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Sample records for pyrimidine dimer formation

  1. Pyrimidine dimer formation and repair in human skin

    SciTech Connect

    Sutherland, B.M.; Harber, L.C.; Kochevar, I.E.

    1980-09-01

    Cyclobutyl pyrimidine dimers have been detected in the DNA of human skin following in vivo irradiation with suberythermal doses of ultraviolet (UV) radiation from FS-20 sun lamp fluorescent tubes. Dimers were assayed by treatment of extracted DNA with Micrococus luteus UV-specific endonuclease, alkaline agarose electrophoresis, and ethidum bromide staining. This technique, in contrast to conventional dimer assays, can be used with nonradioactive DNA and is optimal at low UV light doses. These data suggest that some dimer disappearance by excision repair occurs within 20 min of UV irradiation and that photoreactivation of dimers can make a contribution to the total repair process.

  2. Photosensitized [2 + 2] cycloaddition of N-acetylated cytosine affords stereoselective formation of cyclobutane pyrimidine dimer

    PubMed Central

    Yamamoto, Junpei; Nishiguchi, Kosuke; Manabe, Koichiro; Masutani, Chikahide; Hanaoka, Fumio; Iwai, Shigenori

    2011-01-01

    Photocycloaddition between two adjacent bases in DNA produces a cyclobutane pyrimidine dimer (CPD), which is one of the major UV-induced DNA lesions, with either the cis-syn or trans-syn structure. In this study, we investigated the photosensitized intramolecular cycloaddition of partially-protected thymidylyl-(3′→5′)-N4-acetyl-2′-deoxy-5-methylcytidine, to clarify the effect of the base modification on the cycloaddition reaction. The reaction resulted in the stereoselective formation of the trans-syn CPD, followed by hydrolysis of the acetylamino group. The same result was obtained for the photocycloaddition of thymidylyl-(3′→5′)-N4-acetyl-2′-deoxycytidine, whereas both the cis-syn and trans-syn CPDs were formed from thymidylyl-(3′→5′)-thymidine. Kinetic analyses revealed that the activation energy of the acid-catalyzed hydrolysis is comparable to that reported for the thymine-cytosine CPD. These findings provided a new strategy for the synthesis of oligonucleotides containing the trans-syn CPD. Using the synthesized oligonucleotide, translesion synthesis by human DNA polymerase η was analyzed. PMID:20880992

  3. UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10. 3 bases

    SciTech Connect

    Gale, J.M.; Nissen, K.A.; Smerdon, M.J.

    1987-10-01

    We have determined the distribution of the major UV-induced photoproducts in nucleosome core DNA using the 3'----5' exonuclease activity of T4 DNA polymerase, which has been shown to stop digestion immediately 3' to UV-induced pyrimidine dimers. This assay is extremely sensitive since all DNA fragments without photoproducts (background) are reduced to small oligonucleotides, which can be separated from those fragments containing photoproducts. The results show that the distribution of UV-induced photoproducts (primarily cyclobutane dipyrimidines) is not uniform throughout core DNA but displays a striking 10.3 (+/- 0.1) base periodicity. Furthermore, this characteristic distribution of photoproducts was obtained regardless of whether nucleosome core DNA was isolated from UV-irradiated intact chromatin fibers, histone H1-depleted chromatin fibers, isolated mononucleosomes, or cells in culture. The yield of pyrimidine dimers along the DNA seems to be modulated in a manner that reflects structural features of the nucleosome unit, possibly core histone-DNA interactions, since this pattern was not obtained for UV-irradiated core DNA either free in solution or bound tightly to calcium phosphate crystals. Based on their location relative to DNase I cutting sites, the sites of maximum pyrimidine dimer formation in core DNA mapped to positions where the phosphate backbone is farthest from the core histone surface. These results indicate that within the core region of nucleosomes, histone-DNA interactions significantly alter the quantum yield of cyclobutane dipyrimidines, possibly by restraining conformational changes in the DNA helix required for formation of these photoproducts.

  4. Ultraviolet light action spectra for neoplastic transformation and lethality of Syrian hamster embryo cells correlate with spectrum for pyrimidine dimer formation in cellular DNA.

    PubMed Central

    Doniger, J; Jacobson, E D; Krell, K; DiPaolo, J A

    1981-01-01

    Action spectra were determined for neoplastic transformation, production of pyrimidine dimers, and lethality in Syrian hamster embryo cells. Of wavelengths between 240 and 313 nm, the most effective were 265 and 270. The relative sensitivities per quantum for transformation, pyrimidine dimer production, and lethality were essentially the same at each of the wavelengths tested. This action spectrum for transformation, which is relevant to carcinogenesis, is similar to spectra obtained previously by measuring other cellular responses in either microbial or mammalian systems. Because the action spectra for cytotoxicity and transformation are the same as the spectrum for dimer production, DNA is suggested as the target for all these processes. PMID:6941297

  5. Excision repair of UV-induced pyrimidine dimers in human skin in vivo

    SciTech Connect

    D'Ambrosio, S.M.; Slazinski, L.; Whetstone, J.W.; Lowney, E.

    1981-09-01

    The induction and loss of pyrimidine dimers in human skin in vivo was determined using UV endonuclease, alkaline sucrose sedimentations, and the fluorescent detection of nonradiolabeled DNA. The number of dimers induced following exposure of the skin to radiation emitted from a Burdick UV-800 sunlamp was quantitated by reacting the extracted DNA with Micrococcus luteus endonuclease specific for pyrimidine dimers. Exposure to 15 and 30 seconds of radiation emitted from this lamp produced the formation of 12.8 and 23.6 dimers per 10(8) daltons DNA, respectively. Approximately 50% of the dimers induced were lost 58 min after irradiation. Only a small percentage (less than 10) remained 24 hr postirradiation. These data partially characterize the process by which pyrimidine dimers are excised from human skin DNA in vivo.

  6. Human white blood cells contain cyclobutyl pyrimidine dimer photolyase

    SciTech Connect

    Sutherland, B.M.; Bennett, P.V.

    1995-10-10

    Although enzymatic photoreactivation of cyclobutyl pyrimidine dimers in DNA is present in almost all organisms, its presence in placental mammals is controversial. We tested human white blood cells for photolyase by using three defined DNAs (suprecoiled pET-2, nonsupercoiled bacteriphage {lambda}, and a defined-sequence 287-bp oligonucleotide), two dimer-specific endonucleases (T4 endonuclease V and UV endonuclease from Micrococcus luteus), and three assay methods. We show that human white blood cells contain photolyase that can photorepair pyrimidine dimers in defined supercoiled and linear DNAs and in a 287-bp oligonucleotide and that human photolyase is active on genomic DNA in intact human cells. 44 refs., 3 figs.

  7. UVA Generates Pyrimidine Dimers in DNA Directly

    PubMed Central

    Jiang, Yong; Rabbi, Mahir; Kim, Minkyu; Ke, Changhong; Lee, Whasil; Clark, Robert L.; Mieczkowski, Piotr A.; Marszalek, Piotr E.

    2009-01-01

    There is increasing evidence that UVA radiation, which makes up ∼95% of the solar UV light reaching the Earth's surface and is also commonly used for cosmetic purposes, is genotoxic. However, in contrast to UVC and UVB, the mechanisms by which UVA produces various DNA lesions are still unclear. In addition, the relative amounts of various types of UVA lesions and their mutagenic significance are also a subject of debate. Here, we exploit atomic force microscopy (AFM) imaging of individual DNA molecules, alone and in complexes with a suite of DNA repair enzymes and antibodies, to directly quantify UVA damage and reexamine its basic mechanisms at a single-molecule level. By combining the activity of endonuclease IV and T4 endonuclease V on highly purified and UVA-irradiated pUC18 plasmids, we show by direct AFM imaging that UVA produces a significant amount of abasic sites and cyclobutane pyrimidine dimers (CPDs). However, we find that only ∼60% of the T4 endonuclease V-sensitive sites, which are commonly counted as CPDs, are true CPDs; the other 40% are abasic sites. Most importantly, our results obtained by AFM imaging of highly purified native and synthetic DNA using T4 endonuclease V, photolyase, and anti-CPD antibodies strongly suggest that CPDs are produced by UVA directly. Thus, our observations contradict the predominant view that as-yet-unidentified photosensitizers are required to transfer the energy of UVA to DNA to produce CPDs. Our results may help to resolve the long-standing controversy about the origin of UVA-produced CPDs in DNA. PMID:19186150

  8. Quantitation of pyrimidine dimer contents of nonradioactive deoxyribonucleic acid by electrophoresis in alkaline agarose gels

    SciTech Connect

    Sutherland, B.M.; Shih, A.G.

    1983-02-15

    We have developed a method of quantitating the pyrimidine dimer content of nonradioactive DNAs. DNA samples are treated with the UV-endonuclease from Micrococcus luteus and then separated according to molecular weight by electrophoresis on alkaline agarose gels. From their migration relative to known molecular weight standards, their median molecular weight and thus the number of dimers per DNA molecule in each sample can be calculated. Results of action spectra for dimer formation in T7 bacteriophage measured by this method agree well with action spectra for T7 killing. In addition, the method gives dimer yields in good agreement with those obtained by others using alkaline sucrose gradient sedimentation.

  9. Photoreactivation of ultraviolet radiation-induced pyrimidine dimers in neonatal BALB/c mouse skin

    SciTech Connect

    Ananthaswamy, H.N.; Fisher, M.S.

    1981-05-01

    The numbers of ultraviolet light (uv)-induced pyrimidine dimers in the DNA of neonatal BALB/c mouse skin were measured by assessing the sensitivity of the DNA to Micrococcus luteus uv endonuclease. Irradiation of neonatal BALB/c mice with FS40 sunlamps caused a dose-dependent induction of endonuclease-sensitive sites (pyrimidine dimers) in DNA extracted from back skin. Exposure of these uv-irradiated neonatal mice to photoreactivating (PR) light (cool white fluorescent lamp and incandescent lamp) caused a reduction in the number of pyrimidine dimers in the DNA, as revealed by a shift in low-molecular-weight DNA to high-molecular-weight DNA. In contrast, DNA profiles of the skin of either uv-irradiated mice or uv-irradiated mice kept in the dark for the same duration as those exposed to PR light did not show a loss of uv-induced endonuclease-sensitive sites. Furthermore, reversing the order of treatment, i.e., administering PR light first and then uv, did not produce a reduction in pyrimidine dimers. These results demonstrate that PR or uv-induced pyrimidine dimers occurs in neonatal BALB/c mouse skin. The optimal wavelength range for in vivo PR appears to be in the visible region of the spectrum (greater than 400 nm). Although dimer formation could be detected in both dermis and epidermis, PR occurred only in the dermis. Furthermore, the PR phenomenon could not be detected in the skin of adult mice from the same inbred strain.

  10. Quantitation of pyrimidine dimers in DNA from UVB-irradiated alfalfa (@ L. ) seedlings

    SciTech Connect

    Quaite, F.E.; Sutherland, B.M.; Sutherland, J.C.

    1991-01-01

    Depletion of stratospheric ozone will increase the solar ultraviolet radiation in the range from 290-320 nm (UVB) that reaches the surface of the earth, placing an increased UV burden on exposed organisms. One consequence of increased UVB may be decreased productivity of crop plants. A principal lesion caused by UV in DNA is the cyclobutyl pyrimidine dimer. We have adapted a method for measuring these dimers in nanogram quantities of non-radioactive DNA for use in UV-irradiated plants. We find that biologically relevant doses of broad band UVB radiation induce easily detectable frequencies of pyrimidine dimers in the DNA of irradiated alfalfa sprout leaves and that the dose response for dimer formation is linear up to doses of at least 690 J/m{sup 2}. We also find easily measurable frequencies of dimers in the leaves of seedlings grown in glass filtered sunlight but not exposed to additional UVB, suggesting that significant number of dimers are formed in plants exposed to normal sunlight. 27 refs., 3 figs., 1 tab.

  11. Induction of pyrimidine dimers in epidermal DNA of hairless mice by UVB: an action spectrum

    SciTech Connect

    Ley, R.D.; Peak, M.J.; Lyon, L.L.

    1983-03-01

    An action spectrum for the induction of pyrimidine dimers in the epidermis of hairless mice was determined between 288 and 307 nm. The presence of pyrimidine dimers in tritium-labeled DNA extracted from exposed SKH:hairless-1 mouse skin was determined using dimer-specific nucleases from Micrococcus luteus in conjunction with sedimentation of the irradiated DNA in alkaline sucrose gradients. The rate of induction of pyrimidine dimers was maximal at 293 nm. These values were used to propose a UVB transmission curve for mouse epidermis.

  12. Molecular mechanisms of pyrimidine dimer excision in Saccharomyces cerevisiae: excision of dimers in cell extracts

    SciTech Connect

    Reynolds, R.J.; Love, J.D.; Friedberg, E.C.

    1981-08-01

    Cell-free extracts prepared from rad1-19, rad2-2, rad3-1, rad4-3, rad7-1, rad10-1, rad14-1, rad16-1, and cycl-1 (rad7) mutants of Saccharomyces cerevisiae all catalyze the preferential excision of thymine-containing pyrimidine dimers from ultraviolet-irradiated DNA specifically incised with M. luteus ultraviolet deoxyribonucleic acid incising activity.

