond energies are

  13. Anxiolytic- and antidepressant-like effects of the methadone metabolite 2-ethyl-5-methyl-3,3-diphenyl-1-pyrroline (EMDP).

    PubMed

    Forcelli, Patrick A; Turner, Jill R; Lee, Bridgin G; Olson, Thao T; Xie, Teresa; Xiao, Yingxian; Blendy, Julie A; Kellar, Kenneth J

    2016-02-01

    The enhancement of GABAergic and monoaminergic neurotransmission has been the mainstay of pharmacotherapy and the focus of drug-discovery for anxiety and depressive disorders for several decades. However, the significant limitations of drugs used for these disorders underscores the need for novel therapeutic targets. Neuronal nicotinic acetylcholine receptors (nAChRs) may represent one such target. For example, mecamylamine, a non-competitive antagonist of nAChRs, displays positive effects in preclinical tests for anxiolytic and antidepressant activity in rodents. In addition, nicotine elicits similar effects in rodent models, possibly by receptor desensitization. Previous studies (Xiao et al., 2001) have identified two metabolites of methadone, EMDP (2-ethyl-5-methyl-3,3-diphenyl-1-pyrroline) and EDDP (2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine), which are considered to be inactive at opiate receptors, as relatively potent noncompetitive channel blockers of rat α3β4 nAChRs. Here, we show that these compounds are likewise highly effective blockers of human α3β4 and α4β2 nAChRs. Moreover, we show that they display relatively low affinity for opiate binding sites labeled by [(3)H]-naloxone. We then evaluated these compounds in rats and mice in preclinical behavioral models predictive of potential anxiolytic and antidepressant efficacy. We found that EMDP, but not EDDP, displayed robust effects predictive of anxiolytic and antidepressant efficacy without significant effects on locomotor activity. Moreover, EMDP at behaviorally active doses, unlike mecamylamine, did not produce eyelid ptosis, suggesting it may produce fewer autonomic side effects than mecamylamine. Thus, the methadone metabolite EMDP may represent a novel therapeutic avenue for the treatment of some affective disorders.

  14. EGAR, A Food Protein-Derived Tetrapeptide, Reduces Seizure Activity in Pentylenetetrazole-Induced Epilepsy Models Through α-Amino-3-Hydroxy-5-Methyl-4-Isoxazole Propionate Receptors.

    PubMed

    Cai, Song; Ling, Chuwen; Lu, Jun; Duan, Songwei; Wang, Yingzhao; Zhu, Huining; Lin, Ruibang; Chen, Liang; Pan, Xingchang; Cai, Muyi; Gu, Huaiyu

    2017-01-01

    A primary pathogeny of epilepsy is excessive activation of α-amino-3-hydroxy-5-methyl-4-isoxazole propionate receptors (AMPARs). To find potential molecules to inhibit AMPARs, high-throughput screening was performed in a library of tetrapeptides in silico. Computational results suggest that some tetrapeptides bind stably to the AMPAR. We aligned these sequences of tetrapeptide candidates with those from in vitro digestion of the trout skin protein. Among salmon-derived products, Glu-Gly-Ala-Arg (EGAR) showed a high biological affinity toward AMPAR when tested in silico. Accordingly, natural EGAR was hypothesized to have anticonvulsant activity, and in vitro experiments showed that EGAR selectively inhibited AMPAR-mediated synaptic transmission without affecting the electrophysiological properties of hippocampal pyramidal neurons. In addition, EGAR reduced neuronal spiking in an in vitro seizure model. Moreover, the ability of EGAR to reduce seizures was evaluated in a rodent epilepsy model. Briefer and less severe seizures versus controls were shown after mice were treated with EGAR. In conclusion, the promising experimental results suggest that EGAR inhibitor against AMPARs may be a target for antiepilepsy pharmaceuticals. Epilepsy is a common brain disorder characterized by the occurrence of recurring, unprovoked seizures. Twenty to 30 % of persons with epilepsy do not achieve adequate seizure control with any drug. Here we provide a possibility in which a natural and edible tetrapeptide, EGAR, can act as an antiepileptic agent. We have combined computation with in vitro experiments to show how EGAR modulates epilepsy. We also used an animal model of epilepsy to prove that EGAR can inhibit seizures in vivo. This study suggests EGAR as a potential pharmaceutical for the treatment of epilepsy.

  15. Clinical Spectrum of Encephalitis Associated With Antibodies Against the α-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid Receptor: Case Series and Review of the Literature.

    PubMed

    Joubert, Bastien; Kerschen, Philippe; Zekeridou, Anastasia; Desestret, Virginie; Rogemond, Véronique; Chaffois, Marie-Océane; Ducray, François; Larrue, Vincent; Daubail, Benoit; Idbaih, Ahmed; Psimaras, Dimitri; Antoine, Jean-Christophe; Delattre, Jean-Yves; Honnorat, Jérôme

    2015-10-01

    The clinical features of autoimmune encephalitis associated with antibodies against the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR-Abs) remain poorly defined. To describe 7 patients with encephalitis and AMPAR-Abs and to provide a review of the literature on this disease entity. The setting was the Centre National de Référence pour les Syndromes Neurologiques Paranéoplasiques (Lyon, France), and participants were 7 consecutive patients diagnosed as having encephalitis and AMPAR-Abs between January 1, 2010, and December 1, 2014. Patients' clinical data were analyzed, with a median follow-up period of 12 months (range, 2-31 months). Relevant articles were identified in the MEDLINE database using the keywords autoimmune encephalitis and AMPA receptor antibodies until February 15, 2015. Modes of onset, full clinical presentations, and cancer prevalence. The patients included 4 women and 3 men (median age, 56 years). Four main modes of encephalitis onset were observed, including confusion (3 patients), epileptic (1 patient), amnestic (1 patient), and a severe form of fulminant encephalitis (2 patients). In contrast with previous reports, we observed only 1 patient with seizures. Two patients had cancer (1 lung carcinoma and the other thymic carcinoma). Analysis of the literature identified 35 published cases of encephalitis and AMPAR-Abs, including 18 with clinical data. The same modes of encephalitis onset were observed, including confusion (12 patients), epileptic (1 patient), amnestic (3 patients), and fulminant encephalitis (2 patients). Eleven patients were initially seen with a neoplasm (lung, breast, thymoma, or ovary). The clinical spectrum of AMPAR encephalitis is variable. Cancer was found in 13 of 27 patients (48%) with known cancer status. Most patients are seen with symptoms suggestive of autoimmune limbic encephalitis, although they can be paucisymptomatic or may manifest severe panencephalitis that evolves to a minimally

  16. Glutamate regulates intracellular calcium and gene expression in oligodendrocyte progenitors through the activation of DL-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors.

    PubMed Central

    Pende, M; Holtzclaw, L A; Curtis, J L; Russell, J T; Gallo, V

    1994-01-01

    Oligodendrocytes and their progenitors (O-2A) express functional kainate- and DL-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-preferring glutamate receptors. The physiological consequences of activation of these receptors were studied in purified rat cortical O-2A progenitors and in the primary oligodendrocyte cell line CG-4. Changes in the mRNA levels of a set of immediate early genes were studied and were correlated to intracellular Ca2+ concentration, as measured by fura-2 Ca2+ imaging. Both in CG-4 and in cortical O-2A progenitors, basal mRNA levels of NGFI-A were much higher than c-fos, c-jun, or jun-b. Glutamate, kainate, and AMPA greatly increased NGFI-A mRNA and protein by activation of membrane receptors in a Ca(2+)-dependent fashion. Agonists at non-N-methyl-D-aspartate receptors promoted transmembrane Ca2+ influx through voltage-dependent channels as well as kainate and/or AMPA channels. The influx of Ca2+ ions occurring through glutamate-gated channels was sufficient by itself to increase the expression of NGFI-A mRNA. AMPA receptors were found to be directly involved in intracellular Ca2+ and NGFI-A mRNA regulation, because the effects of kainate were greatly enhanced by cyclothiazide, an allosteric modulator that selectively suppresses desensitization of AMPA but not kainate receptors. Our results indicate that glutamate acting at AMPA receptors regulates immediate early gene expression in cells of the oligodendrocyte lineage by increasing intracellular calcium. Consequently, modulation of these receptor channels may have immediate effects at the genomic level and regulate oligodendrocyte development at critical stages. Images PMID:8159727

  17. Study of dynamics and crystallization kinetics of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile at ambient and elevated pressure

    NASA Astrophysics Data System (ADS)

    Adrjanowicz, K.; Kaminski, K.; Paluch, M.; Ngai, K. L.; Yu, Lian

    2012-06-01

    The organic liquid ROY, i.e., 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, has been a subject of detailed study in the last few years. One interest in ROY lies in its polymorph-dependent fast crystal growth mode below and above the glass transition temperature. This growth mode is not diffusion controlled, and the possibility that it is enabled by secondary relaxation had been suggested. However, a previous study by dielectric relaxation spectroscopy had not been able to find any resolved secondary relaxation. The present paper reports new dielectric measurements of ROY in the liquid and glassy states at ambient pressure and elevated pressure, which were performed to provide more insight into the molecular dynamics as well as the crystallization tendency of ROY. In the search of secondary relaxation, a special glassy state of ROY was prepared by applying high pressure to the liquid state, from which secondary relaxation was possibly resolved. Thus, the role of secondary relaxation in crystallization of ROY remains to be clarified. Notwithstanding, the secondary relaxation present is not necessarily the sole enabler of crystallization. In an effort to search for possible cause of crystallization other than secondary relaxation, we also performed crystallization kinetics studies of ROY at different T and P combinations while keeping the structural relaxation time constant. The results show that crystallization of ROY speeds up with pressure, opposite to the trend found in the crystallization of ibuprofen studied up to 1 GPa. The dielectric relaxation and thermodynamic properties of ROY with phenolphthalein dimethylether (PDE) are similar in many respects, but PDE does not crystallize. Taking all the above into account, besides the secondary relaxation, the specific chemical structure, molecular interactions and packing of the molecules are additional factors that could affect the kinetics of crystallization found in ROY.

  18. Potent methyl oxidation of 5-methyl-2'-deoxycytidine by halogenated quinoid carcinogens and hydrogen peroxide via a metal-independent mechanism.

    PubMed

    Shao, Jie; Huang, Chun-Hua; Kalyanaraman, Balaraman; Zhu, Ben-Zhan

    2013-07-01

    Halogenated quinones are a class of carcinogenic intermediates and are newly identified chlorination disinfection by-products in drinking water. We found recently that the highly reactive and biologically important hydroxyl radical ((•)OH) can be produced by halogenated quinones and H2O2 independent of transition metal ions. However, it is not clear whether these quinoid carcinogens and H2O2 can oxidize the nucleoside 5-methyl-2'-deoxycytidine (5mdC) to its methyl oxidation products and, if so, what the underlying molecular mechanism is. Here we show that three methyl oxidation products, 5-(hydroperoxymethyl)-, 5-(hydroxymethyl)-, and 5-formyl-2'-deoxycytidine, could be produced when 5mdC was treated with tetrachloro-1,4-benzoquinone (TCBQ) and H2O2. The formation of the oxidation products was markedly inhibited by typical (•)OH scavengers and under anaerobic conditions. Analogous effects were observed with other halogenated quinones and the classic Fenton system. Based on these data, we propose that the oxidation of 5mdC by TCBQ/H2O2 might be through the following mechanism: (•)OH produced by TCBQ/H2O2 may first abstract hydrogen from the methyl group of 5mdC, leading to the formation of 5-(2'-deoxycytidylyl)methyl radical, which may combine with O2 to form the peroxyl radical. The unstable peroxyl radical transforms into the corresponding hydroperoxide 5-(hydroperoxymethyl)-2'-deoxycytidine, which reacts with TCBQ and results in the formation of 5-(hydroxymethyl)-2'-deoxycytidine and 5-formyl-2'-deoxycytidine. This is the first report that halogenated quinoid carcinogens and H2O2 can induce potent methyl oxidation of 5mdC via a metal-independent mechanism, which may partly explain their potential carcinogenicity. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Generation of AcGFP fusion with single-chain Fv selected from a phage display library constructed from mice hyperimmunized against 5-methyl 2'-deoxycytidine.

    PubMed

    Ohshima, Motohiro; Inoue, Kazuyuki; Hayashi, Hideki; Tsuji, Daiki; Mizugaki, Michinao; Itoh, Kunihiko

    2010-11-01

    DNA methylation is involved in many diseases such as cancer and autoimmunity. We generated recombinant single-chain Fv (scFv) antibodies against 5-methyl-2'-deoxycytidine (m(5)dCyd) using phage display technology and a hyperimmunized mouse, and the scFv of most interest were constructed as fusion proteins with green fluorescent protein obtained from Aequorea coerulescens GFP (AcGFP). Using RNA isolated from mouse spleens, we constructed a scFv library consisting of λ light chains. The scFv library was selected against m(5)Cyd-BSA and enriched through four rounds of panning. The scFv library was concentrated about 390-fold and an individual clone was reacted with m(5)Cyd-BSA. Two scFvs with high reactivity for m(5)Cyd-BSA termed 1-2 and 1-12 were produced. Furthermore, methylated DNA-binding activities of the scFvs were confirmed using an indirect immunofluorescence assay. Additionally, N- and C-terminal scFv 1-2 fusion with AcGFP were constructed, and we observed the N-terminal AcGFP exhibited much higher fluorescence intensity than the C-terminal fusions. The AcGFP-scFv 1-2 modified N-terminus of scFv with AcGFP had high fluorescence intensity, but the scFv 1-2-AcGFP modified C-terminus of scFv with AcGFP had low fluorescence intensity. The cross-reactivity of AcGFP-scFv 1-2 was similar to scFv 1-2, and thus, AcGFP-scFv 1-2 could be used in a direct immunofluorescence assay. The scFv fusion proteins may be useful for the detection and quantification of cellular methylated DNA in various specimens.

  20. Anxiolytic- and Antidepressant-like Effects of the Methadone Metabolite 2-ethyl-5-methyl-3,3-diphenyl-1-pyrroline (EMDP)

    PubMed Central

    Lee, Bridgin G.; Olson, Thao T.; Xie, Teresa; Xiao, Yingxian; Blendy, Julie A.; Kellar, Kenneth J.

    2015-01-01

    The enhancement of GABAergic and monoaminergic neurotransmission has been the mainstay of pharmacotherapy and the focus of drug-discovery for anxiety and depressive disorders for several decades. However, the significant limitations of drugs used for these disorders underscores the need for novel therapeutic targets. Neuronal nicotinic acetylcholine receptors (nAChRs) may represent one such target. For example, mecamylamine, a non-competitive antagonist of nAChRs, displays positive effects in preclinical tests for anxiolytic and antidepressant activity in rodents. In addition, nicotine elicits similar effects in rodent models, possibly by receptor desensitization. Previous studies (Xiao et al., 2001) have identified two metabolites of methadone, EMDP (2-ethyl-5-methyl-3,3-diphenyl-1-pyrroline) and EDDP (2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine), which are considered to be inactive at opiate receptors, as relatively potent noncompetitive channel blockers of rat α3β4 nAChRs. Here, we show that these compounds are likewise highly effective blockers of human α3β4 and α4β2 nAChRs. Moreover, we show that they display relatively low affinity for opiate binding sites labeled by [3H]-naloxone. We then evaluated these compounds in rats and mice in preclinical behavioral models predictive of potential anxiolytic and antidepressant efficacy. We found that EMDP, but not EDDP, displayed robust effects predictive of anxiolytic and antidepressant efficacy without significant effects on locomotor activity. Moreover, EMDP at behaviorally active doses, unlike mecamylamine, did not produce eyelid ptosis, suggesting it may produce fewer autonomic side effects than mecamylamine. Thus, the methadone metabolite EMDP may represent a novel therapeutic avenue for the treatment of some affective disorders. PMID:26365569

  1. Positive alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor modulators have different impact on synaptic transmission in the thalamus and hippocampus.

    PubMed

    Xia, Yan-Fang; Kessler, Markus; Arai, Amy C

    2005-04-01

    Earlier studies showed that positive modulators of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors enhance synaptic responses and facilitate synaptic plasticity. Those studies focused mainly on hippocampal functions. However, AMPA receptors have regionally distinct subunit compositions and thus potencies and efficacies of modulators may vary across the brain. The present study compared the effects of CX546 [1-(1,4-benzodioxan-6-ylcarbonyl) piperidine], a benzamide-type modulator, on synaptic transmission in neurons of the reticular thalamic nucleus (RTN), which regulates the firing mode of relay cells in other thalamic nuclei, and on hippocampal CA1 pyramidal cells. CX546 greatly prolonged synaptic responses in CA1 pyramidal cells, but at the same concentration it had only weak modulatory effects in RTN neurons. Effects on miniature excitatory postsynaptic currents (EPSCs) were similar to those on EPSCs in both regions, suggesting that variations in neuronal morphology and transmitter release kinetics do not account for the differences. Relay cells in the ventrobasal thalamus also exhibited weak modulatory effects that were comparable with those in RTN neurons. Regionally different effects on response duration were also observed with CX516 [BDP-12, 1-(quinoxalin-6-ylcarbonyl)piperidine], a second benzamide drug. In contrast, 100 microM cyclothiazide produced comparable synaptic enhancements in hippocampus and RTN. The regional selectivity of benzamide drugs (ampakines) may be explained, at least in part, by a lower potency at thalamic AMPA receptors, perhaps due to the prevalence of the subunits GluR3 and 4. Although regional preferences of the ampakines were modest in their extent, they may be sufficient to be of relevance when considering future therapeutic applications of such compounds.

  2. A novel diterpene skeleton: identification of a highly aromatic, cytotoxic and antioxidant 5-methyl-10-demethyl-abietane-type diterpene from Premna serratifolia.

    PubMed

    Habtemariam, Solomon; Varghese, George K

    2015-01-01

    Premna serratifolia Linn. (syn: . P. corymbosa (Burm. f.) Merr., P. integrifolia L. and P. obtusifolia R. Br.) is a member of the Verbenaceae family that is extensively used in the Ayurvedic system of medicine in India. As part of our continuous pharmacological and phytochemical studies on medicinal plants, we have screened the methanolic extracts of leaves, root bark (RB) and root wood of P. serratifolia for cytotoxic activity against two cancer cell lines: SHSY-5Y neuroblastoma and B16 melanoma cells. The RB extract that showed promising activity was fractionated using solvents of increasing polarity followed by a combination of Sephadex LH-20 column and Combiflash chromatography as well as HPLC to afford the active principle. Comprehensive spectroscopic analysis including 1D and 2D NMR (COSY, HMQC, HMBC, NOESY) and MS analysis revealed the identity of the isolated compound as 11,12,16-trihydroxy-2-oxo-5-methyl-10-demethyl-abieta-1[10],6,8,11,13-pentene that appears to be a novel compound based on a new diterpene skeleton. The cytotoxic activity of the isolated compound was 21 and 23 times higher than the crude extract against the SHSY-5Y and B16 cells, respectively. The novel compound also possesses in vitro antioxidant effects as evidenced by the DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging effect where an IC50 value of 20.4 ± 1.3 μM was obtained. In comparison, the positive control, caffeic acid, showed an IC50 value of 14.4 ± 1.6 μM.

  3. Studies of the environmental fate and effect of aircraft deicing fluids: Detection of 5-methyl-1H-benzotriazole in the fathead minnow (Pimephales promelas)

    USGS Publications Warehouse

    Cancilla, Devon A.; Baird, J.C.; Geis, S.W.; Corsi, Steven R.

    2003-01-01

    This paper presents the results of a number of field and laboratory studies to evaluate the environmental impact of aircraft deicing and anti-icing fluids (ADAFs) on aquatic systems. Both 5-methyl-1H-benzotriazole (5-MeBt) and 4-methyl-1H-benzotriazole (4-MeBt), known additives to ADAFs, were found in whole-tissue extracts from minnows placed downstream of an effluent outfall that receives ADAF contaminated runoff from General Mitchell International Airport (Milwaukee, WI, USA). Neither of these compounds was detected in tissues from minnows placed upstream from the airport. A toxicity assessment of water collected during the minnow exposure studies utilizing Hyalella azteca, Pimephales promelas, and Ceriodaphnia dubia showed greater toxicity in a secondary airport outfall containing ADAFs when compared to upstream non-ADAF-contaminated samples. In two 28-d static renewal tests using 5-MeBt laboratory-fortified waters, 5-MeBt was detected in whole-tissue extracts of minnows at all concentrations tested. In studies using laboratory water fortified with 5-MeBt, the median lethal concentration (LC50) of 5-MeBt for P. promelas was found to be 22.0 mg/L. The LC50 for C. dubia to 5-MeBt laboratory-fortified water was found to be 81.3 mg/L. The 25% inhibition concentration (IC25) of 5-MeBt for the green alga Selenastrum capricornutum was 23.2 mg/L, and the average median effective concentration (EC50) for Microtox was 4.25 mg/L. The results of these field and lab studies indicate that additives, other than glycols, used in aircraft deicing fluids can be found in aquatic systems and may be of greater risk than previously believed.

  4. Remodeling of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor subunit composition in hippocampal neurons after global ischemia

    PubMed Central

    Optiz, Thoralf; Grooms, Sonja Y.; Bennett, Michael V. L.; Zukin, R. Suzanne

    2000-01-01

    Transient global ischemia induces selective delayed cell death, primarily of principal neurons in the hippocampal CA1. However, the molecular mechanisms underlying ischemia-induced cell death are as yet unclear. The present study shows that global ischemia triggers a pronounced and cell-specific reduction in GluR2 [the subunit that limits Ca2+ permeability of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors] in vulnerable CA1 neurons, as evidenced by immunofluorescence of brain sections and Western blot analysis of microdissected hippocampal subfields. At 72 h after ischemia (a time before cell death), virtually all CA1 pyramidal neurons exhibited greatly reduced GluR2 immunolabeling throughout their somata and dendritic processes. GluR2 immunolabeling was unchanged in pyramidal cells of the CA3 and granule cells of the dentate gyrus, regions resistant to ischemia-induced damage. Immunolabeling of the AMPA receptor subunit GluR1 was unchanged in CA1, CA3, and dentate gyrus. Western analysis indicated that GluR2 subunit abundance was markedly reduced in CA1 at 60 and 72 h after the ischemic insult; GluR1 abundance was unchanged in all subfields at all times examined. These findings, together with the previous observation of enhanced AMPA-elicited Ca2+ influx in postischemic CA1 neurons, show that functional GluR2-lacking, Ca2+-permeable AMPA receptors are expressed in vulnerable neurons before cell death. Thus, the present study provides an important link in the postulated causal chain between global ischemia and delayed death of CA1 pyramidal neurons. PMID:11087875

  5. Synthesis, structural characterization and theoretical approach of 3-(2,6-dichlorobenzyl)-5-methyl-N-nitro-1,3,5-oxadiazinan-4-imine.

    PubMed

    Ni, Haiwei; Zhang, Yu; Zhang, Fang; Zhao, Jianying; Wu, Liubi; Chu, Xiaozhong

    2015-03-05

    3-(2,6-Dichlorobenzyl)-5-methyl-N-nitro-1,3,5-oxadiazinan-4-imine (DNOI) was synthesized and characterized by X-ray diffraction, FT-IR, FT-Raman and UV-Vis spectra. The X-ray diffraction study showed that DNOI has a one dimensional configuration, due to the intermolecular C9H⋯O1 and N4H⋯O2 hydrogen bonds. The benzene ring and the oxadiazine rings are tilted with respect to each other by 63.07° (C3N1C5C6). Vibrational spectra and electronic spectra measurements were made for the compound. Optimized geometrical structure and harmonic vibrational frequencies were computed with DFT (B3LYP, B3P86, and M062X) methods using 6-311++G(d,p) basis set. Assignments of the observed spectra were proposed. The equilibrium geometries computed by all of the methods were compared with X-ray diffraction results. The absorption spectra of the title compound were computed both in gas phase and in CH3OH solution using TD-B3LYP/6-311++G(d,p) and PCM-B3LYP/6-311++G(d,p) approaches, respectively. The calculated results provide a good description of positions of the bands maxima in the observed electronic spectrum. Temperature dependence of thermodynamic parameters in the range of 100-1000K were determined, entropy, heat capacity and enthalpy changes were increasing with temperature increasing, while for Gibbs free energy is decreasing with temperature increasing. The bond orbital occupancies, contribution from parent natural bond orbital (NBO), the natural atomic hybrids was calculated and discussed.

  6. Inroads into base excision repair II. The discovery of DNA glycosylases. "An N-glycosidase from Escherichia coli that releases free uracil from DNA containing deaminated cytosine residues," Proc. Nat. Acad. Sci. USA, 1974.

    PubMed

    Friedberg, Errol C; Lindahl, Tomas

    2004-11-02

    The discovery of a DNA glycosylase that specifically removes uracil from DNA, opened the door for uncovering a large class of such enzymes that are fundamental to the process of base excision repair of DNA.

  7. Visual and light scattering spectrometric method for the detection of melamine using uracil 5‧-triphosphate sodium modified gold nanoparticles

    NASA Astrophysics Data System (ADS)

    Liang, Lijiao; Zhen, Shujun; Huang, Chengzhi

    2017-02-01

    A highly selective method was presented for colorimetric determination of melamine using uracil 5‧-triphosphate sodium modified gold nanoparticles (UTP-Au NPs) in this paper. Specific hydrogen-bonding interaction between uracil base (U) and melamine resulted in the aggregation of AuNPs, displaying variations of localized surface plasmon resonance (LSPR) features such as color change from red to blue and enhanced localized surface plasmon resonance light scattering (LSPR-LS) signals. Accordingly, the concentration of melamine could be quantified based on naked eye or a spectrometric method. This method was simple, inexpensive, environmental friendly and highly selective, which has been successfully used for the detection of melamine in pretreated liquid milk products with high recoveries.

  8. Synthesis of novel 1H-1,2,3-triazole tethered C-5 substituted uracil-isatin conjugates and their cytotoxic evaluation.

    PubMed

    Kumar, Kewal; Sagar, Sunil; Esau, Luke; Kaur, Mandeep; Kumar, Vipan

    2012-12-01

    The present manuscript describes the synthesis of uracil-isatin hybrids via azide-alkyne cycloadditions and their cytotoxic evaluation against three human cancer cell lines viz. HeLa (cervix), MCF-7 (breast) and DU145 (prostate) using MTT assay. The evaluation studies revealed the dependence of cytotoxicity on C-5 substituents of both uracil and isatin as well as the alkyl chain length with compounds 6g and 6k showing IC(50) values 18.21 and 13.90 μM respectively against DU145 cell lines. Most of the synthesized conjugates exhibited considerable selectivity against MCF-7 and DU145 cell lines. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  9. Comment on ‘To stack or not to stack: Performance of a new density functional for the uracil and thymine dimers’ [Chem. Phys. Lett. 459 (2008) 164

    NASA Astrophysics Data System (ADS)

    van Mourik, Tanja

    2009-04-01

    A Letter by Gu et al. [J. Gu, J. Wang, J. Leszczynski, Y. Xie, H.F. Schaefer III, Chem. Phys. Lett. 459 (2008) 164] presented MP2/6-31+G(d) and MP2/TZVPP stacking energies for the uracil and thymine dimers, with the aim to assess the performance of the new M06-2X density functional. However, the stacking energies were not corrected for the basis set superposition error (BSSE). Here we show that correction for this error dramatically changes the results. BSSE correction severely reduces the stacking energy of the thymine dimer, whereas the stacked uracil dimer structure considered by Gu et al. is not even a minimum on the MP2/6-31+G(d) potential energy surface.

  10. [125I]2-(2-chloro-4-iodo-phenylamino)-5-methyl-pyrroline (LNP 911), a high-affinity radioligand selective for I1 imidazoline receptors.

    PubMed

    Greney, Hugues; Urosevic, Dragan; Schann, Stephan; Dupuy, Laurence; Bruban, Véronique; Ehrhardt, Jean-Daniel; Bousquet, Pascal; Dontenwill, Monique

    2002-07-01

    The I1 subtype of imidazoline receptors (I1R) is a plasma membrane protein that is involved in diverse physiological functions. Available radioligands used so far to characterize the I(1)R were able to bind with similar affinities to alpha2-adrenergic receptors (alpha2-ARs) and to I1R. This feature was a major drawback for an adequate characterization of this receptor subtype. New imidazoline analogs were therefore synthesized and the present study describes one of these compounds, 2-(2-chloro-4-iodo-phenylamino)-5-methyl-pyrroline (LNP 911), which was of high affinity and selectivity for the I1R. LNP 911 was radioiodinated and its binding properties characterized in different membrane preparations. Saturation experiments with [125I]LNP 911 revealed a single high affinity binding site in PC-12 cell membranes (K(D) = 1.4 nM; B(max) = 398 fmol/mg protein) with low nonspecific binding. [125I]LNP 911 specific binding was inhibited by various imidazolines and analogs but was insensitive to guanosine-5'-O-(3-thio)triphosphate. The rank order of potency of some competing ligands [LNP 911, PIC, rilmenidine, 4-chloro-2-(imidazolin-2-ylamino)-isoindoline (BDF 6143), lofexidine, and clonidine] was consistent with the definition of [125I]LNP 911 binding sites as I1R. However, other high-affinity I1R ligands (moxonidine, efaroxan, and benazoline) exhibited low affinities for these binding sites in standard binding assays. In contrast, when [125I]LNP 911 was preincubated at 4 degrees C, competition curves of moxonidine became biphasic. In this case, moxonidine exhibited similar high affinities on [125I]LNP 911 binding sites as on I1R defined with [125I]PIC. Moxonidine proved also able to accelerate the dissociation of [125I]LNP 911 from its binding sites. These results suggest the existence of an allosteric modulation at the level of the I1R, which seems to be corroborated by the dose-dependent enhancement by LNP 911 of the agonist effects on the adenylate cyclase pathway

  11. Identification of ozonation by-products of 4- and 5-methyl-1H-benzotriazole during the treatment of surface water to drinking water.

    PubMed

    Müller, Alexander; Weiss, Stefan C; Beisswenger, Judith; Leukhardt, H Georg; Schulz, Wolfgang; Seitz, Wolfram; Ruck, Wolfgang K L; Weber, Walter H

    2012-03-01

    During the treatment of surface water to drinking water, ozonation is often used for disinfection and to remove organic trace substances, whereby oxidation by-products can be formed. Here we use the example of tolyltriazole to describe an approach for identifying relevant oxidation by-products in the laboratory and subsequently detecting them in an industrial-scale process. The identification process involves ozonation experiments with pure substances at laboratory level (concentration range mg L(-1)). The reaction solutions from different ozone contact times were analyzed by high performance liquid chromatography - quadrupole time-of-flight mass spectrometry (HPLC-QTOF-MS) in full scan mode. Various approaches were used to detect the oxidation by-products: (i) target searches of postulated oxidation by-products, (ii) comparisons of chromatograms (e.g., UV/VIS) of the different samples, and (iii) color-coded abundance time courses (kinetic) of all detected compounds were illustrated in a kind of a heat map. MS/MS, H/D exchange, and derivatization experiments were used for structure elucidation for the detected by-product. Due to the low contaminant concentrations (ng L(-1)-range) of contaminants in the untreated water, the conversion of results from laboratory experiments to an industrial-scale required the use of HPLC-MS/MS with sample enrichment (e.g., solid phase extraction.) In cases where reference substances were not available or oxidation by-products without clear structures were detected, reaction solutions from laboratory experiments were used to optimize the analytical method to detect ng L(-1) in the samples of the industrial processes. We exemplarily demonstrated the effectiveness of the methodology with the industrial chemicals 4- and 5-methyl-1H-benzotriazole (4- and 5-MBT) as an example. Moreover, not only did we identify several oxidation by-products in the laboratory experiments tentatively, but also detected three of the eleven reaction

  12. Synthesis of 5-[3-(2-aminopyrimidin-4-yl)aminopropyn-1-yl]uracil derivative that recognizes Ade-Thy base pairs in double-stranded DNA.

    PubMed

    Ito, Yu; Masaki, Yoshiaki; Kanamori, Takashi; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

    2016-01-01

    5-[3-(2-Aminopyrimidin-4-yl)aminopropyn-1-yl]uracil (Ura(Pyr)) was designed as a new nucleobase to recognize Ade-Thy base pair in double-stranded DNA. We successfully synthesized the dexoynucleoside phosphoramidite having Ura(Pyr) and incorporated it into triplex forming oligonucleotides (TFOs). Melting temperature analysis revealed that introduction of Ura(Pyr) into TFOs could effectively stabilize their triplex structures without loss of base recognition capabilities.

  13. In silico studies to explore the mutagenic ability of 5-halo/oxy/li-oxy-uracil bases with guanine of DNA base pairs.

    PubMed

    Jana, Kalyanashis; Ganguly, Bishwajit

    2014-10-16

    DNA nucleobases are reactive in nature and undergo modifications by deamination, oxidation, alkylation, or hydrolysis processes. Many such modified bases are susceptible to mutagenesis when formed in cellular DNA. The mutagenesis can occur by mispairing with DNA nucleobases by a DNA polymerase during replication. We have performed a study of mispairing of DNA bases with unnatural bases computationally. 5-Halo uracils have been studied as mispairs in mutagenesis; however, the reports on their different forms are scarce in the literature. The stability of mispairs with keto form, enol form, and ionized form of 5-halo-uracil has been computed with the M06-2X/6-31+G** level of theory. The enol form of 5-halo-uracil showed remarkable stability toward DNA mispair compared to the corresponding keto and ionized forms. (F)U-G mispair showed the highest stability in the series and (Halo)(U(enol/ionized)-G mispair interactions energies are more stable than the natural G-C basepair of DNA. To enhance the stability of DNA mispairs, we have introduced the hydroxyl group in the place of halogen atoms, which provides additional hydrogen-bonding interactions in the system while forming the 5-membered ring. The study has been further extended with lithiated 5-hydroxymethyl-uracil to stabilize the DNA mispair. (CH2OLi)U(ionized)-G mispair has shown the highest stability (ΔG = -32.4 kcal/mol) with multi O-Li interactions. AIM (atoms in molecules) and EDA (energy decomposition analysis) analysis has been performed to examine the nature of noncovalent interactions in such mispairs. EDA analysis has shown that electrostatic energy mainly contributes toward the interaction energy of mispairs. The higher stability achieved in these studied mispairs can play a pivotal role in the mutagenesis and can help to attain the mutation for many desired biological processes.

  14. VUV and mid-UV photoabsorption cross sections of thin films of guanine and uracil: application on their photochemistry in the solar system.

    PubMed

    Saïagh, Kafila; Cottin, Hervé; Aleian, Aicha; Fray, Nicolas

    2015-04-01

    We present a photostability study of two nucleobases, guanine and uracil. For the first time, the photoabsorption cross-section spectra of these molecules in the solid phase were measured in the VUV and mid-UV domain (115≤λ≤300 nm). They show a quite similar absorption level throughout this wavelength range, highlighting the importance of considering the whole VUV and UV domain during photolysis experiments in the laboratory. Their photolysis constant (J) can be estimated from those measurements as follows: 2.2×10(-2) s(-1)±11% for guanine and 5.3×10(-2) s(-1)±14% for uracil. This work shows that (i) measuring kinetic constants from a direct and "traditional" photolysis of a thin sample in the laboratory suffers strong limitations and (ii) achieving this measurement requires comprehensive modeling of the radiative transfer that occurs in any sample not optically thin (i.e.,≤2 nm). Moreover, this work has provided other data of interest: the refractive index of solid guanine and of uracil at 650 nm are 1.52 (±0.01) and 1.39 (±0.02), respectively, and the integrated IR band strengths (A) of solid guanine between 3700 and 2120 cm(-1) (3.4×10(-16) cm·molecule(-1)±13%) and of solid uracil between 3400 and 1890 cm(-1) (2.1×10(-16) cm·molecule(-1)±21%).

  15. Substituent effects on the regioselectivity of the Paternò-Büchi reaction of 5- or/and 6-methyl substituted uracils with 4,4'-disubstituted benzophenones.

    PubMed

    Kong, Feng-Feng; Zhai, Bao-Chang; Song, Qin-Hua

    2008-11-01

    The [2 + 2] photochemical cycloadditions (the Paternò-Büchi reaction) of 5- or/and 6-methyl substituted uracil derivatives with 4,4'-disubstituted benzophenones generate two series of regioisomeric oxetanes, 3 and 4. The regioselectivity (3/4) and the photochemical efficiency are strongly dependent on methyl substituent(s) at the C5-C6 double bond of the uracils. The more the methyl groups at the C5-C6 double bond, the higher the efficiency. The regioselectivity (3/4) ranges from ca. 20 : 80 for 1,3,6-trimethyluracil (1C) to ca. 80 : 20 for 1,3,6-trimethylthymine (1D). The substituent effects would derive from the hyperconjugation of the methyl group(s) at C5 or/and C6 of the uracils, which influences the stability of intermediary triplet 1,4-biradicals and the nucleophilicity of C5 and C6 sites of the double bond. Computational studies reveal that potential energies of triplet 1,4-biradicals forming oxetanes 3, BR5, are 1-4 kcal mol(-1) higher than those of 1,4-biradicals forming oxetanes 4, BR6, and electron densities at C5 are 0.1-0.3 unit higher than those at C6, of the double bond of the uracils, i.e. BR5 are less stable than BR6, and BR5 form more easily than BR6. Temperature effects on the regioselectivity of the Paternò-Büchi reaction of 1D with three benzophenones (2a-c) reveal that efficiencies of oxetanes 3 are higher at a lower reaction temperature, and efficiencies of 4 are higher at a higher temperature. Therefore, triplet biradicals BR5 and BR6 would be regarded as intermediates of kinetic control and thermodynamic control, respectively.

  16. Influence of methylation on the properties of uracil and its noncovalent interactions with alkali metal ions: Threshold collision-induced dissociation and theoretical studies

    NASA Astrophysics Data System (ADS)

    Yang, Zhibo; Rodgers, M. T.

    2005-03-01

    The influence of methylation on the properties of uracil and its noncovalent interactions with alkali metal ions is investigated both experimentally and theoretically. Threshold collision-induced dissociation (CID) of M+(xMeU) with Xe is studied in a guided ion beam mass spectrometer. M+ include the following alkali metal ions: Li+, Na+, and K+. Five methylated uracils are examined, xMeU = 1-methyluracil, 3-methyluracil, 6-methyluracil, 1,3-dimethyluracil, and 5,6-dimethyluracil. In all cases endothermic loss of the intact nucleobase is the dominant reaction pathway, while ligand exchange to produce MXe+ is observed as a minor reaction pathway. The threshold regions of the cross sections are interpreted to extract 0 and 298 K bond dissociation energies (BDEs) for M+xMeU after accounting for the effects of multiple ion-neutral collisions, kinetic and internal energies of the reactants, and dissociation lifetimes. Ab initio calculations at the MP2(full)/6-31G* level of theory are used to determine the structures of these complexes and provide molecular constants required for the thermochemical analysis of the experimental data. Theoretical bond dissociation energies are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the MP2(full)/6-31G* geometries. Excellent agreement between theory and experiment is found for the Na+ and K+ systems, while theory systematically underestimates the strength of binding in the Li+ systems. Theoretical calculations are also performed to examine the influence of methylation on the acidities, proton affinities, and Watson-Crick base pairing energies. The present results are compared to earlier studies of uracil and 5-methyluracil to more fully elucidate the influence of methylation on the properties of uracil, its noncovalent interactions with alkali metal ions, and nucleic acid stability.

  17. Using structural-based protein engineering to modulate the differential inhibition effects of SAUGI on human and HSV uracil DNA glycosylase.

    PubMed

    Wang, Hao-Ching; Ho, Chun-Han; Chou, Chia-Cheng; Ko, Tzu-Ping; Huang, Ming-Fen; Hsu, Kai-Cheng; Wang, Andrew H-J

    2016-05-19

    Uracil-DNA glycosylases (UDGs) are highly conserved proteins that can be found in a wide range of organisms, and are involved in the DNA repair and host defense systems. UDG activity is controlled by various cellular factors, including the uracil-DNA glycosylase inhibitors, which are DNA mimic proteins that prevent the DNA binding sites of UDGs from interacting with their DNA substrate. To date, only three uracil-DNA glycosylase inhibitors, phage UGI, p56, and Staphylococcus aureus SAUGI, have been determined. We show here that SAUGI has differential inhibitory effects on UDGs from human, bacteria, Herpes simplex virus (HSV; human herpesvirus 1) and Epstein-Barr virus (EBV; human herpesvirus 4). Newly determined crystal structures of SAUGI/human UDG and a SAUGI/HSVUDG complex were used to explain the differential binding activities of SAUGI on these two UDGs. Structural-based protein engineering was further used to modulate the inhibitory ability of SAUGI on human UDG and HSVUDG. The results of this work extend our understanding of DNA mimics as well as potentially opening the way for novel therapeutic applications for this kind of protein.

  18. Mechanism for the abiotic synthesis of uracil via UV-induced oxidation of pyrimidine in pure H{sub 2}O ices under astrophysical conditions

    SciTech Connect

    Bera, Partha P.; Nuevo, Michel; Sandford, Scott A.; Lee, Timothy J.; Milam, Stefanie N.

    2010-09-14

    The UV photoirradiation of pyrimidine in pure H{sub 2}O ices has been explored using second-order Moeller-Plesset perturbation theory and density functional theory methods, and compared with experimental results. Mechanisms studied include those starting with neutral pyrimidine or cationic pyrimidine radicals, and reacting with OH radical. The ab initio calculations reveal that the formation of some key species, including the nucleobase uracil, is energetically favored over others. The presence of one or several water molecules is necessary in order to abstract a proton which leads to the final products. Formation of many of the photoproducts in UV-irradiated H{sub 2}O:pyrimidine=20:1 ice mixtures was established in a previous experimental study. Among all the products, uracil is predicted by quantum chemical calculations to be the most favored, and has been identified in experimental samples by two independent chromatography techniques. The results of the present study strongly support the scenario in which prebiotic molecules, such as the nucleobase uracil, can be formed under abiotic processes in astrophysically relevant environments, namely in condensed phase on the surface of icy, cold grains before being delivered to the telluric planets, like Earth.

  19. [A case of recurrent lung cancer with bone metastases treated with tegafur-uracil and zoledronic acid for long-term survival].

    PubMed

    Shiono, Satoshi; Harada, Mayumi; Abiko, Masami; Sato, Toru; Takanashi, Imi

    2014-06-01

    We present the case of an 84-year-old man with lumbago due to bone metastases from lung cancer that recurred three years after surgery. The patient received carboplatin-paclitaxel combination as first-line chemotherapy for the treatment of lung cancer, and palliative radiotherapy for the treatment of bone metastases. Gemcitabine was administered as second-line chemotherapy. However, disease progression was observed after three years, and he developed pulmonary metastases. The general condition of the patient worsened, and tegafur-uracil chemotherapy was initiated. Zoledronic acid was also administered. The tegafur-uracil treatment resulted in the disappearance of pulmonary metastases, and a stabilization of the bone metastases. Disease progression was observed after 6 years with a recurrence of pulmonary metastases; however, this did not have a negative impact on the patient's quality of life. Although slow progression may be inherent to lung cancers, it is also possible that the tegafur-uracil and zoledronic acid combination might have contributed to the patient's improved performance.

  20. Genotyping of a family with a novel deleterious DPYD mutation supports the pretherapeutic screening of DPD deficiency with dihydrouracil/uracil ratio.

    PubMed

    Thomas, F; Hennebelle, I; Delmas, C; Lochon, I; Dhelens, C; Garnier Tixidre, C; Bonadona, A; Penel, N; Goncalves, A; Delord, J P; Toulas, C; Chatelut, E

    2016-02-01

    Despite the growing evidence that dihydropyrimidine dehydrogenase deficiency (DPD, encoded by the DPYD gene) confers a higher risk of developing severe toxicity, most patients are not screened for DPD deficiency before fluoropyrimidine treatment. We report here the genetic and phenotypic analyses of DPD in a family related to a patient who died after a first cycle of 5-fluorouracil and in 15 additional retrospective patients having a partial DPD deficiency (as measured by plasma dihydrouracil/uracil ratio). The patient with lethal toxicity was found to be a compound heterozygote for two DPYD mutations: a novel 8-bp duplication (c.168_175dupGAATAATT, p.Phe59Ter) and c.1679T>G (Ile560Ser). The patient's dihydrouracil/uracil ratio indicates complete DPD deficiency. The novel mutation was found in two members of the patient's family. Deleterious DPYD mutations were identified in 9 out of the 15 patients. The relationship between genotype and dihydrouracil/uracil values in the 22 patients of the present study was significant (P = 0.01).

  1. Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine.

    PubMed

    Müller, Andreas; Frey, Jann A; Leutwyler, Samuel

    2005-06-16

    The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give

  2. Quantifying weak hydrogen bonding in uracil and 4-cyano-4'-ethynylbiphenyl: a combined computational and experimental investigation of NMR chemical shifts in the solid state.

    PubMed

    Uldry, Anne-Christine; Griffin, John M; Yates, Jonathan R; Pérez-Torralba, Marta; María, M Dolores Santa; Webber, Amy L; Beaumont, Maximus L L; Samoson, Ago; Claramunt, Rosa María; Pickard, Chris J; Brown, Steven P

    2008-01-23

    Weak hydrogen bonding in uracil and 4-cyano-4'-ethynylbiphenyl, for which single-crystal diffraction structures reveal close CH...O=C and C[triple bond]CH...N[triple bond]C distances, is investigated in a study that combines the experimental determination of 1H, 13C, and 15N chemical shifts by magic-angle spinning (MAS) solid-state NMR with first-principles calculations using plane-wave basis sets. An optimized synthetic route, including the isolation and characterization of intermediates, to 4-cyano-4'-ethynylbiphenyl at natural abundance and with 13C[triple bond]13CH and 15N[triple bond]C labeling is described. The difference in chemical shifts calculated, on the one hand, for the full crystal structure and, on the other hand, for an isolated molecule depends on both intermolecular hydrogen bonding interactions and aromatic ring current effects. In this study, the two effects are separated computationally by, first, determining the difference in chemical shift between that calculated for a plane (uracil) or an isolated chain (4-cyano-4'-ethynylbiphenyl) and that calculated for an isolated molecule and by, second, calculating intraplane or intrachain nucleus-independent chemical shifts that quantify the ring current effects caused by neighboring molecules. For uracil, isolated molecule to plane changes in the 1H chemical shift of 2.0 and 2.2 ppm are determined for the CH protons involved in CH...O weak hydrogen bonding; this compares to changes of 5.1 and 5.4 ppm for the NH protons involved in conventional NH...O hydrogen bonding. A comparison of CH bond lengths for geometrically relaxed uracil molecules in the crystal structure and for geometrically relaxed isolated molecules reveals differences of no more than 0.002 A, which corresponds to changes in the calculated 1H chemical shifts of at most 0.1 ppm. For the C[triple bond]CH...N[triple bond]C weak hydrogen bonds in 4-cyano-4'-ethynylbiphenyl, the calculated molecule to chain changes are of similar magnitude

  3. Meta-analysis of five studies on tegafur plus uracil (UFT) as post-operative adjuvant chemotherapy for breast cancer.

    PubMed

    Kasumi, Fujio; Yoshimoto, Masataka; Uchino, Junichi; Abe, Rikiya; Nomura, Yasuo; Sugimachi, Keizo; Nakazato, Hiroaki; Abe, Osahiko

    2003-01-01

    Meta-analysis of 5 studies on postoperative breast cancer cases (2 studies on surgery alone vs. tegafur plus uracil (UFT) and 3 studies on tamoxifen (TAM) alone vs. TAM + UFT) were carried out to evaluate the anticancer drug UFT in oral postoperative adjuvant chemotherapy. Of the 1973 patients enrolled, 1898 were eligible and 75 were excluded (exclusion rate 3.8%). There was no bias in major background factors in either the UFT-treated (965) or non-UFT-treated (933) groups. The reduction in the odds of death and the odds of recurrence were 17 +/- 17% (p = 0.33) and 21 +/- 11% (p = 0.060), respectively. Multivariate analysis using Cox's proportional hazards model emphasized the effectiveness of UFT treatment for suppression of recurrence compared with non-treatment with UFT (p = 0.038). Suppression of recurrence was remarkable in the group treated with UFT for 2 years. (the reduction in the odds of recurrence: 23 +/- 11%, p = 0.048) Stratified analysis was applied concerning recurrence, and improved results were obtained in premenopausal cases (the reduction in the odds of recurrence: 33 +/- 11%, p = 0.019). These results suggested that UFT treatment for 2 years was effective as postoperative adjuvant chemotherapy for stage I - IIIA breast cancer for the prolongation of the recurrence-free survival period. Copyright 2003 S. Karger AG, Basel

  4. Extracellular palladium-catalysed dealkylation of 5-fluoro-1-propargyl-uracil as a bioorthogonally activated prodrug approach

    NASA Astrophysics Data System (ADS)

    Weiss, Jason T.; Dawson, John C.; MacLeod, Kenneth G.; Rybski, Witold; Fraser, Craig; Torres-Sánchez, Carmen; Patton, E. Elizabeth; Bradley, Mark; Carragher, Neil O.; Unciti-Broceta, Asier

    2014-02-01

    A bioorthogonal organometallic reaction is a biocompatible transformation undergone by a synthetic material exclusively through the mediation of a non-biotic metal source; a selective process used to label biomolecules and activate probes in biological environs. Here we report the in vitro bioorthogonal generation of 5-fluorouracil from a biologically inert precursor by heterogeneous Pd0 catalysis. Although independently harmless, combined treatment of 5-fluoro-1-propargyl-uracil and Pd0-functionalized resins exhibits comparable antiproliferative properties to the unmodified drug in colorectal and pancreatic cancer cells. Live-cell imaging and immunoassay studies demonstrate that the cytotoxic activity of the prodrug/Pd0-resin combination is due to the in situ generation of 5-fluorouracil. Pd0-resins can be carefully implanted in the yolk sac of zebrafish embryos and display excellent biocompatibility and local catalytic activity. The in vitro efficacy shown by this masking/activation strategy underlines its potential to develop a bioorthogonally activated prodrug approach and supports further in vivo investigations.

  5. Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase.

    PubMed

    Olufsen, Magne; Papaleo, Elena; Smalås, Arne Oskar; Brandsdal, Bjørn Olav

    2008-05-15

    MD simulations and continuum electrostatics calculations have been used to study the observed differences in thermostability of cold- and warm-active uracil DNA glycosylase (UDG). The present study focuses on the role of ion pairs and how they affect the thermal stability of the two enzymes. Analysis of the MD generated structural ensembles show that cod UDG (cUDG) and human UDG (hUDG) have 11 and 12 ion pairs which are present in at least 30% of the conformations. The electrostatic contribution of the ion pairs, computed using continuum electrostatics, is slightly more favorable in cUDG at 298 K. This is primarily attributed to more optimized interactions between the ion pairs and nearby dipoles/charges in cUDG. More global salt bridges are found in hUDG and are more stabilizing when compared to cUDG, possibly playing a role in maintaining overall stability and reducing conformational entropy. Both enzymes contain one three-member ionic network, but the one found in hUDG is far more stabilizing. Our results also suggest that care should be taken when performing statistical analysis of crystal structures with respect to ion pairs, and that crystallization conditions must be carefully examined when performing such analysis.

  6. Resonant photoelectron imaging of deprotonated uracil anion via vibrational levels of a dipole-bound excited state

    NASA Astrophysics Data System (ADS)

    Huang, Dao-Ling; Liu, Hong-Tao; Ning, Chuan-Gang; Dau, Phuong Diem; Wang, Lai-Sheng

    2017-01-01

    We report both non-resonant and resonant high-resolution photoelectron imaging of cryogenically-cooled deprotonated uracil anions, N1[U-H]-, via vibrational levels of a dipole-bound excited state. Photodetachment spectroscopy of N1[U-H]- was reported previously (Liu et al., 2014), in which forty-six vibrational autodetachment resonances due to the excited dipole-bound state were observed. By tuning the detachment laser to the vibrational levels of the dipole-bound state, we obtained high-resolution resonant photoelectron spectra, which are highly non-Franck-Condon. The resonant photoelectron spectra reveal many Franck-Condon inactive vibrational modes, significantly expanding the capability of photoelectron spectroscopy. A total of twenty one fundamental vibrational frequencies for the N1[U-H]rad radical are obtained, including all eight low-frequency out-of-plane modes, which are forbidden in non-resonant photoelectron spectroscopy. Furthermore, the breakdown of the Δv = -1 propensity rule is observed for autodetachment from many vibrational levels of the dipole-bound state, due to anharmonic effects. In particular, we have observed intramolecular electron rescattering in a number of resonant photoelectron spectra, leading to excitations of low-frequency vibrational modes. Further theoretical study may be warranted, in light of the extensive experimental data and new observations, to provide further insight into the autodetachment dynamics and vibronic coupling in dipole-bound states, as well as electron molecule interactions.

  7. Extracellular palladium-catalysed dealkylation of 5-fluoro-1-propargyl-uracil as a bioorthogonally activated prodrug approach

    PubMed Central

    Weiss, Jason T.; Dawson, John C.; Macleod, Kenneth G.; Rybski, Witold; Fraser, Craig; Torres-Sánchez, Carmen; Patton, E. Elizabeth; Bradley, Mark; Carragher, Neil O.; Unciti-Broceta, Asier

    2014-01-01

    A bioorthogonal organometallic reaction is a biocompatible transformation undergone by a synthetic material exclusively through the mediation of a non-biotic metal source; a selective process used to label biomolecules and activate probes in biological environs. Here we report the in vitro bioorthogonal generation of 5-fluorouracil from a biologically inert precursor by heterogeneous Pd0 catalysis. Although independently harmless, combined treatment of 5-fluoro-1-propargyl-uracil and Pd0-functionalized resins exhibits comparable antiproliferative properties to the unmodified drug in colorectal and pancreatic cancer cells. Live-cell imaging and immunoassay studies demonstrate that the cytotoxic activity of the prodrug/Pd0-resin combination is due to the in situ generation of 5-fluorouracil. Pd0-resins can be carefully implanted in the yolk sac of zebrafish embryos and display excellent biocompatibility and local catalytic activity. The in vitro efficacy shown by this masking/activation strategy underlines its potential to develop a bioorthogonally activated prodrug approach and supports further in vivo investigations. PMID:24522696

  8. High-performance liquid chromatographic assay with UV detection for measurement of dihydrouracil/uracil ratio in plasma.

    PubMed

    Déporte, R; Amiand, M; Moreau, A; Charbonnel, C; Campion, L

    2006-04-13

    A rapid, robust and sensitive HPLC method for analysis of uracil (U) and dihydrouracil (UH2) in plasma was developed using solid phase extraction and ultraviolet detection. Separation was achieved with a SymmetryShield RP18 column and an Atlantis dC18 column using a 10 mM potassium phosphate buffer as mobile phase. Compounds were eluted within 15 min without interference. Recovery was 80.4 and 80.6% for U and UH2. Calibration curves were linear from 2.5 to 80 ng/mL for U and 6.75 to 200 ng/mL for UH2. The LLQ was, respectively, 2.5 ng/mL for U, and 6.75 ng/mL for UH2. Within-run and between-run precision were less than 5.94% and inaccuracy did not exceed 7.80%. The overall procedure has been applied to correlate UH2/U ratio with dihydropyrimidine dehydrogenase activity in 165 cancer patients.

  9. C(5) modified uracil derivatives showing antiproliferative and erythroid differentiation inducing activities on human chronic myelogenous leukemia K562 cells

    PubMed Central

    Brognara, Eleonora; Lampronti, Ilaria; Breveglieri, Giulia; Accetta, Alessandro; Corradini, Roberto; Manicardi, Alex; Borgatti, Monica; Canella, Alessandro; Multineddu, Chiara; Marchelli, Rosangela; Gambari, Roberto

    2011-01-01

    The K562 cell line has been proposed as a useful experimental system to identify anti-tumor compounds acting by inducing terminal erythroid differentiation. K562 cells exhibit a low proportion of hemoglobin-synthesizing cells under standard cell growth conditions, but are able to undergo terminal erythroid differentiation when treated with a variety of anti-tumor compounds. In this paper we report a screening study on a set of different modified C(5) uracil derivatives for the evaluation of their antiproliferative effect in connection with erythroid differentiation pathways, and for defining a new class of drug candidates for the treatment of chronic myelogenous leukemia. Activity of the derivatives tested can be classified in two effect: an antiproliferative effect linked to a high level of erythroid differentiation activity and an antiproliferative effect without activation of gamma globin genes The highest antiproliferative effect and erythroid induction was shown by compound 9, a thymine derivative bearing a n-octyl chain on nitrogen N(1), whereas thymine did not show any effect, suggesting the importance of the linear alkyl chain in position N(1). To our knowledge this compound should be considered among the most efficient inducers of erythroid differentiation of K562 cells. This work is the starting point for the quest of more effective and specific drugs for the induction of terminal erythroid differentiation, for leading new insights in the treatment of neoplastic diseases with molecules acting by inducing differentiation rather than by simply exerting cytotoxic effects. PMID:21958870

  10. Infrared depletion spectra of 2-aminopyridineṡ2-pyridone, a Watson-Crick mimic of adenineṡuracil

    NASA Astrophysics Data System (ADS)

    Frey, Jann A.; Müller, Andreas; Frey, Hans-Martin; Leutwyler, Samuel

    2004-11-01

    The 2-aminopyridineṡ2-pyridone (2APṡ2PY) dimer is linked by N-H⋯O=C and N-H⋯N hydrogen bonds, providing a model for the Watson-Crick hydrogen bond configuration of the adenineṡthymine and adenineṡuracil nucleobase pairs. Mass-specific infrared spectra of 2APṡ2PY and its seven N-H deuterated isotopomers have been measured between 2550 and 3650 cm-1 by IR laser depletion combined with UV two-color resonant two-photon ionization. The 2PY amide N-H stretch is a very intense band spread over the range 2700-3000 cm-1 due to large anharmonic couplings. It is shifted to lower frequency by 710 cm-1 or ≈20% upon H bonding to 2AP. On the 2AP moiety, the "bound" amino N-H stretch gives rise to a sharp band at 3140 cm-1, which is downshifted by 354 cm-1 or ≈10% upon H bonding to 2PY. The amino group "free" N-H stretch and the H-N-H bend overtone are sharp bands at ≈3530 cm-1 and 3320 cm-1. Ab initio structures and harmonic vibrations were calculated at the Hartree-Fock level and with the PW91 and B3LYP density functionals. The PW91/6-311++G(d,p) method provides excellent predictions for the frequencies and IR intensities of all the isotopomers.

  11. An extended version of Boyd's force field method applicable to heteroatomic molecules. Part 1. Adenine and uracil

    NASA Astrophysics Data System (ADS)

    Espinosa-Müller, A. W.; Bravo, A. N.

    The force field method developed by Boyd is extended to include molecules containing atoms other than C and H (e.g., N, O, P, S, Cl, Br,…). A new set of force field parameters is determined in order to redefine the potential energy functions that govern the dynamics of the internal (valence coordinates) degrees of freedom of a molecule. It is shown that the minimum of the partial potential energy surface is significantly affected by electrostatic intramolecular interactions. In this regard the non-bonded interactions appears to be less important than the dipole-dipole type interactions for a given interatomic distance when heteroatoms are present in the molecular framework. The reliability of the extended method as regards minimized structure, vibrational spectra and thermodynamic properties has been checked for more than 20 polyatomic molecules. From the correlation between calculated and experimental properties it is concluded that the method has good potential for further applications on polyatomic molecules with increasing size and topological compexities such as adenine and uracil.

  12. Ugene, a newly identified protein that is commonly over-expressed in cancer, and that binds uracil DNA-glycosylase

    PubMed Central

    Guo, Chunguang; Zhang, Xiaodong; Fink, Stephen P; Platzer, Petra; Wilson, Keith; Willson, James K. V.; Wang, Zhenghe; Markowitz, Sanford D

    2008-01-01

    Expression microarrays identified a novel transcript, designated as Ugene, whose expression is absent in normal colon and colon adenomas, but that is commonly induced in malignant colon cancers. These findings were validated by real-time PCR and Northern blot analysis in an independent panel of colon cancer cases. In addition, Ugene expression was found to be elevated in many other common cancer types, including, breast, lung, uterus, and ovary. Immunofluorescence of V5-tagged Ugene revealed it to have a nuclear localization. In a pull-down assay, uracil DNA-glycosylase 2 (UNG2), an important enzyme in the base excision repair pathway, was identified as a partner protein that binds to Ugene. Co-immunoprecipitation and Western blot analysis confirmed the binding between the endogenous Ugene and UNG2 proteins. Using deletion constructs, we find that Ugene binds to the first 25 amino acids of the UNG2 NH2-terminus. We suggest Ugene induction in cancer may contribute to the cancer phenotype by interacting with the base excision repair pathway. PMID:18676834

  13. Insertional mutagenesis and marker rescue in a protozoan parasite: cloning of the uracil phosphoribosyltransferase locus from Toxoplasma gondii.

    PubMed Central

    Donald, R G; Roos, D S

    1995-01-01

    Nonhomologous integration vectors have been used to demonstrate the feasibility of insertional mutagenesis in haploid tachyzoites of the protozoan parasite Toxoplasma gondii. Mutant clones resistant to 5-fluorouracil were identified at a frequency of approximately 10(-6) (approximately 2 x 10(-5) of the stable transformants). Four independent mutants were isolated, all of which were shown to lack uracil phosphoribosyl-transferase (UPRT) activity and harbor transgenes integrated at closely linked loci, suggesting inactivation of the UPRT-encoding gene. Genomic DNA flanking the insertion point (along with the integrated vector) was readily recovered by bacterial transformation with restriction-digested, self-ligated total genomic DNA. Screening of genomic libraries with the recovered fragment identified sequences exhibiting high homology to known UPRT-encoding genes from other species, and cDNA clones were isolated that contain a single open reading frame predicted to encode the 244-amino acid enzyme. Homologous recombination vectors were exploited to create genetic knock-outs at the UPRT locus, which are deficient in enzyme activity but can be complemented by transient transformation with wild-type sequences--formally confirming identification of the functional UPRT gene. Mapping of transgene insertion points indicates that multiple independent mutants arose from integration at distinct sites within the UPRT gene, suggesting that nonhomologous integration is sufficiently random to permit tagging of the entire parasite genome in a single transformation. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:7777580

  14. Structures of protonated thymine and uracil and their monohydrated gas-phase ions from ultraviolet action spectroscopy and theory.

    PubMed

    Pedersen, Sara Øvad; Byskov, Camilla Skinnerup; Turecek, Frantisek; Brøndsted Nielsen, Steen

    2014-06-19

    The strong UV chromophores thymine (Thy) and uracil (Ura) have identical heteroaromatic rings that only differ by one methyl substituent. While their photophysics has been elucidated in detail, the effect on the excited states of base protonation and single water molecules is less explored. Here we report gas-phase absorption spectra of ThyH(+) and UraH(+) and monohydrated ions and demonstrate that the substituent is not only responsible for spectral shifts but also influences the tautomer distribution, being different for bare and monohydrated ions. Spectra interpretation is aided by calculations of geometrical structures and transition energies. The lowest free-energy tautomer (denoted 178, enol-enol form) accounts for 230-280 nm (ThyH(+)) and 225-270 nm (UraH(+)) bands. ThyH(+) hardly absorbs above 300 nm, whereas a discernible band is measured for UraH(+) (275-320 nm), ascribed to the second lowest free-energy tautomer (138, enol-keto form) comprising a few percent of the UraH(+) population at room temperature. Band widths are similar to those measured of cold ions in support of very short excited-state lifetimes. Attachment of a single water increases the abundance of 138 relative to 178, 138 now clearly present for ThyH(+). 138 resembles more the tautomer present in aqueous solution than 178 does, and 138 may indeed be a relevant transition structure. The band of ThyH(+)(178) is unchanged, that of UraH(+)(178) is nearly unchanged, and that of UraH(+)(138) blue-shifts by about 10 nm. In stark contrast to protonated adenine, more than one solvating water molecule is required to re-establish the absorption of ThyH(+) and UraH(+) in aqueous solution.

  15. Classical trajectory Monte Carlo model calculations for ionization of the uracil molecule by impact of heavy ions

    NASA Astrophysics Data System (ADS)

    Sarkadi, L.

    2016-09-01

    The ionization of the uracil molecule induced by heavy-ion impact has been investigated using the classical trajectory Monte Carlo (CTMC) method. Assuming the validity of the independent-particle model approximation, the collision problem is solved by considering the three-body dynamics of the projectile, an active electron and the molecule core. The interaction of the molecule core with the other two particles is described by a multi-center potential built from screened atomic potentials. The cross section differential with respect to the energy and angle of the electrons ejected in the ionization process has been calculated for an impact of 3.5 MeV u-1 {{{C}}}6+ ions. Total electron emission cross sections (TCS) are presented for {{{C}}}q+ (q=0-6) and {{{O}}}6+ projectiles as a function of the impact energy in the range from 10 keV u-1 to 10 MeV u-1. The dependence of the TCS on the charge state of the projectile has been investigated for 2.5 MeV u-1 {{{O}}}q+ (q=4-8) and {{{F}}}q+ (q=5-9) ions. The results of the calculations are compared with available experimental data and the predictions of other theoretical models: the first Born approximation with correct boundary conditions (CB1), the continuum-distorted-wave-eikonal-initial-state approach (CDW-EIS), and the combined classical-trajectory Monte Carlo-classical over-the-barrier model (CTMC-COB).

  16. Theoretical study of the hydroxyl radical addition to uracil and photochemistry of the formed U6OH• adduct.

    PubMed

    Francés-Monerris, Antonio; Merchán, Manuela; Roca-Sanjuán, Daniel

    2014-03-20

    Hydroxyl radical ((•)OH) is produced in biological systems by external or endogenous agents. It can damage DNA/RNA by attacking pyrimidine nucleobases through the addition to the C5═C6 double bond. The adduct resulting from the attachment at the C5 position prevails in the experimental measurements, although the reasons for this preference remain unclear. The first aim of this work is therefore to shed light on the comprehension of this important process. Thus, the thermal (•)OH addition to the C5═C6 double bond of uracil has been studied theoretically by using DFT, MP2, and the multiconfigurational CASPT2//CASSCF methodologies. The in-vacuo results obtained with the latter protocol plus the analysis of solvent effects support the experimental observation. A significant lower barrier height is predicted for the C5 pathway with respect to that of the C6 route. In contrast to the C5 adduct, the C6 adduct is able to absorb visible light. Hence, the second aim of the work is to study the photochemistry of this species using the CASPT2//CASSCF methodology within the framework of the photochemical reaction path approach (PRPA). The nonradiative decay to the ground state of this compound has been characterized. A photoreactive character is predicted for the C6 adduct in the excited states according to the presence of excited-state minima along the main decay channel. Finally, a new mechanism of photodissociation has been explored, which implies the photoinduced regeneration of the canonical nucleobase by irradiating with visible light, being therefore relevant in RNA protection against damage by reactive oxygen species.

  17. Tautomeric equilibrium of uracil and thymine in model protein-nucleic acid contacts. Spectroscopic and quantum chemical approach.

    PubMed

    Samijlenko, Svitlana P; Yurenko, Yevgen P; Stepanyugin, Andriy V; Hovorun, Dmytro M

    2010-01-28

    This work deals with tautomeric transformations of uracil (Ura) and thymine (Thy) in their model complexes with the deprotonated carboxylic group. Essential changes in the UV spectra of the bases upon their interaction with NaAc, vanishing signals of both imino protons in (1)H NMR spectra, and a perceptible decrease in intensity of both IR bands, related to the stretching vibrations nu(C=O) of the carbonyl groups, imply involvement of enolic tautomers. Results of quantum chemical calculations of the double complexes of the Ura(Thy) tautomers with CH(3)COO(-) at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory proved to be incompatible with the spectral features: despite the fact that the complexes of the enolic tautomers are much closer in energy to the diketo ones as compared to isolated tautomers, the energy gap between them is such that in tautomeric equilibrium dominate diketo forms. Calculations of triple complexes of the type CH(3)COO(-):Ura(Thy) tautomer:Na(+), taking into account the effect of the Na(+) coordination with tautomers, show that three triple complexes formed by enolic tautomers appeared more stable than those formed by diketo ones. This makes the UV and (1)H NMR data understandable, but the high residual intensity of the nu(C=O) bands in the IR spectra remains unclear. At that ion, Na(+) itself was not able to disturb the tautomeric equilibrium in the coordination complexes of the type Ura(Thy) tautomer:Na(+). To evaluate the DMSO effect, the CPCM solvation model was applied to triple complexes of the Ura tautomers. It appeared that in the solution there is coexistence between the diketo and enolic tautomers in a ratio of 53%:47%. This makes possible reconciliation of our experimental data. The biological significance of high-energy tautomers of nucleotide bases is discussed.

  18. Studies on molecular properties prediction and histamine H3 receptor affinities of novel ligands with uracil-based motifs.

    PubMed

    Lipani, Luca; Odadzic, Dalibor; Weizel, Lilia; Schwed, Johannes-Stephan; Sadek, Bassem; Stark, Holger

    2014-10-30

    The histamine H3 receptor (H3R) plays a role in cognitive and memory processes and is involved in different neurological disorders, including Alzheimer's disease, schizophrenia, and narcolepsy. Therefore, several hH3R antagonists/inverse agonists entered clinical phases for a broad spectrum of mainly centrally occurring diseases. However, many other promising candidates failed due to their pharmacokinetic profile, mostly because of their strong lipophilicity accompanied with low solubility. Analysis of previous potential H3R selective antagonists/inverse agonists, e.g. pitolisant, revealed promising results concerning physicochemical properties and drug-likeness. Herein, a series of new hH3R ligands 8-20 consisting of piperidin-1-yl or piperidin-1-yl-propoxyphenyl coupled to different uracil, thymine, and 5,6-dimethyluracil related moieties, were synthesized, evaluated on their binding properties at the hH3R and the estimation of different physicochemical and drug-likeness properties. Due to the coupling to various positions at pyrimidine-2,4-(1H,3H)-dione, affinity at hH3Rs and drug-likeness parameters have been improved. For instance, compound 9 showed in addition to high affinity at the hH3R (pKi (hH3R) = 8.14) clog S, clog P, LE, LipE, and drug-likeness score values of -4.36, 3.47, 0.34, 4.63, and 1.54, respectively. Also, the methyl substituted analog 17 (pKi (hH3R) = 8.15) revealed LE, LipE and drug-likeness score values of -3.29, 2.47, 0.49, 5.52, and 1.76, respectively.

  19. Variability in the anti-tumor effect of tegafur-uracil depending on histologic types of lung cancer

    PubMed Central

    Lee, Bo-Ram; Yu, Jin-Yeong; Yoon, Seong-Hoon; Ban, Hee-Jung; Kwon, Yong-Soo; Kim, Kyu-Sik; Kim, Yu-Il; Lim, Sung-Chul; Kim, Young-Chul

    2015-01-01

    Background Tegafur-uracil (UFT) is an anticancer agent that inhibits thymidylate synthase (TS). The degree of TS expression in primary lung cancer (LC) is different according to histologic cell type. In this study, we examined the variability of the anti-tumor efficacy of UFT monotherapy depending on histological subtypes of LC. Methods In the current single-institution, retrospective study, we assigned the patients with LC to three histologic groups [the squamous (Sq) non-small cell lung cancer (NSCLC)] group, the non-Sq NSCLC group and the SCLC group] and then compared the clinical response to UFT monotherapy between the three groups. Results Our clinical series of 149 patients include 54 cases of Sq NSCLC, 67 cases of non-Sq NSCLC and 28 cases of SCLC. For Sq NSCLC, non-Sq NSCLC and SCLC group, the overall response rates (ORRs) were 1%, 1% and 0% (P=0.522), respectively. The disease control rates (DCRs) were 38.9%, 31.3% and 10.7% (P=0.012), respectively. The median progression-free survivals (PFSs) were 2.68, 2.25 and 1.46 months (P=0.004 for three groups and P=0.773 for two groups except for the SCLC group at the log-rank test), respectively. There was no significant difference between the groups in median overall survival (OS). Conclusions Our results indicate that the degree of the anti-tumor effect of UFT was higher in patients with NSCLC as compared with SCLC. But it showed no significant difference between the patients with Sq NSCLC and those with non-Sq NSCLC. PMID:25922722

  20. Maternal nicotinamide supplementation causes global DNA hypomethylation, uracil hypo-incorporation and gene expression changes in fetal rats.

    PubMed

    Tian, Yan-Jie; Luo, Ning; Chen, Na-Na; Lun, Yong-Zhi; Gu, Xin-Yi; Li, Zhi; Ma, Qiang; Zhou, Shi-Sheng

    2014-05-01

    Recent evidence shows that excess nicotinamide can cause epigenetic changes in developing rats. The aim of the present study was to investigate the effects of maternal nicotinamide supplementation on the fetus. Female rats were randomised into four groups fed a standard chow diet (control group) or diets supplemented with 1 g/kg of nicotinamide (low-dose group), 4 g/kg of nicotinamide (high-dose group) or 4 g/kg of nicotinamide plus 2 g/kg of betaine (betaine group) for 14-16 d before mating and throughout the study. Fetal tissue samples were collected on the 20th day of pregnancy. Compared with the control group, the high-dose group had a higher fetal death rate, and the average fetal body weight was higher in the low-dose group but lower in the high-dose group. Nicotinamide supplementation led to a decrease in placental and fetal hepatic genomic DNA methylation and genomic uracil contents (a factor modifying DNA for diversity) in the placenta and fetal liver and brain, which could be completely or partially prevented by betaine. Moreover, nicotinamide supplementation induced tissue-specific alterations in the mRNA expression of the genes encoding nicotinamide N-methyltransferase, DNA methyltransferase 1, catalase and tumour protein p53 in the placenta and fetal liver. High-dose nicotinamide supplementation increased fetal hepatic α-fetoprotein mRNA level, which was prevented by betaine supplementation. It is concluded that maternal nicotinamide supplementation can induce changes in fetal epigenetic modification and DNA base composition. The present study raises the concern that maternal nicotinamide supplementation may play a role in the development of epigenetic-related diseases in the offspring.

  1. Neoadjuvant therapy of rectal cancer using oral tegaful-uracil (UFT) plus concomitant radiotherapy--a case report.

    PubMed

    Yamaguchi, Yoshiyuki; Ohshita, Akiko; Hironaka, Katsuji; Emi, Manabu; Kawabuchi, Yoshiharu; Sakatani, Akio; Arihiro, Koji

    2005-09-01

    A 59-year-old male patient with rectal cancer 2 cm in diameter (T2) at the peritoneal reflection with suspicious left lateral node metastasis was treated with 400 mg of preoperative oral uracil and tegaful (UFT) for 5 weeks, 5 days a week in combination with concomitant radiotherapy of 45 Gy per 25 fractions for 5 weeks. After resting for another 5 weeks, colon fiberscopy, barium enema, and computed tomography revealed a trace of the primary tumor and a 40% shrinkage of the lateral metastasis. The serum CEA level decreased to the normal range during treatment. The adverse effects were nausea, bloody stool and elevation of transaminase, all at grade 1. Low anterior resection with a left hemi-lateral lymphadenectomy was performed through a suprapubic, one hand-size incision without laparoscopy. The preoperative treatment did not affect any operative procedures, and no postoperative complications occurred. The surgical specimen showed that the rectal tumor had been remarkably shrunk by the preoperative treatment, to the level of a superficial type tumor. Histological analysis indicated moderately differentiated adenocarcinoma cells that were present at only 2 mm in diameter in the mucosal layer, 6 mm in the submucosal layer, and 1 mm or less in the muscular layer with scar formation. No metastasis was detected in the 16 lymph nodes dissected, but an organizing tumor thrombus, which had preoperatively been diagnosed as lateral node metastasis, was detected. These results suggest that preoperative oral UFT plus concomitant radiotherapy may be a feasible, tolerable and effective treatment for patients with rectal cancer.

  2. Molecular Dynamics Simulations of the Bacterial UraA H+-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin

    PubMed Central

    Kalli, Antreas C.; Sansom, Mark S. P.; Reithmeier, Reinhart A. F.

    2015-01-01

    The Escherichia coli UraA H+-uracil symporter is a member of the nucleobase/ascorbate transporter (NAT) family of proteins, and is responsible for the proton-driven uptake of uracil. Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1) 1-palmitoyl 2-oleoyl-phosphatidylcholine (POPC); 2) 1-palmitoyl 2-oleoyl-phosphatidylethanolamine (POPE); and 3) a mixture of 75% POPE, 20% 1-palmitoyl 2-oleoyl-phosphatidylglycerol (POPG); and 5% 1-palmitoyl 2-oleoyl-diphosphatidylglycerol/cardiolipin (CL) to mimic the lipid composition of the bacterial inner membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal structure of this membrane transport protein, followed by atomistic simulations. The overall fold of the protein in lipid bilayers remained similar to the crystal structure in detergent on the timescale of our simulations. Simulations were performed in the absence of uracil, and resulted in a closed state of the transporter, due to relative movement of the gate and core domains. Anionic lipids, including POPG and especially CL, were found to associate with UraA, involving interactions between specific basic residues in loop regions and phosphate oxygens of the CL head group. In particular, three CL binding sites were identified on UraA: two in the inner leaflet and a single site in the outer leaflet. Mutation of basic residues in the binding sites resulted in the loss of CL binding in the simulations. CL may play a role as a “proton trap” that channels protons to and from this transporter within CL-enriched areas of the inner bacterial membrane. PMID:25729859

  3. The methyl- and aza-substituent effects on nonradiative decay mechanisms of uracil in water: a transient absorption study in the UV region.

    PubMed

    Hua, XinZhong; Hua, LinQiang; Liu, XiaoJun

    2016-05-18

    The nonradiative decay dynamics of photo-excited uracil (Ura) and its derivatives, i.e., thymine (5-methyluracil, Thy), 6-methyluracil (6-MU) and 6-azauracil (6-AU) in water, has been studied using a femtosecond transient absorption method. The molecules are populated in the lowest (1)ππ* state by a pump pulse at 266 nm, and a broadband continuum in the deep UV region is then employed as the probe. The extension of the continuous UV probe down to 250 nm enables us to investigate comprehensively the population dynamics of the ground states for those molecules and to uncover the substituent effects on nonradiative decay dynamics of uracil. Vibrational cooling in the ground states of Ura, Thy and 6-MU has been directly observed for the first time, providing solid evidence of the ultrafast (1)ππ* → S0 decay. In combination with the ground state bleaching signals, it is consolidated that their lowest (1)ππ* state decays via two parallel pathways, i.e., (1)ππ* → S0 and (1)ππ* → (1)nπ*. Moreover, the contribution of the (1)ππ* → (1)nπ* channel is found to be much smaller for Thy or 6-MU than for Ura. Different from methyl-substitution, the initial (1)ππ* state of the aza-substituent 6-AU decays primarily to the (1)nπ* state, while the (1)ππ* → S0 channel can be negligible. Our study provides a comprehensive understanding of the substituent effects on the excited-state dynamics of uracil in water.

  4. Concomitant chemoradiotherapy using carboplatin, tegafur-uracil and leucovorin for stage III and IV head-and-neck cancer: results of GORTEC Phase II study.