  13. Determination of pyrimidine dimers in DNA by high-performance liquid chromatography/gas chromatography and electron capture detection

    SciTech Connect

    Ramsey, R.S.; Ho, C. )

    1989-11-01

    Exposure of DNA to uv radiation results in the formation of a number of photoproducts including the cyclobutyl pyrimidine dimers. At low uv fluences the concentrations of these dimeric compounds are only a small fraction of the corresponding DNA pyrimidine concentration (e.g., as low as 0.02% or less of the total thymine content). Sensitive methods of analysis are therefore required for accurate determinations. Analytical methodology based upon HPLC fractionation and electrophore labeling followed by GC/electron capture detection (ECD) has been developed to quantitate these species. Separation of thymine-thymine, thymine-uracil, and uracil-uracil from the monomeric bases and from other constituents present in acid-hydrolyzed DNA is achieved by reversed-phase HPLC. Isolation of the dimeric fractions is followed by off-line derivatization to form pentafluorobenzyl products for analysis by GC/ECD. All active hydrogens are alkylated, yielding products with high response factors and detection limits in the low femtomole range. The overall analytical scheme for the determination of pyrimidine dimers in DNA is presented.

  14. Photoreactivation of UV-induced pyrimidine dimers and erythema in the marsupial Monodelphis domestica

    SciTech Connect

    Ley, R.D.

    1985-04-01

    Post-UV treatment of the gray, short-tailed opossum Monodelphis domestica with photoreactivating light (320-400 nm) suppressed the appearance of UV-induced erythema as evidenced by an increase in the dose of UV required to elicit an erythemal response. Pre-UV exposure to photoreactivating light had no effect on the UV induction of erythema. The dose-response for the photoreversal of pyrimidine dimers in epidermal DNA of M. domestica was similar to that for the photoreactivation of erythema induction. These data not only support the notion that DNA is the primary chromophore involved in the induction of erythema but also identify pyrimidine dimers as the major DNA change responsible for its induction. These results also identify M. domestica as a useful whole-animal system with which to determine the role of pyrimidine dimers in other photobiological responses of mammalian skin.

  15. UVA-induced cyclobutane pyrimidine dimers in DNA: a direct photochemical mechanism?

    PubMed

    Mouret, Stéphane; Philippe, Coralie; Gracia-Chantegrel, Jocelyne; Banyasz, Akos; Karpati, Szilvia; Markovitsi, Dimitra; Douki, Thierry

    2010-04-07

    The carcinogenic action of UVA radiation is commonly attributed to DNA oxidation mediated by endogenous photosensitisers. Yet, it was recently shown that cyclobutane pyrimidine dimers (CPD), well known for their involvement in UVB genotoxicity, are produced in larger yield than oxidative lesions in UVA-irradiated cells and skin. In the present work, we gathered mechanistic information on this photoreaction by comparing formation of all possible bipyrimidine photoproducts upon UVA irradiation of cells, purified genomic DNA and dA(20):dT(20) oligonucleotide duplex. We observed that the distribution of photoproducts, characterized by the sole formation of CPD and the absence of (6-4) photoproducts was similar in the three types of samples. The CPD involving two thymines represented 90% of the amount of photoproducts. Moreover, the yields of formation of the DNA lesions were similar in cells and isolated DNA. In addition, the effect of the wavelength of the incident photons was found to be the same in isolated DNA and cells. This set of data shows that UVA-induced cyclobutane pyrimidine dimers are formed via a direct photochemical mechanism, without mediation of a cellular photosensitiser. This is possible because the double-stranded structure increases the capacity of DNA bases to absorb UVA photons, as evidenced in the case of the oligomer dA(20):dT(20). These results emphasize the need to consider UVA in the carcinogenic effects of sunlight. An efficient photoprotection is needed that can only be complete by completely blocking incident photons, rather than by systemic approaches such as antioxidant supplementation.

  16. Determination of pyrimidine dimers in Escherichia coli and Cryptosporidium parvum during UV light inactivation, photoreactivation, and dark repair.

    PubMed

    Oguma, K; Katayama, H; Mitani, H; Morita, S; Hirata, T; Ohgaki, S

    2001-10-01

    UV inactivation, photoreactivation, and dark repair of Escherichia coli and Cryptosporidium parvum were investigated with the endonuclease sensitive site (ESS) assay, which can determine UV-induced pyrimidine dimers in the genomic DNA of microorganisms. In a 99.9% inactivation of E. coli, high correlation was observed between the dose of UV irradiation and the number of pyrimidine dimers induced in the DNA of E. coli. The colony-forming ability of E. coli also correlated highly with the number of pyrimidine dimers in the DNA, indicating that the ESS assay is comparable to the method conventionally used to measure colony-forming ability. When E. coli were exposed to fluorescent light after a 99.9% inactivation by UV irradiation, UV-induced pyrimidine dimers in the DNA were continuously repaired and the colony-forming ability recovered gradually. When kept in darkness after the UV inactivation, however, E. coli showed neither repair of pyrimidine dimers nor recovery of colony-forming ability. When C. parvum were exposed to fluorescent light after UV inactivation, UV-induced pyrimidine dimers in the DNA were continuously repaired, while no recovery of animal infectivity was observed. When kept in darkness after UV inactivation, C. parvum also showed no recovery of infectivity in spite of the repair of pyrimidine dimers. It was suggested, therefore, that the infectivity of C. parvum would not recover either by photoreactivation or by dark repair even after the repair of pyrimidine dimers in the genomic DNA.

  17. Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer.

    PubMed

    Horikoshi, Naoki; Tachiwana, Hiroaki; Kagawa, Wataru; Osakabe, Akihisa; Matsumoto, Syota; Iwai, Shigenori; Sugasawa, Kaoru; Kurumizaka, Hitoshi

    2016-02-26

    The cyclobutane pyrimidine dimer (CPD) is induced in genomic DNA by ultraviolet (UV) light. In mammals, this photolesion is primarily induced within nucleosomal DNA, and repaired exclusively by the nucleotide excision repair (NER) pathway. However, the mechanism by which the CPD is accommodated within the nucleosome has remained unknown. We now report the crystal structure of a nucleosome containing CPDs. In the nucleosome, the CPD induces only limited local backbone distortion, and the affected bases are accommodated within the duplex. Interestingly, one of the affected thymine bases is located within 3.0 Å from the undamaged complementary adenine base, suggesting the formation of complementary hydrogen bonds in the nucleosome. We also found that UV-DDB, which binds the CPD at the initial stage of the NER pathway, also efficiently binds to the nucleosomal CPD. These results provide important structural and biochemical information for understanding how the CPD is accommodated and recognized in chromatin.

  18. On the Pyrazine and Pyrazine-Pyrimidine Dimers.

    DTIC Science & Technology

    1986-06-01

    Lennard - Jones -hydrogen-bonding (LJ-HB) potential energy calculations. The pyrazine isotopic hetero- and homo-dimers possess nearly identical spectra with the exception that the perpendicular dimer features are displaced to the red by approx. 11 cm. Exchange or exciton interactions in this system are vanishingly small (less than 1/cm). The geometrics suggested by the isotopically substituted pyrazine dimer spectra are the same as those found for the pyrazine-h sub 4 homo-dimer: a parallel planar hydrogen bonded and a perpendicular dimer. The pyrazine-h sub 4 and pyrazine-h

  19. One pyrimidine dimer inactivates expression of a transfected gene in xeroderma pigmentosum cells

    SciTech Connect

    Protic-Sabljic, M.; Kraemer, K.H.

    1985-10-01

    The authors have developed a host cell reactivation assay of DNA repair utilizing UV-treated plasmid vectors. The assay primarily reflects cellular repair of transcriptional activity of damaged DNA measured indirectly as enzyme activity of the transfected genes. They studied three plasmids (pSV2cat, 5020 base pairs; pSV2catSVgpt, 7268 base pairs; and pRSVcat, 5027 base pairs) with different sizes and promoters carrying the bacterial cat gene (CAT, chloramphenicol acetyltransferase) in a construction that permits cat expression in human cells. All human simian virus 40-transformed cells studied expressed high levels of the transfected cat gene. UV treatment of the plasmids prior to transfection resulted in differential decrease in CAT activity in different cell lines. With pSV2catSVgpt, UV inactivation of CAT expression was greater in the xeroderma pigmentosum group A and D lines than in the other human cell lines tested. The D0 of the CAT inactivation curve was 50 J X m-2 for pSV2cat and for pRSVcat in the xeroderma pigmentosum group A cells. The similarity of the D0 data in the xeroderma pigmentosum group A cells for three plasmids of different size and promoters implies they all have similar UV-inactivation target size. UV-induced pyrimidine dimer formation in the plasmids was quantified by assay of the number of UV-induced T4 endonuclease V-sensitive sites. In the most sensitive xeroderma pigmentosum cells, with all three plasmids, one UV-induced pyrimidine dimer inactivates a target of about 2 kilobases, close to the size of the putative CAT mRNA.

  20. Quantitation of ultraviolet radiation-induced cyclobutyl pyrimidine dimers in DNA by video and photographic densitometry

    SciTech Connect

    Freeman, S.E.; Thompson, B.D. )

    1990-05-01

    We have compared video and photographic methods for calculating the number of ultraviolet radiation (uv)-induced pyrimidine dimers in DNA from the bacteriophage T7 exposed to uv (0 to 800 J/m2) from an FS40 sunlamp. DNA was incubated with a pyrimidine dimer-specific Micrococcus luteus uv endonuclease, subjected to alkaline agarose gel electrophoresis, neutralized, and stained with ethidium bromide, and the DNA fluorescence was recorded either with a video camera or on photographic film. The slopes of the dose-response curves for the number of uv-endonuclease-sensitive sites per 10(3) bases (pyrimidine dimers) was 1.2 (+/- 0.1) X 10(-4) uv-endonuclease-sensitive sites per J/m2 for the video analysis and 1.3 (+/- 0.04) X 10(-4) uv-endonuclease-sensitive sites per J/m2 for the photographic analysis. Results for pyrimidine dimer determination by either method were statistically comparable.

  1. Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics.

    PubMed

    Goto, Noriko; Bazar, Gyorgy; Kovacs, Zoltan; Kunisada, Makoto; Morita, Hiroyuki; Kizaki, Seiichiro; Sugiyama, Hiroshi; Tsenkova, Roumiana; Nishigori, Chikako

    2015-07-02

    Ultraviolet (UV) radiation causes cellular DNA damage, among which cyclobutane pyrimidine dimers (CPDs) are responsible for a variety of genetic mutations. Although several approaches have been developed for detection of CPDs, conventional methods require time-consuming steps. Aquaphotomics, a new approach based on near-infrared spectroscopy (NIRS) and multivariate analysis that determines interactions between water and other components of the solution, has become an effective method for qualitative and quantitative parameters measurement in the solutions. NIR spectral patterns of UVC-irradiated and nonirradiated DNA solutions were evaluated using aquaphotomics for detection of UV-induced CPDs. Groups of UV-irradiated and nonirradiated DNA samples were classified (87.5% accuracy) by soft independent modeling of class analogy (SIMCA). A precise regression model calculated from NIR water spectral patterns based on UVC doses (r Val = 0.9457) and the concentration of cis-syn cyclobutane thymine dimers (cis-syn T<>Ts; r Val = 0.9993) was developed using partial least squares regression (PLSR), while taking advantage of water spectral patterns, particularly around 1400-1500 nm. Our results suggested that, in contrast to DNA, the formation of cis-syn T<>Ts increased the strongly hydrogen bonded water. Additionally, NIRS could qualitatively and quantitatively detect cis-syn T<>Ts in isolated DNA aqueous solutions upon UVC exposure.

  2. Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics

    PubMed Central

    Goto, Noriko; Bazar, Gyorgy; Kovacs, Zoltan; Kunisada, Makoto; Morita, Hiroyuki; Kizaki, Seiichiro; Sugiyama, Hiroshi; Tsenkova, Roumiana; Nishigori, Chikako

    2015-01-01

    Ultraviolet (UV) radiation causes cellular DNA damage, among which cyclobutane pyrimidine dimers (CPDs) are responsible for a variety of genetic mutations. Although several approaches have been developed for detection of CPDs, conventional methods require time-consuming steps. Aquaphotomics, a new approach based on near-infrared spectroscopy (NIRS) and multivariate analysis that determines interactions between water and other components of the solution, has become an effective method for qualitative and quantitative parameters measurement in the solutions. NIR spectral patterns of UVC-irradiated and nonirradiated DNA solutions were evaluated using aquaphotomics for detection of UV-induced CPDs. Groups of UV-irradiated and nonirradiated DNA samples were classified (87.5% accuracy) by soft independent modeling of class analogy (SIMCA). A precise regression model calculated from NIR water spectral patterns based on UVC doses (r Val = 0.9457) and the concentration of cis-syn cyclobutane thymine dimers (cis-syn T<>Ts; r Val = 0.9993) was developed using partial least squares regression (PLSR), while taking advantage of water spectral patterns, particularly around 1400–1500 nm. Our results suggested that, in contrast to DNA, the formation of cis-syn T<>Ts increased the strongly hydrogen bonded water. Additionally, NIRS could qualitatively and quantitatively detect cis-syn T<>Ts in isolated DNA aqueous solutions upon UVC exposure. PMID:26133899

  3. Differences in pyrimidine dimer removal between rat skin cells in vitro and in vivo

    SciTech Connect

    Mullaart, E.; Lohman, P.H.; Vijg, J.

    1988-03-01

    Pyrimidine dimers, the most abundant type of DNA lesions induced by ultraviolet light (UV), are rapidly repaired in human skin fibroblasts in vitro. In the same cell type from rats, however, there is hardly any removal of such dimers. To investigate whether this low capacity of rat skin cells to repair lesions in their DNA is an inherent characteristic of this species or an artifact due to cell culturing, we measured the removal of UV-induced pyrimidine dimers from rat epidermal keratinocytes both in vitro and in vivo. Epidermal keratinocytes in vitro were unable to remove any dimers over the first 3 h after UV-irradiation, while only about 20% was removed during a repair period of 24 h. In this respect, these cells were not different from cultured rat fibroblasts. In contrast to the results obtained with keratinocytes in vitro, we observed a rapid repair of pyrimidine dimers in UV-irradiated keratinocytes in vivo over the first 3 h; this rapid repair phase was followed by a much slower repair phase between 3 and 24 h. These results are discussed in terms of the possibility that mammalian cells are able to switch from one DNA repair pathway to another.

  4. Ultraviolet B-sensitive rice cultivar deficient in cyclobutyl pyrimidine dimer repair

    SciTech Connect

    Hidema, Jun; Kumagai, Tadashi; Sutherland, J.C.; Sutherland, B.M.

    1997-01-01

    Repair of cyclobutyl pyrimidine dimers (CPDs) in DNA is essential in most organisms to prevent biological damage by ultraviolet (UV) light. In higher plants tested thus far, UV-sensitive strains had higher initial damage levels or deficient repair of nondimer DNA lesions but normal CPD repair. This suggested that CPDs might not be important for biological lesions. The photosynthetic apparatus has also been proposed as a critical target. We have analyzed CPD induction and repair in the UV-sensitive rice (Oryza sativa L.) cultivar Norin 1 and its close relative UV-resistant Sasanishiki using alkaline agarose gel electrophoresis. Norin 1 is deficient in cyclobutyl pyrimidine dimer photoreactivation and excision; thus, UV sensitivity correlates with deficient dimer repair. 38 refs., 3 figs.

  5. Control of pyrimidine nucleotide formation in Pseudomonas fulva.

    PubMed

    West, Thomas P

    2010-03-01

    Control of pyrimidine formation was examined in Pseudomonas fulva ATCC 31418. Pyrimidine supplementation lowered pyrimidine biosynthetic pathway enzyme activities in cells grown on glucose or succinate as a carbon source indicating possible repression of enzyme synthesis. Pyrimidine limitation experiments were conducted using an orotidine 50-monophosphate decarboxylase mutant strain isolated in this study. Compared to uracil-supplemented, glucose-grown mutant cells, pyrimidine limitation of this strain caused aspartate transcarbamoylase, dihydroorotase, dihydroorotate dehydrogenase and orotate phosphoribosyltransferase activities to increase about 6-, 13-, 3-, 15-fold, respectively, which confirmed regulation of enzyme synthesis by pyrimidines. At the level of enzyme activity, transcarbamoylase activity in Ps. fulva was strongly inhibited by pyrophosphate, CTP, GTP and GDP under saturating substrate concentrations.

  6. Accommodation of pyrimidine dimers during replication of UV-damaged simian virus 40 DNA.

    PubMed Central

    Stacks, P C; White, J H; Dixon, K

    1983-01-01

    UV irradiation of simian virus 40-infected cells at fluences between 20 and 60 J/m2, which yield one to three pyrimidine dimers per simian virus 40 genome, leads to a fluence-dependent progressive decrease in simian virus 40 DNA replication as assayed by incorporation of [3H]deoxyribosylthymine into viral DNA. We used a variety of biochemical and biophysical techniques to show that this decrease is due to a block in the progression of replicative-intermediate molecules to completed form I molecules, with a concomitant decrease in the entry of molecules into the replicating pool. Despite this UV-induced inhibition of replication, some pyrimidine dimer-containing molecules become fully replicated after UV irradiation. The fraction of completed molecules containing dimers goes up with time such that by 3 h after a UV fluence of 40 J/m2, more than 50% of completed molecules contain pyrimidine dimers. We postulate that the cellular replication machinery can accommodate limited amounts of UV-induced damage and that the progressive decrease in simian virus 40 DNA synthesis after UV irradiation is due to the accumulation in the replication pool of blocked molecules containing levels of damage greater than that which can be tolerated. PMID:6621531

  7. UV light-induced cyclobutane pyrimidine dimers are mutagenic in mammalian cells

    SciTech Connect

    Protic-Sabljic, M.; Tuteja, N.; Munson, P.J.; Hauser, J.; Kraemer, K.H.; Dixon, K.

    1986-10-01

    We used a simian virus 40-based shuttle vector plasmid, pZ189, to determine the role of pyrimidine cyclobutane dimers in UV light-induced mutagenesis in monkey cells. The vector DNA was UV irradiated and then introduced into monkey cells by transfection. After replication, vector DNA was recovered from the cells and tested for mutations in its supF suppressor tRNA marker gene by transformation of Escherichia coli carrying a nonsense mutation in the beta-galactosidase gene. When the irradiated vector was treated with E. coli photolyase prior to transfection, pyrimidine cyclobutane dimers were removed selectively. Removal of approximately 90% of the pyrimidine cyclobutane dimers increased the biological activity of the vector by 75% and reduced its mutation frequency by 80%. Sequence analysis of 72 mutants recovered indicated that there were significantly fewer tandem double-base changes and G X C----A X T transitions (particularly at CC sites) after photoreactivation of the DNA. UV-induced photoproducts remained (although at greatly reduced levels) at all pyr-pyr sites after photoreactivation, but there was a relative increase in photoproducts at CC and TC sites and a relative decrease at TT and CT sites, presumably due to a persistence of (6-4) photoproducts at some CC and TC sites. These observations are consistent with the fact that mutations were found after photoreactivation at many sites at which only cyclobutane dimers would be expected to occur. From these results we conclude that UV-induced pyrimidine cyclobutane dimers are mutagenic in DNA replicated in monkey cells.

  8. Excision repair of pyrimidine dimers induced by simulated solar radiation in the skin of patients with basal cell carcinoma

    SciTech Connect

    Alcalay, J.; Freeman, S.E.; Goldberg, L.H.; Wolf, J.E. )

    1990-11-01

    One prominent lesion induced in DNA by ultraviolet (UV) radiation is the cyclobutyl pyrimidine dimer formed between adjacent pyrimidines on the same DNA strand. We investigated whether people who have developed basal cell carcinoma on sun-exposed skin have an altered ability to repair UV-induced pyrimidine dimers in DNA. Twenty-two patients with at least one basal cell carcinoma, aged 31-84 years, and 19 healthy volunteers, aged 25-61 years, took part in the study. Both groups were given one minimal erythema dose (MED) of simulated solar radiation on the lower back. DNA was extracted from the irradiated skin 0 to 6 h later, and the number of UV-induced pyrimidine dimers was determined using a dimer-specific endonuclease. At time 0, the average number of dimers per unit of DNA was similar in the two groups. After 6 h, an average of 22 +/- 4% of the dimers were removed in the group with basal cell carcinoma compared to 33 +/- 4% in the cancer-free group. In the basal cell carcinoma group, only 23% of the patients repaired more than 30% of the dimers after 6 h, compared with 53% of the cancer-free subjects (p less than 0.05). We conclude that patients who develop basal cell carcinoma on sun-exposed skin may have a decreased ability to repair pyrimidine dimers induced in skin exposed to simulated solar radiation.

  9. Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4 and Micrococcus luteus uv-specific endonucleases

    SciTech Connect

    Gordon, L.K.; Haseltine, W.A.

    1980-12-25

    A comparison was made of the activity of the uv-specific endonucleases of bacteriophage T4 (T4 endonuclease V) and of Micrococcus luteus on ultraviolet light-irradiated DNA substrates of defined sequence. The two enzyms cleave DNA at the site of pyrimidine dimers with the same frequency. The products of the cleavage reaction are the same. The pyrimidine dimer DNA-glycosylase activity of both enzymes is more active on double-stranded DNA than it is on single-stranded DNA.

  10. UV Radiation–Sensitive Norin 1 Rice Contains Defective Cyclobutane Pyrimidine Dimer Photolyase

    PubMed Central

    Hidema, Jun; Kumagai, Tadashi; Sutherland, Betsy M.

    2000-01-01

    Norin 1, a progenitor of many economically important Japanese rice strains, is highly sensitive to the damaging effects of UVB radiation (wavelengths 290 to 320 nm). Norin 1 seedlings are deficient in photorepair of cyclobutane pyrimidine dimers. However, the molecular origin of this deficiency was not known and, because rice photolyase genes have not been cloned and sequenced, could not be determined by examining photolyase structural genes or upstream regulatory elements for mutations. We therefore used a photoflash approach, which showed that the deficiency in photorepair in vivo resulted from a functionally altered photolyase. These results were confirmed by studies with extracts, which showed that the Norin 1 photolyase–dimer complex was highly thermolabile relative to the wild-type Sasanishiki photolyase. This deficiency results from a structure/function alteration of photolyase rather than of nonspecific repair, photolytic, or regulatory elements. Thus, the molecular origin of this plant DNA repair deficiency, resulting from a spontaneously occurring mutation to UV radiation sensitivity, is defective photolyase. PMID:11006332

  11. Molecular mechanisms of pyrimidine dimer excision in Saccharomyces cerevisiae: incision of ultraviolet-irradiated deoxyribonucleic acid in vivo

    SciTech Connect

    Reynolds, R.J.; Friedberg, E.C.

    1981-05-01

    A group of genetically related ultraviolet (uv)-sensitive mutants of Saccharomyces cerevisiae has been examined in terms of their survival after exposure to uv radiation, their ability to carry out excision repair or pyrimidine dimers as measured by the loss of sites (pyrimidine dimers) sensitive to a dimer-specific enzyme probe, and in terms of their ability to effect incision of their deoxyribonucleic acid (DNA) during post-uv incubation in vivo (as measured by the detection of single-strand breaks in nuclear DNA). In addition to a haploid RAD/sup +/ strain (S288C), 11 different mutants representing six RAD loci (RAD1, RAD2, RAD3, RAD4, RAD14, and RAD18) were examined. Quantitative analysis of excision repair capacity, as determined by the loss of sites in DNA sensitive to an enzyme preparation from M. luteus which is specific for pyrimidine dimers, revealed a profound defect in this parameter in all but three of the strains examined. The rad14-1 mutant showed reduced but significant residual capacity to remove enzyme-sensitive sites as did the rad2-4 mutant. The latter was the only one of three different rad2 alleles examined which was leaky in this respect. The uv-sensitive strain carrying the mutant allele rad18-1 exhibited normal loss of enzyme-sensitive sites consistent with its assignment to the RAD6 rather than the RAD3 epistatic group. All strains having mutant alleles of the RAD1, RAD2, RAD3, RAD4, and RAD14 loci showed no detectable incubation-dependent strand breaks in nuclear DNA after exposure to uv radiation. These experiments suggest that the RAD1, RAD2, RAD3, RAD4 (and probably RAD14) genes are all required for the incision of uv-irradiated DNA during pyrimidine dimer excision in vivo.

  12. Induction of pyrimidine dimers and unscheduled DNA synthesis in cultured mouse epithelial cells exposed to 254-nm- and u. v. -B radiation

    SciTech Connect

    Yotti, L.P.; Ley, R.D.

    1983-01-01

    The induction and fate of pyrimidine dimers and unscheduled DNA synthesis were measured in u.v.-irradiated primary, newborn SENCAR mouse epithelial cells. Unscheduled DNA synthesis was induced in a dose responsive manner by two u.v. sources, a germicidal lamp (254 nm) and an FS40 sunlamp (280--400 nm). Using the endonuclease-sensitive site assay to detect pyrimidine dimer production and excision, we examined the response of the newborn mouse cells to both u.v. sources. We were unable to detect the removal of pyrimidine dimers with either of the two sources of u.v. The speculation is made that primary, newborn mouse epidermal cells excise u.v.-induced pyrimidine dimers to an extent below the level of detection of the endonuclease-sensitive site assay but to an extent sufficient to induce unscheduled DNA synthesis.