    PubMed

    Fesneau, Melanie; Pointreau, Yoann; Chapet, Sophie; Martin, Laurent; Pommier, Pascal; Alfonsi, Marc; Laguerre, Brigitte; Feham, Nasreddine; Berger, Christine; Garaud, Pascal; Calais, Gilles

    2010-01-01

    Concomitant chemoradiotherapy is the standard treatment of locally advanced, nonresectable, head-and-neck squamous cell carcinoma. However, the optimal chemotherapy regimen is still controversial. The objective of this Phase II study was to evaluate the feasibility and efficacy of a concomitant treatment using tegafur-uracil, leucovorin, carboplatin, and radiotherapy. A total of 77 patients with head-and-neck squamous cell carcinoma Stage III and IVA were enrolled between October 2003 and July 2005. Of the 77 patients, 72 were eligible. They were treated with tegafur-uracil (300 mg/m(2)/d) and leucovorin (75 mg/d) from Days 1 to 19 and from Days 29 to 47 and carboplatin (70 mg/m(2) intravenously for 4 consecutive days), in three cycles every 21 days. Conventional radiotherapy was delivered to a total dose of 70 Gy in 35 fractions. With a mean follow-up of 22.8 months, the 3-year locoregional control, overall survival and disease-free survival actuarial rate was 33.1%, 41.9%, and 27.2%, respectively. The compliance of the treatment was correct. The main acute toxicity was mucositis, with 62% Grade 3-4. Three patients (4.2%) died of acute toxicity. The incidence and severity of late toxicity was acceptable, with 32% Grade 3 and no Grade 4 toxicity. The protocol of concomitant chemoradiotherapy using tegafur-uracil, leucovorin, and carboplatin for locally advanced unresectable head-and-neck squamous cell carcinoma is feasible. The compliance was correct. The incidence and severity of the acute and late toxicities were acceptable, but not improved. The efficacy of this regimen seems equivalent to the main protocols of concurrent chemoradiotherapy. It represents a possible alternative for patients without an intravenous catheter.

  5. Gamma-irradiated and nonirradiated Eimeria tenella sporozoites exhibit differential uracil uptake and expression of a 7- to 10-kDa metabolic antigen.

    PubMed

    Jenkins, M C; Chute, M B; Danforth, H D; Lillehoj, H S

    1995-06-01

    Eimeria tenella sporozoites were exposed in the oocyst form to either an optimum (15 kRad) or a high (25 kRad) dose of gamma irradiation and used to infect cultured chicken embryo fibroblasts (CEF). The sporozoite-infected CEF monolayer was pulsed at time of infection or 24 hr postinfection with [3H]uracil and harvested 24 hr later to measure sporozoite metabolic activity. Sporozoites exposed to either 0 or 15 kRad gamma irradiation incorporated similar (P > 0.05) amounts of [3H]uracil during the first and second 24-hr periods after infection. However, there was a significant decrease (P < 0.05) in [3H]uracil uptake by 25 kRad-exposed sporozoites compared to nonirradiated and 15 kRad-irradiated sporozoites. Indirect immunofluorescence (IFA) staining of E. tenella sporozoite-infected CEFs using monoclonal antibodies (MAb) specific for somatic or "metabolic" antigens showed that gamma irradiation also affected the release of intracellular metabolites. Regardless of irradiation dose, extracellular sporozoites exhibited similar intensity of immunofluorescence when stained with either somatic antigen- or metabolic antigen-reactive MAb. Also, somatic antigen expression was similar for intracellular parasites irrespective of radiation dose. However, metabolic 7- to 10-kDa antigen expression by 25 kRad-irradiated sporozoites was markedly reduced compared to nonirradiated or 15 kRad-irradiated intracellular sporozoites. These results were corroborated by immunostaining sporozoite/CEF protein-impregnated Immobilon membrane with somatic or metabolic 7- to 10-kDa antigen-reactive MAb. These findings may indicate that the metabolic 7- to 10-kDa antigen is involved in protective immunity elicited by nonirradiated and/or 15 kRad-irradiated E. tenella sporozoites.

  6. Highly Accurate CCSD(T) and DFT–SAPT Stabilization Energies of H-Bonded and Stacked Structures of the Uracil Dimer

    SciTech Connect

    Pitonak, Michal; Riley, Kevin E.; Neogrady, Pavel; Hobza, Pavel

    2008-06-23

    The CCSD(T) interaction energies for the H-bonded and stacked structures of the uracil dimer are determined at the aug-cc-pVDZ and aug-cc-pVTZ levels. On the basis of these calculations we can construct the CCSD(T) interaction energies at the complete basis set (CBS) limit. The most accurate energies, based either on direct extrapolation of the CCSD(T) correlation energies obtained with the aug-cc-pVDZ and aug-cc-pVTZ basis sets or on the sum of extrapolated MP2 interaction energies (from aug-cc-pVTZ and aug-cc-pVQZ basis sets) and extrapolated ΔCCSD(T) correction terms [difference between CCSD(T) and MP2 interaction energies] differ only slightly, which demonstrates the reliability and robustness of both techniques. The latter values, which represent new standards for the H-bonding and stacking structures of the uracil dimer, differ from the previously published data for the S22 set by a small amount. This suggests that interaction energies of the S22 set are generated with chemical accuracy. The most accurate CCSD(T)/CBS interaction energies are compared with interaction energies obtained from various computational procedures, namely the SCS–MP2 (SCS: spin-component-scaled), SCS(MI)–MP2 (MI: molecular interaction), MP3, dispersion-augmented DFT (DFT–D), M06–2X, and DFT–SAPT (SAPT: symmetry-adapted perturbation theory) methods. Among these techniques, the best results are obtained with the SCS(MI)–MP2 method. Remarkably good binding energies are also obtained with the DFT–SAPT method. Both DFT techniques tested yield similarly good interaction energies. The large magnitude of the stacking energy for the uracil dimer, compared to that of the benzene dimer, is explained by attractive electrostatic interactions present in the stacked uracil dimer. These interactions force both subsystems to approach each other and the dispersion energy benefits from a shorter intersystem separation.

  7. Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments.

    PubMed

    Molina, Estefanía Rossich; Ortiz, Daniel; Salpin, Jean-Yves; Spezia, Riccardo

    2015-12-01

    In this study we have coupled mixed quantum-classical (quantum mechanics/molecular mechanics) direct chemical dynamics simulations with electrospray ionization/tandem mass spectrometry experiments in order to achieve a deeper understanding of the fragmentation mechanisms occurring during the collision induced dissociation of gaseous protonated uracil. Using this approach, we were able to successfully characterize the fragmentation pathways corresponding to ammonia loss (m/z 96), water loss (m/z 95) and cyanic or isocyanic acid loss (m/z 70). Furthermore, we also performed experiments with isotopic labeling completing the fragmentation picture. Remarkably, fragmentation mechanisms obtained from chemical dynamics simulations are consistent with those deduced from isotopic labeling.

  8. Efficacy of preoperative radiation therapy for resectable rectal adenocarcinoma when combined with oral tegafur-uracil modulated with leucovorin: results from a phase II study.

    PubMed

    Uzcudun, Ana Escribano; Batlle, Jaime Feliu; Velasco, Jesús Calvillo; Sánchez Santos, María Elena; Carpeño, Javier De Castro; Grande, Antonio García; Juberías, Alberto Mata; Piñeiro, Elena Hernández; Olivar, Lara Miralles; García, Alfredo García

    2002-10-01

    The aim of this study was to evaluate the efficacy of preoperative radiation therapy for resectable rectal adenocarcinoma (T3-T4) when delivered in combination with chemotherapy (oral tegafur-uracil modulated with leucovorin). Thirty-eight patients (23 males; mean age, 62 years.) with histologically proven rectal adenocarcinoma with primary tumor clinical classification T3-T4 (resectable) and N0 or N1-N2, according to TNM staging system, took part in the present clinical trial. After tumor and metastasis resectability confirmation, radiation therapy was administered by delivering a dose of 45 Gy in 25 fractions for 5 weeks. Chemotherapy treatment was initiated on the same day as radiotherapy and consisted of intravenous infusion of 6S-steroisomer of leucovorin 250 mg/m /day in 2 hours on Day 1, followed by oral 350 or 300 mg/m /day of tegafur (a 5-fluorouracil prodrug) plus uracil on Days 1 to 14 divided into 2 daily doses, and oral 6S-steroisomer of leucovorin 7.5 mg/12 hours on Days 2 to 14, with a total of 102 courses of neoadjuvant chemotherapy (, mean of 2.7 courses per patient). Six additional courses of tegafur-uracil were given postoperatively to all 38 patients but 1 who refused. As a result of preoperative chemoradiation treatment, 4 (10.5 percent) complete responses, 20 (52.6 percent) partial responses, and 14 (36.8 percent) patients with disease stabilization were observed. No patients had preoperative disease progression. Histologically proven downstaging was observed in 23 (60 percent) patients. On initial evaluation, only 39 percent of patients were considered as being good candidates for sphincter-preserving surgery; however, on preoperative chemoradiation completion this figure increased up to 60 percent. For the 23 patients eventually undergoing sphincter-preserving surgery, postoperative sphincter function assessment showed excellent function in 15 (65 percent) patients, good in 5 (22 percent), fair in 2 (9 percent), and poor in 1(4 percent

  9. Crystal structure of 3-[({2-[bis-(2-hy-droxy-benz-yl)amino]-eth-yl}(2-hy-droxy-benz-yl)amino)-meth-yl]-2-hydroxy-5-methyl-benzaldehyde.

    PubMed

    Fonseca, Alexandra S; Bortoluzzi, Adailton J

    2014-12-01

    The non-symmetric title mol-ecule, C32H34N2O5, is based on a tetra-substituted ethyl-enedi-amine backbone. The mol-ecular structure consists of three hy-droxy-benzyl groups and one 2-hy-droxy-5-methyl-benzaldehyde group bonded to the N atoms of the di-amine unit. The ethyl-enedi-amine skeleton shows a regular extended conformation, while the spatial orientation of the phenol arms is governed by hydrogen bonds. In the 2-hy-droxy-5-methyl-benzaldehyde group, an intra-molecular S(6) O-H⋯O hydrogen bond is observed between the alcohol and aldehyde functions, and the neighbouring phenol arm participates in an intra-molecular S(6) O-H⋯N hydrogen bond. The third phenol group is involved in a bifurcated intra-molecular hydrogen bond with graph-set notation S(6) for O-H⋯N and O-H⋯O intra-molecular hydrogen bonds between neighbouring amine and phenol arms, respectively. Finally, the fourth phenol group acts as an acceptor in a bifurcated intra-molecular hydrogen bond and also acts as donor in an inter-molecular hydrogen bond, which connects inversion-related mol-ecules into dimers with R 4 (4)(8) ring motifs.

  10. Intramolecular vibrational redistribution in the non-radiative excited state decay of uracil in the gas phase: an ab initio molecular dynamics study.

    PubMed

    Carbonniere, Philippe; Pouchan, Claude; Improta, Roberto

    2015-05-07

    We report a study of intramolecular vibrational distribution (IVR) occurring in the electronic ground state of uracil (S0) in the gas phase, following photoexcitation in the lowest energy bright excited state (Sπ) and decay through the ethylene-like Sπ/S0 Conical Intersection (CI-0π). To this aim we have performed 20 independent ab initio molecular dynamics simulations starting from CI-0π (ten of them with 1 eV kinetic energy randomly distributed over the different molecular degrees of freedom) and 10 starting from the ground state minimum (Franck-Condon, FC, point), with the excess kinetic energy equal to the energy gap between CI-0π and the FC point. The simulations, exploiting PBE0/6-31G(d) calculations, were performed over an overall period of 10 ps. A thorough statistical analysis of the variation of the geometrical parameters of uracil during the simulation time and of the distribution of the kinetic energy among the different vibrational degrees of freedom provides a consistent picture of the IVR process. In the first 0-200 fs the structural dynamics involve mainly the recovery of the average planarity. In the 200-600 fs time range, a substantial activation of CO and NH degrees of freedom is observed. After 500-600 fs most of the geometrical parameters reach average values similar to those found after 10 ps, though the system cannot be considered to be in equilibrium yet.

  11. RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines.

    PubMed

    Shimada, Tomohiro; Hirao, Kiyo; Kori, Ayako; Yamamoto, Kaneyoshi; Ishihama, Akira

    2007-11-01

    Using the genomic SELEX, a total of six Escherichia coli DNA fragments have been identified, which formed complexes with transcription factor RutR. The RutR regulon was found to include a large number of genes encoding components for not only degradation of pyrimidines but also transport of glutamate, synthesis of glutamine, synthesis of pyrimidine nucleotides and arginine, and degradation of purines. DNase I footprinting indicated that RutR recognizes a palindromic sequence of TTGACCAnnTGGTCAA. The RutR box in P1 promoter of carAB encoding carbamoyl phosphate synthetase, a key enzyme of pyrimidine synthesis, overlaps with the PepA (CarP) repressor binding site, implying competition between RutR and PepA. Adding either uracil or thymine abolished RutR binding in vitro to the carAB P1 promoter. Accordingly, in the rutR-deletion mutant or in the presence of uracil, the activation in vivo of carAB P1 promoter was markedly reduced. Northern blot analysis of the RutR target genes indicated that RutR represses the Gad system genes involved in glutamate-dependent acid resistance and allantoin degradation. Altogether we propose that RutR is the pyrimidine sensor and the master regulator for a large set of the genes involved in the synthesis and degradation of pyrimidines.

  12. Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose.

    PubMed

    Yi, Gang-Shun; Wang, Wei-Wei; Cao, Wei-Guo; Wang, Feng-Ping; Liu, Xi-Peng

    2017-01-18

    Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2' hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2'-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs' catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes.

  13. Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose

    PubMed Central

    Yi, Gang-Shun; Wang, Wei-Wei; Cao, Wei-Guo; Wang, Feng-Ping; Liu, Xi-Peng

    2017-01-01

    Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2′ hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2′-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs’ catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes. PMID:28106786

  14. Tritritionikkomycin Z, (uracil-5- sup 3 H,pyridyl-2,4- sup 3 H sub 2 ): Radiolabeling of a potent inhibitor of fungal and insect chitin synthetase

    SciTech Connect

    Ando, Tetsu; Tecle, B.; Toia, R.F.; Casida, J.E. )

    1990-08-01

    Nikkomycin Z (NZ) (a potent fungicide, insecticide, miticide, and inhibitor of fungal and insect chitin synthetase) was converted to a mixture of specific mono-, di-, and tribromo derivatives (BrNZ, Br{sub 2}NZ, and Br{sub 3}NZ, respectively) on reaction with N-bromosuccinimide in N,N-dimethylformamide. Substitution by bromine occurred first at the 2-position of the 3-hydroxypyridyl moiety, second at the 5-position of the uracil moiety, and finally at the 4-position of the 3-hydroxypyridyl moiety as observed both for NZ and for mixtures of uridine and 3-hydroxy-6-methylpyridine as model compounds representative of the moieties of NZ. Following fractionation of the various bromonikkomycin derivatives by HPLC, their structures were assigned by NMR, MS, and UV analyses. Catalytic reductive debromination of Br{sub 3}NZ with tritium gas over palladium on carbon gave (uracil-5-{sup 3}H,pyridyl-2,4-{sup 3}H{sub 2})NZ. This material has sufficiently high specific activity ({approximately}60 Ci/mmol) and suitable positions of labeling to study its uptake, distribution, metabolism, and possible target site interactions in fungal and insect systems.

  15. Influence of halogenation on the properties of uracil and its noncovalent interactions with alkali metal ions. Threshold collision-induced dissociation and theoretical studies.

    PubMed

    Yang, Zhibo; Rodgers, M T

    2004-12-15

    The influence of halogenation on the properties of uracil and its noncovalent interactions with alkali metal ions is investigated both experimentally and theoretically. Bond dissociation energies of alkali metal ion-halouracil complexes, M+(XU), are determined using threshold collision-induced dissociation techniques in a guided ion beam mass spectrometer, where M+ = Li+, Na+, and K+ and XU = 5-fluorouracil, 5-chlorouracil, 6-chlorouracil, 5-bromouracil, and 5-iodouracil. The structures and theoretical bond dissociation energies of these complexes are determined from ab initio calculations. Theoretical calculations are also performed to examine the influence of halogenation on the acidities, proton affinities, and Watson-Crick base pairing energies. Halogenation of uracil is found to produce a decrease in the proton affinity, an increase in the alkali metal ion binding affinities, an increase in the acidity, and stabilization of the A::U base pair. In addition, alkali metal ion binding is expected to lead to an increase in the stability of nucleic acids by reducing the charge on the nucleic acid in a zwitterion effect as well as through additional noncovalent interactions between the alkali metal ion and the nucleobases.

  16. [Over-expression of uracil DNA glycosylase 2 (UNG2) enhances the resistance to oxidative damage in HepG2 cells].

    PubMed

    Cao, Liyan; Cheng, Shan; Du, Juan; Guo, Yanhai; Huang, Xiaofeng

    2017-04-01

    Objective To investigate the uracil glycosidic enzyme activity of uracil DNA glycosylase 2 (UNG2) and study the role of UNG2 in the resistance of antioxidant stress of HepG2 cells. Methods The UNG2-expressing vector was built. Western blotting was used to detect the expression of UNG2. Immunofluorescence staining was performed to observe the cellular location of UNG2. Oligonucleotide was used as substrate for the determination of the UNG2 glycosidic enzyme activity. H2O2 toxicity assay was done to study the function of UNG2 in the antioxidant resistance of hepatocellular carcinoma HepG2 cells. Results UNG2 was successfully over-expressed in HEK293FT cells, and UNG2 was found to be mainly located in nucleus. Enzyme activity assay showed that UNG2 had significant oligonucleotide dU glycosidic enzyme activity. H2O2 toxicity assay showed that over-expressed UNG2 could remarkably increase the survival of HepG2 cells after exposed to H2O2. Conclusion UNG2 possesses specific DNA glycosidic enzyme activity, and it can protect HepG2 cells against oxidative stress damage.

  17. Initial excited-state structural dynamics of 6-substituted uracil derivatives: femtosecond angle and bond lengthening dynamics in pyrimidine nucleobase photochemistry.

    PubMed

    Teimoory, Faranak; Loppnow, Glen R

    2014-12-26

    Substituents on the pyrimidine ring of nucleobases appear to play a major role in determining their initial excited-state structural dynamics and resulting photochemistry. To better understand the determinants of nucleobase initial excited-state structural dynamics, we have measured the absorption and resonance Raman excitation profiles of 6-deuterouracil (6-d-U) and 6-methyluracil (6-MeU). Simulation of the resonance Raman excitation profiles and absorption spectrum with a self-consistent, time-dependent formalism shows the effect of the deuterium and methyl group on the photochemically active internal coordinates, i.e. C5C6 stretch and C5X and C6X bends. The methyl group on either the C5 or C6 position of uracil equally increases the excited-state reorganization energies along the C5C6 stretch. However, a lower reorganization energy of the C5X + C6X bends in 6-MeU than uracil and 5-MeU shows that C6 methyl substituents reduce the bending reorganization energy. In addition, deuterium substitution at either C5 or C6 has a much smaller effect on the initial excited-state structural dynamics than methyl substitution, consistent with a mass effect. These results will be discussed in light of the resulting photochemistry of pyrimidine nucleobases.

  18. Unravelling the potential of a new uracil phosphoribosyltransferase (UPRT) from Arabidopsis thaliana in sensitizing HeLa cells towards 5-fluorouracil.

    PubMed

    Narayanan, Sharmila; Sanpui, Pallab; Sahoo, Lingaraj; Ghosh, Siddhartha Sankar

    2016-10-01

    In silico studies with uracil phosphoribosyltransferase from Arabidopsis thaliana (AtUPRT) revealed its lower binding energies for uracil and 5-fluorouracil (5-FU) as compared to those of bacterial UPRT indicating the prospective of AtUPRT in gene therapy implications. Hence, AtUPRT was cloned and stably expressed in cervical cancer cells (HeLa) to investigate the effect of prodrug 5-FU on these transfected cancer cells. The treatment of AtUPRT-expressing HeLa (HeLa-UPP) cells with 5-FU for 72h resulted in significant decrease in cell viability. Moreover, 5-FU was observed to induce apoptosis and perturb mitochondrial membrane potential in HeLa-UPP cells. While cell cycle analysis revealed significant S-phase arrest as a result of 5-FU treatment in HeLa-UPP cells, quantitative gene expression analysis demonstrated simultaneous upregulation of important cell cycle related genes, cyclin D1 and p21. The survival fractions of non-transfected, vector-transfected and AtUPRT-transfected HeLa cells, following 5-FU treatment, were calculated to be 0.425, 0.366 and 0.227, respectively.

  19. Synthesis of analogues of the O-beta-D-ribofuranosyl nucleoside moiety of liposidomycins. Part 1: contribution of the amino group and the uracil moiety upon the inhibition of MraY.

    PubMed

    Dini, C; Drochon, N; Feteanu, S; Guillot, J C; Peixoto, C; Aszodi, J

    2001-02-26

    The O-beta-D-ribofuranosyl nucleoside I is the minimal structural entity of liposidomycins maintaining enzyme inhibitory activity. Modifications performed on both the primary amine and the uracil moieties clearly demonstrate their major contribution to the inhibition of the bacterial translocase (MraY).

  20. Nucleic acid related compounds. 65. New syntheses of 1-(beta-D-arabinofuranosyl)-5(E)-(2-iodovinyl)uracil (IVAraU) from vinylsilane precursors. Radioiodine uptake as a marker for thymidine kinase positive herpes viral infections

    SciTech Connect

    Robins, M.J.; Manfredini, S.; Wood, S.G.; Wanklin, R.J.; Rennie, B.A.; Sacks, S.L. )

    1991-07-01

    (Trimethylsilyl)acetylene was coupled with 1-(2,3,5-tri-O-acetyl-beta-D- arabinofuranosyl)-5-iodouracil to give 1- (2,3,5-tri-O-acetyl-beta-D-arabinofuranosyl)-5-(2-(trimethylsilyl)eth yny l) uracil. Lindlar hydrogenation of 4 gave 1-(2,3,4-tri-O-acetyl-beta-D-arabinofuranosyl)-5(Z)-(2- (trimethylsilyl)vinyl)uracil. Treatment of 5 with iodine monochloride (or sodium iodide/phenyliodine(III) dichloride) in benzene gave 1-(2,3,5-tri-O-acetyl-beta-D-arabinofuranosyl)-5(E)-(2-iodovinyl)uracil (7), whereas polar solvents favored the (Z)-iodovinyl isomer 8. Deacetylation of 7 gave 1-(beta-D-arabinofuranosyl)-5(E)-(2-iodovinyl)uracil (IVAraU, 9). A microscale in situ synthesis with Na{asterisk}I gave ({asterisk}I)IVAraU. Treatment of HSV-infected cells with (125I)IVAraU resulted in virus-dependent uptake associated with nucleoside phosphorylation by wild type or acyclovir-resistant DNA polymerase mutants (but not with TK-HSV-1 mutants). Uptake was virus-inoculum dependent and was detectable within 4 h postinfection. The process was not completely reversible. Virus-specified uptake of (125I)IVAraU may allow automated in vitro detection of HSV isolates.

  1. Synthesis and Characterization of bis[(2-ethyl-5-methyl-imidazo-4-yl)methyl]Sulfide and Its Coordination Behavior toward Cu(II) as a Possible Approach of a Copper Site Type I

    PubMed Central

    Barrón-Garcés, Juan D.; Mendoza-Díaz, Guillermo; Vilchez-Aguado, Florina; Bernès, Sylvain

    2009-01-01

    The synthesis and characterization of a novel ligand, bis[(2-ethyl-5-methyl-imidazo-4-yl)methyl]sulfide (bemims), as well as a bemims-containing copper(II) coordination complex are described. In this complex, [Cu(bemims)X 2] with X = NO3 −, bemims acts as a tridentate ligand and two monodentate nitrate ions complete the coordination sphere. Both imidazole N atoms and the thioether S atom of bemims participate in coordination. The Cu(II) ion is five-coordinated with a slightly distorted square-pyramidal geometry (τ = .09). Electrochemical studies and spectroscopic data for this complex are compared with some blue copper proteins in order to assess its ability to mimic the copper center of type I copper proteins. PMID:19587830

  2. Alum Catalyzed Simple, Efficient, and Green Synthesis of 2-[3-Amino-5-methyl-5-(pyridin-3-yl)-1,5-dihydro-4H-1,2,4-triazol-4-yl]propanoic Acid Derivatives in Aqueous Media

    PubMed Central

    Sachdeva, Harshita; Dwivedi, Diksha; Saroj, Rekha

    2013-01-01

    Alum (KAl(SO4)2·12H2O) is an inexpensive, efficient, and nontoxic catalyst used for the synthesis of 2-[3-amino-5-methyl-5-(pyridin-3-yl)-1,5-dihydro-4H-1,2,4-triazol-4-yl]propanoic acid derivatives in aqueous media by the reaction of 3-acetyl pyridine (1), amino acids (2)/(6), and thiosemicarbazide (4) at 80°C. This methodology offers significant improvements for the synthesis of products with regards to the yield of products, simplicity in operation, and green aspects by avoiding toxic catalysts which uphold the motto of green chemistry. Synthesized compounds have been characterized by FT-IR, 13C NMR, and 1HNMR spectroscopy. PMID:24288503

  3. Crystal structure of N-(7-di­bromo­methyl-5-methyl-1,8-naphthyridin-2-yl)benzamide–pyrrolidine-2,5-dione (1/1)

    PubMed Central

    Wang, Bang Zhong; Zhou, Jun Ping; Zhou, Yong; Luo, Jian Song; Yang, Jun Jie; Chi, Shao M.ing

    2017-01-01

    The title compound, C17H13Br2N3O·C4H5NO2, is a co-crystal of N-(7-di­bromo­methyl-5-methyl-1,8-naphthyridin-2-yl)benzamide and pyrrolidine-2,5-dione (succinimide). The benzamide mol­ecule exhibits pseudo-mirror symmetry, with an r.m.s. deviation of the non-H atoms of 0.09 Å (except for the two Br atoms). The angle between the least-squares planes of the two mol­ecules is 26.2 (2)°. In the crystal, the two mol­ecules are mutually linked by N—H⋯O and N—H⋯N hydrogen bonds. The packing is consolidated by C—H⋯(O,N) hydrogen bonds and π–π stacking inter­actions. PMID:28083121

  4. Synthesis, characterization and investigation of electrochemical and spectroelectrochemical properties of non-peripherally tetra-5-methyl-1,3,4-thiadiazole substituted copper(II) iron(II) and oxo-titanium (IV) phthalocyanines

    NASA Astrophysics Data System (ADS)

    Demirbaş, Ümit; Akyüz, Duygu; Akçay, Hakkı Türker; Barut, Burak; Koca, Atıf; Kantekin, Halit

    2017-09-01

    In this study novel substituted phthalonitrile (3) and non-peripherally tetra 5-Methyl-1,3,4-thiadiazole substituted copper(II) (4), iron(II) (5) and oxo-titanium (IV) (6) phthalocyanines were synthesized. These novel compounds were fully characterized by FT-IR, 1H NMR, UV-vis and MALDI-TOF mass spectroscopic techniques. Voltammetric and in situ spectroelectrochemical measurements were performed for metallo-phthalocyanines (4-6). TiIVOPc and FeIIPc showed metal-based and ligand-based electron transfer reactions while CuIIPc shows only ligand-based electron transfer reaction. Voltammetric measurements indicated that the complexes have reversible, diffusion controlled and one-electron redox reactions. The assignments of the redox processes and color of the electrogenerated species of the complexes were determined with in-situ spectroelectrochemical and electrocolorimetric measurements. These measurements showed that the complexes can be used as the electrochromic materials for various display technologies.

  5. Aquatic toxicity of nine aircraft deicer and anti-icer formulations and relative toxicity of additive package ingredients alkylphenol ethoxylates and 4,5-methyl-1H-benzotriazoles

    USGS Publications Warehouse

    Corsi, S.R.; Geis, S.W.; Loyo-Rosales, J. E.; Rice, C.P.

    2006-01-01

    Characterization of the effects of aircraft deicer and anti-icer fluid (ADAF) runoff on aquatic organisms in receiving streams is a complex issue because the identities of numerous toxic additives are proprietary and not publicly available. Most potentially toxic and endocrine disrupting effects caused by ADAF are due to the numerous additive package ingredients which vary among manufacturers and types of ADAF formulation. Toxicity investigations of nine ADAF formulations indicate that endpoint concentrations for formulations of different manufacturers are widely variable. Type IV ADAF (anti-icers) are more toxic than Type I (deicers) for the four organisms tested (Vibrio fischeri, Pimephales promelas, Ceriodaphnia dubia, and Selenastrum capricornutum). Acute toxicity endpoint concentrations ranged from 347 to 7700 mg/L as ADAF for Type IV and from 1550 to 45 100 mg/L for Type I formulations. Chronic endpoint concentrations ranged from 70 to 1300 mg/L for Type IV and from 37 to 18 400 mg/L for Type I formulations. Alkylphenol ethoxylates and tolyltriazoles are two known classes of additives. Nonylphenol, nonylphenol ethoxylates, octylphenol, octylphenol ethoxylates, and 4,5-methyl-1H-benzotriazoles were quantified in the nine ADAF formulations, and toxicity tests were conducted with nonylphenol ethoxylates and 4,5-methyl-1H-benzotriazoles. Toxicity units computed for glycol and these additives, with respect to toxicity of the ADAF formulations, indicate that a portion of ADAF toxicity can be explained by the known additives and glycols, but much of the toxicity is due to unidentified additives. ?? 2006 American Chemical Society.

  6. Insights into the mechanisms of ifosfamide encephalopathy: drug metabolites have agonistic effects on alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)/kainate receptors and induce cellular acidification in mouse cortical neurons.

    PubMed

    Chatton, J Y; Idle, J R; Vågbø, C B; Magistretti, P J

    2001-12-01

    Therapeutic value of the alkylating agent ifosfamide has been limited by major side effects including encephalopathy. Although the underlying biochemical processes of the neurotoxic side effects are still unclear, they could be attributed to metabolites rather than to ifosfamide itself. In the present study, the effects of selected ifosfamide metabolites on indices of neuronal activity have been investigated, in particular for S-carboxymethylcysteine (SCMC) and thiodiglycolic acid (TDGA). Because of structural similarities of SCMC with glutamate, the Ca(2+)(i) response of single mouse cortical neurons to SCMC and TDGA was investigated. SCMC, but not TDGA, evoked a robust increase in Ca(2+)(i) concentration that could be abolished by the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)/kainate receptor antagonist 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX), but only partly diminished by the N-methyl-D-aspartate receptor antagonist 10,11-dihydro-5-methyl-5H-dibenzo[a,d]cyclohepten-5,10-imine (MK=801). Cyclothiazide (CYZ), used to prevent AMPA/kainate receptor desensitization, potentiated the response to SCMC. Because activation of AMPA/kainate receptors is known to induce proton influx, the intracellular pH (pH(i)) response to SCMC was investigated. SCMC caused a concentration-dependent acidification that was amplified by CYZ. Since H(+)/monocarboxylate transporter (MCT) activity leads to similar cellular acidification, we tested its potential involvement in the pH(i) response. Application of the lactate transport inhibitor quercetin diminished the pH(i) response to SCMC and TDGA by 43 and 51%, respectively, indicating that these compounds may be substrates of MCTs. Taken together, this study indicates that hitherto apparently inert ifosfamide metabolites, in particular SCMC, activate AMPA/kainate receptors and induce cellular acidification. Both processes could provide the biochemical basis of the observed ifosfamide-associated encephalopathy.

  7. DNA Repair Enzyme Uracil DNA Glycosylase Is Specifically Incorporated into Human Immunodeficiency Virus Type 1 Viral Particles through a Vpr-Independent Mechanism

    PubMed Central

    Willetts, Karen E.; Rey, Françoise; Agostini, Isabelle; Navarro, Jean-Marc; Baudat, Yves; Vigne, Robert; Sire, Joséphine

    1999-01-01

    The Vpr protein, encoded by the human immunodeficiency virus type 1 (HIV-1) genome, is one of the nonstructural proteins packaged in large amounts into viral particles. We have previously reported that Vpr associates with the DNA repair enzyme uracil DNA glycosylase (UDG). In this study, we extended these observations by investigating whether UDG is incorporated into virions and whether this incorporation requires the presence of Vpr. Our results, with highly purified viruses, show that UDG is efficiently incorporated either into wild-type virions or into Vpr-deficient HIV-1 virions, indicating that Vpr is not involved in UDG packaging. Using an in vitro protein-protein binding assay, we reveal a direct interaction between the precursor form of UDG and the viral integrase (IN). Finally, we demonstrate that IN-defective viruses fail to incorporate UDG, indicating that IN is required for packaging of UDG into virions. PMID:9882380

  8. The pH optimum of native uracil-DNA glycosylase of Archaeoglobus fulgidus compared to recombinant enzyme indicates adaption to cytosolic pH.

    PubMed

    Knævelsrud, Ingeborg; Kazazic, Sabina; Birkeland, Nils-Kåre; Bjelland, Svein

    2014-01-01

    Uracil-DNA glycosylase of Archaeoglobus fulgidus (Afung) in cell extracts exhibited maximal activity around pH 6.2 as compared to pH 4.8 for the purified recombinant enzyme expressed in Escherichia coli. Native Afung thus seems to be adapted to the intracellular pH of A. fulgidus, determined to be 7.0±0.1. Both recombinant and native Afung exhibited a broad temperature optimum for activity around 80°C, reflecting the A. fulgidus optimal growth temperature of 83°C. Adaption to the neutral conditions in the A. fulgidus cytoplasm might be due to covalent modifications or accessory factors, or due to a different folding when expressed in the native host.

  9. Biasing Simulations of DNA Base Pair Parameters with Application to Propellor Twisting in AT/AT, AA/TT, and AC/GT Steps and Their Uracil Analogs.

    PubMed

    Peguero-Tejada, Alfredo; van der Vaart, Arjan

    2017-01-23

    An accurate and efficient implementation of the six DNA base pair parameters as order parameters for enhanced sampling simulations is presented. The parameter definitions are defined by vector algebra operations on a reduced atomic set of the base pair, and correlate very well with standard definitions. Application of the model is illustrated by umbrella sampling simulations of propeller twisting within AT/AT, AA/TT, and AC/GT steps and their uracil analogs. Strong correlations are found between propeller twisting and a number of conformational parameters, including buckle, opening, BI/BII backbone configuration, and sugar puckering. The thymine methyl group is observed to notably alter the local conformational free energy landscape, with effects within and directly upstream of the thymine containing base pair.

  10. Uracil-DNA glycosylase-treated reverse transcription loop-mediated isothermal amplification for rapid detection of avian influenza virus preventing carry-over contamination.

    PubMed

    Kim, Eun-Mi; Jeon, Hyo-Sung; Kim, Ji-Jung; Shin, Yeun-Kyung; Lee, Youn-Jeong; Yeo, Sang-Geon; Park, Choi-Kyu

    2016-09-30

    Here, we describe a uracil-DNA glycosylase (UNG)-treated reverse transcription loop-mediated isothermal amplification (uRT-LAMP) for the visual detection of all subtypes of avian influenza A virus (AIV). The uRT-LAMP assay can prevent unwanted amplification by carryover contamination of the previously amplified DNA, although the detection limit of the uRT-LAMP assay is 10-fold lower than that of the RT-LAMP without a UNG treatment. To the best of our knowledge, this is the first successful application of deoxyuridine triphosphate/UNG strategy in RT-LAMP for AIV detection, and the assay can be applied for the rapid, and reliable diagnosis of AIVs, even in contaminated samples.

  11. Uracil-DNA glycosylase-treated reverse transcription loop-mediated isothermal amplification for rapid detection of avian influenza virus preventing carry-over contamination

    PubMed Central

    Kim, Eun-Mi; Jeon, Hyo-Sung; Kim, Ji-Jung; Shin, Yeun-Kyung; Lee, Youn-Jeong; Yeo, Sang-Geon

    2016-01-01

    Here, we describe a uracil-DNA glycosylase (UNG)-treated reverse transcription loop-mediated isothermal amplification (uRT-LAMP) for the visual detection of all subtypes of avian influenza A virus (AIV). The uRT-LAMP assay can prevent unwanted amplification by carryover contamination of the previously amplified DNA, although the detection limit of the uRT-LAMP assay is 10-fold lower than that of the RT-LAMP without a UNG treatment. To the best of our knowledge, this is the first successful application of deoxyuridine triphosphate/UNG strategy in RT-LAMP for AIV detection, and the assay can be applied for the rapid, and reliable diagnosis of AIVs, even in contaminated samples. PMID:26726027

  12. Evaluation of the Role of the Vaccinia Virus Uracil DNA Glycosylase and A20 Proteins as Intrinsic Components of the DNA Polymerase Holoenzyme*

    PubMed Central

    Boyle, Kathleen A.; Stanitsa, Eleni S.; Greseth, Matthew D.; Lindgren, Jill K.; Traktman, Paula

    2011-01-01

    The vaccinia virus DNA polymerase is inherently distributive but acquires processivity by associating with a heterodimeric processivity factor comprised of the viral A20 and D4 proteins. D4 is also an enzymatically active uracil DNA glycosylase (UDG). The presence of an active repair protein as an essential component of the polymerase holoenzyme is a unique feature of the replication machinery. We have shown previously that the A20-UDG complex has a stoichiometry of ∼1:1, and our data suggest that A20 serves as a bridge between polymerase and UDG. Here we show that conserved hydrophobic residues in the N′ terminus of A20 are important for its binding to UDG. Our data argue against the assembly of D4 into higher order multimers, suggesting that the processivity factor does not form a toroidal ring around the DNA. Instead, we hypothesize that the intrinsic, processive DNA scanning activity of UDG tethers the holoenzyme to the DNA template. The inclusion of UDG as an essential holoenzyme component suggests that replication and base excision repair may be coupled. Here we show that the DNA polymerase can utilize dUTP as a substrate in vitro. Moreover, uracil moieties incorporated into the nascent strand during holoenzyme-mediated DNA synthesis can be excised by the viral UDG present within this holoenzyme, leaving abasic sites. Finally, we show that the polymerase stalls upon encountering an abasic site in the template strand, indicating that, like many replicative polymerases, the poxviral holoenzyme cannot perform translesion synthesis across an abasic site. PMID:21572084

  13. Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi)

    SciTech Connect

    Assefa, Netsanet Gizaw; Niiranen, Laila; Johnson, Kenneth A.; Leiros, Hanna-Kirsti Schrøder; Smalås, Arne Oskar; Willassen, Nils Peder; Moe, Elin

    2014-08-01

    A structural and biophysical study of the interactions between cod and human uracil-DNA N-glycosylase (UNG) and their inhibitor Ugi is presented. The stronger interaction between cod UNG and Ugi can be explained by a greater positive electrostatic surface potential. Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme–substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi) has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG–Ugi was determined to a resolution of 1.9 Å with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG–Ugi complex with previously determined structures of UNG–Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (K{sub b}) which is one order of magnitude larger than that for hUNG–Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein–Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.

  14. Quantitative assessment of the effect of uracil-DNA glycosylase on amplicon DNA degradation and RNA amplification in reverse transcription-PCR.

    PubMed

    Kleiboeker, Steven B

    2005-04-11

    Although PCR and RT-PCR provided a valuable approach for detection of pathogens, the high level of sensitivity of these assays also makes them prone to false positive results. In addition to cross-contamination with true positive samples, false positive results are also possible due to "carry-over" contamination of samples with amplicon DNA generated by previous reactions. To reduce this source of false positives, amplicon generated by reactions in which dUTP was substituted for dTTP can be degraded by uracil DNA glycosylase (UNG). UNG does not degrade RNA but will cleave contaminating uracil-containing DNA while leaving thymine-containing DNA intact. The availability of heat-labile UNG makes use of this approach feasible for RT-PCR. In this study, real-time RT-PCR was used to quantify UNG degradation of amplicon DNA and the effect of UNG on RNA detection. Using the manufacturers' recommended conditions, complete degradation of DNA was not observed for samples containing 250 copies of amplicon DNA. Doubling the UNG concentration resulted in degradation of the two lowest concentrations of DNA tested, but also resulted in an increase of 1.94 cycles in the CT for RNA detection. To improve DNA degradation while minimizing the effect on RNA detection, a series of time, temperature and enzyme concentrations were evaluated. Optimal conditions were found to be 0.25 U UNG per 25 microl reaction with a 20 min, 30 degrees C incubation prior to RT-PCR. Under these conditions, high concentrations of amplicon DNA could be degraded while the CT for RNA detection was increased by 1.2 cycles.