  13. Removal of cyclobutane pyrimidine dimers from a UV-irradiated shuttle vector introduced into human cells

    SciTech Connect

    Ganesan, A.K.; Hanawalt, P.C. )

    1994-05-01

    A shuttle vector (pZH-1) carrying the E. Coli lacZ gene under control of the SV40 early promoter was irradiated with UV and introduced into repair-proficient or repair-deficient human cell lines. The expression of irradiated lacZ compared to unirradiated lacZ was greater in repair-proficient cells (HT-1080) than in repair-deficient cells (XP12RO-SV40) belonging to xeroderma pigmentosum complementation group A. To ascertain whether the expression of lacZ in the repair-proficient cells was correlated with the removal of cyclobutane pyrimidine dimers (CPDs), the authors purified DNA from the recipient cells and used the CPD-specific enzyme T4 endonuclease V to measure the frequency of CPDs remaining in the plasmid as a whole and in two restriction fragments derived from it. They found that removal of CPDs occurred in both fragments in the repair-proficient cells but not in the repair-deficient cells. The results provide the first direct evidence for the removal of CPDs from UV irradiated plasmids introduced into human cells and support the notion that expression of the UV-damaged lacZ gene in repair-proficient human cells reflects the removal of transcription blocking lesions from the gene.

  14. Cyclobutane Pyrimidine Dimer Density as a Predictive Biomarker of the Biological Effects of Ultraviolet Radiation in Normal Human Fibroblast

    PubMed Central

    Sproul, Christopher D.; Mitchell, David L.; Rao, Shangbang; Ibrahim, Joseph G.; Kaufmann, William K.; Cordeiro-Stone, Marila

    2015-01-01

    This study compared biological responses of normal human fibroblasts (NHF1) to three sources of ultraviolet radiation (UVR), emitting UVC wavelengths, UVB wavelengths, or a combination of UVA and UVB (solar simulator; emission spectrum, 94.3% UVA and 5.7% UVB). The endpoints measured were cytotoxicity, intra-S checkpoint activation, inhibition of DNA replication and mutagenicity. Results show that the magnitude of each response to the indicated radiation sources was best predicted by the density of DNA cyclobutane pyrimidine dimers (CPD). The density of 6-4 pyrimidine–pyrimidone photoproducts was highest in DNA from UVC-irradiated cells (14% of CPD) as compared to those exposed to UVB (11%) or UVA–UVB (7%). The solar simulator source, under the experimental conditions described here, did not induce the formation of 8-oxo-7,8-dihydroguanine in NHF1 above background levels. Taken together, these results suggest that CPD play a dominant role in DNA damage responses and highlight the importance of using endogenous biomarkers to compare and report biological effects induced by different sources of UVR. PMID:24148148

  15. Rapid deamination of cyclobutane pyrimidine dimer photoproducts at TCG sites in a translationally and rotationally positioned nucleosome in vivo.

    PubMed

    Cannistraro, Vincent J; Pondugula, Santhi; Song, Qian; Taylor, John-Stephen

    2015-10-30

    Sunlight-induced C to T mutation hot spots in skin cancers occur primarily at methylated CpG sites that coincide with sites of UV-induced cyclobutane pyrimidine dimer (CPD) formation. The C and 5-methyl-C in CPDs are not stable and deaminate to U and T, respectively, which leads to the insertion of A by the DNA damage bypass polymerase η, thereby defining a probable mechanism for the origin of UV-induced C to T mutations. Deamination rates for T(m)CG CPDs have been found to vary 12-fold with rotational position in a nucleosome in vitro. To determine the influence of nucleosome structure on deamination rates in vivo, we determined the deamination rates of CPDs at TCG sites in a stably positioned nucleosome within the FOS promoter in HeLa cells. A procedure for in vivo hydroxyl radical footprinting with Fe-EDTA was developed, and, together with results from a cytosine methylation protection assay, we determined the translational and rotational positions of the TCG sites. Consistent with the in vitro observations, deamination was slower for one CPD located at an intermediate rotational position compared with two other sites located at outside positions, and all were much faster than for CPDs at non-TCG sites. Photoproduct formation was also highly suppressed at one site, possibly due to its interaction with a histone tail. Thus, it was shown that CPDs of TCG sites deaminate the fastest in vivo and that nucleosomes can modulate both their formation and deamination, which could contribute to the UV mutation hot spots and cold spots.

  16. Xeroderma pigmentosum complementation group C cells remove pyrimidine dimers selectively from the transcribed strand of active genes

    SciTech Connect

    Venema, J.; van Hoffen, A.; Karcagi, V.; Natarajan, A.T.; van Zeeland, A.A.; Mullenders, L.H. )

    1991-08-01

    The authors have measured the removal of UV-induced pyrimidine dimers from DNA fragments of the adenosine deaminase (ADA) and dihydrofolate reductase (DHFR) genes in primary normal human and xeroderma pigmentosum complementation group C (XP-C) cells. Using strand-specific probes, we show that in normal cells, preferential repair of the 5{prime} part of the ADA gene is due to the rapid and efficient repair of the transcribed strand. Within 8 h after irradiation with UV at 10 J m-2, 70% of the pyrimidine dimers in this strand are removed. The nontranscribed strand is repaired at a much slower rate, with 30% dimers removed after 8 h. Repair of the transcribed strand in XP-C cells occurs at a rate indistinguishable from that in normal cells, but the nontranscribed strand is not repaired significantly in these cells. Similar results were obtained for the DHFR gene. In the 3{prime} part of the ADA gene, however, both normal and XP-C cells perform fast and efficient repair of either strand, which is likely to be caused by the presence of transcription units on both strands. The factor defective in XP-C cells is apparently involved in the processing of DNA damage in inactive parts of the genome, including nontranscribed strands of active genes. These findings have important implications for the understanding of the mechanism of UV-induced excision repair and mutagenesis in mammalian cells.

  17. Repair of UV-induced pyrimidine dimers in the individual genes Gart, Notch and white from Drosophila melanogaster cell lines.

    PubMed Central

    de Cock, J G; Klink, E C; Ferro, W; Lohman, P H; Eeken, J C

    1991-01-01

    The excision repair of UV-induced pyrimidine dimers was investigated in three genes: Gart, Notch and white in a permanent Drosophila cell line Kc, derived from wild type Drosophila melanogaster embryonic cells. In this cell line Gart and Notch are actively transcribed, whereas white is not expressed. In all three genes UV-induced pyrimidine dimers were removed with the same rate and to the same extent: 60% removal within 16 hours, up to 80-100% in 24 hours after irradiation with 10 or 15 J/m2 UV. These kinetics are similar to the time course of dimer removal measured in the genome overall. No difference in repair of the inactive white locus compared to the active Gart and Notch genes was found. Similar results were obtained using a different wild type cell line, SL2, although repair appeared to be somewhat slower in this cell line. The results are discussed with respect to the data found for gene specific repair in other eukaryotic systems. Images PMID:1648203

  18. Synthesis of monomeric and dimeric steroids containing [1,2,4]triazolo[1,5-a]pyrimidines.

    PubMed

    Arenas-González, Ailed; Mendez-Delgado, Luis Antonio; Merino-Montiel, Penélope; Padrón, José M; Montiel-Smith, Sara; Vega-Báez, José Luis; Meza-Reyes, Socorro

    2016-12-01

    The synthesis of several monomeric and dimeric steroidal [1,2,4]triazolo[1,5-a]pyrimidines (TPs) derived from steroids are described. These derivatives were prepared from α,β-unsaturated carbonyl compounds through a Claisen Schmidt condensation and rearrangement of the spiro moiety followed by a cycloaddition with 3-amino-1,2,4-triazole. The antiproliferative activity of compounds 7, 13-15 was tested against human cancer cells; several IG50 values were below 10μM.

  19. As(III) inhibits ultraviolet radiation-induced cyclobutane pyrimidine dimers repair via generation of nitric oxide in human keratinocytes

    PubMed Central

    Ding, Wei; Hudson, Laurie G.; Sun, Xi; Feng, Changjian; Liu, Ke Jian

    2008-01-01

    Inorganic arsenic enhances skin tumor formation when combined with other carcinogens including ultraviolet radiation (UVR). The inhibition of DNA damage repair by arsenic has been hypothesized to contribute to the co-carcinogenic activities of arsenic observed in vivo. Cyclobutane pyrimidine dimers (CPDs) are an important mutagenic UVR photoproduct and implicated in the genesis of non-melanoma skin cancer. The current study demonstrates that low concentrations of arsenite (As(III)) inhibit UVR-induced CPDs repair in a human keratinocyte cell line via nitric oxide (NO) and inducible nitric oxide synthase (iNOS). Following As(III) treatment, NO production and iNOS expression are elevated. Little is known about regulation of iNOS by As(III) and further investigations indicated that p38 mitogen-activated protein kinase (p38 MAPK) and NF-κB are required for As(III) induction of iNOS expression. This As(III)-stimulated signaling cascade was involved in inhibition of UVR-induced CPDs repair as disruption of p38 MAPK activity and NF-κB nuclear translocation counteracted the effects of As(III) on CPD repair. Selective inhibition of iNOS ameliorated As(III) inhibition of CPDs repair thereby suggesting that iNOS is a downstream mediator of As(III) activity. These findings provide evidence that an As(III) stimulated signal transduction cascade culminating in elevated iNOS expression and NO generation is an underlying mechanism for inhibition of UVR-induced DNA damage repair by arsenic. PMID:18621123

  20. Enzymatic analysis of isomeric trithymidylates containing ultraviolet light-induced cyclobutane pyrimidine dimers. II. Phosphorylation by phage T4 polynucleotide kinase

    SciTech Connect

    Weinfeld, M.; Liuzzi, M.; Paterson, M.C.

    1989-04-15

    Phage T4 polynucleotide kinase proved incapable of catalyzing the phosphorylation of thymidylyl-(3'----5')-thymidine containing either a cis-syn-cyclobutane pyrimidine dimer (d-T less than p greater than T) or a 6-4'-(pyrimidin-2'-one)pyrimidine photoproduct (d-T(p)-T), and similarly the UV-modified compounds of (dT)3 bearing either photoproduct at their 5'-end (d-T less than p greater than TpT and d-T(p)TpT). In contrast, the 3'-structural isomers of these trinucleotides (d-TpT less than p greater than T and d-TpT(p)T) were phosphorylated at the same rate as the parent compound. These phosphorylatable lesion-containing oligonucleotides are quantitatively released from UV-irradiated poly(dA):poly(dT) by enzymatic hydrolysis with snake venom phosphodiesterase and alkaline phosphatase. By combining this digestion regimen with phosphorylation by polynucleotide kinase and (gamma-/sup 32/P)ATP, pyrimidine dimers were quantitated at the fmol level following exposure of poly(dA):poly(dT) and herring sperm DNA to biologically relevant UV fluences. The rate of dimer induction in the synthetic polymer, approximately 10 dimers/10(6) nucleotides/Jm-2, was in close agreement with that obtained by conventional methods. Dimers were induced at one-fourth of this rate in the natural DNA. Further treatment of the phosphorylated oligonucleotides derived from irradiated herring sperm DNA with nuclease P1 released the labeled 5'-nucleotide, thus permitting analysis of the nearest-neighbor bases 5' to the lesions. We observed a ratio for pyrimidine-to-purine bases of almost 6:1, implicating tripyrimidine stretches as hotspots for UV-induced DNA damage.

  1. Major Roles for Pyrimidine Dimers, Nucleotide Excision Repair, and ATR in the Alternative Splicing Response to UV Irradiation.

    PubMed

    Muñoz, Manuel J; Nieto Moreno, Nicolás; Giono, Luciana E; Cambindo Botto, Adrián E; Dujardin, Gwendal; Bastianello, Giulia; Lavore, Stefania; Torres-Méndez, Antonio; Menck, Carlos F M; Blencowe, Benjamin J; Irimia, Manuel; Foiani, Marco; Kornblihtt, Alberto R

    2017-03-21

    We have previously found that UV irradiation promotes RNA polymerase II (RNAPII) hyperphosphorylation and subsequent changes in alternative splicing (AS). We show now that UV-induced DNA damage is not only necessary but sufficient to trigger the AS response and that photolyase-mediated removal of the most abundant class of pyrimidine dimers (PDs) abrogates the global response to UV. We demonstrate that, in keratinocytes, RNAPII is the target, but not a sensor, of the signaling cascade initiated by PDs. The UV effect is enhanced by inhibition of gap-filling DNA synthesis, the last step in the nucleotide excision repair pathway (NER), and reduced by the absence of XPE, the main NER sensor of PDs. The mechanism involves activation of the protein kinase ATR that mediates the UV-induced RNAPII hyperphosphorylation. Our results define the sequence UV-PDs-NER-ATR-RNAPII-AS as a pathway linking DNA damage repair to the control of both RNAPII phosphorylation and AS regulation.

  2. Inhibition of semiconservative DNA synthesis in ICR 2A frog cells by pyrimidine dimers and nondimer photoproducts induced by ultraviolet radiation

    SciTech Connect

    Rosenstein, B.S.

    1984-11-01

    DNA synthesis was examined in ultraviolet (uv)-irradiated ICR 2A frog cells in which either pyrimidine dimers or nondimer photoproducts represented the major class of DNA lesions. In addition, cells were exposed to /sup 60/Co ..gamma.. rays. The cultures were pulse-labeled and the size distribution of the DNA synthesized was estimated using both sucrose gradient sedimentation and alkaline step elution. Using either of these techniques, it was found that the presence of dimers resulted in a reduction principally in the synthesis of high molecular weight (MW) DNA. In contrast, nondimer photoproducts caused a strong inhibition in the synthesis of low MW DNA, as was also observed in ..gamma..-irradiated cells. Hence the induction of pyrimidine dimers in DNA mainly affected the elongation of replicons, whereas nondimer lesions primarily caused an inhibition of replicon initiation.

  3. Fibrillar dimer formation of islet amyloid polypeptides

    NASA Astrophysics Data System (ADS)

    Chiu, Chi-cheng; de Pablo, Juan J.

    2015-09-01

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 - 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 - 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  4. Fibrillar dimer formation of islet amyloid polypeptides

    SciTech Connect

    Chiu, Chi -cheng; de Pablo, Juan J.

    2015-05-08

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  5. Faster DNA Repair of Ultraviolet-Induced Cyclobutane Pyrimidine Dimers and Lower Sensitivity to Apoptosis in Human Corneal Epithelial Cells than in Epidermal Keratinocytes

    PubMed Central

    Mallet, Justin D.; Bastien, Nathalie; Gendron, Sébastien P.; Rochette, Patrick J.

    2016-01-01

    Absorption of UV rays by DNA generates the formation of mutagenic cyclobutane pyrimidine dimers (CPD) and pyrimidine (6–4) pyrimidone photoproducts (6-4PP). These damages are the major cause of skin cancer because in turn, they can lead to signature UV mutations. The eye is exposed to UV light, but the cornea is orders of magnitude less prone to UV-induced cancer. In an attempt to shed light on this paradox, we compared cells of the corneal epithelium and the epidermis for UVB-induced DNA damage frequency, repair and cell death sensitivity. We found similar CPD levels but a 4-time faster UVB-induced CPD, but not 6-4PP, repair and lower UV-induced apoptosis sensitivity in corneal epithelial cells than epidermal. We then investigated levels of DDB2, a UV-induced DNA damage recognition protein mostly impacting CPD repair, XPC, essential for the repair of both CPD and 6-4PP and p53 a protein upstream of the genotoxic stress response. We found more DDB2, XPC and p53 in corneal epithelial cells than in epidermal cells. According to our results analyzing the protein stability of DDB2 and XPC, the higher level of DDB2 and XPC in corneal epithelial cells is most likely due to an increased stability of the protein. Taken together, our results show that corneal epithelial cells have a better efficiency to repair UV-induced mutagenic CPD. On the other hand, they are less prone to UV-induced apoptosis, which could be related to the fact that since the repair is more efficient in the HCEC, the need to eliminate highly damaged cells by apoptosis is reduced. PMID:27611318

  6. Photochemistry of Pyrimidine in Astrophysical Ices: Formation of Nucleobases and Other Prebiotic Species

    NASA Technical Reports Server (NTRS)

    Nuevo, Michel; Sandford, Scott A.; Materese, Christopher K.; Milam, Stefanie N.

    2012-01-01

    Nucleobases are N-heterocycles that are the informational subunits of DNA and RNA. They are divided into two molecular groups: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites, and their extraterrestrial origin confirmed by isotopic measurements. Although no N-heterocycles have ever been observed in the ISM, the positions of the 6.2- m interstellar emission features suggest a population of such molecules is likely to be present. However, laboratory experiments have shown that the ultraviolet (UV) irradiation of pyrimidine in ices of astrophysical relevance such as H2O, NH3, CH3OH, CH4, CO, or combinations of these at low temperature (less than or equal to 20 K) leads to the formation of several pyrimidine derivatives including the nucleobases uracil and cytosine, as well as precursors such as 4(3H)-pyrimidone and 4-aminopyrimidine. Quantum calculations on the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in pure H2O ices are in agreement with their experimental formation pathways.10 In those residues, other species of prebiotic interest such as urea as well as the amino acids glycine and alanine could also be identified. However, only very small amounts of pyrimidine derivatives containing CH3 groups could be detected, suggesting that the addition of methyl groups to pyrimidine is not an efficient process. For this reason, the nucleobase thymine was not observed in any of the samples. In this work, we study the formation of nucleobases and other photo-products of prebiotic interest from the UV irradiation of pyrimidine in ices containing H2O, NH3, CH3OH, and CO, mixed in astrophysical proportions.

  7. Fibrillar dimer formation of islet amyloid polypeptides

    DOE PAGES

    Chiu, Chi -cheng; de Pablo, Juan J.

    2015-05-08

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimentalmore » and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.« less

  8. Detection of distinct α-helical rearrangements of cyclobutane pyrimidine dimer photolyase upon substrate binding by Fourier transform infrared spectroscopy.

    PubMed

    Wijaya, I M Mahaputra; Zhang, Yu; Iwata, Tatsuya; Yamamoto, Junpei; Hitomi, Kenichi; Iwai, Shigenori; Getzoff, Elizabeth D; Kandori, Hideki

    2013-02-12

    Photolyases (PHRs) utilize near-ultraviolet (UV)-blue light to specifically repair the major photoproducts (PPs) of UV-induced damaged DNA. The cyclobutane pyrimidine dimer PHR (CPD-PHR) from Escherichia coli binds flavin adenine dinucleotide (FAD) as a cofactor and 5,10-methenyltetrahydrofolate as a light-harvesting pigment and specifically repairs CPD lesions. By comparison, a second photolyase known as (6-4) PHR, present in a range of higher organisms, uniquely repairs (6-4) PPs. To understand the repair mechanism and the substrate specificity that distinguish CPD-PHR from (6-4) PHR, we applied Fourier transform infrared (FTIR) spectroscopy to bacterial CPD-PHR in the presence or absence of a well-defined DNA substrate, as we have studied previously for vertebrate (6-4) PHR. PHRs show light-induced reduction of FAD, and photorepair by CPD-PHR involves the transfer of an electron from the photoexcited reduced FAD to the damaged DNA for cleaving the dimers to maintain the DNA's integrity. Here, we measured and analyzed difference FTIR spectra for the photoactivation and DNA photorepair processes of CPD-PHR. We identified light-dependent signals only in the presence of substrate. The signals, presumably arising from a protonated carboxylic acid or the DNA substrate, implicate conformational rearrangements of the protein and substrate during the repair process. Deuterium exchange FTIR measurements of CPD-PHR highlight potential differences in the photoactivation and photorepair mechanisms in comparison to those of (6-4) PHR. Although CPD-PHR and (6-4) PHR appear to exhibit similar overall structures, our studies indicate that distinct conformational rearrangements, especially in the α-helices, are initiated within these enzymes upon binding of their respective DNA substrates.

  9. Little or No Repair of Cyclobutyl Pyrimidine Dimers Is Observed in the Organellar Genomes of the Young Arabidopsis Seedling.

    PubMed Central

    Chen, J. J.; Jiang, C. Z.; Britt, A. B.

    1996-01-01

    A Southern-blot-based, site-specific assay for ultraviolet (UV)-induced cyclobutyl pyrimidine dimers (CPDs), employing the CPD-specific enzyme T4 endonuclease V, was used to follow the repair of this lesion in particular DNA sequences in 5- to 6-d-old Arabidopsis thaliana seedlings. CPDs, measured as enzyme-sensitive sites, in nuclear sequences were removed rapidly in the light but were repaired slowly, if at all, in the dark. This result was identical to that obtained in prior analyses of CPDs in total cellular DNA. Assay of representative chloroplast and mitochondrial sequences in the same DNA preparations revealed that, in contrast to nuclear sequences, enzyme-sensitive sites are inefficiently eliminated in both the presence and absence of visible light. These observations suggest that Arabidopsis seedlings possess little or no capacity for the repair of CPDs in the organellar genomes. Given the fact that the UV dose employed only marginally affected the growth of the seedlings, we suggest that Arabidopsis seedlings must possess very efficient mechanism(s) for the tolerance of UV-induced DNA damage. PMID:12226273

  10. Methyl-CpG binding domain protein acts to regulate the repair of cyclobutane pyrimidine dimers on rice DNA

    PubMed Central

    Fang, Changxun; Chen, Weisi; Li, Chengxun; Jian, Xin; Li, Yingzhe; Lin, Hongmei; Lin, Wenxiong

    2016-01-01

    UVB radiation causes cyclobutane pyrimidine dimers (CPDs) to form on the DNA of living organisms. This study found that overexpression of the silicon absorbance gene Lsi1 reduced the accumulation of CPDs in rice, which profited from the reactivation by photolyase. The transcript abundance of deoxyribodipyrimidine photolyase (Os10g0167600) was generally correlated with the silicon content of the rice, and the up-regulation of Os10g0167600 was found to be highest in the UVB-treated Lsi1-overexpressed (Lsi1-OX) rice. A trans-acting factor, methyl-CpG binding domain protein (OsMeCP), was found to interact with the cis-element of Os10g0167600. The nucleic location of OsMeCP effectively enabled the transcriptional regulation. Compared with the WT, the level of OsMeCP was lower in the Lsi1-OX rice but higher in the Lsi1-RNAi line. Rice cultured in a high silicate-concentration solution also exhibited less OsMeCP abundance. Overexpression of OsMeCP led to lower Os10g0167600 transcript levels and a higher CPD content than in the WT, but the reverse was true in the OsMeCP-RNAi line. These findings indicate that OsMeCP acts as a negative regulator of silicon, and can mediate the repression of the transcription from Os10g0167600, which inhibits the photoreactivation of the photolyase involved in the repair of CPDs. PMID:27694845

  11. Chemical modification of the third strand: differential effects on purine and pyrimidine triple helix formation.

    PubMed

    Mills, Martin; Arimondo, Paola B; Lacroix, Laurent; Garestier, Thérèse; Klump, Horst; Mergny, Jean-Louis

    2002-01-08

    DNA triple helices offer exciting perspectives toward oligonucleotide-directed control of gene expression. Oligonucleotide analogues are routinely used with modifications in either the backbone or the bases to form more stable triple-helical structures or to prevent their degradation in cells. In this article, different chemical modifications are tested in a model system, which sets up a competition between the purine and pyrimidine motifs. For most modifications, the DeltaH degrees of purine triplex formation is close to zero, implying a nearly temperature-independent affinity constant. In contrast, the pyrimidine triplex is strongly favored at lower temperatures. The stabilization induced by modifications previously known to be favorable to the pyrimidine motif was quantified. Interestingly, modifications favorable to the GT motif (propynyl-U and dU replacing T) were also discovered. In a system where two third strands compete for triplex formation, replacement of the GA or GT strand by a pyrimidine strand may be observed at neutral pH upon lowering the temperature. This purine-to-pyrimidine triplex conversion depends on the chemical nature of the triplex-forming strands and the stability of the corresponding triplexes.

  12. Selective inhibition by methoxyamine of the apurinic/apyrimidinic endonuclease activity associated with pyrimidine dimer-DNA glycosylases from Micrococcus luteus and bacteriophage T4

    SciTech Connect

    Liuzzi, M.; Weinfeld, M.; Paterson, M.C.

    1987-06-16

    The UV endonucleases from Micrococcus luteus and bacteriophage T4 possess two catalytic activities specific for the site of cyclobutane pyrimidine dimers in UV-irradiated DNA: a DNA glycosylase that cleaves the 5'-glycosyl bond of the dimerized pyrimidines and an apurinic/apyrimidinic (AP) endonuclease that thereupon incises the phosphodiester bond 3' to the resulting apyrimidinic site. The authors have explored the potential use of methoxyamine, a chemical that reacts at neutral pH with AP sites in DNA, as a selective inhibitor of the AP endonuclease activities residing in the M. luteus and T4 enzymes. The presence of 50 mM methoxyamine during incubation of UV-treated, (/sup 3/H)thymine-labeled poly(dA) x poly(dT) with either enzyme preparation was found to protect completely the irradiated copolymer from endonucleolytic attack at dimer sites, as assayed by yield of acid-soluble radioactivity. In contrast, the dimer-DNA glycosylase activity of each enzyme remained fully functional, as monitored retrospectively by release of free thymine after either photochemical-(5 kJ/m/sup 2/, 254 nm) or photoenzymic- (Escherichia coli photolyase plus visible light) induced reversal of pyrimidine dimers in the UV-damaged substrate. The data demonstrate that the inhibition of the strand-incision reaction arises because of chemical modification of the AP sites and is not due to inactivation of the enzyme by methoxyamine. The results, combined with earlier findings for 5'-acting AP endonucleases, strongly suggest that methoxyamine is a highly specific inhibitor of virtually all AP endonucleases, irrespective of their modes of action, and may therefore prove useful in a wide variety of DNA repair studies.

  13. Inhibition of RNA and DNA synthesis in UV-irradiated normal human fibroblasts is correlated with pyrimidine (6-4) pyrimidone photoproduct formation.