  15. The stress hormone corticosterone increases synaptic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors via serum- and glucocorticoid-inducible kinase (SGK) regulation of the GDI-Rab4 complex.

    PubMed

    Liu, Wenhua; Yuen, Eunice Y; Yan, Zhen

    2010-02-26

    Corticosterone, the major stress hormone, plays an important role in regulating neuronal functions of the limbic system, although the cellular targets and molecular mechanisms of corticosteroid signaling are largely unknown. Here we show that a short treatment of corticosterone significantly increases alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR)-mediated synaptic transmission and AMPAR membrane trafficking in pyramidal neurons of prefrontal cortex, a key region involved in cognition and emotion. This enhancing effect of corticosterone is through a mechanism dependent on Rab4, the small GTPase-controlling receptor recycling between early endosome and plasma membrane. Guanosine nucleotide dissociation inhibitor (GDI), which regulates the cycle of Rab proteins between membrane and cytosol, forms an increased complex with Rab4 after corticosterone treatment. Corticosterone also triggers an increased GDI phosphorylation at Ser-213 by the serum- and glucocorticoid-inducible kinase (SGK). Moreover, AMPAR synaptic currents and surface expression and their regulation by corticosterone are altered by mutating Ser-213 on GDI. These results suggest that corticosterone, via SGK phosphorylation of GDI at Ser-213, increases the formation of GDI-Rab4 complex, facilitating the functional cycle of Rab4 and Rab4-mediated recycling of AMPARs to the synaptic membrane. It provides a potential mechanism underlying the role of corticosteroid stress hormone in up-regulating excitatory synaptic efficacy in cortical neurons.

  16. 2-(3-Methoxyphenyl)-5-methyl-1,8-naphthyridin-4(1H)-one (HKL-1) induces G2/M arrest and mitotic catastrophe in human leukemia HL-60 cells

    SciTech Connect

    Hsu, Mei-Hua; Liu, Chin-Yu; Lin, Chiao-Min; Chen, Yen-Jung; Chen, Chun-Jen; Lin, Yu-Fu; Huang, Li-Jiau; Lee, Kuo-Hsiung; Kuo, Sheng-Chu

    2012-03-01

    2-(3-Methoxyphenyl)-5-methyl-1,8-naphthyridin-4(1H)-one (HKL-1), a 2-phenyl-1,8-naphthyridin-4-one (2-PN) derivative, was synthesized and evaluated as an effective antimitotic agent in our laboratory. However, the molecular mechanisms are uncertain. In this study, HKL-1 was demonstrated to induce multipolar spindles, sustain mitotic arrest and generate multinucleated cells, all of which indicate mitotic catastrophe, in human leukemia HL-60 cells. Western blotting showed that HKL-1 induces mitotic catastrophe in HL-60 cells through regulating mitotic phase-specific kinases (down-regulating CDK1, cyclin B1, CENP-E, and aurora B) and regulating the expression of Bcl-2 family proteins (down-regulating Bcl-2 and up-regulating Bax and Bak), followed by caspase-9/-3 cleavage. These findings suggest that HKL-1 appears to exert its cytotoxicity toward HL-60 cells in culture by inducing mitotic catastrophe. Highlights: ► HKL-1 is a potential antimitotic agent against HL-60 cells. ► HKL-1 induces spindle disruption and sustained resulted in mitotic catastrophe. ► CENP-E and aurora B protein expressions significantly reduced. ► Bcl-2 family protein expressions altered and caspase-9/-3 activation. ► HKL-1 is an attractive candidate for possible use as a novel antimitotic agent.

  17. Lanthanide complexes containing 5-methyl-1,2,4-triazolo[1,5-a] pyrimidin-7(4H)-one and their therapeutic potential to fight leishmaniasis and Chagas disease.

    PubMed

    Caballero, Ana B; Rodríguez-Diéguez, Antonio; Salas, Juan M; Sánchez-Moreno, Manuel; Marín, Clotilde; Ramírez-Macías, Inmaculada; Santamaría-Díaz, Noelia; Gutiérrez-Sánchez, Ramón

    2014-09-01

    In the last years, numerous and significant advances in lanthanide coordination chemistry have been achieved. The unique chemical nature of these metal ions which is conferred by their f-electrons has led to a wide range of coordination compounds with interesting structural, physical and also biological properties. Consequently, lanthanide complexes have found applications mainly in catalysis, gas adsorption, photochemistry and as diagnostic tools. However, research on their therapeutic potential and the understanding of their mechanism of action is still taking its first steps, and there is a distinct lack of research in the parasitology field. In the present work, we describe the synthesis and physical properties of seven new lanthanide complexes with the anionic form of the bioactive ligand 5-methyl-1,2,4-triazolo[1,5-a]pyrimidin-7(4H)-one (HmtpO), namely [Ln(mtpO)3(H2O)6]·9H2O (Ln=La(III), Nd(III), Eu(III), Gd(III), Tb(III), Dy(III) and Er(III)). In addition, results on the in vitro antiproliferative activity against Leishmania spp. and Trypanosoma cruzi are described. The high activity of the new compounds against parasite proliferation and their low cytotoxicity against reference host cell lines show a great potential of this type of compounds to become a new generation of highly effective and non-toxic antiparasitic agents to fight the so considered neglected diseases leishmaniasis and Chagas disease.

  18. Expression of N-methyl-D-aspartate (NMDA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) GluR2/3 receptors in the developing rat pineal gland.

    PubMed

    Kaur, C; Sivakumar, V; Ling, E A

    2005-10-01

    The expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) type glutamate (GluR2/3) receptors and N-methyl-D-aspartate receptor subtype 1 (NMDAR1) was carried out by immunohistochemistry, double immunofluorescence and real-time RT-PCR analysis in the pineal glands of 1-day to 6-wk-old rats in the present study. GluR2/3 immunopositive cells were distributed throughout the pineal gland and showed branching processes in all age groups. The NMDAR1 immunoreactivity, however, was observed in fewer branched cells. A constitutive mRNA expression of NMDAR1, GluR2 and GluR3 was detected in the pineal glands of various ages and showed no significant difference between the age groups studied. Immunohistochemical and double immunofluorescence results showed that the GluR2/3 were mainly expressed and co-localized with OX-42-positive microglia/macrophages and the glial fibrillary acidic protein (GFAP)-positive astrocytes. Co-localization of NMDAR1 with OX-42- and GFAP-positive cells was much less. The expression of these receptors on the glial cells suggests that they may be involved in the development and growth of the pineal gland in the early postnatal period (1 day to 3 wk) and subsequently in the regulation of melatonin synthesis.

  19. Extraction studies of selected actinide ions from aqueous solutions with 4-benzoyl-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione and tri-n-octylphosphine oxide

    SciTech Connect

    Hannink, N.J.; Hoffman, D.C. |; Smith, B.F.

    1991-11-01

    The first measurements of distribution coefficients (K{sub d}) for Cm(III), Bk(III), Cf(III), Es(III), and Fm(III) between aqueous perchlorate solutions and solutions of 4-benzoyl-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione (BMPPT) and the synergist tri-n-octylphosphine oxide (TOPO) in toluene are reported. Curium-243, berkelium-250, californium-249, einsteinium-254, and fermium-253 were used in these studies. The K{sub d} for {sup 241}Am was also measured and is in agreement with previously published results. Our new results show that the K{sub d}`s decrease gradually with increasing atomic number for the actinides with a dip at Cf. In general, the K{sub d}`s for these actinides are about a factor of 5 to 10 greater than the K{sub d}`s for the homologous lanthanides at a pH of 2.9, a BMPPT concentration of 0.2 M, and a TOPO concentration of 0.04 M. The larger K{sub d}`s for the actinides are consistent with greater covalent bonding between the actinide metal ion and the sulfur bonding site in the ligand.

  20. Extraction studies of selected actinide ions from aqueous solutions with 4-benzoyl-2,4-Dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione and Tri-n-octylphosphine oxide

    SciTech Connect

    Hannink, N.J.; Hoffman, D.C.; Smith, B.F.

    1992-07-01

    The first measurements of distribution coefficients (k{sub d}) for Cm(III), Bk(III), Cf(III), Es(III), and Fm(III) between aqueous perchlorate solutions and solutions of 4-benzoyl-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione (BMPPT) and the synergist tri-n-octylphosphine oxide (TOPO) in toluene are reported. Curium-243, berkelium-250, californium-249, einsteinium-254, and fermium-253 were used in these studies. The K{sub d} for {sup 241}Am was also measured and is in agreement with previously published results. Our new results show that the K{sub d}`s decrease gradually with increasing atomic number for the actinides with a dip at Cf. In general, the K{sub d}`s for these actinides are about about a factor of 10 greater than the K{sub d}`s for the homologous lanthanides at a pH of 2.9, a BMPPT concentration of 0.2 M, and a TOPO concentration of 0.04 M. The larger K{sub d}`s for the actinides are consistent with greater covalent bonding between the actinide metal ion and the sulfur bonding site in the ligand. 9 refs., 2 figs., 1 tab.

  1. Extraction studies of selected actinide ions from aqueous solutions with 4-benzoyl-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione and tri-n-octylphosphine oxide

    SciTech Connect

    Hannink, N.J.; Hoffman, D.C. California Univ., Berkeley, CA . Dept. of Chemistry); Smith, B.F. )

    1991-11-01

    The first measurements of distribution coefficients (K{sub d}) for Cm(III), Bk(III), Cf(III), Es(III), and Fm(III) between aqueous perchlorate solutions and solutions of 4-benzoyl-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione (BMPPT) and the synergist tri-n-octylphosphine oxide (TOPO) in toluene are reported. Curium-243, berkelium-250, californium-249, einsteinium-254, and fermium-253 were used in these studies. The K{sub d} for {sup 241}Am was also measured and is in agreement with previously published results. Our new results show that the K{sub d}'s decrease gradually with increasing atomic number for the actinides with a dip at Cf. In general, the K{sub d}'s for these actinides are about a factor of 5 to 10 greater than the K{sub d}'s for the homologous lanthanides at a pH of 2.9, a BMPPT concentration of 0.2 M, and a TOPO concentration of 0.04 M. The larger K{sub d}'s for the actinides are consistent with greater covalent bonding between the actinide metal ion and the sulfur bonding site in the ligand.

  2. In vivo antitumor effects of 4,7-dimethoxy-5-methyl-1,3-benzodioxole isolated from the fruiting body of Antrodia camphorata through activation of the p53-mediated p27/Kip1 signaling pathway.

    PubMed

    Tu, Shih-Hsin; Wu, Chih-Hsiung; Chen, Li-Ching; Huang, Ching-Shui; Chang, Hui-Wen; Chang, Chien-Hsi; Lien, Hsiu-Man; Ho, Yuan-Soon

    2012-04-11

    In this study, 4,7-dimethoxy-5-methyl-1,3-benzodioxole (SY-1) was isolated from three different sources of dried Antrodia camphorata (AC) fruiting bodies. AC is a medicinal mushroom that grows on the inner heartwood wall of Cinnamomum kanehirai Hay (Lauraceae), which is an endemic species that is used in Chinese medicine for its antitumor properties. We demonstrated that SY-1 [given as a 1-30 mg/kg body weight intraperitoneal (ip) injection three times per week] profoundly decreased the growth of COLO-205 human colon cancer cell tumor xenografts in an athymic nude mouse model. We further demonstrated that significant AC extract-mediated antitumor effects were observed at the highest concentration (5 g/kg body weight/day). No gross toxicity signs were observed (i.e., body weight changes, general appearance, or individual organ effects). Frozen COLO-205 xenograft tumors were pulverized in liquid N(2), and the expression of cell cycle regulatory proteins was detected by immunoblotting. We found that the p53-mediated p27/Kip1 protein was significantly induced in the low-dose (1 mg/kg body weight) SY-1-treated tumors, whereas the p21/Cip1 protein levels did not change. The G0/G1 phase cell cycle regulators induced by SY-1 were also associated with a significant decrease in cyclins D1, D3, and A. These results provide further evidence that SY-1 may have significance for cancer chemotherapy.

  3. 4,7-Dimethoxy-5-methyl-1,3-benzodioxole from Antrodia camphorata inhibits LPS-induced inflammation via suppression of NF-κB and induction HO-1 in RAW264.7 cells.

    PubMed

    Shie, Pei-Hsin; Wang, Sheng-Yang; Lay, Horng-Liang; Huang, Guan-Jhong

    2016-02-01

    Several benzenoid compounds have been isolated from Antrodia camphorata are known to have excellent anti-inflammatory activity. In this study, we investigated the anti-inflammatory potential of 4,7-dimethoxy-5-methyl-1,3-benzodioxole (DMB), one of the major benzenoid compounds isolated from the mycelia of A. camphorata. DMB significantly decreased the LPS-induced production of pro-inflammatory molecules, such as nitric oxide (NO), interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α) in RAW264.7 cells. In addition, DMB suppressed the protein levels of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) in a dose dependent manner. Moreover, DMB significantly suppressed LPS-induced nuclear translocation of nuclear factor-κB (NF-κB), and this inhibition was found to be associated with decreases in the phosphorylation and degradation of its inhibitor, inhibitory κB-α (IκB-α). Moreover, we found that DMB markedly inhibited the protein expression level of Toll-like receptor 4 (TLR4). Furthermore, treatment with DMB significantly increased hemoxygenase-1 (HO-1) expression in RAW264.7 cells, which is further confirmed by hemin, a HO-1 enhancer, significantly attenuated the LPS-induced pro-inflammatory molecules and iNOS and TLR4 protein levels. Taken together, the present study suggests that DMB may have therapeutic potential for the treatment of inflammatory diseases.

  4. Effects of (R)-(-)-5-methyl-1-nicotinoyl-2-pyrazoline on glutamate transporter 1 and cysteine/glutamate exchanger as well as ethanol drinking behavior in male, alcohol-preferring rats.

    PubMed

    Aal-Aaboda, Munaf; Alhaddad, Hasan; Osowik, Francis; Nauli, Surya M; Sari, Youssef

    2015-06-01

    Alcohol consumption is largely associated with alterations in the extracellular glutamate concentrations in several brain reward regions. We recently showed that glutamate transporter 1 (GLT-1) is downregulated following chronic exposure to ethanol for 5 weeks in alcohol-preferring (P) rats and that upregulation of the GLT-1 levels in nucleus accumbens and prefrontal cortex results, in part, in attenuating ethanol consumption. Cystine glutamate antiporter (xCT) is also downregulated after chronic ethanol exposure in P rats, and its upregulation could be valuable in attenuating ethanol drinking. This study examines the effect of a synthetic compound, (R)-(-)-5-methyl-1-nicotinoyl-2-pyrazoline (MS-153), on ethanol drinking and expressions of GLT-1 and xCT in the amygdala and the hippocampus of P rats. P rats were exposed to continuous free-choice access to water, 15% and 30% ethanol, and food for 5 weeks, after which they received treatments of MS-153 or vehicle for 5 days. The results show that MS-153 treatment significantly reduces ethanol consumption. It was revealed that GLT-1 and xCT expressions were downregulated in both the amygdala and the hippocampus of ethanol-vehicle-treated rats (ethanol-vehicle group) compared with water-control animals. MS-153 treatment upregulated GLT-1 and xCT expressions in these brain regions. These findings demonstrate an important role for MS-153 in these glutamate transporters for the attenuation of ethanol-drinking behavior.

  5. Design, synthesis, and biological evaluation of novel transrepression-selective liver X receptor (LXR) ligands with 5,11-dihydro-5-methyl-11-methylene-6H-dibenz[b,e]azepin-6-one skeleton.

    PubMed

    Aoyama, Atsushi; Endo-Umeda, Kaori; Kishida, Kenji; Ohgane, Kenji; Noguchi-Yachide, Tomomi; Aoyama, Hiroshi; Ishikawa, Minoru; Miyachi, Hiroyuki; Makishima, Makoto; Hashimoto, Yuichi

    2012-09-13

    To obtain novel transrepression-selective liver X receptor (LXR) ligands, we adopted a strategy of reducing the transactivational agonistic activity of the 5,11-dihydro-5-methyl-11-methylene-6H-dibenz[b,e]azepin-6-one derivative 10, which exhibits LXR-mediated transrepressional and transactivational activity. Structural modification of 10 based on the reported X-ray crystal structure of the LXR ligand-binding domain led to a series of compounds, of which almost all exhibited transrepressional activity at 1 or 10 μM but showed no transactivational activity even at 30 μM. Among the compounds obtained, 18 and 22 were confirmed to have LXR-dependent transrepressional activity by using peritoneal macrophages from wild-type and LXR-null mice. A newly developed fluorescence polarization assay indicated that they bind directly to LXRα. Next, further structural modification was performed with the guidance of docking simulations with LXRα, focusing on enhancing the binding of the ligands with LXRα through the introduction of substituents or heteroatom(s). Among the compounds synthesized, compound 48, bearing a hydroxyl group, showed potent, selective, and dose-dependent transrepressional activity.

  6. 1-(1,3-Benzodioxol-5-yl-carbo-nyl) piperidine, a modulator of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor, ameliorates exercise-induced fatigue in mice.

    PubMed

    Fan, Wutu; Wu, Xianglong; Pan, Yalei; Li, Chenrui; Niu, Yinbo; Zhai, Yuankun; Mei, Qibing

    2014-01-01

    The current study was designed to investigate the effects of 1-(1,3-benzodioxol-5-yl-carbonyl) piperidine (1-BCP) on swimming endurance capacity which as one indicator of fatigue in the weight-loaded forced swimming mice. Mice were given either vehicle or 1-BCP (0.1, or 0.2 mmol/kg body weight daily) by intraperitoneal injection once daily for 2 weeks. The 1-BCP groups showed a significant increase in swimming time to exhaustion compared with the control group. 1-BCP increased the liver glycogen (LG) and muscle glycogen (MG) contents significantly, while decreased the lactic acid (LA) and blood urea nitrogen (BUN) levels notably compared with control group. Besides, 1-BCP treatment also significantly improved the endogenous cellular antioxidant enzymes in mice by increasing the activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px). Therefore, this study demonstrated for the first time that the supplementation of 1-BCP, as a positive allosteric modulator of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, could enhance the endurance capacity of mice and facilitated them recovery from fatigue. Thus, we provide a new effective therapeutic strategy for fatigue.

  7. Synthesis and biological evaluation of the 1-arylpyrazole class of σ(1) receptor antagonists: identification of 4-{2-[5-methyl-1-(naphthalen-2-yl)-1H-pyrazol-3-yloxy]ethyl}morpholine (S1RA, E-52862).

    PubMed

    Díaz, José Luis; Cuberes, Rosa; Berrocal, Joana; Contijoch, Montserrat; Christmann, Ute; Fernández, Ariadna; Port, Adriana; Holenz, Jörg; Buschmann, Helmut; Laggner, Christian; Serafini, Maria Teresa; Burgueño, Javier; Zamanillo, Daniel; Merlos, Manuel; Vela, José Miguel; Almansa, Carmen

    2012-10-11

    The synthesis and pharmacological activity of a new series of 1-arylpyrazoles as potent σ(1) receptor (σ(1)R) antagonists are reported. The new compounds were evaluated in vitro in human σ(1)R and guinea pig σ(2) receptor (σ(2)R) binding assays. The nature of the pyrazole substituents was crucial for activity, and a basic amine was shown to be necessary, in accordance with known receptor pharmacophores. A wide variety of amines and spacer lengths between the amino and pyrazole groups were tolerated, but only the ethylenoxy spacer and small cyclic amines provided compounds with sufficient selectivity for σ(1)R vs σ(2)R. The most selective compounds were further profiled, and compound 28, 4-{2-[5-methyl-1-(naphthalen-2-yl)-1H-pyrazol-3-yloxy]ethyl}morpholine (S1RA, E-52862), which showed high activity in the mouse capsaicin model of neurogenic pain, emerged as the most interesting candidate. In addition, compound 28 exerted dose-dependent antinociceptive effects in several neuropathic pain models. This, together with its good physicochemical, safety, and ADME properties, led compound 28 to be selected as clinical candidate.

  8. Separation studies of yttrium(III) and lanthanide(III) ions with 4-benzoyl-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione and trioctylphosphine oxide using a robotic extraction system

    SciTech Connect

    Nekimken, H.L.; Smith, B.F.; Jarvinen, G.D.; Bartholdi, C.S.

    1992-07-01

    We studied the extraction of trivalent Y, La, Pr, Nd, Sm, Eu, Gd, Dy, Er, and Lu from aqueous perchlorate solutions using a mixture of 4-benzoyl-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione (HBMPPT) and trioctylphosphine oxide (TOPO). The metal ion distribution coefficients (D-values) as a function of increasing lanthanide atomic number increased initially, reached a maximum value at Nd, then decreased to a nearly constant value for Gd and the later lanthanides. The D-values vary slightly across the lanthanide series, the maximum difference being a factor of 14 between La and Nd. Analysis of slopes of plots of log D versus pH, log [HBMPPT], and log [TOPO] indicated that the stoichiometries of the extraction complexes varied across the lanthanide series showing a decrease in the number of HBMPPT (and/or BMPPT) units and an increase in the number of TOPO molecules involved in the major extraction species. This extraction system can provide a good way to separate the trivalent actinides from the trivalent lanthanides. 21 refs., 2 figs., 3 tabs.

  9. Normal coordinate analysis and vibrational spectroscopy (FT-IR and FT-Raman) studies of 5-methyl-N-[4-(trifluoromethyl) phenyl]-isoxazole-4-carboxamide using density functional method.

    PubMed

    Shahidha, R; Muthu, S; Elamurugu Porchelvi, E; Govindarajan, M

    2014-11-11

    Vibrational spectral analysis of 5-methyl-N-[4-(trifluoromethyl) phenyl]-isoxazole-4-carboxamide is (5MN4TPI4C) molecule was carried out using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry, harmonic vibrational wavenumbers, various bonding features have been computed using density functional B3LYP method with 6-311G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFFM). Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The non-linear optical (NLO) behavior of 5MN4TPI4C has been studied by determination of the electric dipole moment (μ) and hyperpolarizability (β) by using B3LYP/6-311G(d,p) method. The molecular orbital compositions and their contributions to the chemical bonding are studied by Total density of energy states (TDOS), sum of α and β electron (αβDOS) density of states. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are calculated.

  10. Efficient and regioselective one-step synthesis of 7-aryl-5-methyl- and 5-aryl-7-methyl-2-amino-[1,2,4]triazolo[1,5-a]pyrimidine derivatives.

    PubMed

    Massari, Serena; Desantis, Jenny; Nannetti, Giulio; Sabatini, Stefano; Tortorella, Sara; Goracci, Laura; Cecchetti, Violetta; Loregian, Arianna; Tabarrini, Oriana

    2017-09-26

    Two facile and efficient one-step procedures for the regioselective synthesis of 7-aryl-5-methyl- and 5-aryl-7-methyl-2-amino-[1,2,4]triazolo[1,5-a]pyrimidines have been developed, via reactions of 3,5-diamino-1,2,4-triazole with variously substituted 1-aryl-1,3-butanediones and 1-aryl-2-buten-1-ones, respectively. The excellent yield and/or regioselectivity shown by the reactions decreased when ethyl 5-amino-1,2,4-triazole-3-carboxylate was used. [1,2,4]Triazolo[1,5-a]pyrimidine being a privileged scaffold, the procedures herein reported may be useful for the preparation of biologically active compounds. In this study, the preparation of a set of compounds based on the [1,2,4]triazolo[1,5-a]pyrimidine scaffold led to the identification of compound 20 endowed with a very promising ability to inhibit influenza virus RNA polymerase PA-PB1 subunit heterodimerization.

  11. Uracil DNA Glycosylase BKRF3 Contributes to Epstein-Barr Virus DNA Replication through Physical Interactions with Proteins in Viral DNA Replication Complex

    PubMed Central

    Su, Mei-Tzu; Liu, I-Hua; Wu, Chia-Wei; Chang, Shu-Ming; Tsai, Ching-Hwa; Yang, Pei-Wen; Chuang, Yu-Chia; Lee, Chung-Pei

    2014-01-01

    ABSTRACT Epstein-Barr virus (EBV) BKRF3 shares sequence homology with members of the uracil-N-glycosylase (UNG) protein family and has DNA glycosylase activity. Here, we explored how BKRF3 participates in the DNA replication complex and contributes to viral DNA replication. Exogenously expressed Flag-BKRF3 was distributed mostly in the cytoplasm, whereas BKRF3 was translocated into the nucleus and colocalized with the EBV DNA polymerase BALF5 in the replication compartment during EBV lytic replication. The expression level of BKRF3 increased gradually during viral replication, coupled with a decrease of cellular UNG2, suggesting BKRF3 enzyme activity compensates for UNG2 and ensures the fidelity of viral DNA replication. In immunoprecipitation-Western blotting, BKRF3 was coimmunoprecipitated with BALF5, the polymerase processivity factor BMRF1, and the immediate-early transactivator Rta. Coexpression of BMRF1 appeared to facilitate the nuclear targeting of BKRF3 in immunofluorescence staining. Residues 164 to 255 of BKRF3 were required for interaction with Rta and BALF5, whereas residues 81 to 166 of BKRF3 were critical for BMRF1 interaction in glutathione S-transferase (GST) pulldown experiments. Viral DNA replication was defective in cells harboring BKRF3 knockout EBV bacmids. In complementation assays, the catalytic mutant BKRF3(Q90L,D91N) restored viral DNA replication, whereas the leucine loop mutant BKRF3(H213L) only partially rescued viral DNA replication, coupled with a reduced ability to interact with the viral DNA polymerase and Rta. Our data suggest that BKRF3 plays a critical role in viral DNA synthesis predominantly through its interactions with viral proteins in the DNA replication compartment, while its enzymatic activity may be supplementary for uracil DNA glycosylase (UDG) function during virus replication. IMPORTANCE Catalytic activities of both cellular UDG UNG2 and viral UDGs contribute to herpesviral DNA replication. To ensure that the enzyme

  12. Homooligomeric dA.dU and dA.dT sequences in parallel and antiparallel strand orientation: consequence of the 5-methyl groups on stability, structure and interaction with the minor groove binding drug Hoechst 33258.

    PubMed

    Germann, M W; Kalisch, B W; van de Sande, J H

    1996-06-01

    Oligodeoxyribonucleotides containing dA.dU base combinations were shown to form parallel stranded DNA. CD spectra and hyperchromicity profiles provide evidence that the structure is very similar to that of a related parallel stranded dA.dT oligomer. Thermal denaturation studies show that these parallel dA.dU sequences are significantly less stable than their dA.dT analogues in either antiparallel or parallel stranded orientations. The stabilizing effect of the 5-methyl group is similar for parallel and antiparallel sequences. The minor groove binding drug Hoechst 33258 binds with similar affinity to APS dA.dT and APS dA.dU sequences. However, binding to the PS dA.dT hairpin is significantly impaired as a consequence of the different groove dimensions and the presence of thymine methyl groups at the binding site. This results in an 8.6 kJmol-1 reduced free energy of binding for the PS dA.dT sequence. Replacement of the bulky methyl group with a hydrogen (ie. T-->U) results in significantly stronger Hoechst 33258 binding to the parallel dA.dU sequences with a penalty of only 4.1 kJmol-1. Our data demonstrate that although Hoechst 33258 detects the altered groove, it is still able to bind a PS duplex containing dA.dU base pairs with high affinity, despite the large structural differences from its regular binding site in APS DNA.

  13. An experimental and DFT computational study on 4-(3-(1H-imidazol-1-yl)propyl)-5-methyl-2H-1,2,4-triazol-3(4H)-one monohydrate

    NASA Astrophysics Data System (ADS)

    Tanak, Hasan; Köysal, Yavuz; Ünver, Yasemin; Yavuz, Metin; Işık, Şamil; Sancak, Kemal

    2010-01-01

    The triazole compound 4-(3-(1H-imidazol-1-yl)propyl)-5-methyl-2H-1,2,4-triazol-3(4H)-one monohydrate has been synthesised and characterised by 1H-NMR, 13C-NMR, IR, and X-ray single-crystal determination. The compound crystallizes in the triclinic space group ? with a = 9.0366(7) Å, b = 11.5690(8) Å, c = 12.0571(9) Å, α = 110.733(6)°, β = 94.172(6)°, γ = 98.085(6)° and Z = 4. In addition to the molecular geometry from X-ray determination, the molecular geometry, vibrational frequencies and gauge, including atomic orbital (GIAO) 1H- and 13C-NMR chemical shift values of the title compound in the ground state, were calculated using the density functional method (B3LYP) with the 6-31G(d) basis set. The calculated results show that the optimised geometries can well reproduce the crystal structure, and the theoretical vibrational frequencies and chemical shift values show good agreement with experimental values. The energetic behaviour of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager model. The total energy of the title compound decreases with increasing polarity of the solvent. The predicted nonlinear optical properties of the title compound are greater than those of urea. In addition, DFT calculations of the molecular electrostatic potentials, frontier molecular orbitals and thermodynamic properties of the title compound were carried out at the B3LYP/6-31G(d) level of theory.

  14. Motor Skills Training Enhances α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid Receptor Subunit mRNA Expression in the Ipsilateral Sensorimotor Cortex and Striatum of Rats Following Intracerebral Hemorrhage.

    PubMed

    Tamakoshi, Keigo; Ishida, Kazuto; Kawanaka, Kentaro; Takamatsu, Yasuyuki; Tamaki, Hiroyuki

    2017-10-01

    We investigated the effects of acrobatic training (AT) on expression of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) subunits in the sensorimotor cortex and striatum after intracerebral hemorrhage (ICH). Male Wistar rats were divided into 4 groups: ICH without AT (ICH), ICH with AT (ICH + AT), sham operation without AT (SHAM), and sham operation with AT (SHAM + AT). ICH was induced by collagenase injection into the left striatum. The ICH + AT group performed 5 acrobatic tasks daily on days 4-28 post ICH. Forelimb sensorimotor function was evaluated using the forelimb placing test. On days 14 and 29, mRNA expression levels of AMPAR subunits GluR1-4 were measured by real-time reverse transcription-polymerase chain reaction. Forelimb placing test scores were significantly higher in the ICH + AT group than in the ICH group. Expression levels of all AMPAR subunit mRNAs were significantly higher in the ipsilateral sensorimotor cortex of rats in the ICH + AT group than in that of rats in the ICH group on day 29. GluR3 and GluR4 expression levels were reduced in the ipsilateral striatum of rats in the ICH group compared with that of rats in the SHAM group on day 14. These changes may play a critical role in motor skills training-induced recovery after ICH. Copyright © 2017 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  15. Roles of fragile X mental retardation protein in dopaminergic stimulation-induced synapse-associated protein synthesis and subsequent alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-4-propionate (AMPA) receptor internalization.

    PubMed

    Wang, Hansen; Kim, Susan S; Zhuo, Min

    2010-07-09

    Fragile X syndrome, the most common form of inherited mental retardation, is caused by the absence of the RNA-binding protein fragile X mental retardation protein (FMRP). FMRP regulates local protein synthesis in dendritic spines. Dopamine (DA) is involved in the modulation of synaptic plasticity. Activation of DA receptors can regulate higher brain functions in a protein synthesis-dependent manner. Our recent study has shown that FMRP acts as a key messenger for DA modulation in forebrain neurons. Here, we demonstrate that FMRP is critical for DA D1 receptor-mediated synthesis of synapse-associated protein 90/PSD-95-associated protein 3 (SAPAP3) in the prefrontal cortex (PFC). DA D1 receptor stimulation induced dynamic changes of FMRP phosphorylation. The changes in FMRP phosphorylation temporally correspond with the expression of SAPAP3 after D1 receptor stimulation. Protein phosphatase 2A, ribosomal protein S6 kinase, and mammalian target of rapamycin are the key signaling molecules for FMRP linking DA D1 receptors to SAPAP3. Knockdown of SAPAP3 did not affect surface expression of alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-4-propionate (AMPA) GluR1 receptors induced by D1 receptor activation but impaired their subsequent internalization in cultured PFC neurons; the subsequent internalization of GluR1 was also impaired in Fmr1 knock-out PFC neurons, suggesting that FMRP may be involved in subsequent internalization of GluR1 through regulating the abundance of SAPAP3 after DA D1 receptor stimulation. Our study thus provides further insights into FMRP involvement in DA modulation and may help to reveal the molecular mechanisms underlying impaired learning and memory in fragile X syndrome.

  16. A study of the oligomeric state of the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-preferring glutamate receptors in the synaptic junctions of porcine brain.

    PubMed Central

    Wu, T Y; Liu, C I; Chang, Y C

    1996-01-01

    The number of the subunits in an alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-preferring L-glutamate receptor in the synaptic junctions of porcine brain was investigated in this study. Upon incubation of the synaptic junctions with three cross-linking regents, dimethyl adipimidate (DMA), dimethyl suberimidate (DMS) and N-succinimidyl-(4-azidophenyl)-1,3'-dithiopropionate (SADP), AMPA receptor subunits in higher-molecular-mass aggregates were detected by immunoblotting. These aggregates migrated as proteins of approx. 200, 300 and 400 kDa. The number and identity of the subunits in a solubilized AMPA receptor were also investigated here. Two samples, W1 and W2, enriched in AMPA receptors were prepared from synaptic junctions by a combination of detergent-solubilization, anion-exchange chromatography and wheatgerm agglutinin affinity chromatography. Hydrodynamic behaviour analyses revealed that the majority of the AMPA receptors in either one of these samples were asymmetrical detergent-surrounded particles with a protein mass around 350 kDa. SDS/PAGE analysis revealed that the majority of AMPA receptors in the W1 sample were comprised of dimers of 106 kDa subunits which were covalently linked by disulphide bonds. Cross-linking these receptors with SADP yielded a new band of approx. 400 kDa. The results obtained here, either from the studies of AMPA receptors embedding in synaptic junctions or from those of detergent-solubilized and partially purified receptors, suggest that AMPA receptors contain a basic core structure comprising of four 106 kDa subunits. PMID:8920974

  17. Involvement of p38 MAPK and ATF-2 signaling pathway in anti-inflammatory effect of a novel compound bis[(5-methyl)2-furyl](4-nitrophenyl)methane on lipopolysaccharide-stimulated macrophages.

    PubMed

    Udompong, Sarinporn; Mankhong, Sakulrat; Jaratjaroonphong, Jaray; Srisook, Klaokwan

    2017-09-01

    Activated macrophages produce various pro-inflammatory mediators such as inducible nitric oxide synthase (iNOS)-derived nitric oxide (NO) and cyclooxygenase (COX)-2-derived prostaglandin E2 (PGE2) during inflammatory response. However, overproduction of NO and PGE2 appears to be involved in pathogenesis of various inflammatory diseases. Therefore, inhibition of NO and PGE2 production might be useful for the treatment of inflammatory-related diseases. In this study, the bis[(5-methyl)2-furyl](4-nitrophenyl)methane or BFNM was evaluated for the anti-inflammatory activity and mechanism of action in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophage. BFNM inhibited NO and PGE2 production in a concentration-dependent manner and down-regulated the expression of iNOS and COX-2 at mRNA and protein levels. BFNM suppressed nuclear translocation of NF-κB p65 subunit only very slightly, and failed to decrease NF-κB DNA binding activity. In contrast, the compound significantly reduced phosphorylation of p38 MAPK and ATF-2, a component of AP-1 known to be involved in the transcriptional regulation of iNOS and COX-2, in a dose-dependent manner in LPS-induced cells. Collectively, these results suggest that BFNM has an anti-inflammatory effect in RAW 264.7 macrophages, at least in part, by suppression of NO and PGE2 production. The inhibitory effect of BFNM is mediated mainly via the p38 MAPK/ATF-2 signaling pathway. Thus, BFNM would be a lead compound for the development of novel anti-inflammatory agents. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Poly(ADP-Ribose)Polymerase 1 (PARP-1) Activation and Ca(2+) Permeable α-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid (AMPA) Channels in Post-Ischemic Brain Damage: New Therapeutic Opportunities?

    PubMed

    Gerace, Elisabetta; Pellegrini-Giampietro, Domenico E; Moroni, Flavio; Mannaioni, Guido

    2015-01-01

    A significant number of laboratories observed that poly (ADP-ribose) polymerase (PARP) inhibitors, administered a few hours after ischemic or traumatic brain injury, may drastically reduce the subsequent neurological damage. It has also been shown that PARP inhibitors, administered for 24 hours to rats with permanent middle cerebral artery occlusion (MCAO), may reduce the number of dying neurons for a long period after surgery, thus suggesting that these agents could reduce the delayed brain damage and the neurological and cognitive impairment (dementia) frequently observed a few months after a stroke. In organotypic hippocampal slices exposed to N-methyl-N'-nitro-N'-nitrosoguanidine (MNNG), an alkylating agent able to activate PARP, a selective and delayed degeneration of the CA1 pyramidal cells which was anatomically similar to that observed after a short period of oxygen and glucose deprivation (OGD) has been described. Biochemical and electrophysiological approaches showed that MNNG exposure caused an increased expression and function of the calcium permeable α-amino- 3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) channels in the CA1 but not in the CA3 hippocampal region. PARP inhibitors prevented this increase and reduced CA1 cell death. The AMPA receptor antagonist 2,3-dihydroxy-6- nitro-7-sulfamoyl-benzo[f]quinoxaline-2,3-dione or the selective Ca(2+) permeable AMPA channel blocker 1-Naphthyl acetyl spermine (NASPM), also reduced the MNNG-induced CA1 pyramidal cell death. Since activation of PARP-1 facilitate the expression of Ca(2+) permeable channels and the subsequent delayed cell death, PARP inhibitors administered a few hours after a stroke may not only reduce the early post-ischemic brain damage but also the late neuronal death frequently occurring after severe stroke.

  19. Linking supply to demand: the neuronal monocarboxylate transporter MCT2 and the alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-propionic acid receptor GluR2/3 subunit are associated in a common trafficking process.

    PubMed

    Pierre, Karin; Chatton, Jean-Yves; Parent, Annabelle; Repond, Cendrine; Gardoni, Fabrizio; Di Luca, Monica; Pellerin, Luc

    2009-05-01

    MCT2 is the major neuronal monocarboxylate transporter (MCT) that allows the supply of alternative energy substrates such as lactate to neurons. Recent evidence obtained by electron microscopy has demonstrated that MCT2, like alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-propionic acid (AMPA) receptors, is localized in dendritic spines of glutamatergic synapses. Using immunofluorescence, we show in this study that MCT2 colocalizes extensively with GluR2/3 subunits of AMPA receptors in neurons from various mouse brain regions as well as in cultured neurons. It also colocalizes with GluR2/3-interacting proteins, such as C-kinase-interacting protein 1, glutamate receptor-interacting protein 1 and clathrin adaptor protein. Coimmunoprecipitation of MCT2 with GluR2/3 and C-kinase-interacting protein 1 suggests their close interaction within spines. Parallel changes in the localization of both MCT2 and GluR2/3 subunits at and beneath the plasma membrane upon various stimulation paradigms were unraveled using an original immunocytochemical and transfection approach combined with three-dimensional image reconstruction. Cell culture incubation with AMPA or insulin triggered a marked intracellular accumulation of both MCT2 and GluR2/3, whereas both tumor necrosis factor alpha and glycine (with glutamate) increased their cell surface immunolabeling. Similar results were obtained using Western blots performed on membrane or cytoplasm-enriched cell fractions. Finally, an enhanced lactate flux into neurons was demonstrated after MCT2 translocation on the cell surface. These observations provide unequivocal evidence that MCT2 is linked to AMPA receptor GluR2/3 subunits and undergoes a similar translocation process in neurons upon activation. MCT2 emerges as a novel component of the synaptic machinery putatively linking neuroenergetics to synaptic transmission.

  20. Uracil DNA glycosylase interacts with the p32 subunit of the replication protein A complex to modulate HIV-1 reverse transcription for optimal virus dissemination.

    PubMed

    Herate, Cecile; Vigne, Clarisse; Guenzel, Carolin A; Lambele, Marie; Rouyez, Marie-Christine; Benichou, Serge

    2016-04-12

    Through incorporation into virus particles, the HIV-1 Vpr protein participates in the early steps of the virus life cycle by influencing the reverse transcription process. We previously showed that this positive impact on reverse transcription was related to Vpr binding to the uracil DNA glycosylase 2 enzyme (UNG2), leading to enhancement of virus infectivity in established CD4-positive cell lines via a nonenzymatic mechanism. We report here that Vpr can form a trimolecular complex with UNG2 and the p32 subunit (RPA32) of the replication protein A (RPA) complex and we explore how these cellular proteins can influence virus replication and dissemination in the primary target cells of HIV-1, which express low levels of both proteins. Virus infectivity and replication in peripheral blood mononuclear cells and monocyte-derived macrophages (MDMs), as well as the efficiency of the viral DNA synthesis, were significantly reduced when viruses were produced from cells depleted of endogenous UNG2 or RPA32. Moreover, viruses produced in macrophages failed to replicate efficiently in UNG2- and RPA32-depleted T lymphocytes. Reciprocally, viruses produced in UNG2-depleted T cells did not replicate efficiently in MDMs confirming the positive role of UNG2 for virus dissemination. Our data show the positive effect of UNG2 and RPA32 on the reverse transcription process leading to optimal virus replication and dissemination between the primary target cells of HIV-1.

  1. Advanced loop-mediated isothermal amplification method for sensitive and specific detection of Tomato chlorosis virus using a uracil DNA glycosylase to control carry-over contamination.

    PubMed

    Kil, Eui-Joon; Kim, Sunhoo; Lee, Ye-Ji; Kang, Eun-Ha; Lee, Minji; Cho, Sang-Ho; Kim, Mi-Kyeong; Lee, Kyeong-Yeoll; Heo, Noh-Youl; Choi, Hong-Soo; Kwon, Suk-Tae; Lee, Sukchan

    2015-03-01

    In 2013, Tomato chlorosis virus (ToCV) was identified in symptomatic tomato plants in Korea. In the present study, a loop-mediated isothermal amplification (LAMP) method was developed using four specific primers designed against ORF6 in ToCV RNA2 to detect ToCV rapidly and with high sensitivity. The optimized reaction involved incubation of a reaction mixture containing 2U Bst DNA polymerase and 4mM MgSO4 for 1h at 60-62 °C. Although specific and rapid detection of ToCV by LAMP was confirmed, false-positive reactions caused by carry-over contamination sometimes occurred because of the high sensitivity of LAMP compared with other detection methods. To prevent false-positive reactions, dUTP was substituted for dTTP and uracil-DNA glycosylase (UDG) was added to the LAMP reaction. First, the LAMP reaction was conducted successfully with substitution of dUTP for dTTP. Before the next reaction, LAMP products with incorporated dUTP were cleaved selectively by UDG without any effect on thymine-containing DNA (template DNA). This modified LAMP method complemented with UDG treatment to prevent carry-over contamination offers a potentially powerful method for detecting plant viruses. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Probing the Conical Intersection Dynamics of the RNA Base Uracil by UV-Pump Stimulated-Raman-Probe Signals; Ab Initio Simulations

    PubMed Central

    2015-01-01

    Nonadiabatic electron and nuclear dynamics of photoexcited molecules involving conical intersections is of fundamental importance in many reactions such as the self-protection mechanism of DNA and RNA bases against UV irradiation. Nonlinear vibrational spectroscopy can provide an ultrafast sensitive probe for these processes. We employ a simulation protocol that combines nonadiabatic on-the-fly molecular dynamics with a mode-tracking algorithm for the simulation of femtosecond stimulated Raman spectroscopy (SRS) signals of the high frequency C–H- and N–H-stretch vibrations of the photoexcited RNA base uracil. The simulations rely on a microscopically derived expression that takes into account the path integral of the excited state evolution and the pulse shapes. Analysis of the joint time/frequency resolution of the technique reveals a matter chirp contribution that limits the inherent temporal resolution. Characteristic signatures of relaxation dynamics mediated in the vicinity of conical intersection are predicted. The C–H and N–H spectator modes provide high sensitivity to their local environment and act as local probes with submolecular and high temporal resolution. PMID:24803857

  3. 20-150-keV proton-impact-induced ionization of uracil: Fragmentation ratios and branching ratios for electron capture and direct ionization

    SciTech Connect

    Tabet, J.; Eden, S.; Feil, S.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Ouaskit, S.; Maerk, T. D.

    2010-01-15

    Fragmentation ratios and branching ratios are measured for ionization and dissociative ionization for 20-150 keV (0.9-2.4v{sub 0}) proton collisions with gas-phase uracil molecules. Through event-by-event determination of the postcollision projectile charge, it is possible for such a key biomolecule to distinguish between electron capture (EC) by the incident proton and direct ionization (DI) without projectile neutralization. While the same fragment ion groups are observed in the mass spectra for both processes, EC induces dissociation with greater efficiency than DI in the impact energy range of 35-150 keV (1.2-2.4v{sub 0}). In this range EC is also less abundant than DI with a branching ratio for EC/total ionization of <50%. Moreover, whereas fragmentation ratios do not change with energy in the case of EC, DI mass spectra show a tendency for increased fragmentation at lower impact energies.

  4. WW domains of Rsp5p define different functions: determination of roles in fluid phase and uracil permease endocytosis in Saccharomyces cerevisiae.

    PubMed

    Gajewska, B; Kamińska, J; Jesionowska, A; Martin, N C; Hopper, A K; Zoładek, T

    2001-01-01

    Rsp5p, ubiquitin-protein ligase, an enzyme of the ubiquitination pathway, contains three WW domains that mediate protein-protein interactions. To determine if these domains adapt Rsp5p to a subset of substrates involved in numerous cellular processes, we generated mutations in individual or combinations of the WW domains. The rsp5-w1, rsp5-w2, and rsp5-w3 mutant alleles complement RSP5 deletions at 30 degrees. Thus, individual WW domains are not essential. Each rsp5-w mutation caused temperature-sensitive growth. Among variants with mutations in multiple WW domains, only rsp5-w1w2 complemented the deletion. Thus, the WW3 domain is sufficient for Rsp5p essential functions. To determine whether rsp5-w mutations affect endocytosis, fluid phase and uracil permease (Fur4p) endocytosis was examined. The WW3 domain is important for both processes. WW2 appears not to be important for fluid phase endocytosis whereas it is important for Fur4p endocytosis. In contrast, the WW1 domain affects fluid phase endocytosis, but it does not appear to function in Fur4p endocytosis. Thus, various WW domains play different roles in the endocytosis of these two substrates. Rsp5p is located in the cytoplasm in a punctate pattern that does not change during the cell cycle. Altering WW domains does not change the location of Rsp5p.

  5. Therapeutic usefulness of postoperative adjuvant chemotherapy with Tegafur-Uracil (UFT) in patients with breast cancer: focus on the results of clinical studies in Japan.

    PubMed

    Nakayama, Takahiro; Noguchi, Shinzaburo

    2010-01-01

    In Japan, the history of postoperative chemotherapy for breast cancer started with 5-fluorouracil (5-FU), launched in the 1980s. Currently, oral fluoropyrimidine-based regimens indicated for the treatment of breast cancer in Japan include tegafur plus uracil (UFT); tegafur, gimeracil, and oteracil (TS-1); doxifluridine; and capecitabine. In particular, UFT represents an important option for long-term treatment because of minimal adverse events and the potential for long-term maintenance of effective plasma concentrations of 5-FU to inhibit micrometastasis after surgery. Therefore, various clinical studies of postoperative adjuvant chemotherapy with UFT have been conducted in patients with completely resected tumors. Recent studies have shown that UFT prolongs survival after tumor resection in patients with gastric cancer, colorectal cancer, and lung cancer. In patients with breast cancer, large clinical trials of UFT-based postoperative chemotherapy conducted in Japan have shown that UFT is useful for the treatment of intermediate-risk patients with no lymph node metastasis. This paper reviews the results of clinical studies of UFT conducted in Japan to assess the therapeutic usefulness of this oral 5-FU. The types of patients most likely to benefit from UFT are discussed on the basis of currently available evidence and a global consensus of treatment recommendations. The optimal timing of endocrine therapy and strategies for postoperative adjuvant chemotherapy with UFT in patients with breast cancer are also discussed.

  6. Structural and Energetic Impact of Non-Natural 7-Deaza-8-Azaadenine and Its 7-Substituted Derivatives on H-Bonding Potential with Uracil in RNA Molecules.

    PubMed

    Chawla, Mohit; Credendino, Raffaele; Oliva, Romina; Cavallo, Luigi

    2015-10-15

    Non-natural (synthetic) nucleobases, including 7-ethynyl- and 7-triazolyl-8-aza-7-deazaadenine, have been introduced in RNA molecules for targeted applications, and have been characterized experimentally. However, no theoretical characterization of the impact of these modifications on the structure and energetics of the corresponding H-bonded base pair is available. To fill this gap, we performed quantum mechanics calculations, starting with the analysis of the impact of the 8-aza-7-deaza modification of the adenine skeleton, and we moved then to analyze the impact of the specific substituents on the modified 8-aza-7-deazaadenine. Our analysis indicates that, despite of these severe structural modifications, the H-bonding properties of the modified base pair gratifyingly replicate those of the unmodified base pair. Similar behavior is predicted when the same skeleton modifications are applied to guanine when paired to cytosine. To stress further the H-bonding pairing in the modified adenine-uracil base pair, we explored the impact of strong electron donor and electron withdrawing substituents on the C7 position. Also in this case we found minimal impact on the base pair geometry and energy, confirming the validity of this modification strategy to functionalize RNAs without perturbing its stability and biological functionality.

  7. [Utilization of Uracil-DNA glycosylase for combining reverse transcription and anti-contamination with polymerase chain reaction in hepatitis C virus].

    PubMed

    DU, Shao Cai; Zhang, Rui; Li, Jun Qiang; Wei, Lai

    2007-08-18

    To develop a hepatitis C virus(HCV) reverse transcription-polymerase chain reaction (RT-PCR) assay using Uracil-DNA glycosylase (UDG) for amplicon contamination control and evaluate the temperature and UDG concentrations for anti-contamination. In this new HCV RT-PCR assay, reverse transcription, UDG anti-contamination and the first PCR were carried out at the same time. The layer candles were used to prevent the contamination in the second PCR. dU-DNA was used as quality control for UDG anti-contamination and templates to determine the sensitivity of the new HCV RT-PCR assay. HCV cDNA was detected by DNA enzyme immunoassay (DNA-EIA). Complete degradation of amplicon DNA was observed on the conditions of 0.2au UDG per reaction volume respectively at 37 degrees C and 42 degrees C for 40 min. The anti-contamination condition also could eliminate all detectible dU-DNA, including the highest concentration of amplicon DNA.The 1:10(4) dilution of the HCV RNA sample containing 2.110x 10(5)copies /mL copies of RNA could be detected. Our results indicate that this new RT-PCR assay can control the contamination stringently and is sensitive as well.

  8. Polymeric Cd(II), trinuclear and mononuclear Ni(II) complexes of 5-methyl-4-phenyl-1,2,4-triazole-3-thione: Synthesis, structural characterization, thermal behaviour, fluorescence properties and antibacterial activity

    NASA Astrophysics Data System (ADS)

    Bharty, M. K.; Paswan, S.; Dani, R. K.; Singh, N. K.; Sharma, V. K.; Kharwar, R. N.; Butcher, R. J.

    2017-02-01

    Syntheses of a polymeric Cd(II) complex, [Cd(mptt)2]n (1), a trinuclear Ni(II) complex, [Ni3(μ-mptt)4(μ-H2O)2(H2O)2(ttfa)2]·3H2O (2) and a mononuclear Ni(II) complex [Ni(mptt)2(en)2] (3) have been performed using the ligand 5-methyl-4-phenyl-1,2,4-triazole-3-thione (Hmptt) and nickel(II)/cadmium(II) salts {ttfa = thenoyltrifluroacetonate). The ligand and the complexes have been characterized by various physicochemical methods in addition to their single crystal X-ray structure. The Cd centre in complex 1 adopts a distorted tetrahedral geometry with one sulfur atom and two mptt ligands provide three nitrogen atoms from three triazole units. The sulfur atom of the ligand binds covalently and overall the ligand acts as uninigative N,S/N,N bidentate moiety. The polymeric structure of complex 1 results from the N atoms of the neighboring triazole units coordinating with the Cd(II) centre. The three Ni(II) centres in the trinuclear Ni(II) complex 2 form a linear arrangement and all have six coordinated arrangements. The middle Ni(II) binds with four deprotonated triazole ring nitrogens and two water molecules form two bridges. The terminal Ni(II) centres bind through two thenoyl oxygens, two triazole nitrogens and water molecules that formed bridges with the middle Ni centre. In complex 3, the nickel(II) centre is covalently bonded through two deprotonated triazole ring nitrogens from two ligand moieties and other four sites are occupied by four nitrogens from two bidentate en ligands. Thermogravimetric analyses (TGA) of the complexes indicated for NiO as the final residue. The bioefficacy of the ligand and complexes 2 and 3 have been examined against the growth of bacteria to evaluate their anti-microbial potential. Complex 2 showed high antibacterial activity as compared to the ligand and complex 3. Complexes 1, 2 and 3 are fluorescent materials with maximum emissions at 425, 421 and 396 nm at an excitation wavelength of 323, 348 and 322 nm, respectively.

  9. Elevated levels of plasma homocysteine, deficiencies in dietary folic acid and uracil-DNA glycosylase impair learning in a mouse model of vascular cognitive impairment.

    PubMed

    Jadavji, Nafisa M; Farr, Tracy D; Lips, Janet; Khalil, Ahmed A; Boehm-Sturm, Philipp; Foddis, Marco; Harms, Christoph; Füchtemeier, Martina; Dirnagl, Ulrich

    2015-04-15

    Dietary deficiencies in folic acid result in elevated levels of plasma homocysteine, which has been associated with the development of dementia and other neurodegenerative disorders. Previously, we have shown that elevated levels of plasma homocysteine in mice deficient for a DNA repair enzyme, uracil-DNA glycosylase (UNG), result in neurodegeneration. The goal of this study was to evaluate how deficiencies in folic acid and UNG along with elevated levels of homocysteine affect vascular cognitive impairment, via chronic hypoperfursion in an animal model. Ung(+/+) and Ung(-/-) mice were placed on either control (CD) or folic acid deficient (FADD) diets. Six weeks later, the mice either underwent implantation of microcoils around both common carotid arteries. Post-operatively, behavioral tests began at 3-weeks, angiography was measured after 5-weeks using MRI to assess vasculature and at completion of study plasma and brain tissue was collected for analysis. Learning impairments in the Morris water maze (MWM) were observed only in hypoperfused Ung(-/-) FADD mice and these mice had significantly higher plasma homocysteine concentrations. Interestingly, Ung(+/+) FADD produced significant remodeling of the basilar artery and arterial vasculature. Increased expression of GFAP was observed in the dentate gyrus of Ung(-/-) hypoperfused and FADD sham mice. Chronic hypoperfusion resulted in increased cortical MMP-9 protein levels of FADD hypoperfused mice regardless of genotypes. These results suggest that elevated levels of homocysteine only, as a result of dietary folic acid deficiency, don't lead to memory impairments and neurobiochemical changes. Rather a combination of either chronic hypoperfusion or UNG deficiency is required.

  10. Electron configuration and hydrogen-bonding pattern in several thymine and uracil analogues studied by 1H-14N NQDR and DFT/QTAIM.

    PubMed

    Seliger, Janez; Žagar, Veselko; Latosińska, Magdalena; Latosińska, Jolanta Natalia

    2012-08-02

    Some thio- and aza-derivatives of natural nucleobases uracil and thymine: 2-thiouracil, 4-thiouracil, 6-methyl-2-thiouracil, 6-azauracil, and 6-aza-2-thiothymine have been studied experimentally in solid state by (1)H-(14)N NMR-NQR double resonance (NQDR) and theoretically by the Density Functional Theory (DFT)/Quantum Theory of Atoms in Molecules (QTAIM). The (14)N resonance frequencies have been measured at 173 and 295 K and assigned to particular nitrogen sites (-N═ and -NH-). The temperature factor has been found negligible. The changes in the molecular skeletons, electric charge distribution, intermolecular interactions pattern, and molecular aggregations caused by oxygen replacement with sulfur and carbon replacement with nitrogen are discussed in detail. Correlations between all the principal components of the (14)N quadrupole coupling tensor have been found helpful in the search for the experimental (14)N NQR frequencies, their assignment to a particular nitrogen positions and estimation of the strength of the inter- and intramolecular interactions. The variation in the NQR parameters have been mainly related to the variation in the population of π-electron orbital. For thiouracil derivatives a general trend is that the stronger the hydrogen bond is, the lower is the asymmetry parameter, while for thymine and 6-aza-2-thiotymine, the opposite relation holds. Differences in correlations of the principal components of the (14)N quadrupole coupling tensor at the amino and iminonitrogen positions in heterocyclic rings are discussed. The effect of C→H and C→N substitution at the amino nitrogen position and C→N substitution at the iminonitrogen position on the quadrupole coupling tensor is analyzed. This study also demonstrates the advantages of combining NQR and DFT/QTAIM to predict an unsolved crystalline structure of 4-thiouracil.

  11. Differences in nitric oxide steady states between arginine, hypoxanthine, uracil auxotrophs (AHU) and non-AHU strains of Neisseria gonorrhoeae during anaerobic respiration in the presence of nitrite.

    PubMed

    Barth, Kenneth; Clark, Virginia L

    2008-08-01

    Neisseria gonorrhoeae can grow by anaerobic respiration using nitrite as an alternative electron acceptor. Under these growth conditions, N. gonorrhoeae produces and degrades nitric oxide (NO), an important host defense molecule. Laboratory strain F62 has been shown to establish and maintain a NO steady-state level that is a function of the nitrite reductase/NO reductase ratio and is independent of cell number. The nitrite reductase activities (122-197 nmol NO2 reduced x min(-1) x OD600(-1)) and NO reductase activities (88-155 nmol NO reduced x min(-1) x OD600(-1)) in a variety of gonococcal clinical isolates were similar to the specific activities seen in F62 (241 nmol NO2 reduced x min(-1) x OD600(-1) and 88 nmol NO reduced x min(-1) x OD600(-1), respectively). In seven gonococcal strains, the NO steady-state levels established in the presence of nitrite were similar to that of F62 (801-2121 nmol x L-1 NO), while six of the strains, identified as arginine, hypoxanthine, and uracil auxotrophs (AHU), that cause asymptomatic infection in men had either two- to threefold (373-579 nmol x L-1 NO) or about 100-fold (13-24 nmol x L-1 NO) lower NO steady-state concentrations. All tested strains in the presence of a NO donor, 2,2'-(hydroxynitrosohydrazono)bis-ethanimine/NO, quickly lowered and maintained NO levels in the noninflammatory range of NO (<300 nmol x L-1). The generation of a NO steady-state concentration was directly affected by alterations in respiratory control in both F62 and an AHU strain, although differences in membrane function are suspected to be responsible for NO steady-state level differences in AHU strains.

  12. Adsorption of adenine, cytosine, thymine, and uracil on sulfide-modified montmorillonite: FT-IR, Mössbauer and EPR spectroscopy and X-ray diffractometry studies.

    PubMed

    Carneiro, Cristine E A; Berndt, Graciele; de Souza Junior, Ivan G; de Souza, Cláudio M D; Paesano, Andrea; da Costa, Antonio C S; di Mauro, Eduardo; de Santana, Henrique; Zaia, Cássia T B V; Zaia, Dimas A M

    2011-10-01

    In the present work the interactions of nucleic acid bases with and adsorption on clays were studied at two pHs (2.00, 7.00) using different techniques. As shown by Mössbauer and EPR spectroscopies and X-ray diffractometry, the most important finding of this work is that nucleic acid bases penetrate into the interlayer of the clays and oxidize Fe(2+) to Fe(3+), thus, this interaction cannot be regarded as a simple physical adsorption. For the two pHs the order of the adsorption of nucleic acid bases on the clays was: adenine ≈ cytosine > thymine > uracil. The adsorption of adenine and cytosine on clays increased with decreasing of the pH. For unaltered montmorillonite this result could be explained by electrostatic forces between adenine/cytosine positively charged and clay negatively charged. However for montmorillonite modified with Na(2)S, probably van der Waals forces also play an important role since both adenine/cytosine and clay were positively charged. FT-IR spectra showed that the interaction between nucleic acid bases and clays was through NH(+) or NH (2) (+) groups. X-ray diffractograms showed that nucleic acid bases adsorbed on clays were distributed into the interlayer surface, edge sites and external surface functional groups (aluminol, silanol) EPR spectra showed that the intensity of the line g ≈ 2 increased probably because the oxidation of Fe(2+) to Fe(3+) by nucleic acid bases and intensity of the line g = 4.1 increased due to the interaction of Fe(3+) with nucleic acid bases. Mössbauer spectra showed a large decreased on the Fe(2+) doublet area of the clays due to the reaction of nucleic acid bases with Fe(2+).

  13. X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

    NASA Astrophysics Data System (ADS)

    Prokofev, I. I.; Lashkov, A. A.; Gabdulkhakov, A. G.; Balaev, V. V.; Seregina, T. A.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

    2016-11-01

    In many types of human tumor cells and infectious agents, the demand for pyrimidine nitrogen bases increases during the development of the disease, thus increasing the role of the enzyme uridine phosphorylase in metabolic processes. The rational use of uridine phosphorylase and its ligands in pharmaceutical and biotechnology industries requires knowledge of the structural basis for the substrate specificity of the target enzyme. This paper summarizes the results of the systematic study of the three-dimensional structure of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae in complexes with substrates of enzymatic reactions—uridine, phosphate anion, thymidine, uracil, and thymine. These data, supplemented with the results of molecular modeling, were used to consider in detail the structural basis for the substrate specificity of uridine phosphorylases. It was shown for the first time that the formation of a hydrogen-bond network between the 2'-hydroxy group of uridine and atoms of the active-site residues of uridine phosphorylase leads to conformational changes of the ribose moiety of uridine, resulting in an increase in the reactivity of uridine compared to thymidine. Since the binding of thymidine to residues of uridine phosphorylase causes a smaller local strain of the β-N1-glycosidic bond in this the substrate compared to the uridine molecule, the β-N1-glycosidic bond in thymidine is more stable and less reactive than that in uridine. It was shown for the first time that the phosphate anion, which is the second substrate bound at the active site, interacts simultaneously with the residues of the β5-strand and the β1-strand through hydrogen bonding, thus securing the gate loop in a conformation

  14. Maintenance treatment of Uracil and Tegafur (UFT) in responders following first-line fluorouracil-based chemotherapy in metastatic gastric cancer: a randomized phase II study.

    PubMed

    Li, Wenhua; Zhao, Xiaoying; Wang, Huijie; Liu, Xin; Zhao, Xinmin; Huang, Mingzhu; Qiu, Lixin; Zhang, Wen; Chen, Zhiyu; Guo, Weijian; Li, Jin; Zhu, Xiaodong

    2017-06-06

    Maintenance therapy proves to be effective in advanced lung and breast cancer after initial chemotherapy. The purpose of this phase II study was to evaluate the efficacy and safety of Uracil and Tegafur (UFT) maintenance in metastatic gastric cancer patients following the first-line fluorouracil-based chemotherapy. Metastatic gastric cancer patients with stable disease or a better response after the completion of first-line chemotherapy were randomized to oral UFT (360mg/m2 × 2 weeks) every 3 weeks until disease progression/intolerable toxicity or to observation (OBS). The primary endpoint was progression-free survival (PFS); the secondary endpoints were overall survival (OS) and safety. The trial was closed after the interim analysis of the 58 enrolled (120 planned) patients. Median PFS was not improved in the UFT group compared with the OBS group (3.2 months versus 3.6 months, P = 0.752), as well as the median OS (14.2 months for both, P = 0.983). However, subgroup analysis showed that low baseline hemoglobin (< 120 g/L) was associated with poorer PFS with maintenance therapy (P = 0.032), while the normal hemoglobin patients benefit from the UFT treatment (P = 0.008). Grade 3 to 4 toxicities in the UFT group were anemia (3.4%), thrombocytopenia (3.4%) and diarrhea (6.9%). This trial did not show superiority of UFT maintenance in non-selected patients responding to fluorouracil-based first-line chemotherapy. The normal hemoglobin level at baseline is a predictive biomarker for favorable patient subsets from the maintenance treatment.

  15. Polymerization of non-complementary RNA: systematic symmetric nucleotide exchanges mainly involving uracil produce mitochondrial RNA transcripts coding for cryptic overlapping genes.

    PubMed

    Seligmann, Hervé

    2013-03-01

    Usual DNA→RNA transcription exchanges T→U. Assuming different systematic symmetric nucleotide exchanges during translation, some GenBank RNAs match exactly human mitochondrial sequences (exchange rules listed in decreasing transcript frequencies): C↔U, A↔U, A↔U+C↔G (two nucleotide pairs exchanged), G↔U, A↔G, C↔G, none for A↔C, A↔G+C↔U, and A↔C+G↔U. Most unusual transcripts involve exchanging uracil. Independent measures of rates of rare replicational enzymatic DNA nucleotide misinsertions predict frequencies of RNA transcripts systematically exchanging the corresponding misinserted nucleotides. Exchange transcripts self-hybridize less than other gene regions, self-hybridization increases with length, suggesting endoribonuclease-limited elongation. Blast detects stop codon depleted putative protein coding overlapping genes within exchange-transcribed mitochondrial genes. These align with existing GenBank proteins (mainly metazoan origins, prokaryotic and viral origins underrepresented). These GenBank proteins frequently interact with RNA/DNA, are membrane transporters, or are typical of mitochondrial metabolism. Nucleotide exchange transcript frequencies increase with overlapping gene densities and stop densities, indicating finely tuned counterbalancing regulation of expression of systematic symmetric nucleotide exchange-encrypted proteins. Such expression necessitates combined activities of suppressor tRNAs matching stops, and nucleotide exchange transcription. Two independent properties confirm predicted exchanged overlap coding genes: discrepancy of third codon nucleotide contents from replicational deamination gradients, and codon usage according to circular code predictions. Predictions from both properties converge, especially for frequent nucleotide exchange types. Nucleotide exchanging transcription apparently increases coding densities of protein coding genes without lengthening genomes, revealing unsuspected functional DNA

  16. Is GPR17 a P2Y/Leukotriene Receptor? Examination of Uracil Nucleotides, Nucleotide Sugars, and Cysteinyl Leukotrienes as Agonists of GPR17

    PubMed Central

    Qi, Ai-Dong; Harden, T. Kendall

    2013-01-01

    The orphan receptor GPR17 has been reported to be activated by UDP, UDP-sugars, and cysteinyl leukotrienes, and coupled to intracellular Ca2+ mobilization and inhibition of cAMP accumulation, but other studies have reported either a different agonist profile or lack of agonist activity altogether. To determine if GPR17 is activated by uracil nucleotides and leukotrienes, the hemagglutinin-tagged receptor was expressed in five different cell lines and the signaling properties of the receptor were investigated. In C6, 1321N1, or Chinese hamster ovary (CHO) cells stably expressing GPR17, UDP, UDP-glucose, UDP-galactose, and cysteinyl leukotriene C4 (LTC4) all failed to promote inhibition of forskolin-stimulated cAMP accumulation, whereas both UDP and UDP-glucose promoted marked inhibition (>80%) of forskolin-stimulated cAMP accumulation in C6 and CHO cells expressing the P2Y14 receptor. Likewise, none of these compounds promoted accumulation of inositol phosphates in COS-7 or human embryonic kidney 293 cells transiently transfected with GPR17 alone or cotransfected with Gαq/i5, which links Gi-coupled receptors to the Gq-regulated phospholipase C (PLC) signaling pathway, or PLCε, which is activated by the Gα12/13 signaling pathway. Moreover, none of these compounds promoted internalization of GPR17 in 1321N1-GPR17 cells. Consistent with previous reports, coexpression experiments of GPR17 with cysteinyl leukotriene receptor 1 (CysLTR1) suggested that GPR17 acts as a negative regulator of CysLTR1. Taken together, these data suggest that UDP, UDP-glucose, UDP-galactose, and LTC4 are not the cognate ligands of GPR17. PMID:23908386

  17. Preoperative Chemoradiotherapy for Rectal Cancer: Randomized Trial Comparing Oral Uracil and Tegafur and Oral Leucovorin Vs. Intravenous 5-Fluorouracil and Leucovorin

    SciTech Connect

    Torre, Alejandro de la Garcia-Berrocal, Maria Isabel; Arias, Fernando; Marino, Alfonso; Valcarcel, Francisco; Magallon, Rosa; Regueiro, Carlos A.; Romero, Jesus; Zapata, Irma; Fuente, Cristina de la; Fernandez-Lizarbe, Eva; Vergara, Gloria; Belinchon, Belen; Veiras, Maria; Moleron, Rafael; Millan, Isabel

    2008-01-01

    Purpose: To compare, in a randomized trial, 5-fluorouracil (FU) plus leucovorin (LV) (FU+LV) vs. oral uracil and tegafur (UFT) plus LV (UFT+LV) given concomitantly with preoperative irradiation in patients with cT3-4 or N+ rectal cancer. Methods and Materials: A total of 155 patients were entered onto the trial. Patients received pelvic radiotherapy (4500-5,040 cGy in 5 to 6 weeks) and chemotherapy consisting of two 5-day courses of 20 mg/m{sup 2}/d LV and 350 mg/m{sup 2}/d FU in the first and fifth weeks of radiotherapy (77 patients) or one course of 25 mg/d oral LV and 300 mg/m{sup 2}/d UFT for 4 weeks beginning in the second week of radiotherapy (78 patients). The primary endpoints were pathologic complete response (pCR) and resectability rate. Secondary endpoints included downstaging rate, toxicity, and survival. Results: Grade 3-5 acute hematologic toxicity occurred only with FU+LV (leukopenia 9%; p = 0.02). There were no differences in resectability rates (92.1% vs. 93.4%; p = 0.82). The pCR rate was 13.2% in both arms. Tumor downstaging was more frequent with UFT+LV (59.2% vs. 43.3%; p = 0.04). Three-year overall survival was 87% with FU+LV and 74% with UFT+LV (p = 0.37). The 3-year cumulative incidences of local recurrence were 7.5% and 8.9%, respectively (p = 0.619; relative risk, 1.46; 95% confidence interval 0.32-6.55). Conclusion: Although this study lacked statistical power to exclude clinically significant differences between both groups, the outcome of patients treated with UFT+LV did not differ significantly from that of patients treated with FU+LV, and hematologic toxicity was significantly lower in the experimental arm.

  18. Effect of Hydrogen Bonding on Barrier-Free Proton Transfer in Anionic Complexes of Uracil with Weak Acids: (U...HCN){sup -} versus (U...H{sub 2}S){sup -}

    SciTech Connect

    Haranczyk, Maciej; Rak, Janusz; Gutowski, Maciej S.; Radisic, Dunja; Stokes, Sarah T.; Bowen, Kit H.

    2004-10-26

    A photoelectron spectrum is reported for an anionic complex of uracil (U) with HCN. The effects of electron attachment to a complex of U with HA (A = CN, NC) have been studied at the density functional theory level with 6-31++G** basis sets and the B3LYP and MPW1K exchange correlation functionals. Critical anionic structures have been reexamined at the MP2/6-31++G** level. The B3LYP gas phase deprotonation enthalpies are equal to 14.56, 15.13, and 15.12 eV for HNC, HCN, and H{sub 2}S, respectively. The experimental deprotonation enthalpies are 15.100 {+-} 0.008 and 15.214 {+-}0.125 eV for HCN and H{sub 2}S, respectively. Hence, HCN and H{sub 2}S have very similar deprotonation enthalpies. The photoelectron spectra of anionic complexes of uracil with HCN and H{sub 2}S are, however, very different. The (UHCN){sup -} spectrum reveals a broad feature with a maximum between 1.2-1.4 eV, whereas the main feature of the (UH{sub 2}S){sup -} spectrum has a maximum between 1.7 and 2.1 eV. We suggest that barrier-free proton transfer (BFPT) [Eur. Phys. J. D 2002, 20, 431-439; J. Phys. Chem. B 2003, 107, 7889-7895] occurs in the (UH{sub 2}S){sup -} complex but not in (UHCN){sup -}. Critical factors for the occurrence of BFPT have been analyzed. The difference between the (UHCN){sup -} and (UH{sub 2}S){sup -} complexes is attributed to differences in hydrogen bonds formed by HCN and H{sub 2}S with uracil.

  19. Palladium(II) and platinum(II) organometallic complexes with 4,7-dihydro-5-methyl-7-oxo[1,2,4]triazolo[1,5-a]pyrimidine. Antitumor activity of the platinum compounds.

    PubMed

    Ruiz, José; Villa, María Dolores; Cutillas, Natalia; López, Gregorio; de Haro, Concepción; Bautista, Delia; Moreno, Virtudes; Valencia, Laura

    2008-06-02

    Palladium and platinum complexes with HmtpO (where HmtpO=4,7-dihydro-5-methyl-7-oxo[1,2,4]triazolo[1,5-a]pyrimidine, an analogue of the natural occurring nucleobase hypoxanthine) of the types [M(dmba)(PPh3)(HmtpO)]ClO4[dmba=N,C-chelating 2-(dimethylaminomethyl)phenyl; M=Pd or Pt], [Pd(N-N)(C6F5)(HmtpO)]ClO4[N-N=2,2'-bipyridine (bpy), 4,4'-dimethyl-2,2'-bipyridine (Me2bpy), or N, N, N', N'-tetramethylethylenediamine (tmeda)] and cis-[M(C6F5)2(HmtpO)2] (M=Pd or Pt) (head-to-head atropisomer in the solid state) have been obtained. Pd(II) and Pt(II) complexes with the anion of HmtpO of the types [Pd(tmeda)(C6F5)(mtpO)], [Pd(dmba)(micro-mtpO)] 2, and [NBu4]2[M(C6F5)2(micro-mtpO)]2(M=Pd or Pt) have been prepared starting from the corresponding hydroxometal complexes. Complexes containing simultaneously both the neutral HmtpO ligand and the anionic mtpO of the type [NBu4][M(C6F5)2(HmtpO)(mtpO)] (M=Pd or Pt) have been also obtained. In these mtpO-HmtpO metal complexes, for the first time, prototropic exchange is observed between the two heterocyclic ligands. The crystal structures of [Pd(dmba)(PPh 3)(HmtpO)]+, cis-[Pt(C6F5)2(HmtpO)2].acetone, [Pd(C6F5)(tmeda)(mtpO)].2H2O, [Pd(dmba)(micro-mtpO)]2, [NBu4]2[Pd(C6F5)2(micro-mtpO)]2.CH2Cl2.toluene, [NBu4]2[Pt(C6F5)2(micro-mtpO)](2).0.5(toluene), and [NBu4][Pt(C6F5)2(mtpO)(HmtpO)] have been established by X-ray diffraction. Values of IC50 were calculated for the new platinum complexes cis-[Pt(C6F5)2(HmtpO)2] and [Pt(dmba)(PPh3)(HmtpO)]ClO4 against a panel of human tumor cell lines representative of ovarian (A2780 and A2780 cisR), lung (NCI-H460), and breast cancers (T47D). At 48 h incubation time, both complexes were about 8-fold more active than cisplatin in T47D and show very low resistance factors against an A2780 cell line, which has acquired resistance to cisplatin. The DNA adduct formation of cis-[Pt(C6F5)2(HmtpO)2] and [Pt(dmba)(PPh3)(HmtpO)]ClO4 was followed by circular dichroism and electrophoretic mobility. Atomic

  20. Uracil/ftorafur/leucovorin combined with irinotecan (TEGAFIRI) or oxaliplatin (TEGAFOX) as first-line treatment for metastatic colorectal cancer patients: results of randomised phase II study

    PubMed Central

    Bajetta, E; Di Bartolomeo, M; Buzzoni, R; Mariani, L; Zilembo, N; Ferrario, E; Lo Vullo, S; Aitini, E; Isa, L; Barone, C; Jacobelli, S; Recaldin, E; Pinotti, G; Iop, A

    2007-01-01

    This randomised phase II study evaluates the safety and efficacy profile of uracil/tegafur/leucovorin combined with irinotecan (TEGAFIRI) or with oxaliplatin (TEGAFOX). One hundred and forty-three patients with measurable, non-resectable metastatic colorectal cancer were randomised in a multicentre study to receive TEGAFIRI (UFT 250 mg m−2 day days 1–14, LV 90 mg day days 1–14, irinotecan 240 mg m−2 day 1; q21) or TEGAFOX (UFT 250 mg m−2 day days 1–14, LV 90 mg day days 1–14, oxaliplatin 120 mg m−2 day 1; q21). Among 143 randomised patients, 141 were analysed (68 received TEGAFIRI and 73 TEGAFOX). The main characteristics of the two arms were well balanced. The most common grade 3–4 treatment-related adverse events were neutropenia (13% of cases with TEGAFIRI; 1% in the TEGAFOX group). Diarrhoea was prevalent in the TEGAFIRI arm (16%) vs TEGAFOX (4%). Six complete remission (CR) and 19 partial remission (PR) were recorded in the TEGAFIRI arm (odds ratio (OR): 41.7; 95% confidence limit (CL), 29.1–55.1%), and six CR and 22 PR were recorded in the TEGAFOX group, (OR: 38.9; 95% CL, 27.6–51.1). At a median time follow-up of 17 months (intequartile (IQ) range 12–23), a median survival probability of 20 and 19 months was obtained in the TEGAFIRI and TEGAFOX groups, respectively. Median time to progression was 8 months for both groups. TEGAFIRI and TEGAFOX are both effective and tolerable first-line therapies in MCRC patients. The employment of UFT/LV given in doublet combination is interesting and the presented data appear comparable to equivalent infusion regimens described in the literature. The safety profile of the two combinations also allows an evaluation with other biological agents such as monoclonal antibodies. PMID:17245343

  1. Liquid chromatography-tandem mass spectrometric assay for the analysis of uracil, 5,6-dihydrouracil and beta-ureidopropionic acid in urine for the measurement of the activities of the pyrimidine catabolic enzymes.

    PubMed

    Sparidans, Rolf W; Bosch, T M; Jörger, M; Schellens, Jan H M; Beijnen, Jos H

    2006-07-24

    A liquid chromatography-tandem mass spectrometric assay for the determination of uracil, 5,6-dihydrouracil and beta-ureidopropionic acid in urine was developed to measure the activities of enzymes involved in pyrimidine breakdown. The assay was required to investigate the relation between the uracil-dihydrouracil ratio and toxicities observed after treatment with fluoropyrimidines drugs. After addition of stable isotopically labelled internal standards, the analytes were isolated from a 100-microl urine sample using liquid-liquid extraction with ethyl acetate-2-propanol. Compounds were separated on an Atlantis dC18 column, using ammonium acetate-formic acid in water as the eluent. The eluate was totally led into an electrospray interface with positive ionisation and the analytes were quantified using triple quadrupole mass spectrometry. The assay was validated in the range 1.6-1600 microM, using both, artificial urine and pooled urine as matrices. Intra-day precisions were < or = 8% and inter-day precisions were < or = 10%. Accuracies between 91 and 108% were found. The analytes were chemically stable under all relevant conditions and the assay was successfully applied in two clinical studies of cancer patients treated with 5-fluorouracil or capecitabine.