    PubMed

    Petit Frère, C; Clingen, P H; Arlett, C F; Green, M H

    1996-07-05

    UV-irradiation of living cells results in an inhibition of RNA and DNA synthesis. The purpose of this study was to determine whether specific photoproducts or the total combined yield of lesions were responsible for these effects. Asynchronously dividing human fibroblasts from normal donors were irradiated with UVC (254 nm), broad spectrum UVB (290-320 + nm, Westinghouse FS20 lamp) or narrow spectrum UVB (310-315 nm, Philips TL01 lamp) at fluences which induce known yields of cyclobutane pyrimidine dimers, pyrimidine (6-4) pyrimidone photoproducts or Dewar isomers. DNA synthesis was approximately 3-4 times more sensitive to both UVC and UVB irradiation than RNA synthesis. The immediate inhibition of RNA and DNA synthesis was correlated with (6-4) rather than overall photoproduct formation suggesting that the (6-4) photoproduct is the mediator of these inhibitory effects. In support of this suggestion we found that photoreactivation of cells cultured from the marsupial, mouse Sminthopsis crassicaudata, resulted in removal of 70% of pyrimidine dimers from the overall genome, but had only a slight effect on the recovery of RNA synthesis.

  14. Assessment of cyclobutane pyrimidine dimers by digital photography in human skin.

    PubMed

    ten Berge, Onno; van Velsen, Sara G A; Giovannone, Barbara; Bruijnzeel-Koomen, Carla A F M; Knol, Edward F; Guikers, Kees; van Weelden, Huib

    2011-10-28

    UV-mediated DNA damage and repair are important mechanisms in research on UV-induced carcinogenesis. UV-induced DNA-damage and repair can be determined by immunohistochemical staining of photoproduct positive nuclei of keratinocytes in the epidermis. We developed a new method of analysing and quantifying thymine dimer (TT-CPD) positive cells in the epidermis. Normal skin of healthy controls was exposed to UVB ex vivo and in vivo. Skin samples were immunohistochemically stained for TT-CPDs. Digital images of the epidermis were quantified for TT-CPDs both visually and digitally. There was a UVB-dose dependent induction of TT-CPDs present in the ex vivo UVB-irradiated skin samples. The linear measurement range of the digital quantification was increased compared to the manual counting. The average 24-hour repair rate of the initiated TT-CPDs elicited by the UVB irradiation at T=0 of the 8 HCs showed a 34% decrease of TT-CPD photoproducts by the manual counting method and a 51% decrease determined by digital counting. The digital quantification method improves immunohistochemical quantification of DNA photo damage. It is more sensitive in measuring the extent of DNA-damage per nucleus.

  15. Quantitation of radiation-, chemical-, or enzyme-induced single strand breaks in nonradioactive DNA by alkaline gel electrophoresis: application to pyrimidine dimers

    SciTech Connect

    Freeman, S.E.; Blackett, A.D.; Monteleone, D.C.; Setlow, R.B.; Sutherland, B.M.; Sutherland, J.C.

    1986-10-01

    The authors have developed an alkaline agarose gel method for quantitating single strand breaks in nanogram quantities of nonradioactive DNA. After electrophoresis together with molecular length standards, the DNA is neutralized, stained with ethidium bromide, photographed, and the density profiles recorded with a computer controller scanner. The medium lengths, number average molecular lengths, and length average molecular lengths of the DNAs can be computed by using the mobilities of the molecular length standards. The frequency of single strand breaks can then be determined by comparison of the corresponding average molecular lengths of DNAs treated and not treated with single stand break-inducing agents (radiation, chemicals, or lesion-specific endonuclease). Single stand break yields (induced at pyrimidine dimer sites in uv-irradiated human fibroblasts DNA by the dimer-specific endonuclease from Micrococcus luteus) from our method agree with values obtained for the same DNAs from alkaline sucrose gradient analysis. The method has been used to determined pyrimidine dimer yields in DNA from biopsies of human skin irradiated in situ. It will be especially useful in determining the frequency of single strand breaks (or lesions convertible to single stand breaks by specific cleaving reagents or enzymes) in small quantities of DNA from cells or tissues not amendable to radioactive labeling.

  16. Formation of cyclobutane thymine dimers photosensitized by pyridopsoralens: Quantitative and qualitative distribution within DNA

    SciTech Connect

    Moysan, A.; Viari, A.; Vigny, P. ); Voituriez, L.; Cadet J. ); Moustacchi, E.; Sage, E. )

    1991-07-23

    As after irradiation with 254-nm UV light, exposure of thymidine and three isomeric pyridopsoralen derivatives to UVA radiation, in the dry state, leads to the formation of the six diastereomers of cyclobutadithymidine as the predominant reaction. This unexpected photosensitized reaction, which also gives rise to both 5R* and 5S* diastereomers of 5,6-dihydro-5-({alpha}-thymidylyl)thymidine (or spore photoproduct), is selective since (2+2) dimerization of 2{prime}-deoxycytidine was not detected under the same experimental conditions. The cis-syn isomer of cyclobutadithymine was also found to be produced within isolated DNA following UVA irradiation in aqueous solutions containing 7-methylpyrido (3,4-c)psoralen. Quantitatively, this photoproduct represents about one-fifth of the overall yield of the furan-side pyridopsoralen (2+2) photocycloadducts the thymine. DNA sequencing methodology was used to demonstrate that pyridopsoralen-photosensitized DNA is a substrate for T4 endonuclease V and Escherichia coli photoreactivating enzyme, two enzymes acting specifically on cyclobutane pyrimidine dimers. The formation of cyclobutane thymine dimers concomitant to that of thymine-furocoumarin photoadducts and their eventual implication in the photobiological effects of the pyridopsoralens are discussed.

  17. Formation of Nucleobases from the UV Irradiation of Pyrimidine in Astrophysical Ice Analogs

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.; Nuevo, Michel; Materese, Christopher K.

    2014-01-01

    Nucleobases are the informational subunits of DNA and RNA. They consist of Nheterocycles that belong to either the pyrimidine-base group (uracil, cytosine, and thymine) or the purinebase group (adenine and guanine). Several nucleobases, mostly purine bases, have been detected in meteorites [1-3], with isotopic signatures consistent with an extraterrestrial origin [4]. Uracil is the only pyrimidine-base compound formally reported in meteorites [2], though the presence of cytosine cannot be ruled out [5,6]. However, the actual process by which the uracil was made and the reasons for the non-detection of thymine in meteorites have yet to be fully explained. Although no N-heterocycles have ever been observed in the ISM [7,8], the positions of the 6.2-µm interstellar emission features suggest a population of such molecules is likely to be present [9]. In this work we study the formation of pyrimidine-based molecules, including the three nucleobases uracil, cytosine, and thymine from the ultraviolet (UV) irradiation of pyrimidine in ices consisting of several combinations of H(sub2)O, NH(sub3), CH(sub3)OH, and CH(sub4) at low temperature, in order to simulate the astrophysical conditions under which prebiotic species may be formed in the interstellar medium, in the protosolar nebula, and on icy bodies of the Solar System.

  18. Self-assembling of cytosine nucleoside into triply-bound dimers in acid media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations.

    PubMed

    Armentano, Donatella; De Munno, Giovanni; Di Donna, Leonardo; Sindona, Giovanni; Giorgi, Gianluca; Salvini, Laura; Napoli, Anna

    2004-02-01

    Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.

  19. 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.; Wu, R.; Ip, W.-H.

    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.

  20. The Role of Pyrimidine Dimers as Premutagenic Lesions: A Study of Targeted VS. Untargeted Mutagenesis in the lacI Gene of ESCHERICHIA COLI

    PubMed Central

    Kunz, Bernard A.; Glickman, Barry W.

    1984-01-01

    We have employed conjugal transfer of an F' lac episome to examine targeted and untargeted mutagenesis in the lacI gene of Escherichia coli and to determine the relative importance of pyrimidine dimers as premutational UV lesions compared to (6-4) photoproducts that also may have a mutational role. This conjugal system allowed us to assess the premutagenic role of UV lesions independently from any role as inducers of SOS functions. F' DNA was transferred to an SOS-induced recipient strain from: unirradiated donor cells, UV-treated donor cells or donor cells that were irradiated and then exposed to photoreactivating light. The results indicate that SOS-related, untargeted events may account for as much as one-third of the nonsense mutations (i.e., base substitutions) recovered after undamaged F' DNA is transferred to UV-irradiated recipients. When the donor strain also is irradiated, in excess of 90% of the mutations detected following conjugation appear to be targeted. Photoreactivation of the UV-treated donor cells, prior to F' transfer to the SOS-induced recipient strain, demonstrated that in this experimental system virtually all recovered UV-induced mutations are targeted by photoreactivable lesions. We presume that these lesions are pyrimidine dimers because (6-4) photoproducts are not photoreactivable. PMID:6368314

  1. Fully functional global genome repair of (6-4) photoproducts and compromised transcription-coupled repair of cyclobutane pyrimidine dimers in condensed mitotic chromatin.

    PubMed

    Komura, Jun-ichiro; Ikehata, Hironobu; Mori, Toshio; Ono, Tetsuya

    2012-03-10

    During mitosis, chromatin is highly condensed, and activities such as transcription and semiconservative replication do not occur. Consequently, the condensed condition of mitotic chromatin is assumed to inhibit DNA metabolism by impeding the access of DNA-transacting proteins. However, about 40 years ago, several researchers observed unscheduled DNA synthesis in UV-irradiated mitotic chromosomes, suggesting the presence of excision repair. We re-examined this subject by directly measuring the removal of UV-induced DNA lesions by an ELISA and by a Southern-based technique in HeLa cells arrested at mitosis. We observed that the removal of (6-4) photoproducts from the overall genome in mitotic cells was as efficient as in interphase cells. This suggests that global genome repair of (6-4) photoproducts is fully functional during mitosis, and that the DNA in mitotic chromatin is accessible to proteins involved in this mode of DNA repair. Nevertheless, not all modes of DNA repair seem fully functional during mitosis. We also observed that the removal of cyclobutane pyrimidine dimers from the dihydrofolate reductase and c-MYC genes in mitotic cells was very slow. This suggests that transcription-coupled repair of cyclobutane pyrimidine dimers is compromised or non-functional during mitosis, which is probably the consequence of mitotic transcriptional repression.

  2. Formation of Nucleobases from the UV Irradiation of Pyrimidine in Interstellar Ice Analogs

    NASA Technical Reports Server (NTRS)

    Milam, Stefanie N.; Nuevo, Michel; Sandford, Scott A.; Elsila, Jamie E.; Dworkin, Jason P.

    2010-01-01

    Previous laboratory simulations showed that complex molecules, including prebiotic compounds/can be formed under interstellar conditions from the vacuum UV irradiation of interstellar ice analogs containing H2O, CO, NH3 etc. Although some complex prebiotic species have not been confirmed In the interstellar medium, they are known to be present in meteorites. Nucleobases, the building blocks of DNA and RNA, have also been detected in meteorites. Here, we present a study of the formation of pyrimidine-based compounds from the UV irradiation of pyrimidine in H2O- and/or NH3-ices at 20-30 K, Our results show that various derivatives, induding the nucleobases uracil and cytosine, are formed under these conditions.

  3. DLTS study of the oxygen dimer formation kinetics in silicon

    NASA Astrophysics Data System (ADS)

    Yarykin, Nikolai; Weber, Jörg

    2009-12-01

    The introduction rates of radiation defects, in particular the X- and M-centers for which the oxygen dimer is a precursor, are investigated as a function of duration of the pre-irradiation heat treatment at 480∘ C in Czochralski-grown silicon both of n- and p-types. The characteristic annealing time to grow the X-center concentration in the n-type crystal is found to be about 1 h in accordance with the model which implies no significant barrier for the dimer formation. The M-center concentration in the p-type crystal is found to be nearly independent of duration of the pre-irradiation annealing after a few minutes transient period. This behavior is ascribed to the stabilization of dimer concentration due to an effective dimer trapping in these samples.

  4. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair.

    PubMed

    Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

    2014-10-03

    The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  5. Fully functional global genome repair of (6-4) photoproducts and compromised transcription-coupled repair of cyclobutane pyrimidine dimers in condensed mitotic chromatin

    SciTech Connect

    Komura, Jun-ichiro; Ikehata, Hironobu; Mori, Toshio; Ono, Tetsuya

    2012-03-10

    During mitosis, chromatin is highly condensed, and activities such as transcription and semiconservative replication do not occur. Consequently, the condensed condition of mitotic chromatin is assumed to inhibit DNA metabolism by impeding the access of DNA-transacting proteins. However, about 40 years ago, several researchers observed unscheduled DNA synthesis in UV-irradiated mitotic chromosomes, suggesting the presence of excision repair. We re-examined this subject by directly measuring the removal of UV-induced DNA lesions by an ELISA and by a Southern-based technique in HeLa cells arrested at mitosis. We observed that the removal of (6-4) photoproducts from the overall genome in mitotic cells was as efficient as in interphase cells. This suggests that global genome repair of (6-4) photoproducts is fully functional during mitosis, and that the DNA in mitotic chromatin is accessible to proteins involved in this mode of DNA repair. Nevertheless, not all modes of DNA repair seem fully functional during mitosis. We also observed that the removal of cyclobutane pyrimidine dimers from the dihydrofolate reductase and c-MYC genes in mitotic cells was very slow. This suggests that transcription-coupled repair of cyclobutane pyrimidine dimers is compromised or non-functional during mitosis, which is probably the consequence of mitotic transcriptional repression. -- Highlights: Black-Right-Pointing-Pointer Global genome repair of (6-4) photoproducts is fully active in mitotic cells. Black-Right-Pointing-Pointer DNA in condensed mitotic chromatin does not seem inaccessible or inert. Black-Right-Pointing-Pointer Mitotic transcriptional repression may impair transcription-coupled repair.