  2. Toward feasible and comprehensive computational protocol for simulation of the spectroscopic properties of large molecular systems: the anharmonic infrared spectrum of uracil in the solid state by the reduced dimensionality/hybrid VPT2 approach.

    PubMed

    Fornaro, Teresa; Carnimeo, Ivan; Biczysko, Malgorzata

    2015-05-28

    Feasible and comprehensive computational protocols for simulating the spectroscopic properties of large and complex molecular systems are very sought after. Indeed, due to the great variety of intra- and intermolecular interactions that may take place, the interpretation of experimental data becomes more and more difficult as the system under study increases in size or is placed in a complex environment, such as condensed phases. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes, with increasing complexity toward condensed phases and monolayers of biomolecules on solid supports. We have resorted to fully anharmonic quantum mechanical computations within the generalized second-order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such an approach has been validated in a previous work ( Phys. Chem. Chem. Phys. 2014 , 16 , 10112 - 10128 ) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended such computational protocol to simulate spectroscopic properties of a molecular solid, namely polycrystalline uracil. First we have selected a realistic molecular model for representing the spectroscopic properties of uracil in the solid state, the uracil heptamer, and then we have computed the relative anharmonic frequencies combining less demanding approaches such as the hybrid B3LYP-D3/DFTBA one, in which the harmonic frequencies are computed at a higher level of theory (B3LYP-D3/N07D) whereas the anharmonic shifts are evaluated at a lower level of theory (DFTBA), and the reduced dimensionality VPT2 (RD-VPT2) approach, where only selected vibrational modes are computed anharmonically along with the couplings with other modes. The good agreement between the

  3. Eight new crystal structures of 5-(hydroxymethyl)uracil, 5-carboxyuracil and 5-carboxy-2-thiouracil: insights into the hydrogen-bonded networks and the predominant conformations of the C5-bound residues.

    PubMed

    Seiler, Vanessa Kristina; Hützler, Wilhelm Maximilian; Bolte, Michael

    2016-05-01

    In order to examine the preferred hydrogen-bonding pattern of various uracil derivatives, namely 5-(hydroxymethyl)uracil, 5-carboxyuracil and 5-carboxy-2-thiouracil, and for a conformational study, crystallization experiments yielded eight different structures: 5-(hydroxymethyl)uracil, C5H6N2O3, (I), 5-carboxyuracil-N,N-dimethylformamide (1/1), C5H4N2O4·C3H7NO, (II), 5-carboxyuracil-dimethyl sulfoxide (1/1), C5H4N2O4·C2H6OS, (III), 5-carboxyuracil-N,N-dimethylacetamide (1/1), C5H4N2O4·C4H9NO, (IV), 5-carboxy-2-thiouracil-N,N-dimethylformamide (1/1), C5H4N2O3S·C3H7NO, (V), 5-carboxy-2-thiouracil-dimethyl sulfoxide (1/1), C5H4N2O3S·C2H6OS, (VI), 5-carboxy-2-thiouracil-1,4-dioxane (2/3), 2C5H4N2O3S·3C6H12O3, (VII), and 5-carboxy-2-thiouracil, C10H8N4O6S2, (VIII). While the six solvated structures, i.e. (II)-(VII), contain intramolecular S(6) O-H...O hydrogen-bond motifs between the carboxy and carbonyl groups, the usually favoured R2(2)(8) pattern between two carboxy groups is formed in the solvent-free structure, i.e. (VIII). Further R2(2)(8) hydrogen-bond motifs involving either two N-H...O or two N-H...S hydrogen bonds were observed in three crystal structures, namely (I), (IV) and (VIII). In all eight structures, the residue at the ring 5-position shows a coplanar arrangement with respect to the pyrimidine ring which is in agreement with a search of the Cambridge Structural Database for six-membered cyclic compounds containing a carboxy group. The search confirmed that coplanarity between the carboxy group and the cyclic residue is strongly favoured.

  4. Toward the discovery of dual HCMV-VZV inhibitors: Synthesis, structure activity relationship analysis, and cytotoxicity studies of long chained 2-uracil-3-yl-N-(4-phenoxyphenyl)acetamides.

    PubMed

    Babkov, Denis A; Khandazhinskaya, Anastasia L; Chizhov, Alexander O; Andrei, Graciela; Snoeck, Robert; Seley-Radtke, Katherine L; Novikov, Mikhail S

    2015-11-01

    The need for novel therapeutic options to fight herpesvirus infections still persists. Herein we report the design, synthesis and antiviral evaluation of a new family of non-nucleoside antivirals, derived from 1-[ω-(4-bromophenoxy)alkyl]uracil derivatives--previously reported inhibitors of human cytomegalovirus (HCMV). Introduction of the N-(4-phenoxyphenyl)acetamide side chain at N(3) increased their potency and widened activity spectrum. The most active compounds in the series exhibit submicromolar activity against different viral strains of HCMV and varicella zoster virus (VZV) replication in HEL cell cultures. Inactivity against other DNA and RNA viruses, including herpes simplex virus 1/2, points to a novel mechanism of antiviral action. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Design, synthesis and anticonvulsant activity of some new 6,8-halo-substituted-2h-[1,2,4]triazino[5,6-b]indole-3(5h)-one/-thione and 6,8-halo-substituted 5-methyl-2h-[1,2,4]triazino[5,6-b]indol-3(5h)-one/-thione

    PubMed Central

    Kumar, Rajeev; Singh, Tejendra; Singh, Hariram; Jain, Sandeep; Roy, R. K.

    2014-01-01

    A new series of 6,8-halo-substituted-2H-[1,2,4]triazino[5,6-b]indole-3(5H)-one/-thione and 6,8-halo-substituted 5-methyl-2H-[1,2,4]triazino[5,6-b]indol-3(5H)-one/-thione (5a-5l) were designed and synthesized keeping in view of the structural requirement of pharmacophore. The above compounds were characterized by thin layer chromatography and spectral analysis. Anticonvulsant activity of the synthesized compounds was evaluated by the maximal electroshock (MES) test. Neurotoxicity and CNS depressant effects were evaluated by the rotarod motor impairment and Porsolt’s force swim tests, respectively. A computational study was carried out, for calculation of pharmacophore pattern, prediction of pharmacokinetic properties and toxicity properties. The above study revealed that the compounds 8-chloro-2H-[1,2,4]triazino[5,6-b]indol-3(5H)-one (5e), 6,8-dibromo-2H-[1,2,4]triazino[5,6-b]indol-3(5H)-one (5i) and 6,8-dibromo-5-methyl-2H-[1,2,4]triazino[5,6-b]indol-3(5H)-one (5k) possess excellent anticonvulsant activity in the series with little CNS depressant effect and no neurotoxicity as compared to standard drugs phenytoin and carbamazepine. PMID:26417257

  6. Crystal structure of 3-[({2-[bis­(2-hy­droxy­benz­yl)amino]­eth­yl}(2-hy­droxy­benz­yl)amino)­meth­yl]-2-hydroxy-5-methyl­benzaldehyde

    PubMed Central

    Fonseca, Alexandra S.; Bortoluzzi, Adailton J.

    2014-01-01

    The non-symmetric title mol­ecule, C32H34N2O5, is based on a tetra­substituted ethyl­enedi­amine backbone. The mol­ecular structure consists of three hy­droxy­benzyl groups and one 2-hy­droxy-5-methyl­benzaldehyde group bonded to the N atoms of the di­amine unit. The ethyl­enedi­amine skeleton shows a regular extended conformation, while the spatial orientation of the phenol arms is governed by hydrogen bonds. In the 2-hy­droxy-5-methyl­benzaldehyde group, an intra­molecular S(6) O—H⋯O hydrogen bond is observed between the alcohol and aldehyde functions, and the neighbouring phenol arm participates in an intra­molecular S(6) O—H⋯N hydrogen bond. The third phenol group is involved in a bifurcated intra­molecular hydrogen bond with graph-set notation S(6) for O—H⋯N and O—H⋯O intra­molecular hydrogen bonds between neighbouring amine and phenol arms, respectively. Finally, the fourth phenol group acts as an acceptor in a bifurcated intra­molecular hydrogen bond and also acts as donor in an inter­molecular hydrogen bond, which connects inversion-related mol­ecules into dimers with R 4 4(8) ring motifs. PMID:25552993

  7. Synthesis, crystal structure, insecticidal activity and DFT study on the geometry and vibration of O-( E)-1-{1-[(6-chloropyridin-3-yl)methyl]-5-methyl-1 H-1,2,3-triazol-4-yl}ethyleneamino- O-ethyl- O-phenylphosphorothioate

    NASA Astrophysics Data System (ADS)

    Shi, De-Qing; Zhu, Xiao-Fei; Song, Yuan-Zhi

    2008-12-01

    The title compound, O-( E)-1-{1-[(6-chloropyridin-3-yl)methyl]-5-methyl-1 H-1,2,3-triazol-4-yl}ethyleneamino- O-ethyl- O-phenylphosphorothioate, has been synthesized via the condensation reaction of 1-{1-[(6-chloropyridin-3-yl)methyl]-5-methyl-1 H-1,2,3-triazol-4-yl}ethanone oxime and O-ethyl- O-phenylphosphorochloridothioate in the presence of NaOH powder in refluxing EtOH. Its structure was characterized by 1H NMR, FTIR, Raman, elemental analysis and X-ray single crystal diffraction. The results of preliminary bioassays indicated that the title compound displays good insecticidal activity. Density functional (DFT) calculations have been carried out for the title compound by using the Becke-Lee-Yang-Parr's three-parameter hybrid functional (B3LYP) method at 6-31G** and 6-31G* basis sets. The calculated results show that the predicted geometry can well reproduce the structural parameters. The vibrational wave numbers of the title compound were calculated at same level. Predicted vibrational frequencies have been assigned and compared with experimental IR and Raman spectra and they are supported each other.

  8. Tamoxifen plus tegafur-uracil (TUFT) versus tamoxifen plus Adriamycin (doxorubicin) and cyclophosphamide (ACT) as adjuvant therapy to treat node-positive premenopausal breast cancer (PreMBC): results of Japan Clinical Oncology Group Study 9404.

    PubMed

    Shien, Tadahiko; Iwata, Hiroji; Fukutomi, Takashi; Inoue, Kenichi; Aogi, Kenjiro; Kinoshita, Takayuki; Ando, Jiro; Takashima, Seiki; Nakamura, Kenichi; Shibata, Taro; Fukuda, Haruhiko

    2014-09-01

    A prospective randomized clinical trial was conducted to evaluate the efficacy of tamoxifen plus doxorubicin and cyclophosphamide compared to tamoxifen plus tegafur-uracil as an adjuvant therapy to treat node-positive premenopausal breast cancer (PreMBC). Eligibility criteria included pathologically node-positive (n = 1-9) preMBC with curative resection, in stages I-IIIA. Patients were randomized to receive either tamoxifen 20 mg/day plus tegafur-uracil 400 mg/day (TU) for 2 years or six courses of a 28-day cycle of doxorubicin 40 mg/m(2) plus cyclophosphamide 500 mg/m(2) on day 1 along with tamoxifen (ACT) given for 2 years as adjuvant therapy. Primary endpoint was overall survival (OS), and secondary endpoint was recurrence-free survival (RFS). In total, 169 patients were recruited (TU arm 87, ACT arm 82) between October 1994 and September 1999. The HR for OS was 0.76 (95 % CI 0.35, 1.66, log-rank p = 0.49) and that for RFS was 0.77 (95 % CI 0.44, 1.36, log-rank p = 0.37), with ACT resulting in a better HR. The 5-year OS was 79.7 % for patients in the TU arm and 83 % for those in the ACT arm. The 5-year RFS was 66.1 % for patients in the TU arm and 70.6 % for those in the ACT arm. A higher proportion of patients in the ACT arm experienced grade 3 leucopenia (0 % in the TU arm, 4 % in the ACT arm). There were no significant differences in the efficacy of TU and ACT as adjuvant therapy.

  9. The methylenetetrahydrofolate reductase C677T mutation induces cell-specific changes in genomic DNA methylation and uracil misincorporation: a possible molecular basis for the site-specific cancer risk modification.

    PubMed

    Sohn, Kyoung-Jin; Jang, Hyeran; Campan, Mihaela; Weisenberger, Daniel J; Dickhout, Jeffrey; Wang, Yi-Cheng; Cho, Robert C; Yates, Zoe; Lucock, Mark; Chiang, En-Pei; Austin, Richard C; Choi, Sang-Woon; Laird, Peter W; Kim, Young-In

    2009-05-01

    The C677T polymorphism in the methylenetetrahydrofolate reductase (MTHFR) gene is associated with a decreased risk of colon cancer although it may increase the risk of breast cancer. This polymorphism is associated with changes in intracellular folate cofactors, which may affect DNA methylation and synthesis via altered one-carbon transfer reactions. We investigated the effect of this mutation on DNA methylation and uracil misincorporation and its interaction with exogenous folate in further modulating these biomarkers of one-carbon transfer reactions in an in vitro model of the MTHFR 677T mutation in HCT116 colon and MDA-MB-435 breast adenocarcinoma cells. In HCT116 cells, the MTHFR 677T mutation was associated with significantly increased genomic DNA methylation when folate supply was adequate or high; however, in the setting of folate insufficiency, this mutation was associated with significantly decreased genomic DNA methylation. In contrast, in MDA-MB-435 cells, the MTHFR 677T mutation was associated with significantly decreased genomic DNA methylation when folate supply was adequate or high and with no effect when folate supply was low. The MTHFR 677T mutation was associated with a nonsignificant trend toward decreased and increased uracil misincorporation in HCT116 and MDA-MB-435 cells, respectively. Our data demonstrate for the first time a functional consequence of changes in intracellular folate cofactors resulting from the MTHFR 677T mutation in cells derived from the target organs of interest, thus providing a plausible cellular mechanism that may partly explain the site-specific modification of colon and breast cancer risks associated with the MTHFR C677T mutation.

  10. Comment on "Structural and vibrational studies on 1-(5-Methyl- [1,3,4] thiadiazol-2-yl)-pyrolidin-2-ol" [Spectrochimica Acta Part A, 152 (2016) 252-261]. The importance of intramolecular OH ⋯ N hydrogen bonding in the conformational properties of thiadiazol-pyrrolidin-2-ol bearing species

    NASA Astrophysics Data System (ADS)

    Laurella, Sergio L.; Erben, Mauricio F.

    2016-07-01

    The title paper [1] reports a study on the spectroscopic and physicochemical properties of 1-(5-methyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (MTPN) based on experimental and theoretical data. The latter ones are based on the computed molecular structure for a rather unusual conformer. Here, after a careful analysis of the conformational space of MTPN, the most stable conformation was determined for the molecule isolated in a vacuum, which results to be 21.9 kJ/mol more stable than the conformer reported previously. Our study also includes the closely related species 1-(5-trifluoromethyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (FMTPN). An intramolecular OH ⋯ N hydrogen bond determines the conformational behavior of the [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol group as demonstrated by Natural Bond Orbital population analysis.

  11. Comment on "Structural and vibrational studies on 1-(5-Methyl- [1,3,4] thiadiazol-2-yl)-pyrolidin-2-ol" [Spectrochimica Acta Part A, 152 (2016) 252-261]. The importance of intramolecular OH⋯N hydrogen bonding in the conformational properties of thiadiazol-pyrrolidin-2-ol bearing species.

    PubMed

    Laurella, Sergio L; Erben, Mauricio F

    2016-07-05

    The title paper [1] reports a study on the spectroscopic and physicochemical properties of 1-(5-methyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (MTPN) based on experimental and theoretical data. The latter ones are based on the computed molecular structure for a rather unusual conformer. Here, after a careful analysis of the conformational space of MTPN, the most stable conformation was determined for the molecule isolated in a vacuum, which results to be 21.9kJ/mol more stable than the conformer reported previously. Our study also includes the closely related species 1-(5-trifluoromethyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (FMTPN). An intramolecular OH⋯N hydrogen bond determines the conformational behavior of the [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol group as demonstrated by Natural Bond Orbital population analysis.

  12. Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

    SciTech Connect

    Morgado, Claudio A.; Jurecka, Petr; Svozil, Daniel; Hobza, Pavel; Sponer, Jiri

    2009-06-09

    We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantummechanics (QM) methods. Nonparallel stacking geometries often occur in nucleic acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the shortrange repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been carried out using the MP2 method extrapolated to the complete basis-set limit and corrected for higher-order electron-correlation contributions using CCSD(T) calculations with a medium-sized basis set. These reference calculations have been used as benchmark data to test the performance of the DFT-D, SCS(MI)-MP2, and DFTSAPT QM methods and of the AMBER molecular-mechanics (MM) force field. The QM methods show close to quantitative agreement with the reference data, albeit the DFT-D method tends to modestly exaggerate the repulsion of steric clashes. The force field in general also provides a good description of base stacking for the systems studied here. However, for geometries with close interatomic contacts and clashes, the repulsion effects are rather severely exaggerated. The discrepancy reported here should not affect the overall stability of MD simulations and qualitative applications of the force field. However, it may affect the description of subtle

  13. Methanocarba Modification of Uracil and Adenine Nucleotides: High Potency of Northern Ring Conformation at P2Y1, P2Y2, P2Y4, and P2Y11 but Not P2Y6 Receptors

    PubMed Central

    Kim, Hak Sung; Ravi, R. Gnana; Marquez, Victor E.; Maddileti, Savitri; Wihlborg, Anna-Karin; Erlinge, David; Malmsjö, Malin; Boyer, José L.; Harden, T. Kendall; Jacobson, Kenneth A.

    2016-01-01

    The potency of nucleotide antagonists at P2Y1 receptors was enhanced by replacing the ribose moiety with a constrained carbocyclic ring (Nandanan, et al. J. Med. Chem. 2000, 43, 829—842). We have now synthesized ring-constrained methanocarba analogues (in which a fused cyclopropane moiety constrains the pseudosugar ring) of adenine and uracil nucleotides, the endogenous activators of P2Y receptors. Methanocarba-adenosine 5′-triphosphate (ATP) was fixed in either a Northern (N) or a Southern (S) conformation, as defined in the pseudorotational cycle. (N)-Methanocarba-uridine was prepared from the 1-amino-pseudosugar ring by treatment with β-ethoxyacryloyl cyanate and cyclization to form the uracil ring. Phosphorylation was carried out at the 5′-hydroxyl group through a multistep process: Reaction with phosphoramidite followed by oxidation provided the 5′-monophosphates, which then were treated with 1,1′-carbonyldiimidazole for condensation with additional phosphate groups. The ability of the analogues to stimulate phospholipase C through activation of turkey P2Y1 or human P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11 receptors stably expressed in astrocytoma cells was measured. At recombinant human P2Y1 and P2Y2 receptors, (N)-methanocarba-ATP was 138- and 41-fold, respectively, more potent than racemic (S)-methanocarba-ATP as an agonist. (N)-methanocarba-ATP activated P2Y11 receptors with a potency similar to ATP. (N)-Methanocarba-uridine 5′-triphosphate (UTP) was equipotent to UTP as an agonist at human P2Y2 receptors and also activated P2Y4 receptors with an EC50 of 85 nM. (N)-Methanocarba-uridine 5′-diphosphate (UDP) was inactive at the hP2Y6 receptor. The vascular effects of (N)-methanocarba-UTP and (N)-methanocarba-UDP were studied in a model of the rat mesenteric artery. The triphosphate was more potent than UTP in inducing a dilatory P2Y4 response (pEC50 = 6.1 ± 0.2), while the diphosphate was inactive as either an agonist or antagonist in a P2Y6

  14. Simultaneous determination of 1-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl) uracil (FAU) and 1-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl) 5-methyluracil (FMAU) in human plasma by liquid chromatography/tandem mass spectrometry.

    PubMed

    Wiegand, Richard; Wu, Jianmei; Shields, Anthony F; Lorusso, Patricia; Li, Jing

    2012-04-01

    A liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) assay was developed and validated for simultaneous determination of 1-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl) uracil (FAU) and its active metabolite 1-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl) 5-methyluracil (FMAU) in human plasma. FAU and FMAU were extracted from plasma samples using solid-phase extraction with Waters Sep-Pak® Vac C₁₈ cartridge. Chromatographic separation was achieved on a Waters Atlantis T3 C₁₈ column with a gradient mobile phase consisting of methanol and water with 0.45% formic acid (v/v) running at a flow rate of 0.2 ml/min. The analytes were monitored by triple quadrupole mass spectrometer under positive ionization mode. The lower limit of quantitation (LLOQ) was 10 and 2 ng/ml for FAU and FMAU in plasma, respectively. Calibration curves were linear over FAU and FMAU plasma concentration range of 10-2000 and 2-1000 ng/ml, respectively. The intra-day and inter-day accuracy and precision were within the generally accepted criteria for bioanalytical method (<15%). The method has been successfully employed to characterize the plasma pharmacokinetics of FAU and FMAU in cancer patients receiving 1-h intravenous infusion of FAU 50 mg/m². Copyright © 2012 Elsevier B.V. All rights reserved.

  15. The products of the reaction between 6-amine-1,3-dimethyl uracil and bis-chalcones induce cytotoxicity with massive vacuolation in HeLa cervical cancer cell line.

    PubMed

    Solano, José D; González-Sánchez, Ignacio; Cerbón, Marco A; Guzmán, Ángel; Martínez-Urbina, Miguel A; Vilchis-Reyes, Miguel A; Martínez-Zuñiga, Eduardo C; Alvarado, Cuauhtémoc; Quintero, Angelina; Díaz, Eduardo

    2013-02-01

    As a part of our research in the chemistry of chalcones we have prepared four pyrimidine monoadducts of bis-chalcones through the reaction with 6-amino-1,3-dimethyl uracil. These compounds displayed cytotoxicity with a massive vacuolation in different human cell lines in vitro. Compound 6 was the most cytotoxic inducer of vacuoles, this compound induced G1 phase cell cycle arrest, and their cytotoxicity went without morphological and biochemical evidence of apoptotic cell death in HeLa cells. In addition, our results showed that this vacuole formation does not require de novo protein synthesis and the content vacuolar is acidic. Compound 6 induce necrotic cell death with excessive vacuolation, similar to a process of autophagy. Spautin-1 an inhibitor of autophagy, decreased the transformation of microtubule-associated protein 1 light chain 3 (LC3B-I) to LC3B-II and the vacuolation induced by compound 6 in HeLa cells, both autophagy processes. These compounds could be of pivotal importance in the study of non-apoptotic cell death with vacuole formation and could be useful in research into new autophagy inhibitors agents.

  16. 2-Amino-5-methyl-pyridinium 2-amino-benzoate.

    PubMed

    Thanigaimani, Kaliyaperumal; Farhadikoutenaei, Abbas; Khalib, Nuridayanti Che; Arshad, Suhana; Razak, Ibrahim Abdul

    2012-11-01

    In the 2-amino-benzoate anion of the title salt, C(6)H(9)N(2) (+)·C(7)H(6)NO(2) (-), an intra-molecular N-H⋯O hydrogen bond is observed. The dihedral angle between the ring and the CO(2) group is 8.41 (13)°. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl-ate O atoms via a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. The ion pairs are further connected via N-H⋯O hydrogen bonds, resulting in a donor-donor-acceptor-acceptor (DDAA) array of quadruple hydrogen bonds. The crystal structure also features a weak N-H⋯O hydrogen bond and a C-H⋯π inter-action, resulting in a three-dimensional network.

  17. N-(2-Chloro-5-methyl-phen-yl)succinamic acid.

    PubMed

    Gowda, B Thimme; Foro, Sabine; Chaithanya, U

    2012-01-01

    In the title compound, C(11)H(12)ClNO(3), the conformation of the N-H bond in the amide segment is syn with respect to the ortho-Cl atom. The amide and carboxyl C=O groups are syn to each other. Furthermore, the C=O and O-H bonds of the carboxyl group are in syn positions with respect to each other. The dihedral angle between the benzene ring and the amide group is 47.8 (2)°. In the crystal, mol-ecules are connected by pairs of O-H⋯O hydrogen bonds, forming inversion dimers. The dimers are further linked by N-H⋯O hydrogen bonds into double chains along the b-axis direction.

  18. Synthesis, biological evaluation, and automated docking of constrained analogues of the opioid peptide H-Dmt-D-Ala-Phe-Gly-NH₂ using the 4- or 5-methyl substituted 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one scaffold.

    PubMed

    De Wachter, Rien; de Graaf, Chris; Keresztes, Atilla; Vandormael, Bart; Ballet, Steven; Tóth, Géza; Rognan, Didier; Tourwé, Dirk

    2011-10-13

    The Phe(3) residue of the N-terminal tetrapeptide of dermorphin (H-Dmt-d-Ala-Phe-Gly-NH(2)) was conformationally constrained using 4- or 5-methyl-substituted 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one (Aba) stereoisomeric scaffolds. Several of the synthesized peptides were determined to be high affinity agonists for the μ opioid receptor (OPRM) with selectivity over the δ opioid receptor (OPRD). Interesting effects of the Aba configuration on ligand binding affinity were observed. H-Dmt-d-Ala-erythro-(4S,5S)-5-Me-Aba-Gly-NH(2)9 and H-Dmt-threo-(4R,5S)-5-Me-Aba-Gly-NH(2)12 exhibited subnanomolar affinity for OPRM, while they possess an opposite absolute configuration at position 4 of the Aba ring. However, in the 4-methyl substituted analogues, H-Dmt-d-Ala-(4R)-Me-Aba-Gly-NH(2)14 was significantly more potent than the (4S)-derivative 13. These unexpected results were rationalized using the binding poses predicted by molecular docking simulations. Interestingly, H-Dmt-d-Ala-(4R)-Me-Aba-Gly-NH(2)14 is proposed to bind in a different mode compared with the other analogues. Moreover, in contrast to Ac-4-Me-Aba-NH-Me, which adopts a β-turn in solution and in the crystal structure, the binding mode of this analogue suggests an alternative receptor-bound conformation.

  19. Synthesis and preliminary CNS depressant activity evaluation of new 3-[(3-substituted-5-methyl-4-thiazolidinon-2-ylidene)hydrazono]-1H-2- indolinones and 3-[(2-thioxo-3-substituted-4,5-imidazolidinedion-1-yl) imino]-1H-2-indolinones.

    PubMed

    Karali, N; Gürsoy, A; Terzioglu, N; Ozkirimli, S; Ozer, H; Ekinci, A C

    1998-01-01

    A series of (+/-) 3-[(3-substituted-5-methyl-4-thiazolidinon-2- ylidene)hydrazono]-1H-2-indolinones (2a-h) and 3-[(2-thioxo-3-substituted-4,5-imidazolidinedion-1-yl)imino] -1H-2-indolinones (3a-g) were synthesized by the cyclization of 3-(4-substituted-thiosemicarbazono)-1H-2-indolinones (1a-h) with ethyl 2-bromopropionate in anydrous ethanolic medium and oxalyl chloride in anhydrous diethyl ether, respectively. The structures of 2 and 3 were confirmed by analytical and spectral data (IR, 1H NMR, 13C NMR, and EIMS). The configuration of 3 was assigned on the basis of 1H NMR and 13C NMR data. 2c, 2d, 2g, 2h, and 3a-g were evaluated for anticonvulsant activity against maximal electroshock (MES) and subcutaneous pentylenetetrazol (ScMet) induced seizures. Among the compounds tested, only 2d exhibited some activity in anticonvulsant identification (Phase I) trials in mice. 2a, 2b, 2d, 2g, 2h, and 3a-g were additionally tested for potentiating effects on pentobarbital induced hypnosis in mice. All of the test compounds increased the sleeping time of pentobarbital significantly (p < 0.05) and the most potent compound was found to be 3a.

  20. Discovery of N-[(4R)-6-(4-chlorophenyl)-7-(2,4-dichlorophenyl)-2,2-dimethyl-3,4-dihydro-2H-pyrano[2,3-b]pyridin-4-yl]-5-methyl-1H-pyrazole-3-carboxamide (MK-5596) as a novel cannabinoid-1 receptor (CB1R) inverse agonist for the treatment of obesity.

    PubMed

    Yan, Lin; Huo, Pei; Debenham, John S; Madsen-Duggan, Christina B; Lao, Julie; Chen, Richard Z; Xiao, Jing Chen; Shen, Chun-Pyn; Stribling, D Sloan; Shearman, Lauren P; Strack, Alison M; Tsou, Nancy; Ball, Richard G; Wang, Junying; Tong, Xinchun; Bateman, Thomas J; Reddy, Vijay B G; Fong, Tung M; Hale, Jeffrey J

    2010-05-27

    This paper describes the discovery of N-[(4R)-6-(4-chlorophenyl)-7-(2,4-dichlorophenyl)-2,2-dimethyl-3,4-dihydro-2H-pyrano[2,3-b]pyridin-4-yl]-5-methyl-1H-pyrazole-3-carboxamide (MK-5596, 12c) as a novel cannabinoid-1 receptor (CB1R) inverse agonist for the treatment of obesity. Structure-activity relationship (SAR) studies of lead compound 3, which had off-target hERG (human ether-a-go-go related gene) inhibition activity, led to the identification of several compounds that not only had attenuated hERG inhibition activity but also were subject to glucuronidation in vitro providing the potential for multiple metabolic clearance pathways. Among them, pyrazole 12c was found to be a highly selective CB1R inverse agonist that reduced body weight and food intake in a DIO (diet-induced obese) rat model through a CB1R-mediated mechanism. Although 12c was a substrate of P-glycoprotein (P-gp) transporter, its high in vivo efficacy in rodents, good pharmacokinetic properties in preclinical species, good safety margins, and its potential for a balanced metabolism profile in man allowed for the further evaluation of this compound in the clinic.

  1. Synthesis, DFT calculations, electronic structure, electronic absorption spectra, natural bond orbital (NBO) and nonlinear optical (NLO) analysis of the novel 5-methyl-8H-benzo[h]chromeno[2,3-b][1,6] naphthyridine-6(5H),8-dione (MBCND)

    NASA Astrophysics Data System (ADS)

    Halim, Shimaa Abdel; Ibrahim, Magdy A.

    2017-02-01

    New derivative of heteroannulated chromone identified as 5-methyl-8H-benzo[h]chromeno[2,3-b][1,6]naphthyridine-6(5H),8-dione (5, MBCND) was easily and efficiently synthesized from DBU catalyzed condensation reaction of 2-aminochromone-3-carboxaldehyde (1) with 4-hydroxy-1-methylquinolin-2(1H)-one (2). The same product 5 was isolated from condensation reaction of aldeyde 1 with 3-(4-hydroxy-1-methyl-2-oxo-1,2-dihydroquinolin-3-yl)-3-oxopropanoic acid (3) or ethyl 4-(4-hydroxy-1-methyl-2-oxo-1,2-dihydroquinolin-3-yl)-2,4-dioxobutanoate (4). Structure of compound (5, MBCND) was deduced based on their elemental analyses and spectral data (IR, 1H NMR and mass spectra). Density Functional Theory (DFT) calculations at the B3LYP/6-311G (d,p) level of theory have been carried out to investigate the equilibrium geometry of the novel compound (5, MBCND). Moreover, total energy, energy of HOMO and LUMO and Mullikan atomic charges were calculated. In addition, the dipole moment, theoretical study of the electronic structure, nonlinear optical properties (NLO), and natural bonding orbital (NBO) analysis and orientation have been performed and discussed. Also the electronic absorption spectra were measured in polar (methanol) as well as non polar (dioxane) solvents and the assignment of the observed bands has been discussed by TD-DFT calculations. The correspondences between calculated and experimental transitions energies are satisfactory.

  2. Differences in nitric oxide steady-states between arginine, hypoxanthine, uracil auxotrophs (AHU) and non-AHU strains of Neisseria gonorrhoeae during anaerobic respiration in the presence of nitrite

    PubMed Central

    Barth, Kenneth; Clark, Virginia L.

    2008-01-01

    Neisseria gonorrhoeae can grow by anaerobic respiration using nitrite as an alternative electron acceptor. Under these growth conditions, N. gonorrhoeae produces and degrades nitric oxide (NO), an important host defense molecule. Laboratory strain F62 has been shown to establish and maintain a NO steady-state level that is a function of the nitrite reductase/nitric oxide reductase ratio and is independent of cell number. The nitrite reductase activities (122–197 nmoles NO2 reduced/ min-OD600) and nitric oxide reductase activities (88–155 nmoles NO reduced/ min-OD600) in a variety of gonococcal clinical isolates were similar to the specific activities seen in F62 (241 nmoles NO2 reduced/ min-OD and 88 nmoles NO reduced/ min-OD, respectively). In 7 gonococcal strains, the NO steady state levels established in the presence of nitrite were similar to that of F62 (801–2121 nM NO), while 6 of the strains, identified as arginine, hypoxanthine, and uracil auxotrophs (AHU), that cause asymptomatic infection in men, had either a 2- to 3-fold (373–579 nM NO) or about 100-fold (13–24 nM NO) lower NO steady state concentrations. All tested strains in the presence of a NO-donor, DETA/NO, quickly lowered and maintained NO levels in the non-inflammatory range of NO (<300 nM). The generation of a NO steady-state concentration was directly affected by alterations in respiratory control in both F62 and an AHU strain, although differences in membrane function are suspected to be responsible for NO steady-state level differences in AHU strains. PMID:18772926

  3. Influence of Transition Metal Cationization versus Sodium Cationization and Protonation on the Gas-Phase Tautomeric Conformations and Stability of Uracil: Application to [Ura+Cu]+ and [Ura+Ag]+

    NASA Astrophysics Data System (ADS)

    Akinyemi, T. E.; Wu, R. R.; Nei, Y.-W.; Cunningham, N. A.; Roy, H. A.; Steill, J. D.; Berden, G.; Oomens, J.; Rodgers, M. T.

    2017-09-01

    The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu]+ and [Ura+Ag]+, were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra were measured over the IR fingerprint and hydrogen-stretching regions. Structures and linear IR spectra of the stable tautomeric conformations of these complexes were initially determined at the B3LYP/6-31G(d) level. The four most stable structures computed were also examined at the B3LYP/def2-TZVPPD level to improve the accuracy of the predicted IR spectra. Two very favorable modes of binding are found for [Ura+Cu]+ and [Ura+Ag]+ that involve O2N3 bidentate binding to the 2-keto-4-hydroxy minor tautomer and O4 monodentate binding to the canonical 2,4-diketo tautomer of Ura. Comparisons between the measured IRMPD and calculated IR spectra enable elucidation of the conformers present in the experiments. These comparisons indicate that both favorable binding modes are represented in the experimental tautomeric conformations of [Ura+Cu]+ and [Ura+Ag]+. B3LYP suggests that Cu+ exhibits a slight preference for O4 binding, whereas Ag+ exhibits a slight preference for O2N3 binding. In contrast, MP2 suggests that both Cu+ and Ag+ exhibit a more significant preference for O2N3 binding. The relative band intensities suggest that O4 binding conformers comprise a larger portion of the population for [Ura+Ag]+ than [Ura+Cu]+. The dissociation behavior and relative stabilities of the [Ura+M]+ complexes, M+ = Cu+, Ag+, H+, and Na+) are examined via energy-resolved collision-induced dissociation experiments. The IRMPD spectra, dissociation behaviors, and binding preferences of Cu+ and Ag+ are compared with previous and present results for those of H+ and Na+. [Figure not available: see fulltext.

  4. Influence of Transition Metal Cationization versus Sodium Cationization and Protonation on the Gas-Phase Tautomeric Conformations and Stability of Uracil: Application to [Ura+Cu](+) and [Ura+Ag]().

    PubMed

    Akinyemi, T E; Wu, R R; Nei, Y-W; Cunningham, N A; Roy, H A; Steill, J D; Berden, G; Oomens, J; Rodgers, M T

    2017-09-11

    The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu](+) and [Ura+Ag](+), were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra were measured over the IR fingerprint and hydrogen-stretching regions. Structures and linear IR spectra of the stable tautomeric conformations of these complexes were initially determined at the B3LYP/6-31G(d) level. The four most stable structures computed were also examined at the B3LYP/def2-TZVPPD level to improve the accuracy of the predicted IR spectra. Two very favorable modes of binding are found for [Ura+Cu](+) and [Ura+Ag](+) that involve O2N3 bidentate binding to the 2-keto-4-hydroxy minor tautomer and O4 monodentate binding to the canonical 2,4-diketo tautomer of Ura. Comparisons between the measured IRMPD and calculated IR spectra enable elucidation of the conformers present in the experiments. These comparisons indicate that both favorable binding modes are represented in the experimental tautomeric conformations of [Ura+Cu](+) and [Ura+Ag](+). B3LYP suggests that Cu(+) exhibits a slight preference for O4 binding, whereas Ag(+) exhibits a slight preference for O2N3 binding. In contrast, MP2 suggests that both Cu(+) and Ag(+) exhibit a more significant preference for O2N3 binding. The relative band intensities suggest that O4 binding conformers comprise a larger portion of the population for [Ura+Ag](+) than [Ura+Cu](+). The dissociation behavior and relative stabilities of the [Ura+M](+) complexes, M(+) = Cu(+), Ag(+), H(+), and Na(+)) are examined via energy-resolved collision-induced dissociation experiments. The IRMPD spectra, dissociation behaviors, and binding preferences of Cu(+) and Ag(+) are compared with previous and present results for those of H(+) and Na(+). Graphical Abstract ᅟ.

  5. A combined experimental and DFT investigation on the structure and CO-releasing properties of mono and binuclear fac-Re(I)(CO)3 complexes with 5-pyridin-2-ylmethylene-amino uracils.

    PubMed

    Jiménez-Pulido, Sonia B; Illán-Cabeza, Nuria A; Hueso-Ureña, Francisco; Maldonado, Carmen R; Sánchez-Sánchez, Purificación; Fernández-Liencres, M Paz; Fernández-Gómez, Manuel; Moreno-Carretero, Miguel N

    2016-09-27

    The synthesis, structure and CO-releasing properties of a number of new tricarbonyl rhenium(i) complexes with 5-substituted-6-amino-1,3-dimethyluracils are reported and their structural features discussed on the basis of both spectral and X-ray crystallographic analyses. The 5-substituent library includes -N[double bond, length as m-dash]CH-2py (DAAUPic) and -CH[double bond, length as m-dash]N-N[double bond, length as m-dash]CH-2py (FDUHzPic) as additional metal binding components and chloride, acetonitrile or pyridine acting as ancillary ligands. The compounds have been identified by elemental analysis, NMR, MS and IR spectroscopy. In addition, [ReCl(CO)3(DAAUPic)], [Re(CO)3(FDUHzPic)py]ClO4, [Re(CO)3(FDUHzPic)py]PF6, [Re2Cl2(CO)6(FDUHzPic)] and [Re2Cl(CO)6(FDUHzPicH-1)(H2O)] structures have been solved by X-ray diffraction methods. These studies have clearly shown that the preferred coordination mode to rhenium takes place through the (N1F,N52)-pyridin-2-yl-methyleneamine moiety, the uracil coordinative availability (O4-N51 or N6-N51) being used only to bind the second metal center. The CO-releasing ability of these rhenium compounds has been investigated by the reaction with myoglobin; the corresponding studies have revealed that two of the mononuclear complexes and their related binuclear analogues are able to release CO to a moderate extent. This ability has also been theoretically assessed through a QTAIM analysis. The results, although non-conclusive, may explain somehow possible different preferences in CO releasing power after a comparison between the nature of Re-CO links in mononuclear and binuclear compounds.

  6. Electron Detachment as a Probe of Intrinsic Nucleobase Dynamics in Dianion-Nucleobase Clusters: Photoelectron Spectroscopy of the Platinum II Cyanide Dianion Bound to Uracil, Thymine, Cytosine, and Adenine.