  6. Enzymatic analysis of isomeric trithymidylates containing ultraviolet light-induced cyclobutane pyrimidine dimers. I. Nuclease P1-mediated hydrolysis of the intradimer phosphodiester linkage

    SciTech Connect

    Liuzzi, M.; Weinfeld, M.; Paterson, M.C.

    1989-04-15

    Our recent findings suggest that enzymatic hydrolysis of the intradimer phosphodiester bond may constitute the initial step in the repair of UV light-induced cyclobutane pyrimidine dimers in human cells. To examine the susceptibility of this phosphodiester linkage to enzyme-mediated hydrolysis, the trinucleotide d-Tp-TpT was UV-irradiated and the two isomeric compounds containing a cis-syn-cyclobutane dimer were isolated by high performance liquid chromatography and treated with various deoxyribonucleases. Snake venom phosphodiesterase hydrolyzed only the 3'-phosphodiester group in the 5'-isomer (d-T less than p greater than TpT) but was totally inactive toward the 3'-isomer (d-TpT less than p greater than T). In contrast, calf spleen phosphodiesterase only operated on the 3'-isomer by cleaving the 5'-internucleotide bond. Kinetic analysis revealed that (i) the activity of snake venom phosphodiesterase was unaffected by a dimer 5' to a phosphodiester linkage, (ii) the action of calf spleen phosphodiesterase was partially inhibited by a dimer 3' to a phosphodiester bond, and (iii) Escherichia coli phr B-encoded DNA photolyase reacted twice as fast with d-T less than p greater than TpT as with d-TpT less than p greater than T. Mung bean nuclease, nuclease S1, and nuclease P1 all cleaved the 5'-internucleotide linkage, but not the intradimer phosphodiester bond, in d-TpT less than p greater than T. Both phosphate groups in d-T less than p greater than TpT were refractory to mung bean nuclease or nuclease S1. Incubation of d-T less than p greater than TpT with nuclease P1, however, generated the novel compound dT less than greater than d-pTpT containing a severed intradimer phosphodiester linkage. Accordingly, nuclease P1 represents the first purified enzyme known to hydrolyze an intradimer phosphodiester linkage.

  7. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair

    SciTech Connect

    Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

    2014-10-03

    Highlights: • ATM phosphorylates the opposite strand of the dimer in response to DNA damage. • The PETPVFRLT box of ATM plays a key role in its dimer dissociation in DNA repair. • The dephosphorylation of ATM is critical for dimer re-formation after DNA repair. - Abstract: The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  8. Resistance of the genome of Escherichia coli and Listeria monocytogenes to irradiation evaluated by the induction of cyclobutane pyrimidine dimers and 6-4 photoproducts using gamma and UV-C radiations

    NASA Astrophysics Data System (ADS)

    Beauchamp, S.; Lacroix, M.

    2012-08-01

    The effect of gamma and UV-C irradiation on the production of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4 PPs) in DNA was investigated to compare the natural resistance of the genome of a Gram-positive bacterium and a Gram-negative bacterium against irradiation. Solution of pure DNA and bacterial strains Listeria monocytogenes and Escherichia coli were irradiated using gamma and UV-C rays. Extracted DNA from bacteria and pure DNA samples were then analysed by ELISA using anti-CPDs and anti-6-4 PPs monoclonal antibodies. The results show that gamma rays, as well as UV-C rays, induce the formation of CPDs and 6-4 PPs in DNA. During UV-C irradiation, the three samples showed a difference in their sensitivity against formation of CPDs (P≤0.05). Pure DNA was the most sensitive while the genome of L. monocytogenes was the most resistant. Also during UV-C irradiation, the genome of L. monocytogenes was the only one to show a significant resistance against formation of 6-4 PPs (P≤0.05). During gamma irradiation, for both types of lesion, pure DNA and the genome of E. coli did not show significant difference in their sensitivity (P>0.05) while the genome of L. monocytogenes showed a resistance against formation of CPDs and 6-4 PPs.

  9. Formation of Nucleobases from the UV Photo-Irradiation of Pyrimidine in Astrophysical Ice Analogs

    NASA Technical Reports Server (NTRS)

    Milam, S. N.; Nuevo, M.; Sandford, S. A.; Elsila, J. E.; Dworkin, J. P.

    2010-01-01

    Astrochemistry laboratory simulations have shown that complex organic molecules including compounds of astrobiological interest can be formed under interstellarl/circumstellar conditions from the vacuum UV irradiation of astrophysical ice analogs containing H2O, CO, CO2, CH3OH, NH13, etc. Of all prebiotic compounds, the formation of amino acids under such experimental conditions has been the most extensively studied. Although the presence of amino acids in the interstellar medium (ISM) has yet to be confirmed, they have been detected in meteorites, indicating that biomolecules and/or their precursors can be formed under extraterrestrial, abiotic conditions. Nucleobases, the building blocks of DNA and RNA, as well as other 1V-heterocycles, have also been detected in meteorites, but like amino acids, they have yet to be observed in the ISM. In this work, we present an experimental study of the formation of pyrimidine-based compounds from the UV photo-irradiation of pyrimidine in ice mixtures containing H2O, NH3, and/or CH3OH at low temperature and pressure.

  10. Excited State Pathways Leading to Formation of Adenine Dimers.

    PubMed

    Banyasz, Akos; Martinez-Fernandez, Lara; Ketola, Tiia-Maaria; Muñoz-Losa, Aurora; Esposito, Luciana; Markovitsi, Dimitra; Improta, Roberto

    2016-06-02

    The reaction intermediate in the path leading to UV-induced formation of adenine dimers A═A and AA* is identified for the first time quantum mechanically, using PCM/TD-DFT calculations on (dA)2 (dA: 2'deoxyadenosine). In parallel, its fingerprint is detected in the absorption spectra recorded on the millisecond time-scale for the single strand (dA)20 (dA: 2'deoxyadenosine).

  11. A Cyclic Disilylated Stannylene: Synthesis, Dimerization, and Adduct Formation

    PubMed Central

    2011-01-01

    Reaction of 1,4-dipotassio-1,1,4,4-tetrakis(trimethylsilyl)tetramethyltetrasilane with [(Me3Si)2N]2Sn led to the formation of an endocyclic distannene via the dimerization of a transient stannylene. In the presence of strong donor molecules such as PEt3, the stannylene could be trapped as adduct. Reaction of the PEt3 derivative with B(C6F5)3 gave rise to the formation of the stannylene B(C6F5)3 adduct. PMID:21438553

  12. Immunological detection of UV induced cyclobutane pyrimidine dimers and (6-4) photoproducts in DNA from reference bacteria and natural aquatic populations.

    PubMed

    Kraft, Stephanie; Stephanie, Kraft; Obst, Ursula; Ursula, Obst; Schwartz, Thomas; Thomas, Schwartz

    2011-03-01

    UV light-caused DNA damage is a widespread field of study. As UV light has the biological effect of inactivating or killing bacteria, it is used for water disinfection. Due to this application, it is important to study the DNA damage efficiencies and regeneration capacities in bacteria after UV irradiation. Two monoclonal antibodies, anti-CPD and anti-(6-4) PP, were applied for an immunoassay of UV-induced DNA modifications. Cyclobutane pyrimidine dimer (CPD) and 6-4 photoproduct (6-4 PP) were detected in the reference bacteria Pseudomonas aeruginosa and Enterococcus faecium, and in natural water communities. The antibody-mediated detection signals increased with the UV doses from 100-400J/m(2). Here, the CPD-specific signals were stronger than the (6-4) PP-specific signals. These immunological results were in accordance with parallel cultivation experiments. All UV-irradiated bacteria showed a reduction of their growth rate depending on UV application by several orders of magnitudes. The immunoassay was also applied to three types of natural aquatic habitats with different cell densities. Besides artificial UV irradiation, it was possible to visualize natural sunlight effects on these natural bacterial communities. Light-dependent and dark repair processes were distinguished using the established immunological assays. The antibody-mediated analyses presented are fast methods to detect UV-induced DNA lesions and repair capacities in selected bacterial species as well as in entire natural mixed populations.

  13. Probing mechanism of α-formylketene dithioacetal towards the facile formation of functionalized pyrimidines: A structural approach

    NASA Astrophysics Data System (ADS)

    Joy, Monu; Adeniyi, Adebayo A.; Mathews, Annie; Mathew, Bijo; Prasanth, S.; Soliman, Mohmoud E. S.; Malayan, Jalaja J.; Anabha, E. R.

    2017-01-01

    α-Formylketene dithioacetal is an active precursor for the synthesis of a variety of organic compounds including pyrimidines and its functionalized materials. The present study deals with the structural versatility of a solid representative compound from the family of α-formylketene dithioacetal to the formation of functionalized pyrimidines derivatives through experimental as well as theoretical methods. 2-(3,4-dimethoxybenzoyl)-3,3-bis(methylsulfanyl)prop-2-enal, the representative compound was synthesized with a reported protocol and characterized through spectral methods. The complete three dimensional solid state structural studies were carried out utilizing single crystal X-ray crystallographic technique along with theoretical methods like classical and accelerated molecular dynamics simulation. Various quantum chemical parameters were also discussed to reveals the complete molecular geometry and reactivity of designated compound.

  14. Ultraviolet Irradiation of Pyrimidine in Interstellar Ice Analogs: Formation and Photo-Stability of Nucleobases

    NASA Technical Reports Server (NTRS)

    Nuevo, Michel; Milam, Stefanie N.; Sandford, Scott A.; Elsila, Jamie E.; Dworkin, Jason P.

    2010-01-01

    Astrochemistry laboratory experiments recently showed that molecules of prebiotic interest can potentially form in space, as supported by the detection of amino acids in organic residues formed by the UV photolysis of ices simulating interstellar and cometary environments (H2O, CO, CO2, CH3OH, NH3, etc.). Although the presence of amino acids in the interstellar medium (ISM) is still under debate, experiments and the detection of amino acids in meteorites both support a scenario in which prebiotic molecules could be of extraterrestrial origin, before they are delivered to planets by comets, asteroids, and interplanetary dust particles. Nucleobases, the informational subunits of DNA and RNA, have also been detected in meteorites, although they have not yet been observed in the ISM. Thus, these molecules constitute another family of prebiotic compounds that can possibly form via abiotical processes in astrophysical environments. Nucleobases are nitrogen-bearing cyclic aromatic species with various functional groups attached, which are divided into two classes: pyrimidines (uracil, cytosine, and thymine) and purines (adenine and guanine). In this work, we study how UV irradiation affects pyrimidine mixed in interstellar ice analogs (H2O, NH3, CH3OH). In particular, we show that the UV irradiation of H2O:pyrimidine mixtures leads to the production of oxidized compounds including uracil, and show that both uracil and cytosine are formed upon irradiation of H2O:NH3:pyrimidine mixtures. We also study the photostability of pyrimidine and its photoproducts formed during these experiments.

  15. Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation

    NASA Astrophysics Data System (ADS)

    Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W.; Lin, Jialing; Li, Jianing

    2016-07-01

    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation.

  16. The reaction of the acrylonitrile ion CH 2dbnd CH-C tbnd N rad + with HCN: Proton-transport catalysis vs formation of ionized pyrimidine

    NASA Astrophysics Data System (ADS)

    Ervasti, Henri K.; Jobst, Karl J.; Gerbaux, Pascal; Burgers, Peter C.; Ruttink, Paul J. A.; Terlouw, Johan K.

    2009-11-01

    The CBS-QB3 model chemistry predicts that the title ion-molecule reaction, of potential interest in astrochemistry, yields a stable head-to-tail dimer, [HC dbnd N-CH 2C(H)C tbnd N] rad + ( D1). Cyclization of D1 into ionized pyrimidine seems possible, but the initiating 1,2-H shift is close in energy to back-dissociation into CH 2dbnd C(H)CN rad + ( AN) + HCN. Less energy demanding is formation of the H-bridged isomers [CH 2dbnd C(CN)H--N tbnd CH] rad + and [HC tbnd N--HC(H) dbnd C(H)CN] rad +, whose HCN component may catalyze isomerization of AN into CH 2dbnd C dbnd C dbnd NH rad + ( AN1) and CH dbnd C(H)C dbnd NH rad + ( AN2) respectively. Tandem mass spectrometry based experiments using 15N/ 13C labelling show that cyclization of D1 does not occur and that AN1 is the predominant reaction product instead.

  17. Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis.

    PubMed

    Desmarais, Samantha M; Leitner, Thomas; Barron, Annelise E

    2012-02-01

    DNA barcodes are short, unique ssDNA primers that "mark" individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 base-pairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive base-pairs formed, yet non-consecutive base-pairs did not create stable dimers even when 20 out of 30 possible base-pairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation.