    PubMed

    Sen, Ananya; Hou, Gao-Lei; Wang, Xue-Bin; Dessent, Caroline E H

    2015-09-03

    We report the first low-temperature photoelectron spectra of isolated gas-phase complexes of the platinum II cyanide dianion bound to nucleobases. These systems are models for understanding platinum-complex photodynamic therapies, and a knowledge of the intrinsic photodetachment properties is crucial for characterizing their broader photophysical properties. Well-resolved, distinct peaks are observed in the spectra, consistent with complexes where the Pt(CN)4(2-) moiety is largely intact. Adiabatic electron detachment energies for the dianion-nucleobase complexes are measured to be 2.39-2.46 eV. The magnitudes of the repulsive Coulomb barriers of the complexes are estimated to be between 1.9 and 2.1 eV, values that are lower than for the bare Pt(CN)4(2-) dianion as a result of charge solvation by the nucleobases. In addition to the resolved spectral features, broad featureless bands indicative of delayed electron detachment are observed in the 193 nm photoelectron spectra of the four dianion-nucleobase complexes and also in the 266 nm spectra of the Pt(CN)4(2-)·thymine and Pt(CN)4(2-)·adenine complexes. The selective excitation of these features in the 266 nm spectra is attributed to one-photon excitation of [Pt(CN)4(2-)·thymine]* and [Pt(CN)4(2-)·adenine]* long-lived excited states that can effectively couple to the electron detachment continuum, producing strong electron detachment signals. We attribute the delayed electron detachment bands observed here for Pt(CN)4(2-)·thymine and Pt(CN)4(2-)·adenine but not for Pt(CN)4(2-)·uracil and Pt(CN)4(2-)·cytosine to fundamental differences in the individual nucleobase photophysics following 266 nm excitation. This indicates that the Pt(CN)4(2-) dianion in the clusters can be viewed as a "dynamic tag" which has the propensity to emit electrons when the attached nucleobase displays a long-lived excited state.

  7. Spectroscopic Studies of Fluorescence Effects in Bioactive 4-(5-Heptyl-1,3,4-Thiadiazol-2-yl)Benzene-1,3-Diol and 4-(5-Methyl-1,3,4-Thiadiazol-2-yl)Benzene-1,3-Diol Molecules Induced by pH Changes in Aqueous Solutions.

    PubMed

    Matwijczuk, Arkadiusz; Kluczyk, Dariusz; Górecki, Andrzej; Niewiadomy, Andrzej; Gagoś, Mariusz

    2017-03-01

    This paper presents the results of stationary fluorescence spectroscopy and time-resolved spectroscopy analyses of two 1,3,4-thiadiazole analogues, i.e. 4-(5-methyl-1,3,4-thiadiazol-2-yl)benzene-1,3-diol (C1) and 4-(5-heptyl-1,3,4-thiadiazol-2-yl)benzene-1,3-diol (C7) in an aqueous medium containing different concentrations of hydrogen ions. An interesting dual florescence effect was observed when both compounds were dissolved in aqueous solutions at pH below 7 for C1 and 7.5 for C7. In turn, for C1 and C7 dissolved in water at pH higher than the physiological value (mentioned above), single fluorescence was only noted. Based on previous results of investigations of the selected 1,3,4-thiadiazole compounds, it was noted that the presented effects were associated with both conformational changes in the analysed molecules and charge transfer (CT) effects, which were influenced by the aggregation factor. However, in the case of C1 and C7, the dual fluorescence effects were visible in a higher energetic region (different than that observed in the 1,3,4-thiadiazoles studied previously). Measurements of the fluorescence lifetimes in a medium characterised by different concentrations of hydrogen ions revealed clear lengthening of the excited-state lifetime in a pH range at which dual fluorescence effects can be observed. An important finding of the investigations presented in this article is the fact that the spectroscopic effects observed not only are interesting from the cognitive point of view but also can help in development of an appropriate theoretical model of molecular interactions responsible for the dual fluorescence effects in the analysed 1,3,4-thiadiazoles. Furthermore, the study will clarify a broad range of biological and pharmaceutical applications of these compounds, which are more frequently used in clinical therapies. Graphical Abstract Upper left corner - C7 molecule at high pH, right upper corner - fluorescence emission spectrum for C7 dissolved in H2

  8. Magnetic behavior of MnPS{sub 3} phases intercalated by [Zn{sub 2}L]{sup 2+} (LH{sub 2}: macrocyclic ligand obtained by condensation of 2-hydroxy-5-methyl-1,3-benzenedicarbaldehyde and 1,2-diaminobenzene)

    SciTech Connect

    Spodine, E.; Valencia-Galvez, P.; Fuentealba, P.; Manzur, J.; Ruiz, D.; Venegas-Yazigi, D.; Paredes-Garcia, V.; Cardoso-Gil, R.; Schnelle, W.; Kniep, R.

    2011-05-15

    The intercalation of the cationic binuclear macrocyclic complex [Zn{sub 2}L]{sup 2+} (LH{sub 2}: macrocyclic ligand obtained by the template condensation of 2-hydroxy-5-methyl-1,3-benzenedicarbaldehyde and 1,2-diaminobenzene) was achieved by a cationic exchange process, using K{sub 0.4}Mn{sub 0.8}PS{sub 3} as a precursor. Three intercalated materials were obtained and characterized: (Zn{sub 2}L){sub 0.05}K{sub 0.3}Mn{sub 0.8}PS{sub 3}(1), (Zn{sub 2}L){sub 0.1}K{sub 0.2}Mn{sub 0.8}PS{sub 3}(2) and (Zn{sub 2}L){sub 0.05}K{sub 0.3}Mn{sub 0.8}PS{sub 3}(3), the latter phase being obtained by an assisted microwave radiation process. The magnetic data permit to estimate the Weiss temperature {theta} of {approx}-130 K for (1); {approx}-155 K for (2) and {approx}-130 K for (3). The spin canting present in the potassium precursor remains unperturbed in composite (3), and spontaneous magnetization is observed under 50 K in both materials. However composites (1) and (2) do not present this spontaneous magnetization at low temperatures. The electronic properties of the intercalates do not appear to be significantly altered. The reflectance spectra of the intercalated phases (1), (2) and (3) show a gap value between 1.90 and 1.80 eV, lower than the value observed for the K{sub 0.4}Mn{sub 0.8}PS{sub 3} precursor of 2.8 eV. -- Graphical Abstract: Microwave assisted synthesis was used to obtain an intercalated MnPS{sub 3} phase with a binuclear Zn(II) macrocyclic complex. A comparative magnetic study of the composites obtained by assisted microwave and traditional synthetic methods is reported. Display Omitted Highlights: {yields} A rapid and efficient preparation of intercalated MnPS{sub 3} composites by assisted microwave synthesis is described. {yields} The exchange of potassium ions of the precursor by the macrocyclic Zn(II) complex is partial. {yields} The composite obtained by assisted microwave synthesis retains the spontaneous magnetization, observed in the low temperature

  9. Communication: Electronic UV-Vis transient spectra of the ∙OH reaction products of uracil, thymine, cytosine, and 5,6-dihydrouracil by using the complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory.

    PubMed

    Francés-Monerris, Antonio; Merchán, Manuela; Roca-Sanjuán, Daniel

    2013-08-21

    Addition of ∙OH radicals to pyrimidine nucleobases is a common reaction in DNA/RNA damage by reactive oxygen species. Among several experimental techniques, transient absorption spectroscopy has been during the last decades used to characterize such compounds. Discrepancies have however appeared in the assignment of the adduct or adducts responsible for the reported transient absorption UV-Vis spectra. In order to get an accurate assignment of the transient spectra and a unified description of the absorption properties of the ∙OH reaction products of pyrimidines, a systematic complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory study has been carried out on the uracil, thymine, and cytosine ∙OH addition adducts, as well as on the 5,6-dihydrouracil hydrogen abstraction products. With the obtained findings, the C5OH contributions to the lowest-energy band can be finally discarded. Instead, a bright (2)(π2) state of the C6OH adducts is determined to be the main responsible in all compounds for the absorption band in the Vis range.

  10. Simultaneous determination of 1-(2′-deoxy-2′-fluoro-β-D-arabinofuranosyl) uracil (FAU) and 1-(2′-deoxy-2′-fluoro- β-D-arabinofuranosyl 5-methyluracil (FMAU) in human plasma by liquid chromatography/tandem mass spectrometry

    PubMed Central

    Wiegand, Richard; Wu, Jianmei; Shields, Anthony F.; LoRusso, Patricia; Li, Jing

    2013-01-01

    A liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) assay was developed and validated for simultaneously determination of 1-(2′-deoxy-2′-fluoro-β-D-arabinofuranosyl) uracil (FAU) and its active metabolite 1-(2′-deoxy-2′-fluoro-β-D-arabinofuranosyl 5-methyluracil (FMAU) in human plasma. FAU and FMAU were extracted from plasma samples using solid-phase extraction with Waters Sep-Pak® Vac C18 cartridge. Chromatographic separation was achieved on a Waters Atlantis T3 C18 column with a gradient mobile phase consisting of methanol and water with 0.45% formic acid (v/v) running at a flow rate of 0.2 ml/min. The analytes were monitored by triple quadrupole mass spectrometer under positive ionization mode. The lower limit of quantitation (LLOQ) was 10 and 2 ng/ml for FAU and FMAU in plasma, respectively. Calibration curves were linear over FAU and FMAU plasma concentration range of 10–2000 and 2 – 1000 ng/ml, respectively. The intra-day and inter-day accuracy and precision were within the generally accepted criteria for bioanalytical method (< 15%). The method has been successfully employed to characterize the plasma pharmacokinetics of FAU and FMAU in cancer patients receiving 1-h intravenous infusion of FAU 50 mg/m2. PMID:22410089

  11. Ca2+ sensitization in idiopathic dilated human myocardium. Differential in vitro effects of (+)-(5-methyl-6-phenyl)-1,3,5,6-tetrahydro-3,6-methano-1,5-benzodiazoci ne-2,4-dione, a novel purely Ca2+sensitizing agent, and (+)-5-(1-(3,4-dimethoxybenzoyl)-1,2,3,4-tetrahydroquinolin-6-yl)-6-meth yl-3, 6-dihydro-2H-1,3,4-thiadiazin-2-one on skinned fibres and isolated ventricular strips.

    PubMed

    Herzig, J W; Chiesi, M; Depersin, H; Grüninger, S; Hasenfuss, G; Kubalek, R; Leutert, T; Pieske, B; Pioch, K; Wenk, P; Holubarsch, C

    1996-06-01

    (+)-(5-Methyl-6-phenyl)-1,3,5,6-tetrahydro-3,6-methano-1, 5-benzodiazocine-2,4-dione (CAS 165755-40-8, CGP 48506) is a novel Ca2+ sensitizing agent devoid of any other positive inotropic mechanism, particularly phosphodiesterase (PDE) III inhibition. 5-(1-(3,4-Dimethoxybenzoyl)-1,2,3,4-tetrahydroquinolin-6-yl)-6-met hyl-3, 6-dihydro-2H-1,3,4-thiadiazin-2-one (CAS 120223-04-3, EMD 53998) is a PDE III inhibitor with a Ca2+ sensitizing activity residing in its (+)-enantiomer, EMD 57033 (CAS 147527-31-9). In skinned fibres and electrically stimulated left ventricular strips from idiopathic dilated human hearts, New York Heart Association (NYHA) class IV, the Ca2+ sensitizing and inotropic effects of the benzodiazocine CGP 48506 and the thiadiazinones EMD 53998 or EMD 57033 were compared. Both CGP 48506 and EMD 53998 induce a left shift of the Ca2+ activation curve of force towards lower Ca2+ concentrations in skinned fibres, which indicates Ca2+ sensitization. Only EMD 53998, but not CGP 48506, increases skinned fibre force at both minimum (resting) and maximally activating Ca2+ concentrations. This is taken as an argument for a principal difference in the mechanisms of the Ca2+ sensitizing actions of the two compounds. CGP 48506 is shown not to influence the amplitude of the Ca2+ transient in rat cardiomyocytes. On the other hand, both CGP 48506 and EMD 57033 show comparable, though quantitatively different, positive inotropic effects in electrically stimulated left ventricular strip preparations. It is unclear whether the PDE III inhibitory component of the profile of actions of EMD 57033 may play a role in preventing the increase in diastolic tension as expected from the skinned fibre experiments. It is noteworthy that both Ca2+ sensitizing agents act as positive inotropic compounds in the end-stage failing human heart where other inotropic agents like beta 1-adrenergic agonists or PDE inhibitors have been described to fail.

  12. 8-Bromo-3-(cyclo­propanylcarbon­yl)-5-methyl­indolizine-1-carbonitrile

    PubMed Central

    Fan, Dahe; Tang, Fan; Wang, Wei

    2012-01-01

    The asymmetric unit of the title compound, C14H11BrN2O, contains three independent mol­ecules with very similar geometries. The dihedral angles between the side chain of the cyclo­propyl plane and the five-membered ring to which it is attached are 55.0 (2), 58.1 (2) and 60.2 (3)° for the three mol­ecules. Each mol­ecule forms an intra­molecular C—H⋯O hydrogen bond. PMID:22719653

  13. 2-Amino-5-methyl­pyridinium 2-amino­benzoate

    PubMed Central

    Thanigaimani, Kaliyaperumal; Farhadikoutenaei, Abbas; Khalib, Nuridayanti Che; Arshad, Suhana; Razak, Ibrahim Abdul

    2012-01-01

    In the 2-amino­benzoate anion of the title salt, C6H9N2 +·C7H6NO2 −, an intra­molecular N—H⋯O hydrogen bond is observed. The dihedral angle between the ring and the CO2 group is 8.41 (13)°. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms via a pair of N—H⋯O hydrogen bonds, forming an R 2 2(8) ring motif. The ion pairs are further connected via N—H⋯O hydrogen bonds, resulting in a donor–donor–acceptor–acceptor (DDAA) array of quadruple hydrogen bonds. The crystal structure also features a weak N—H⋯O hydrogen bond and a C—H⋯π inter­action, resulting in a three-dimensional network. PMID:23284507

  14. 2-Amino-5-methyl­pyridinium 3-chloro­benzoate

    PubMed Central

    Thanigaimani, Kaliyaperumal; Farhadikoutenaei, Abbas; Khalib, Nuridayanti Che; Arshad, Suhana; Razak, Ibrahim Abdul

    2012-01-01

    The 3-chloro­benzoate anion of the title salt, C6H9N2 +·C7H4ClO2 −, is nearly planar with a dihedral angle of 2.44 (13)° between the benzene ring and the carboxyl­ate group. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms of the anion via a pair of N—H⋯O hydrogen bonds with an R 2 2(8) ring motif, forming an approximately planar ion pair with a dihedral angle of 7.92 (5)° between the pyridinium and benzene rings. The ion pairs are further connected via N—H⋯O and C—H⋯O hydrogen bonds, forming a two-dimensional network parallel to the bc plane. PMID:23284506

  15. 2-Amino-5-methyl­pyridinium 4-chloro­benzoate

    PubMed Central

    Thanigaimani, Kaliyaperumal; Farhadikoutenaei, Abbas; Arshad, Suhana; Razak, Ibrahim Abdul

    2013-01-01

    The 4-chloro­benzoate anion of the title salt, C6H9N2 +·C7H4ClO2 −, is nearly planar with a dihedral angle of 5.14 (16)° between the benzene ring and the carboxyl­ate group. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms of the anion via a pair of N—H⋯O hydrogen bonds with an R 2 2(8) ring motif. The ion pairs are further connected via N—H⋯O and weak C—H⋯O hydrogen bonds, forming a two-dimensional network parallel to the bc plane. The crystal structure also features a π–π stacking inter­action between the pyridinium and benzene rings with a centroid–centroid distance of 3.7948 (9) Å. PMID:23476392

  16. 2-Amino-5-methyl­pyridinium 4-methyl­benzoate

    PubMed Central

    Thanigaimani, Kaliyaperumal; Farhadikoutenaei, Abbas; Arshad, Suhana; Razak, Ibrahim Abdul

    2013-01-01

    The 4-methyl­benzoate anion of the title salt, C6H9N2 +·C8H7O2 −, is nearly planar, with a dihedral angle of 6.26 (10)° between the benzene ring and the carboxyl­ate group. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms of the anion via a pair of N—H⋯O hydrogen bonds with an R 2 2(8) ring motif, forming an approximately planar ion pair with a dihedral angle of 9.63 (4)° between the pyridinium and benzene rings. The ion pairs are further connected via N—H⋯O and weak C—H⋯O hydrogen bonds, forming a two-dimensional network parallel to the bc plane. PMID:23476474

  17. 2-Amino-5-methyl­pyridinium trifluoro­acetate

    PubMed Central

    Thanigaimani, Kaliyaperumal; Farhadikoutenaei, Abbas; Khalib, Nuridayanti Che; Arshad, Suhana; Razak, Ibrahim Abdul

    2012-01-01

    In the title salt, C6H9N2 +·C2F3O2 −, the F atoms of the anion are disordered over two sets of sites, with refined occupancies in a ratio of 0.505 (17):0.495 (17). In the crystal, cations and anions are linked via N—H⋯O hydrogen bonds, forming R 2 2(8) ring motifs. The ionic units are linked into a two-dimensional network parallel to (100) by N—H⋯O and weak C—H⋯O hydrogen bonds. The crystal structure is further stabilized by weak C—H⋯F hydrogen bonds, resulting in a three-dimensional network. PMID:23476163

  18. Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expression

    PubMed Central

    Ponnaluri, V. K. Chaithanya; Ehrlich, Kenneth C.; Zhang, Guoqiang; Lacey, Michelle; Johnston, Douglas; Pradhan, Sriharsa; Ehrlich, Melanie

    2017-01-01

    ABSTRACT Differentially methylated or hydroxymethylated regions (DMRs) in mammalian DNA are often associated with tissue-specific gene expression but the functional relationships are still being unraveled. To elucidate these relationships, we studied 16 human genes containing myogenic DMRs by analyzing profiles of their epigenetics and transcription and quantitatively assaying 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) at specific sites in these genes in skeletal muscle (SkM), myoblasts, heart, brain, and diverse other samples. Although most human promoters have little or no methylation regardless of expression, more than half of the genes that we chose to study—owing to their myogenic DMRs—overlapped tissue-specific alternative or cryptic promoters displaying corresponding tissue-specific differences in histone modifications. The 5mC levels in myoblast DMRs were significantly associated with 5hmC levels in SkM at the same site. Hypermethylated myogenic DMRs within CDH15, a muscle- and cerebellum-specific cell adhesion gene, and PITX3, a homeobox gene, were used for transfection in reporter gene constructs. These intragenic DMRs had bidirectional tissue-specific promoter activity that was silenced by in vivo-like methylation. The CDH15 DMR, which was previously associated with an imprinted maternal germline DMR in mice, had especially strong promoter activity in myogenic host cells. These findings are consistent with the controversial hypothesis that intragenic DNA methylation can facilitate transcription and is not just a passive consequence of it. Our results support varied roles for tissue-specific 5mC- or 5hmC-enrichment in suppressing inappropriate gene expression from cryptic or alternative promoters and in increasing the plasticity of gene expression required for development and rapid responses to tissue stress or damage. PMID:27911668

  19. Influence of C5-methylation of cytosine on the formation of cyclobutane pyrimidine dimers

    NASA Astrophysics Data System (ADS)

    Li, Xiaoyi; Eriksson, Leif A.

    2005-01-01

    The reaction pathways for thermal and photochemical formation of 5-methylcytosine (m 5C) pyrimidine dimers (CPD) are explored using density functional theory techniques. It is shown that the methylation of cytosine does not contribute to an increased yield of CPDs after UV irradiation due to an even lower excitation energy at the reactant complex of m 5C as compared to cytosine, a larger barrier to reach the decay channel corresponding to the transition state structure along the ground state reaction path, and a higher-lying decay channel.

  20. 2-Isopropyl-4-meth­oxy-5-methyl­phenyl benzoate

    PubMed Central

    Moumou, Mohamed; Akssira, Mohamed; Elhakmaoui, Ahmed; El Ammari, Lahcen; Benharref, Ahmed; Berraho, Moha

    2010-01-01

    The title compound, C18H20O3, a hemisynthetic product, was obtained by the reaction of benzoyl chloride and p-methoxy­thymol. The structure comprises two benzene rings bridged by a carboxyl group; the dihedral angle between the rings is 73.54 (8)°. PMID:21580674

  1. Crystal structure of N-(2-hy-droxy-5-methyl-phen-yl)benzamide.

    PubMed

    Moreno-Fuquen, Rodolfo; Mariño, Nory J; Kennedy, Alan R

    2015-12-01

    In the title compound, C14H13NO2, the mean plane of the non-H atoms of the central amide fragment C-N-C(=O)-C (r.m.s. deviation = 0.029 Å) forms dihedral angles of 5.63 (6) and 10.20 (5)° with the phenyl and hy-droxy-phenyl rings, respectively. A short intra-molecular N-H⋯O contact is present. In the crystal, the mol-ecules are linked by O-H⋯O hydrogen bonds to generate C(7) chains along [100]. The chains are reinforced by weak C-H⋯O contacts, which together with the O-H⋯O bonds lead to R 2 (2)(7) loops. Very weak N-H⋯O inter-actions link the mol-ecules into inversion dimers.

  2. 9-[3-(Carbazol-9-yl)-5-methyl­phen­yl]carbazole

    PubMed Central

    Kim, Jae Eun; Kim, Jun Hee; Sim, Wonbo; Lee, Jai Young

    2013-01-01

    The title compound, C31H22N2, crystallizes with two symmetry-independent mol­ecules in the asymmetric unit. The mol­ecules have slightly different conformations, the dihedral angles between the central phenyl ring and the carbazolyl groups being 56.29 (4) and 59.57 (4)° in one mol­ecule and 48.71 (4) and 65.47 (4)° in the other. In the crystal, mol­ecules are linked by weak C—H⋯π and π–π [centroid–centroid distances = 3.7698 (10), 3.8292 (9), 3.9429 (10) and 3.9431 (10) Å]. PMID:23795018

  3. Bromidotetra-kis-(1H-2-ethyl-5-methyl-imidazole-κN)copper(II) bromide.

    PubMed

    Godlewska, Sylwia; Baranowska, Katarzyna; Socha, Joanna; Dołęga, Anna

    2011-12-01

    The Cu(II) ion in the title compound, [CuBr(C(6)H(10)N(2))(4)]Br, is coordinated in a square-based-pyramidal geometry by the N atoms of four imidazole ligands and a bromide anion in the apical site. Both the Cu(II) and Br(-) atoms lie on a crystallographic fourfold axis. In the crystal, the [CuBr(C(6)H(10)N(2))(4)](+) complex cations are linked to the uncoordinated Br(-) anions (site symmetry [Formula: see text]) by N-H⋯Br hydrogen bonds, generating a three-dimensional network. The ethyl group of the imidazole ligand was modelled as disordered over two orientations with occupancies of 0.620 (8) and 0.380 (8).

  4. 5-Methyl-N-[2-(trifluoro-meth-yl)phen-yl]isoxazole-4-carboxamide.

    PubMed

    Wang, De-Cai; Qiu, Jiang-Kai; Zhu, Hai-Xi; Wei, Ping; Ou-Yang, Ping-Kai

    2012-05-01

    In the title compound, C(12)H(9)F(3)N(2)O(2), the benzene ring is nearly perpendicular to the isoxazole ring, making a dihedral angle of 82.97 (2)°. In the crystal, mol-ecules are linked by N-H⋯O hydrogen bonds into a supra-molecular chain running along the c axis.

  5. 2-Isopropyl-4-meth-oxy-5-methyl-phenyl acetate.

    PubMed

    Oubabi, Radouane; Auhmani, Aziz; Ait Itto, My Youssef; Driss, Mohamed; Soumhi, El Hassane

    2013-10-26

    In the title compound, C13H18O3, the benzene ring is almost perpendicular to the acet-oxy plane, making a dihedral angle of 89.33 (11)°. In the crystal, mol-ecules are linked by weak C-H⋯O hydrogen bonds, forming a zigzag chain along the c-axis direction.

  6. Nucleosides and nucleotides. 158. 1-(3-C-ethynyl-beta-D-ribo-pentofuranosyl)-cytosine, 1-(3-C-ethynyl-beta-D-ribo-pentofuranosyl)uracil, and their nucleobase analogues as new potential multifunctional antitumor nucleosides with a broad spectrum of activity.

    PubMed

    Hattori, H; Tanaka, M; Fukushima, M; Sasaki, T; Matsuda, A

    1996-12-06

    We previously designed 1-(3-C-ethynyl-beta-D-ribo-pentofuranosyl)uracil (EUrd) as a potential multifunctional antitumor nucleoside antimetabolite. It showed a potent and broad spectrum of antitumor activity against various human tumor cells in vitro and in vivo. To determine the structure-activity relationship, various nucleobase analogues of EUrd, such as 5-fluorouracil, thymine, cytosine, 5-fluorocytosine, adenine, and guanine derivatives, were synthesized by condensation of 1-O-acetyl-2,3,5-tri-O-benzoyl-3-C-ethynyl-alpha,beta-D-ribo-pentofur anose (6) and the corresponding pertrimethylsilylated nucleobases in the presence of SnCl4 or TMSOTf as a Lewis acid in CH3CN followed by debenzoylation. The in vitro tumor cell growth inhibitory activity of these 3'-C-ethynyl nucleosides against mouse leukemia L1210 and human nasopharyngeal KB cells showed that 1-(3-C-ethynyl-beta-D-ribo-pentofuranosyl)cytosine (ECyd) and EUrd were the most potent inhibitors in the series, with IC50 values for L1210 cells of 0.016 and 0.13 microM and for KB cells of 0.028 and 0.029 microM, respectively. 5-Fluorocytosine, 5-fluorouracil, and adenine nucleosides showed much lower activity, with IC50 values of 0.4-2.5 microM, while thymine and guanine nucleosides did not exhibit any activity up to 300 microM. We next evaluated the tumor cell growth inhibitory activity of ECyd and EUrd against 36 human tumor cell lines in vitro and found that they were highly effective against these cell lines with IC50 values in the nanomolar to micromolar range. These nucleosides have a similar inhibitory spectrum. The in vivo antitumor activities of ECyd and EUrd were compared to that of 5-fluorouracil against 11 human tumor xenografts including three stomach, three colon, two pancreas, one renal, one breast, and one bile duct cancers. ECyd and EUrd showed a potent tumor inhibition ratio (73-92% inhibition relative to the control) in 9 of 11 and 8 of 11 human tumors, respectively, when administered

  7. Methotrexate-induced misincorporation of uracil into DNA

    PubMed Central

    Goulian, M.; Bleile, B.; Tseng, B. Y.

    1980-01-01

    A line of human lymphoid cells was tested for the presence of dUMP in DNA with or without treatment with the dihydrofolate reductase inhibitor, methotrexate. Cells treated with methotrexate and labeled with [3H]dUrd contained dUMP in DNA in readily detectable amounts (≈0.8 pmol of dUMP per μmol of total DNA nucleotide), and this was increased ≈3-fold if the cells were also treated with Ura at the same time. No dUMP (<1 fmol/μmol of DNA) could be detected by these methods in DNA from cells not treated with methotrexate, regardless of whether Ura was present or absent. The presence of dUMP in DNA from cells treated with methotrexate is a result of the great increase in intracellular concentration of dUTP and the fall in dTTP that accompany inhibition of thymidylate synthetase (5,10-methylenetetrahydrofolate:dUMP C-methyltransferase; EC 2.1.1.45) by the drug. These changes are apparently sufficient to overcome the normal mechanisms that exclude dUMP from DNA, and the enhancement by Ura reflects suppression of one of the mechanisms, Ura removal from DNA by the enzyme Ura-DNA glycosylase. The results suggest an active lesion of DNA in cells in which thymidylate synthetase is inhibited. Under these conditions there appears to be a cyclic incorporation and removal of dUMP resulting from reinsertion of dUMP during gap repair at sites of Ura removal. This consequence of the normal excision-repair process, which occurs when intracellular levels of dUTP approach those of dTTP, may have effects related to the cytotoxicity of drug inhibitors of thymidylate synthetase, clinical deficiencies of folate and vitamin B-12, and thymineless death, in general. Images PMID:6929529

  8. Increase in the photoreactivity of uracil derivatives by doubling thionation.

    PubMed

    Pollum, M; Jockusch, S; Crespo-Hernández, C E

    2015-11-07

    The ability of 4-thiouracil to strongly absorb UVA radiation and to populate a reactive triplet state in high yield has enabled its use as a versatile photocrosslinker for nearly 50 years. In this contribution, we present a detailed spectroscopic and photochemical investigation of the 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil series in an effort to further advance this chemistry and to scrutinize the photoreactivity of 2,4-dithiouracil. Our results reveal that excitation of 2,4-dithiouracil leads to intersystem crossing to the triplet manifold in 220 ± 40 fs, which enables the population of the reactive triplet state with near unity yield (ΦT = 0.90 ± 0.15) and ultimately leads to a ca. 50% singlet oxygen generation (ΦΔ = 0.49 ± 0.02)-one of the highest singlet oxygen yields reported to date for a photoexcited thiobase. In addition, the long-lived triplet state of 2,4-dithiouracil reacts efficiently with the nucleic acid base adenine 5'-monophosphate through a direct, oxygen-independent photocycloaddition mechanism and at a rate that is at least 3-fold faster than that of 4-thiouracil under equal conditions. The new physico-chemical insights reported for these RNA-thiobase derivatives are compared to those of the DNA and RNA bases and the DNA-thiobase derivatives. Furthermore, the strong near-visible absorption and increased photoreactivity measured for 2,4-dithiouracil lays a solid foundation for developing RNA-targeted photocrosslinking and phototherapeutic agents that are more effective than those currently available.

  9. New Boron-Nitrogen Analogues of Uracil Derivatives

    DTIC Science & Technology

    1989-07-01

    obtained on treatment of the betaine 1,3,5-trimehyl-2-(N, N’, N"- trimetLhlbiuret-l-vi)-1,3,5-triaza-2-boracyclohexa-4,6-dione 6a [5] with anhydrous ...quantitative yield on treatment of the betaine 6a [5] with anhydrous dimethylamine in chloroform solution. After evaporation of excess amine and solvent...of the salts 4a--4c under vacuum, the betaine 5a was obtained. ,F R\\ N- I 11 R’ R II 0 0 5 a: R = RI = CH3 b: R = CH3, RI = C2 H5 c: R = CH 3, RI

  10. Synthesis and crystal structure studies of ethyl 5-methyl-1, 3-diphenyl-1H-pyrazole-4-carboxylate

    SciTech Connect

    Chandra,; Babu, E. A. Jithesh; Mahendra, M.; Srikantamurthy, N.; Umesha, K. B.

    2014-04-24

    The title compound, C{sub 19}H{sub 18}N{sub 2}O{sub 2}, was investigated by single crystal X-ray diffraction method. It crystallizes in monoclinic class under the space group P2{sub 1}/c with cell parameters a= 8.4593(4) Å, b=15.6284(6) Å, c=12.4579(5) Å, α=90°, β=98.241(3)°, γ=90° and Z=2. The ethoxycarbonyl group is slightly twisted from the pyrazole ring, and adopts syn-periplanar conformation. The crystal structure is stabilized by intermolecular C-H….O hydrogen bonds, which help in stabilizing the crystal structure.

  11. Natural folates from biofortified tomato and synthetic 5-methyl-tetrahydrofolate display equivalent bioavailability in a murine model.

    PubMed

    Castorena-Torres, Fabiola; Ramos-Parra, Perla A; Hernández-Méndez, Rogelio V; Vargas-García, Andrés; García-Rivas, Gerardo; de la Garza, Rocío I Díaz

    2014-03-01

    Folate deficiency is a global health problem related to neural tube defects, cardiovascular disease, dementia, and cancer. Considering that folic acid (FA) supply through industrialized foods is the most successful intervention, limitations exist for its complete implementation worldwide. Biofortification of plant foods, on the other hand, could be implemented in poor areas as a complementary alternative. A biofortified tomato fruit that accumulates high levels of folates was previously developed. In this study, we evaluated short-term folate bioavailability in rats infused with this folate-biofortified fruit. Fruit from tomato segregants hyperaccumulated folates during an extended ripening period, ultimately containing 3.7-fold the recommended dietary allowance in a 100-g portion. Folate-depleted Wistar rats separated in three groups received a single dose of 1 nmol of folate/g body weight in the form of lyophilized biofortified tomato fruit, FA, or synthetic 5-CH3-THF. Folate bioavailability from the biofortified tomato was comparable to that of synthetic 5-CH3-THF, with areas under the curve (AUC(0-∞)) of 2,080 ± 420 and 2,700 ± 220 pmol · h/mL, respectively (P = 0.12). Whereas, FA was less bioavailable with an AUC(0-∞) of 750 ± 10 pmol · h/mL. Fruit-supplemented animals reached maximum levels of circulating folate in plasma at 2 h after administration with a subsequent steady decline, while animals treated with FA and synthetic 5-CH3-THF reached maximum levels at 1 h. Pharmacokinetic parameters revealed that biofortified tomato had slower intestinal absorption than synthetic folate forms. This is the first study that demonstrates the bioavailability of folates from a biofortified plant food, showing its potential to improve folate deficiency.

  12. 2-Amino-5-methyl­pyridinium 3-hy­droxy­pyridine-2-carboxyl­ate

    PubMed Central

    Farhadikoutenaei, Abbas; Thanigaimani, Kaliyaperumal; Arshad, Suhana; Razak, Ibrahim Abdul

    2013-01-01

    In the 3-hy­droxy­picolinate anion of the title salt, C6H9N2 +·C6H4NO3 −, an intra­molecular O—H⋯O hydrogen bond with an S(6) graph-set motif is formed, so that the anion is essentially planar, with a dihedral angle of 9.55 (9)° between the pyridine ring and the carboxyl­ate group. In the crystal, the cations and anions are linked via N—H⋯O hydrogen bonds, forming a centrosymmetric 2 + 2 aggregate with R 2 2(8) and R 4 2(8) ring motifs. The crystal structure also features N—H⋯N and weak C—H⋯π inter­actions. PMID:24046674

  13. 2-Amino-5-methyl­pyridinium 2-hy­droxy-5-chloro­benzoate

    PubMed Central

    Thanigaimani, Kaliyaperumal; Farhadikoutenaei, Abbas; Arshad, Suhana; Razak, Ibrahim Abdul

    2013-01-01

    In the 5-chloro­salicylate anion of the title salt, C6H9N2 +·C7H4ClO3 −, an intra­molecular O—H⋯O hydrogen bond with an S(6) graph-set motif is observed and the dihedral angle between the benzene ring and the –CO2 group is 1.6 (6)°. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms via a pair of N—H⋯O hydrogen bonds, forming an R 2 2(8) ring motif. The crystal structure also features N—H⋯O and weak C—H⋯O inter­actions, resulting in a layer parallel to (10-1). PMID:23476391

  14. 4,6-Bis[5-methyl-3-(trifluoro­meth­yl)pyrazol-1-yl]pyrimidine

    PubMed Central

    Li, Yong-Hong; Zhang, Tao; Mei, Xiang-Dong; Ning, Jun

    2009-01-01

    The complete mol­ecule of the the title compound, C14H10F6N6, is generated by crystallographic twofold symmetry, with two C atoms lying on the roatation axis. The dihedral angle between the central and peripheral rings is 25.97 (8)°. PMID:21578452

  15. 1,2-Bis(2-hy­droxy-5-methyl­benzyl­idene)hydrazine

    PubMed Central

    Saravanan, B.; Jayamani, A.; Sengottuvelan, N.; Chakkaravarthi, G.; Manivannan, V.

    2013-01-01

    The mol­ecular structure of the title compound, C16H16N2O2, is stabilized by intra­molecular O—H⋯N hydrogen bonds with S(6) graph-set motifs, so that the mol­ecule is almost planar, with a C=N—N=C torsion angle of −179.7 (2)° and a dihedral angle of 1.82 (12)° between the aromatic rings. In the crystal, weak C—H⋯π inter­actions lead to the formation of a three-dimensional network. PMID:24427035

  16. 2-Hy­droxy-3-meth­oxy­methyl-5-methyl­benzaldehyde

    PubMed Central

    Gunasekaran, B.; Jayamani, A.; Sengottuvelan, N.; Chakkaravarthi, G.

    2013-01-01

    In the title mol­ecule, C10H12O3, all non-H atoms lie in a common plane (r.m.s deviation = 0.010 Å). The mol­ecular conformation is stabilized by an intra­molecular O—H⋯O hydrogen bond. PMID:23424581

  17. 1,1′-Bis(1-acetyl-5-methyl-1H-pyrazol-3-yl)ferrocene

    PubMed Central

    Zhu, Bei-Bei; Shi, Yao-Cheng; Shen, Wen-Bin; Li, Qian-Kun

    2011-01-01

    The title compound, [Fe(C11H11N2O)2], crystallizes with two independent mol­ecules in the asymmetric unit which have have different conformations. In one mol­ecule, the two ferrocene cyclo­penta­dienyl rings are fully eclipsed and the two pyrazole rings are syn to each other; in the other, the two cyclo­penta­dienyl rings are synclinal and the pyrazole rings are anti. In both mol­ecules, the acetyl group attached to the pyrazole ring is oriented away from the iron–cyclo­penta­dienyl group of ferrocene. PMID:22219778

  18. Configuration of the 5'-methyl group modulates the biophysical and biological properties of locked nucleic acid (LNA) oligonucleotides.

    PubMed

    Seth, Punit P; Allerson, Charles R; Siwkowski, Andrew; Vasquez, Guillermo; Berdeja, Andres; Migawa, Michael T; Gaus, Hans; Prakash, Thazha P; Bhat, Balkrishen; Swayze, Eric E

    2010-12-09

    As part of a program aimed at exploring the structure- activity relationships of 2',4'-bridged nucleic acid (BNA) containing antisense oligonucleotides (ASOs), we report the synthesis and biophysical and biological properties of R- and S-5'-Me LNA modified oligonucleotides. We show that introduction of a methyl group in the (S) configuration at the 5'-position is compatible with the high affinity recognition of complementary nucleic acids observed with LNA. In contrast, introduction of a methyl group in the (R) configuration reversed the stabilization effect of LNA. NMR studies indicated that the R-5'-Me group changes the orientation around torsion angle γ from the +sc to the ap range at the nucleoside level, and this may in part be responsible for the poor hybridization behavior exhibited by this modification. In animal experiments, S-5'-Me-LNA modified gapmer antisense olignucleotides showed slightly reduced potency relative to the sequence matched LNA ASOs while improving the therapeutic profile.

  19. Aquadi-n-but­yl(5-methyl­pyrazine-2-carboxyl­ato)tin(IV) methanol solvate

    PubMed Central

    Gao, Zhongjun

    2008-01-01

    In the monomeric title compound, [Sn(C4H9)2(C6H5N2O2)2(H2O)]·CH3OH, the Sn atom is seven-coordinate, displaying a distorted penta­gonal bipyramidal SnC2N2O3 geometry with the two C atoms in the axial sites. In the crystal structure, inter­molecular O—H⋯O hydrogen bonds link the complex and solvent mol­ecules into infinite chains. PMID:21202739

  20. Synthesis and spectroscopy studies of the inclusion complex of 3-amino-5-methyl pyrazole with beta-cyclodextrin.

    PubMed

    Louiz, S; Labiadh, H; Abderrahim, R

    2015-01-05

    Amino pyrazole belongs to anti-inflammatory class, and is characterized by a low solubility in water. (In order to increase its solubility in water, inclusion complex of amino pyrazole with β-CD was obtained.) The inclusion complex obtained between AMP and β-cyclodextrin, was characterized by FT-IR, (1)H NMR, (1)H-(1)H NOESY, (13)C NMR, DEPT, XHCOR, spectra, through TG analysis, DTA, DSC and Scanning Electron Microscopy (SEM). The stoichiometry of inclusion complex is 1:1 (guest-host) and K stability is 1.1 × 10(4)M(-1).

  1. Synthesis and crystal structure studies of ethyl 5-methyl-1, 3-diphenyl-1H-pyrazole-4-carboxylate

    NASA Astrophysics Data System (ADS)

    Chandra, Srikantamurthy, N.; Babu, E. A. Jithesh; Umesha, K. B.; Mahendra, M.

    2014-04-01

    The title compound, C19H18N2O2, was investigated by single crystal X-ray diffraction method. It crystallizes in monoclinic class under the space group P21/c with cell parameters a= 8.4593(4) Å, b=15.6284(6) Å, c=12.4579(5) Å, α=90°, β=98.241(3)°, γ=90° and Z=2. The ethoxycarbonyl group is slightly twisted from the pyrazole ring, and adopts syn-periplanar conformation. The crystal structure is stabilized by intermolecular C-H….O hydrogen bonds, which help in stabilizing the crystal structure.

  2. Synthesis and spectroscopy studies of the inclusion complex of 3-amino-5-methyl pyrazole with beta-cyclodextrin

    NASA Astrophysics Data System (ADS)

    Louiz, S.; Labiadh, H.; Abderrahim, R.

    2015-01-01

    Amino pyrazole belongs to anti-inflammatory class, and is characterized by a low solubility in water. (In order to increase its solubility in water, inclusion complex of amino pyrazole with β-CD was obtained.) The inclusion complex obtained between AMP and β-cyclodextrin, was characterized by FT-IR, 1H NMR, 1H-1H NOESY, 13C NMR, DEPT, XHCOR, spectra, through TG analysis, DTA, DSC and Scanning Electron Microscopy (SEM). The stoichiometry of inclusion complex is 1:1 (guest-host) and K stability is 1.1 × 104 M-1.

  3. QM/MM lineshape simulation of the hydrogen-bonded uracil NH stretching vibration of the adenine:uracil base pair in CDCl3

    NASA Astrophysics Data System (ADS)

    Yan, Yun-an; Krishnan, Gireesh M.; Kühn, Oliver

    2008-10-01

    A hybrid Car-Parrinello QM/MM molecular dynamics simulation has been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. The resulting trajectory is analyzed putting emphasis on the N-H⋯N hydrogen bond geometry. Using an empirical correlation between the N⋯N-distance and the fundamental NH-stretching frequency, the time-dependence of this energy gap along the trajectory is obtained. From the gap-correlation function we determine the infrared absorption spectrum using lineshape theory in combination with a multimode oscillator model. The obtained average transition frequency and the width of the spectrum are in reasonable agreement with recent experimental data.

  4. Hydrogermylation of 5-ethynyluracil nucleosides: formation of 5-(2-germylvinyl)uracil and 5-(2-germylacetyl)uracil nucleosides.

    PubMed

    Liang, Yong; Pitteloud, Jean-Philippe; Wnuk, Stanislaw F

    2013-06-07

    A stereoselective radical-mediated hydrogermylation of the protected 5-ethynyluracil nucleosides with trialkyl-, triaryl,- or tris(trimethylsilyl)germanes gave (Z)-5-(2-germylvinyl)uridine, 2'-deoxyuridine, or ara-uridine as major products. Reaction of the β-triphenylgermyl vinyl radical intermediate with oxygen and fragmentation of the resulting peroxyradical provided also 5-[2-(triphenylgermyl)acetyl]pyrimidine nucleosides in low to moderate yields. Thermal isomerization of the latter in MeOH occurred via a four-centered activated complex, and subsequent hydrolysis of the resulting O-germyl substituted enol yielded 5-acetyluracil nucleosides in quantitative yield.

  5. Contrasting reactions of hydrated electron and formate radical with 2-thio analogues of cytosine and uracil.

    PubMed

    Prasanthkumar, Kavanal P; Alvarez-Idaboy, Juan R; Kumar, Pavitra V; Singh, Beena G; Priyadarsini, K Indira

    2016-10-19

    2-Thiocytosine (TC) and 2-thiouracil (TU) were subjected to hydrated electron (eaq(-)), formate radical (CO2˙(-)) and 2-hydroxypropan-2-yl radical ((CH3)2˙COH) reactions in aqueous medium. Transients were characterized by absorption spectroscopy and the experimental findings were rationalized by DFT calculations at LC-ωPBE and M06-2X levels using a 6-311+G(d,p) basis set and SMD solvation. In eaq(-) reactions, a ring N-atom protonated radical of TC and an exocyclic O-atom protonated radical of TU were observed via addition of eaq(-) and subsequent protonation by solvent molecules. However, two competing but simultaneous mechanisms are operative in CO2˙(-) reactions with TC and TU. The first one corresponds to formations of N(O)-atom protonated radicals (similar to eaq(-) reactions); the second mechanism led to 2 center-3 electron, sulfur-sulfur bonded neutral dimer radicals, TCdim˙ and TUdim˙. DFT calculations demonstrated that H-abstraction by CO2˙(-) from TC(TU) results in S-centered radical which upon combination with TC(TU) provide the dimer radical. In some cases, DFT energy profiles were further validated by CBS-QB3//M06-2X calculations. This is the first time report for a contradictory behavior in the mechanisms of eaq(-) and CO2˙(-) reactions with any pyrimidines or their thio analogues.

  6. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA.

    PubMed

    Rohland, Nadin; Harney, Eadaoin; Mallick, Swapan; Nordenfelt, Susanne; Reich, David

    2015-01-19

    The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 ancient human samples.

  7. Uracil moiety is required for toxicity of the cyanobacterial hepatotoxin cylindrospermopsin.

    PubMed

    Banker, R; Carmeli, S; Werman, M; Teltsch, B; Porat, R; Sukenik, A

    2001-02-23

    A new natural derivative of the sulfated guanidinium zwitterionic toxin cylindrospermopsin, 7-epi-cylindrospermopsin, was recently isolated from the cyanobacterium Aphanizomenon ovalisporum (Forti). The toxicity of the molecule (LD50 ip 5 d), estimated by mouse bioassay, was 200 microg/kg mouse, a value similar to that of cylindrospermopsin. Treatment of cylindrospermopsin with chlorine solution or chlorine-related oxidants produced two new derivatives. The chemical structure of these products was elucidated by nuclear magnetic resonance (NMR) and mass spectrometry (MS) techniques and toxicity was determined. In the first derivative, the vinylic proton at position 5 of the pyrimidine ring was substituted by chlorine to yield 5-chlorocylindrospermopsin. The other product is a truncated one, where C-6 of the pyrimidine ring was oxidized to a carboxylic acid. A trivial name, cylindrospermic acid, was given to this compound. Both products showed no toxic effects even at doses 50 times higher than the LD50 of cylindrospermopsin (10 mg/kg mouse ip). Based on these results, the pyrimidine ring is postulated as the molecule component essential for the toxicity of cylindrospermopsin.

  8. Oligo-2'-deoxyribonucleotides containing uracil modified at the 5-position with linkers ending with guanidinium groups.

    PubMed

    Roig, Victoria; Asseline, Ulysse

    2003-04-16

    We report here the synthesis and binding studies of oligo-2'-deoxyribonucleotides (ODNs) containing 2'-deoxyuridines, modified at the 5-position by linkers ending with either one or two guanidinium groups. Comparison was made with ODNs containing 2'-deoxyuridines modified at the 5-position with linkers ending with either two or one amino groups. One or two modified 2'-deoxyuridines were incorporated into pyrimidine strands, and their influence on the stability of duplex (with both DNA and RNA targets) and triplex structures was studied. The strongest stabilization was obtained with modified ODNs containing guanidinium groups. This result confirms that the reduction of the global negative charge number on one strand is an important parameter in the stability of duplex and triplex structures.

  9. Electron driven reactions in sulphur containing analogues of uracil: the case of 2-thiouracil.

    PubMed

    Kopyra, J; Abdoul-Carime, H; Kossoski, F; Varella, M T do N

    2014-12-07

    The fragmentation of 2-thiouracil (TU) molecules induced by low energy (<12 eV) electrons is investigated experimentally and theoretically. It is observed that most of the damage is localised at the sulphur site and in particular visible via the production of the thiocyanate, SCN(-), anion. Similar to the canonical nucleobases the loss of the hydrogen atom is a predominant dissociation channel already at the subexcitation energies. The theory shows that for incident electron energies below 3 eV dissociative electron attachment is initiated by shape resonances implicating the π* molecular orbitals. It may also arise from the dipole bound supported state as illustrated by the production of the SCN(-), S(-) and (TU-S)(-) fragments observed close to 0 eV but also the formation of (TU-H)(-) species at 0.7 and 1 eV.

  10. 2-((Z)-{3-[(Z)-(2-Hy-droxy-5-methyl-benzyl-idene)amino]-2,2-dimethyl-prop-yl}imino-meth-yl)-4-methyl-phenol.

    PubMed

    Kia, Reza; Kargar, Hadi; Mirkhani, Valiollah; Ganji, Fatemeh; Tahir, Muhammad Nawaz

    2010-12-15

    In the title compound, C(21)H(26)N(2)O(2), the dihedral angle between the two benzene rings is 73.47 (16)°. Strong intra-molecular O-H⋯N hydrogen bonds generate S(6) ring motifs. The substituted benzene rings are twisted around the central quaternary C atom in opposite directions, making a vault geometry.

  11. Piracetam Defines a New Binding Site for Allosteric Modulators of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors§

    PubMed Central

    Ahmed, Ahmed H.; Oswald, Robert E.

    2010-01-01

    Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system and are important potential drug targets for cognitive enhancement and the treatment of schizophrenia. Allosteric modulators of AMPA receptors promote dimerization by binding to a dimer interface and reducing desensitization and deactivation. The pyrrolidine allosteric modulators, piracetam and aniracetam, were among the first of this class of drugs to be discovered. We have determined the structure of the ligand binding domain of the AMPA receptor subtypes GluA2 and GluA3 with piracetam and a corresponding structure of GluA3 with aniracetam. Both drugs bind to both GluA2 and GluA3 in a very similar manner, suggesting little subunit specificity. However, the binding sites for piracetam and aniracetam differ considerably. Aniracetam binds to a symmetrical site at the center of the dimer interface. Piracetam binds to multiple sites along the dimer interface with low occupation, one of which is a unique binding site for potential allosteric modulators. This new site may be of importance in the design of new allosteric regulators. PMID:20163115

  12. Piracetam defines a new binding site for allosteric modulators of alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors.

    PubMed

    Ahmed, Ahmed H; Oswald, Robert E

    2010-03-11

    Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system and are important potential drug targets for cognitive enhancement and the treatment of schizophrenia. Allosteric modulators of AMPA receptors promote dimerization by binding to a dimer interface and reducing desensitization and deactivation. The pyrrolidine allosteric modulators, piracetam and aniracetam, were among the first of this class of drugs to be discovered. We have determined the structure of the ligand binding domain of the AMPA receptor subtypes GluA2 and GluA3 with piracetam and a corresponding structure of GluA3 with aniracetam. Both drugs bind to GluA2 and GluA3 in a very similar manner, suggesting little subunit specificity. However, the binding sites for piracetam and aniracetam differ considerably. Aniracetam binds to a symmetrical site at the center of the dimer interface. Piracetam binds to multiple sites along the dimer interface with low occupation, one of which is a unique binding site for potential allosteric modulators. This new site may be of importance in the design of new allosteric regulators.

  13. Studies on an (S)-2-Amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic Acid (AMPA) Receptor Antagonist IKM-159: Asymmetric Synthesis, Neuroactivity, and Structural Characterization

    PubMed Central

    Juknaitė, Lina; Sugamata, Yutaro; Tokiwa, Kazuya; Ishikawa, Yuichi; Takamizawa, Satoshi; Eng, Andrew; Sakai, Ryuichi; Pickering, Darryl S.; Frydenvang, Karla; Swanson, Geoffrey T.; Kastrup, Jette S.; Oikawa, Masato

    2015-01-01

    IKM-159 was developed and identified as a member of a new class of heterotricyclic glutamate analogues that act as AMPA receptor-selective antagonists. However, it was not known which enantiomer of IKM-159 was responsible for its pharmacological activities. Here, we report in vivo and in vitro neuronal activities of both enantiomers of IKM-159 prepared by enantioselective asymmetric synthesis. By employment of (R)-2-amino-2-(4-methoxyphenyl)ethanol as a chiral auxiliary, (2R)-IKM-159 and the (2S)-counterpart were successfully synthesized in 0.70% and 1.5% yields, respectively, over a total of 18 steps. Both behavioral and electrophysiological assays showed that the biological activity observed for the racemic mixture was reproduced only with (2R)-IKM-159, whereas the (2S)-counterpart was inactive in both assays. Racemic IKM-159 was crystallized with the ligand-binding domain of GluA2, and the structure revealed a complex containing (2R)-IKM-159 at the glutamate binding site. (2R)-IKM-159 locks the GluA2 in an open form, consistent with a pharmacological action as competitive antagonist of AMPA receptors. PMID:23432124

  14. Studies on an (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA) receptor antagonist IKM-159: asymmetric synthesis, neuroactivity, and structural characterization.

    PubMed

    Juknaitė, Lina; Sugamata, Yutaro; Tokiwa, Kazuya; Ishikawa, Yuichi; Takamizawa, Satoshi; Eng, Andrew; Sakai, Ryuichi; Pickering, Darryl S; Frydenvang, Karla; Swanson, Geoffrey T; Kastrup, Jette S; Oikawa, Masato

    2013-03-28

    IKM-159 was developed and identified as a member of a new class of heterotricyclic glutamate analogues that act as AMPA receptor-selective antagonists. However, it was not known which enantiomer of IKM-159 was responsible for its pharmacological activities. Here, we report in vivo and in vitro neuronal activities of both enantiomers of IKM-159 prepared by enantioselective asymmetric synthesis. By employment of (R)-2-amino-2-(4-methoxyphenyl)ethanol as a chiral auxiliary, (2R)-IKM-159 and the (2S)-counterpart were successfully synthesized in 0.70% and 1.5% yields, respectively, over a total of 18 steps. Both behavioral and electrophysiological assays showed that the biological activity observed for the racemic mixture was reproduced only with (2R)-IKM-159, whereas the (2S)-counterpart was inactive in both assays. Racemic IKM-159 was crystallized with the ligand-binding domain of GluA2, and the structure revealed a complex containing (2R)-IKM-159 at the glutamate binding site. (2R)-IKM-159 locks the GluA2 in an open form, consistent with a pharmacological action as competitive antagonist of AMPA receptors.

  15. Synthesis of 2'-deoxy-2'-[.sup.18F]fluoro-5-methyl-1-B-D-arabinofuranosyluracil (.sup.18F-FMAU)

    DOEpatents

    Li, Zibo; Cai, Hancheng; Conti, Peter S

    2014-12-16

    The present invention relates to methods of synthesizing .sup.18F-FMAU. In particular, .sup.18F-FMAU is synthesized using one-pot reaction conditions in the presence of Friedel-Crafts catalysts. The one-pot reaction conditions are incorporated into a fully automated cGMP-compliant radiosynthesis module, which results in a reduction in synthesis time and simplifies reaction conditions. The one-pot reaction conditions are also suitable for the production of 5-substituted thymidine or cytidine analogs. The products from the one-pot reaction (e.g. the labeled thymidine or cytidine analogs) can be used as probes for imaging tumor proliferative activity. More specifically, these [.sup.18F]-labeled thymidine or cytidine analogs can be used as a PET tracer for certain medical conditions, including, but not limited to, cancer disease, autoimmunity inflammation, and bone marrow transplant.

  16. Effect of C5-methylation of cytosine on the photoreactivity of DNA: a joint experimental and computational study of TCG trinucleotides.

    PubMed

    Esposito, Luciana; Banyasz, Akos; Douki, Thierry; Perron, Marion; Markovitsi, Dimitra; Improta, Roberto

    2014-08-06

    DNA methylation, occurring at the 5 position of cytosine, is a natural process associated with mutational hotspots in skin tumors. By combining experimental techniques (optical spectroscopy, HPLC coupled to mass spectrometry) with theoretical methods (molecular dynamics, DFT/TD-DFT calculations in solution), we study trinucleotides with key sequences (TCG/T5mCG) in the UV-induced DNA damage. We show how the extra methyl, affecting the conformational equilibria and, hence, the electronic excited states, increases the quantum yield for the formation of cyclobutane dimers while reducing that of (6-4) adducts.

  17. 1-(2-Hydr­oxy-5-methyl­phen­yl)-3-(3-methylthiophen-2-yl)prop-2-en-1-one

    PubMed Central

    Thippeswamy, G. B.; Vijay Kumar, D.; Jayashree, B. S.; Sridhar, M. A.; Shashidhara Prasad, J.

    2010-01-01

    In the structure of the title compound, C15H14O2S, the benzene ring is nearly coplanar with the thio­phene ring. The hydroxy group substituted at C2 position is in an antiperi­planar conformation with respect to the phenyl ring. The crystal structure exhibits weak intramolecular O—H⋯O hydrogen bonding. PMID:21579466

  18. 3-{[Bis(pyridin-2-ylmeth­yl)amino]­meth­yl}-2-hy­droxy-5-methyl­benz­aldehyde

    PubMed Central

    Wang, Ruo-Xu; Gao, Da-Zhi; Ye, Fan; Wu, Yan-Fei; Zhu, Dun-Ru

    2012-01-01

    In the title compound, C21H21N3O2, the pyridine rings and the benzene ring lie in a propeller arrangement around the central tertiary amine N atom. The dihedral angles formed by the benzene ring with the pyridine rings are 61.0 (3) and 49.6 (3)°, while the dihedral angle between the pyridine rings is 69.7 (3)°. The mol­ecular conformation is stabilized by intramolecular bifurcated O—H⋯N hydrogen bonds. In the crystal, inversion dimers are formed via pairs of C—H⋯N hydrogen bonds. PMID:22719467

  19. 3-Methyl-5-methyl­sulfanyl-1,3,4-thia­diazole-2(3H)-thione

    PubMed Central

    Suarez, Sebastian A.; Hazari, Saroj K. S.; Ganguly, Biplab; Doctorovich, Fabio; G. Roy, Tapashi; Baggio, Ricardo

    2012-01-01

    The title compound, C4H6N2S3, has two very similar mol­ecules per asymmetric unit. The nine non-H atoms in each mol­ecule are coplanar, both having comparable r.m.s. deviations of 0.002 Å. The main inter­est in the rather simple structure resides in a survey of very weak (in some cases, borderline) non-bonding inter­actions of various kinds, viz. S⋯S, C—H⋯π, π–π [centroid–centroid distance = 3.8958 (13) Å] and C—S⋯π [3.7271 (11) Å], which act as the major driving force for the arrangement of mol­ecules in the structure. The role of long, though highly directional, S⋯S contacts (d > 3.60 Å), and their relevance to the stability of the structure is discussed. PMID:23125808

  20. 2-Bromo-1-[1-(4-bromo­phen­yl)-5-methyl-1H-1,2,3-triazol-4-yl]ethanone

    PubMed Central

    Bunev, Alexander S.; Troshina, Marina A.; Ostapenko, Gennady I.; Pavlova, Andzhela P.; Khrustalev, Victor N.

    2014-01-01

    The asymmetric unit of the title compound, C11H9Br2N3O, contains two crystallographically independent mol­ecules with similar geometries; the Br—C—C=O torsion angles are 1.2 (4) and −2.8 (4)°, and the benzene and triazole rings are inclined o one another by 51.90 (16) and 51.88 (16)°. The two molecules are related by a pseudo-screw 21 axis directed along [100]. In the crystal, mol­ecules are linked into a three-dimensional network by weak C—H⋯O and C—H⋯N hydrogen bonds and secondary Br⋯Br [3.5991 (8) and 3.6503 (9) Å] inter­actions. PMID:25161595

  1. 3-Ethyl-2-methyl-5-methyl­ene-6,7-di­hydroindol-4(5H)-one

    PubMed Central

    Sonar, Vijayakumar N.; Parkin, Sean; Crooks, Peter A.

    2008-01-01

    The title compound, C12H15NO, a degradation product of molindone hydro­chloride, was prepared by the reaction of molindone with methyl iodide and subsequent reaction of the resulting quaternary ammonium salt with 2N aqueous sodium hydroxide. The newly formed double bond is exocyclic in nature and the carbonyl group is conjugated with the π-electrons of the pyrrole ring. The six-membered ring is in the half-chair conformation. The H atom attached to the N atom is involved in an inter­molecular hydrogen bond with the O atom of a screw-related mol­ecule, thus forming a continuous chain. PMID:21200723

  2. Potent and Selective Inhibition of a Single α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Subunit by an RNA Aptamer*

    PubMed Central

    Park, Jae-Seon; Wang, Congzhou; Han, Yan; Huang, Zhen; Niu, Li

    2011-01-01

    Inhibitors of AMPA-type glutamate ion channels are useful as biochemical probes for structure-function studies and as drug candidates for a number of neurological disorders and diseases. Here, we describe the identification of an RNA inhibitor or aptamer by an in vitro evolution approach and a characterization of its mechanism of inhibition on the sites of interaction by equilibrium binding and on the receptor channel opening rate by a laser-pulse photolysis technique. Our results show that the aptamer is a noncompetitive inhibitor that selectively inhibits the GluA2Qflip AMPA receptor subunit without any effect on other AMPA receptor subunits or kainate or NMDA receptors. On the GluA2 subunit, this aptamer preferentially inhibits the flip variant. Furthermore, the aptamer preferentially inhibits the closed-channel state of GluA2Qflip with a KI = 1.5 μm or by ∼15-fold over the open-channel state. The potency and selectivity of this aptamer rival those of small molecule inhibitors. Together, these properties make this aptamer a promising candidate for the development of water-soluble, highly potent, and GluA2 subunit-selective drugs. PMID:21402710

  3. WHY DOES 5-METHYL CHRYSENE INTERACT WITH DNA LIKE BOTH A PLANAR AND A NON-PLANAR POLYCYCLIC AROMATIC HYDROCARBON? QUANTUM MECHANICAL STUDIES

    EPA Science Inventory

    Polycyclic aromatic hydrocarbons are a large class of anthropogenic chemicals found in the environment. Some class members are potent animal carcinogens while other similar class members show little carcinogenic activity. When considering a series of in vitro studies of the int...

  4. 40 CFR 721.5590 - Oxirane, [[[(1R,2S,5R)-5-methyl-2- (1-methylethyl)cyclohexyl] oxy]methyl]-.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... activities. Requirements as specified in § 721.80(g). (ii) Release to water. Requirements as specified § 721.90 (a)(1), (b)(1), and (c)(1). (b) Specific requirements. The provisions of subpart A of this part... requirements as specified in § 721.125 (a), (b), (c), (i), and (k) are applicable to manufacturers,...

  5. WHY DOES 5-METHYL CHRYSENE INTERACT WITH DNA LIKE BOTH A PLANAR AND A NON-PLANAR POLYCYCLIC AROMATIC HYDROCARBON? QUANTUM MECHANICAL STUDIES

    EPA Science Inventory

    Polycyclic aromatic hydrocarbons are a large class of anthropogenic chemicals found in the environment. Some class members are potent animal carcinogens while other similar class members show little carcinogenic activity. When considering a series of in vitro studies of the int...

  6. Tautomerism aspect of thione-thiol combined with spectral investigation of some 4-amino-5-methyl-1,2,4-triazole-3-thione Schiff's bases

    NASA Astrophysics Data System (ADS)

    El Ashry, El Sayed H.; Awad, Laila F.; Soliman, Saied M.; Abd Al Moaty, Mohamed N.; Ghabbour, Hazem A.; Barakat, Assem

    2017-10-01

    Reaction of 4-amino-3-methyl-1,2,4-triazole-5-thione with some substituted benzaldehydes in presence of catalytic amount of hydrochloric acid afforded the respective Schiff's bases 3a-e. Computational studies using DFT incorporating the B3LYP/6-311G(d,p) level of theory is used to predict the stability of the possible tautomers. Molecular modeling, natural charge calculations, NMR, Frontier molecular orbitals and electronic spectra were investigated. Analysis of the thermodynamic parameters of the thione-thiol tautomeric reactions of these derivatives was used to predict the tautomers stability. The thione tautomer is the most favored form in gas phase and in solution whatever the nature of solvent used. The electronic spectra were assigned based on the TD-DFT calculations. The GIAO NMR chemical shifts correlated well with the experimental data.

  7. 5-methyl-cytosine and 5-hydroxy-methyl-cytosine in the genome of Biomphalaria glabrata, a snail intermediate host of Schistosoma mansoni.

    PubMed

    Fneich, Sara; Dheilly, Nolwenn; Adema, Coen; Rognon, Anne; Reichelt, Michael; Bulla, Jan; Grunau, Christoph; Cosseau, Céline

    2013-06-06

    Biomphalaria glabrata is the mollusc intermediate host for Schistosoma mansoni, a digenean flatworm parasite that causes human intestinal schistosomiasis. An estimated 200 million people in 74 countries suffer from schistosomiasis, in terms of morbidity this is the most severe tropical disease after malaria. Epigenetic information informs on the status of gene activity that is heritable, for which changes are reversible and that is not based on the DNA sequence. Epigenetic mechanisms generate variability that provides a source for potentially heritable phenotypic variation and therefore could be involved in the adaptation to environmental constraint. Phenotypic variations are particularly important in host-parasite interactions in which both selective pressure and rate of evolution are high. In this context, epigenetic changes are expected to be major drivers of phenotypic plasticity and co-adaptation between host and parasite. Consequently, with characterization of the genomes of invertebrates that are parasite vectors or intermediate hosts, it is also essential to understand how the epigenetic machinery functions to better decipher the interplay between host and parasite. The CpGo/e ratios were used as a proxy to investigate the occurrence of CpG methylation in B. glabrata coding regions. The presence of DNA methylation in B. glabrata was also confirmed by several experimental approaches: restriction enzymatic digestion with isoschizomers, bisulfite conversion based techniques and LC-MS/MS analysis. In this work, we report that DNA methylation, which is one of the carriers of epigenetic information, occurs in B. glabrata; approximately 2% of cytosine nucleotides are methylated. We describe the methylation machinery of B. glabrata. Methylation occurs predominantly at CpG sites, present at high ratios in coding regions of genes associated with housekeeping functions. We also demonstrate by bisulfite treatment that methylation occurs in multiple copies of Nimbus, a transposable element. This study details DNA methylation for the first time, one of the carriers of epigenetic information in B. glabrata. The general characteristics of DNA methylation that we observed in the B. glabrata genome conform to what epigenetic studies have reported from other invertebrate species.

  8. Discovery of the First α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Antagonist Dependent upon Transmembrane AMPA Receptor Regulatory Protein (TARP) γ-8.

    PubMed

    Gardinier, Kevin M; Gernert, Douglas L; Porter, Warren J; Reel, Jon K; Ornstein, Paul L; Spinazze, Patrick; Stevens, F Craig; Hahn, Patric; Hollinshead, Sean P; Mayhugh, Daniel; Schkeryantz, Jeff; Khilevich, Albert; De Frutos, Oscar; Gleason, Scott D; Kato, Akihiko S; Luffer-Atlas, Debra; Desai, Prashant V; Swanson, Steven; Burris, Kevin D; Ding, Chunjin; Heinz, Beverly A; Need, Anne B; Barth, Vanessa N; Stephenson, Gregory A; Diseroad, Benjamin A; Woods, Tim A; Yu, Hong; Bredt, David; Witkin, Jeffrey M

    2016-05-26

    Transmembrane AMPA receptor regulatory proteins (TARPs) are a family of scaffolding proteins that regulate AMPA receptor trafficking and function. TARP γ-8 is one member of this family and is highly expressed within the hippocampus relative to the cerebellum. A selective TARP γ-8-dependent AMPA receptor antagonist (TDAA) is an innovative approach to modulate AMPA receptors in specific brain regions to potentially increase the therapeutic index relative to known non-TARP-dependent AMPA antagonists. We describe here, for the first time, the discovery of a noncompetitive AMPA receptor antagonist that is dependent on the presence of TARP γ-8. Three major iteration cycles were employed to improve upon potency, CYP1A2-dependent challenges, and in vivo clearance. An optimized molecule, compound (-)-25 (LY3130481), was fully protective against pentylenetetrazole-induced convulsions in rats without the motor impairment associated with non-TARP-dependent AMPA receptor antagonists. Compound (-)-25 could be utilized to provide proof of concept for antiepileptic efficacy with reduced motor side effects in patients.

  9. 3-tert-Butyl 5-methyl (2R,4S,5R)-2-(4-methoxyphenyl)-4-(3-nitrophenyl)-1,3-oxazolidine-3,5-dicarboxylate

    PubMed Central

    Montiel-Smith, Sara; Bernès, Sylvain; Sandoval-Ramírez, Jesús; Meza-Reyes, Socorro; Dubois, Joëlle

    2012-01-01

    The title mol­ecule, C23H26N2O8, was synthesized in three steps starting from m-nitro­cinnamic acid. The central oxazolidine ring adopts an almost perfect envelope conformation with the O atom as the flap [puckering parameter ϕ = 0.3 (6)°]. The dihedral angle formed by the benzene rings is 61.81 (9)°. In the crystal, mol­ecules are connected into double chains parallel to [010] by C—H⋯O hydrogen bonds. The absolute configuration was assigned from the synthetic procedure. PMID:23284466

  10. Bromidotetra­kis­(1H-2-ethyl-5-methyl­imidazole-κN 3)copper(II) bromide

    PubMed Central

    Godlewska, Sylwia; Baranowska, Katarzyna; Socha, Joanna; Dołęga, Anna

    2011-01-01

    The CuII ion in the title compound, [CuBr(C6H10N2)4]Br, is coordinated in a square-based-pyramidal geometry by the N atoms of four imidazole ligands and a bromide anion in the apical site. Both the CuII and Br− atoms lie on a crystallographic fourfold axis. In the crystal, the [CuBr(C6H10N2)4]+ complex cations are linked to the uncoordinated Br− anions (site symmetry ) by N—H⋯Br hydrogen bonds, generating a three-dimensional network. The ethyl group of the imidazole ligand was modelled as disordered over two orientations with occupancies of 0.620 (8) and 0.380 (8). PMID:22199662

  11. 21 CFR 73.3122 - 4-[(2,4-dimethylphenyl)azo]-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... in paragraph (a) of this section may be used as a color additive in contact lenses in amounts not to...) of the Federal Food, Drug, and Cosmetic Act with respect to the contact lens in which the...

  12. 1,3-Dimethyl-5-methyl­sulfonyl-1H-pyrazolo­[4,3-e][1,2,4]triazine

    PubMed Central

    Mojzych, Mariusz; Karczmarzyk, Zbigniew; Wysocki, Waldemar

    2010-01-01

    In the title compound, C7H9N5O2S, the pyrazolo­[4,3-e][1,2,4]triazine fused-ring system is essentially planar [maximum deviation = 0.0420 (3) Å]. In the crystal, mol­ecules related by twofold axes are linked into a mol­ecular net via inter­molecular C—H⋯O and C—H⋯N hydrogen bonds. π–π inter­actions are observed between the triazine and pyrazole rings of mol­ecules related by the the twofold axis and inversion symmetry with centroid–centroid distances of 3.778 (3) and 3.416 (3) Å, respectively. PMID:21589516

  13. Crystal structure of 1,3-bis-(3-tert-butyl-2-hy-droxy-5-methyl-benz-yl)-1,3-diazinan-5-ol monohydrate.

    PubMed

    Rivera, Augusto; Miranda-Carvajal, Ingrid; Ríos-Motta, Jaime; Bolte, Michael

    2016-09-01

    In the title hydrate, C28H42N2O3·H2O, the central 1,3-diazinan-5-ol ring adopts a chair conformation with the two benzyl substituents equatorial and the lone pairs of the N atoms axial. The dihedral angle between the aromatic rings is 19.68 (38)°. There are two intra-molecular O-H⋯N hydrogen bonds, each generating an S(6) ring motif. In the crystal, classical O-H⋯O hydrogen bonds connect the 1,3-diazinane and water mol-ecules into columns extending along the b axis. The crystal structure was refined as a two-component twin with a fractional contribution to the minor domain of 0.0922 (18).

  14. The contribution of the methyl groups on thymine bases to binding specificity and affinity by alanine-rich mutants of the bZIP motif.

    PubMed

    Kise, K J; Shin, J A

    2001-09-01

    We have used fluorescence anisotropy to measure in situ the thermodynamics of binding of alanine-rich mutants of the GCN4 basic region/leucine zipper (bZIP) to short DNA duplexes, in which thymines were replaced with uracils, in order to quantify the contributions of the C5 methyl group on thymines with alanine methyl side chains. We simplified the alpha-helical GCN4 bZIP by alanine substitution: 4A, 11A, and 18A contain four, 11, and 18 alanine mutations in their DNA-binding basic regions, respectively. Titration of fluorescein-labeled duplexes with increasing amounts of protein yielded dissociation constants in the low-to-mid nanomolar range for all bZIP mutants in complex with the AP-1 target site (5'-TGACTCA-3'); binding to the nonspecific control duplex was >1000-fold weaker. Small changes of <1 kcal/mol in binding free energies were observed for wild-type bZIP and 4A mutant to uracil-containing AP-1, whereas 11A and 18A bound almost equally well to native AP-1 and uracil-containing AP-1. These modest changes in binding affinities may reflect the multivalent nature of protein-DNA interactions, as our highly mutated proteins still exhibit native-like behavior. These protein mutations may compensate for changes in enthalpic and entropic contributions toward DNA-binding in order to maintain binding free energies similar to that of the native protein-DNA complex.

  15. Crystal structure of (2-{[3,5-bis­(1,1-di­methyl­eth­yl)-4-hy­droxy­phen­yl](5-methyl-2H-pyrrol-2-yl­idene)meth­yl}-5-methyl-1H-pyrrolido-κ2 N,N′)di­fluoridoboron

    PubMed Central

    Morimoto, Yukio; Ogawa, Keizo; Uto, Yoshihiro; Nagasawa, Hideko; Hori, Hitoshi

    2015-01-01

    The title compound, C25H31BF2N2O, is a potential boron tracedrug in boron neutron capture therapy (BNCT), in which the B atom adopts a distorted BN2F2 tetra­hedral geometry: it is soluble in dimethyl sulfoxide, di­methyl­formamide and methanol. The pyrrolyl­idene­methyl­pyrrole triple fused ring system is almost planar (r.m.s. deviation = 0.031 Å) and subtends a dihedral angle of 47.09 (5)° with the plane of the pendant phenol ring. The phenol –OH group is blocked from forming hydrogen bonds by the adjacent bulky tert-butyl groups. In the crystal, inversion dimers linked by pairs of very weak C—H⋯F inter­actions generate R 2 2(22) loops. PMID:26396909

  16. Gene silencing by DNA methylation and dual inheritance in Chinese hamster ovary cells.

    PubMed

    Paulin, R P; Ho, T; Balzer, H J; Holliday, R

    1998-06-01

    Chinese hamster ovary (CHO) cells strain D422, which has one copy of the adenine phosphoribosyl transferase (APRT) gene, were permeabilized by electroporation and treated with 5-methyl deoxycytidine triphosphate. Cells with a silenced APRT gene were selected on 2, 6-diaminopurine. Colonies were isolated and shown to be reactivated to APRT+ by 5-aza-cytidine and by selection in medium containing adenine, aminopterin and thymidine. Genomic DNA was prepared from eight isolates of independent origin and subjected to bisulphite treatment. This deaminates cytosine to uracil in single-stranded DNA but does not deaminate 5-methyl cytosine. PCR, cloning and sequencing revealed the methylation pattern of CpG doublets in the promoter region of the APRT- gene, whereas the active APRT gene had nonmethylated DNA. CHO strain K1, which has two copies of the APRT+ gene, could also be silenced by the same procedure but at a lower frequency. The availability of the 5-methyl dCTP-induced silencing, 5-aza-CR and a standard mutagen, ethyl methane sulphonate, makes it possible to follow concomitantly the inheritance of active, mutant or silenced gene copies. This analysis demonstrates "dual inheritance" at the APRT locus in CHO cells.

  17. UV-MALDI mass spectrometric quantitation of uracil based pesticides in fruit soft drinks along with matrix effects evaluation.

    PubMed

    Ivanova, Bojidarka; Spiteller, Michael

    2014-02-01

    This study focused on the development of the accurate and precise quantitative method for the determination of pesticides bromacil (1), terbacil (2), lenacil (3), butafenacil (4) and flupropacil (5) in fruit based soft drinks. Three different types of drinks are bought from market; huddled orange fruit drink (100%) (I), red-oranges (II) and multivitamin drink containing strawberry, orange, banana and maracuja (III). Samples were analyzed "with" and "without" pulp utilizing LC-ESI (or APCI) MS/MS, HPLC-ESI-(or APCI)-MS/MS and UV-MALDI-Orbitrap-MS methods. The effect of high complexity of the food matrix on the analysis was discussed. Study focuses on the advantages of the UV-MALDI-Orbitrap-MS method compared to the traditionally involved GC alone or hybrid methods such as GC-MS and LC-MS/MS for quantification of pesticides in water and soft drinks. The developed method included the techniques performed for validation, calibration and standardization. The target pesticides are widely used for the treatment of citrus fruits and pineapples, but for soft drink products, there are still no clear regulations on pesticide residues limits. The matrix effects in the analysis of fruit drinks required implementation of the exact standard reference material corresponds to the variety of food matrices. This paper contributed to the broad analytical implementation of the UV-MALDI-Orbitrap-MS method in the quality control and assessment programs for monitoring of pesticide contamination in fruit based sodas. Copyright © 2013 Elsevier Inc. All rights reserved.

  18. Associations between single nucleotide polymorphisms in folate uptake and metabolizing genes with blood folate, homocysteine and DNA uracil concentrations

    USDA-ARS?s Scientific Manuscript database

    Background: Folate is an essential nutrient which supports nucleotide synthesis and biological methylation reactions. Diminished folate status results in chromosome breakage and is associated with several diseases including colorectal cancer. Folate status is also inversely related to plasma homocys...

  19. Molecularly Imprinted Polymers (MIPs) Against Uracils : Functional Monomer Design, Monomer-Template Interactions in Solution and MIP Performance in Chromatography

    DTIC Science & Technology

    2002-04-05

    assessed [4]. Here, the ability of the monomer to form multiple hydrogen-bond interactions with substrate molecules was stressed . The same group has...with (5) has been studied to explore the difference between the amido - and amino- functionalities. l NH2 0H H (1) R = cyclohexyl (5) (2) R = benzyl (4...monomer (5) illustrates the increase in association constant obtained when switching from amino- to amido - functionalities; the association constants

  20. Experimental and theoretical studies on the coordination chemistry of the N1-hexyl substituted pyrimidines (uracil, 5-fluorouracil and cytosine).

    PubMed

    Barceló-Oliver, Miquel; Baquero, Beatriz Adriana; Bauzá, Antonio; García-Raso, Angel; Vich, Roberto; Mata, Ignasi; Molins, Elies; Terrón, Angel; Frontera, Antonio

    2013-06-07

    N(1)-Hexyl substituted pyrimidines were shown to present solubility properties closer to the real bases than the commonly used methyl and ethyl derivatives, yielding bi-layered structures in the solid state. The study of their coordination capabilities, mainly with Ag(I) and Hg(II), is presented in order to prove their reactivity. A series of coordination complexes, namely, [Hg(N(1)-hexyl-5-fluorouracilate)2]4·6H2O (1), (Ag(+))·[Ag(N(1)-hexyl-5-fluorouracilate)2](-) (2), [Ag(NO3)(N(1)-hexyluracil-κO(4))4] (3), [ZnBr2(N(1)-hexylcytosine)2] (4), [CdBr2(N(1)-hexylcytosine)2] (5), [HgBr2(N(1)-hexylcytosine)2] (6) and [CoBr2(N(1)-hexylcytosine)2] (7), have been synthesized in good yields and X-ray characterized. The presence of the hexyl chains and the fluorine atoms causes the formation of interesting 3D architectures in the solid state. Their structures have been further characterized by infrared spectra (IR) and elemental analyses. In addition, DFT-D3 calculations are used to study interesting noncovalent interactions observed in the solid state, like fluorine-fluorine, fluorine-π and hydrophobic interactions.