  18. Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile

    NASA Astrophysics Data System (ADS)

    Hamid, Ahmed M.; Sharma, Pramod; Samy El-Shall, M.; Hilal, Rifaat; Elroby, Shaaban; Aziz, Saadullah G.; Alyoubi, Abdulrahman O.

    2013-08-01

    Equilibrium thermochemical measurements using an ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise hydration of the biologically significant ions pyrimidine radical cation and protonated pyrimidine. The binding energy of the hydrated pyrimidine radical cation is weaker than that of the proton-bound dimer pyrimidineH+(H2O) consistent with the formation of a weak carbon-based CHδ+..OH2 hydrogen bond (11.9 kcal/mol) and a stronger NH+..OH2 hydrogen bond (15.6 kcal/mol), respectively. Other proton-bound dimers such as pyrimidineH+(CH3OH) and pyrimidineH+(CH3CN) exhibit higher binding energies (18.2 kcal/mol and 22.8 kcal/mol, respectively) due to the higher proton affinities and dipole moments of acetonitrile and methanol as compared to water. The measured collisional cross sections of the proton-bound dimers provide experimental-based support for the DFT calculated structures at the M06-2x/6-311++G (d,p) level. The calculations show that the hydrated pyrimidine radical cation clusters form internally solvated structures in which the water molecules are bonded to the C4N2H4•+ ion by weak CHδ+..OH2 hydrogen bonds. The hydrated protonated pyrimidine clusters form externally solvated structures where the water molecules are bonded to each other and the ion is external to the water cluster. Dissociative proton transfer reactions C4N2H4•+(H2O)n-1 + H2O → C4N2H3• + (H2O)nH+ and C4N2H5+(H2O)n-1 + H2O → C4N2H4 + (H2O)nH+ are observed for n ≥ 4 where the reactions become thermoneutral or exothermic. The absence of the dissociative proton transfer reaction within the C4N2H5+(CH3CN)n clusters results from the inability of acetonitrile molecules to form extended hydrogen bonding structures such as those formed by water and methanol due to the presence of the methyl groups which block the extension of hydrogen bonding networks.

  19. Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile.

    PubMed

    Hamid, Ahmed M; Sharma, Pramod; El-Shall, M Samy; Hilal, Rifaat; Elroby, Shaaban; Aziz, Saadullah G; Alyoubi, Abdulrahman O

    2013-08-28

    Equilibrium thermochemical measurements using an ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise hydration of the biologically significant ions pyrimidine radical cation and protonated pyrimidine. The binding energy of the hydrated pyrimidine radical cation is weaker than that of the proton-bound dimer pyrimidineH(+)(H2O) consistent with the formation of a weak carbon-based CH(δ+)··OH2 hydrogen bond (11.9 kcal/mol) and a stronger NH(+)··OH2 hydrogen bond (15.6 kcal/mol), respectively. Other proton-bound dimers such as pyrimidineH(+)(CH3OH) and pyrimidineH(+)(CH3CN) exhibit higher binding energies (18.2 kcal/mol and 22.8 kcal/mol, respectively) due to the higher proton affinities and dipole moments of acetonitrile and methanol as compared to water. The measured collisional cross sections of the proton-bound dimers provide experimental-based support for the DFT calculated structures at the M06-2x/6-311++G (d,p) level. The calculations show that the hydrated pyrimidine radical cation clusters form internally solvated structures in which the water molecules are bonded to the C4N2H4(●+) ion by weak CH(δ+)··OH2 hydrogen bonds. The hydrated protonated pyrimidine clusters form externally solvated structures where the water molecules are bonded to each other and the ion is external to the water cluster. Dissociative proton transfer reactions C4N2H4(●+)(H2O)(n-1) + H2O → C4N2H3(●) + (H2O)(n)H(+) and C4N2H5(+)(H2O)(n-1) + H2O → C4N2H4 + (H2O)(n)H(+) are observed for n ≥ 4 where the reactions become thermoneutral or exothermic. The absence of the dissociative proton transfer reaction within the C4N2H5(+)(CH3CN)n clusters results from the inability of acetonitrile molecules to form extended hydrogen bonding structures such as those formed by water and methanol due to the presence of the methyl groups which block the extension of hydrogen bonding networks.

  20. Formation of Enhanced Uniform Chiral Fields in Symmetric Dimer Nanostructures

    NASA Astrophysics Data System (ADS)

    Tian, Xiaorui; Fang, Yurui; Sun, Mengtao

    2015-12-01

    Chiral fields with large optical chirality are very important in chiral molecules analysis, sensing and other measurements. Plasmonic nanostructures have been proposed to realize such super chiral fields for enhancing weak chiral signals. However, most of them cannot provide uniform chiral near-fields close to the structures, which makes these nanostructures not so efficient for applications. Plasmonic helical nanostructures and blocked squares have been proved to provide uniform chiral near-fields, but structure fabrication is a challenge. In this paper, we show that very simple plasmonic dimer structures can provide uniform chiral fields in the gaps with large enhancement of both near electric fields and chiral fields under linearly polarized light illumination with polarization off the dimer axis at dipole resonance. An analytical dipole model is utilized to explain this behavior theoretically. 30 times of volume averaged chiral field enhancement is gotten in the whole gap. Chiral fields with opposite handedness can be obtained simply by changing the polarization to the other side of the dimer axis. It is especially useful in Raman optical activity measurement and chiral sensing of small quantity of chiral molecule.

  1. Formation of Enhanced Uniform Chiral Fields in Symmetric Dimer Nanostructures

    PubMed Central

    Tian, Xiaorui; Fang, Yurui; Sun, Mengtao

    2015-01-01

    Chiral fields with large optical chirality are very important in chiral molecules analysis, sensing and other measurements. Plasmonic nanostructures have been proposed to realize such super chiral fields for enhancing weak chiral signals. However, most of them cannot provide uniform chiral near-fields close to the structures, which makes these nanostructures not so efficient for applications. Plasmonic helical nanostructures and blocked squares have been proved to provide uniform chiral near-fields, but structure fabrication is a challenge. In this paper, we show that very simple plasmonic dimer structures can provide uniform chiral fields in the gaps with large enhancement of both near electric fields and chiral fields under linearly polarized light illumination with polarization off the dimer axis at dipole resonance. An analytical dipole model is utilized to explain this behavior theoretically. 30 times of volume averaged chiral field enhancement is gotten in the whole gap. Chiral fields with opposite handedness can be obtained simply by changing the polarization to the other side of the dimer axis. It is especially useful in Raman optical activity measurement and chiral sensing of small quantity of chiral molecule. PMID:26621558

  2. Formation of Enhanced Uniform Chiral Fields in Symmetric Dimer Nanostructures.

    PubMed

    Tian, Xiaorui; Fang, Yurui; Sun, Mengtao

    2015-12-01

    Chiral fields with large optical chirality are very important in chiral molecules analysis, sensing and other measurements. Plasmonic nanostructures have been proposed to realize such super chiral fields for enhancing weak chiral signals. However, most of them cannot provide uniform chiral near-fields close to the structures, which makes these nanostructures not so efficient for applications. Plasmonic helical nanostructures and blocked squares have been proved to provide uniform chiral near-fields, but structure fabrication is a challenge. In this paper, we show that very simple plasmonic dimer structures can provide uniform chiral fields in the gaps with large enhancement of both near electric fields and chiral fields under linearly polarized light illumination with polarization off the dimer axis at dipole resonance. An analytical dipole model is utilized to explain this behavior theoretically. 30 times of volume averaged chiral field enhancement is gotten in the whole gap. Chiral fields with opposite handedness can be obtained simply by changing the polarization to the other side of the dimer axis. It is especially useful in Raman optical activity measurement and chiral sensing of small quantity of chiral molecule.

  3. Observation of covalent and electrostatic bonds in nitrogen-containing polycyclic ions formed by gas phase reactions of the benzene radical cation with pyrimidine.

    PubMed

    Attah, Isaac Kwame; Soliman, Abdel-Rahman; Platt, Sean P; Meot-Ner Mautner, Michael; Aziz, Saaudallah G; Samy El-Shall, M

    2017-03-01

    Polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic nitrogen heterocyclics (PANHs) are present in ionizing environments, including interstellar clouds and solar nebulae, where their ions can interact with neutral PAH and PANH molecules leading to the formation of a variety of complex organics including large N-containing ions. Herein, we report on the formation of a covalently-bonded (benzene·pyrimidine) radical cation dimer by the gas phase reaction of pyrimidine with the benzene radical cation at room temperature using the mass-selected ion mobility technique. No ligand exchange reactions with benzene and pyrimidine are observed indicating that the binding energy of the (benzene·pyrimidine)˙(+) adduct is significantly higher than both the benzene dimer cation and the proton-bound pyrimidine dimer. The (benzene·pyrimidine)˙(+) adduct shows thermal stability up to 541 K. Thermal dissociation of the (C6D6·C4H4N2)˙(+) adduct at temperatures higher than 500 K produces C4H4N2D(+) (m/z 82) suggesting the transfer of a D atom from the C6D6 moiety to the C4H4N2 moiety before the dissociation of the adduct. Mass-selected ion mobility of the (benzene·pyrimidine)˙(+) dimer reveals the presence of two families of isomers formed by electron impact ionization of the neutral (benzene·pyrimidine) dimer. The slower mobility peak corresponds to a non-covalent family of isomers with larger collision cross sections (76.0 ± 1.8 Å(2)) and the faster peak is consistent with a family of covalent isomers with more compact structures and smaller collision cross sections (67.7 ± 2.2 Å(2)). The mobility measurements at 509 K show only one peak corresponding to the family of stable covalently bonded isomers characterized by smaller collision cross sections (66.9 ± 1.9 Å(2) at 509 K). DFT calculations at the M06-2X/6-311++G** level show that the most stable (benzene·pyrimidine)˙(+) isomer forms a covalent C-N bond with a binding energy of 49.7 kcal mol(-1) and a

  4. Aggregation of Kanamycin A: dimer formation with physiological cations.

    PubMed

    Dieterich, Johannes M; Gerstel, Ulrich; Schröder, Jens-Michael; Hartke, Bernd

    2011-12-01

    Global cluster geometry optimization has focused so far on clusters of atoms or of compact molecules. We are demonstrating here that present-day techniques also allow to globally optimize clusters of extended, flexible molecules, and that such studies have immediate relevance to experiment. For example, recent experimental findings point to production of larger clusters of an aminoglycoside closely related to Kanamycin A (KA), together with certain preferred physiological cations, by Pseudomonas aeruginosa. The present study provides first theoretical support for KA clustering, with a close examination of the monomer, the bare dimer, and dimers with sodium and potassium cations, employing global cluster structure optimization, in conjunction with force fields, semiempirical methods, DFT and ab-initio approaches. Interestingly, already at this stage the theoretical findings support the experimental observation that sodium cations are preferred over potassium cations in KA clusters, due to fundamentally different cationic embedding. Theoretically predicted NMR and IR spectra for these species indicate that it should be possible to experimentally detect the aggregation state and even the cationic embedding mode in such clusters.

  5. Dimerization Interface of 3-Hydroxyacyl-CoA Dehydrogenase Tunes the Formation of Its Catalytic Intermediate

    PubMed Central

    Jin, Ying-Hua; Fan, Jun; Sun, Fei

    2014-01-01

    3-hydroxyacyl-CoA dehydrogenase (HAD, EC 1.1.1.35) is a homodimeric enzyme localized in the mitochondrial matrix, which catalyzes the third step in fatty acid β-oxidation. The crystal structures of human HAD and subsequent complexes with cofactor/substrate enabled better understanding of HAD catalytic mechanism. However, numerous human diseases were found related to mutations at HAD dimerization interface that is away from the catalytic pocket. The role of HAD dimerization in its catalytic activity needs to be elucidated. Here, we solved the crystal structure of Caenorhabditis elegans HAD (cHAD) that is highly conserved to human HAD. Even though the cHAD mutants (R204A, Y209A and R204A/Y209A) with attenuated interactions on the dimerization interface still maintain a dimerization form, their enzymatic activities significantly decrease compared to that of the wild type. Such reduced activities are in consistency with the reduced ratios of the catalytic intermediate formation. Further molecular dynamics simulations results reveal that the alteration of the dimerization interface will increase the fluctuation of a distal region (a.a. 60–80) that plays an important role in the substrate binding. The increased fluctuation decreases the stability of the catalytic intermediate formation, and therefore the enzymatic activity is attenuated. Our study reveals the molecular mechanism about the essential role of the HAD dimerization interface in its catalytic activity via allosteric effects. PMID:24763278

  6. Dimerization and its role in GMP formation by human guanylate binding proteins.

    PubMed

    Abdullah, Nazish; Balakumari, Meena; Sau, Apurba Kumar

    2010-10-06

    The mechanism of oligomerization and its role in the regulation of activity in large GTPases are not clearly understood. Human guanylate binding proteins (hGBP-1 and 2) belonging to large GTPases have the unique feature of hydrolyzing GTP to a mixture of GDP and GMP with unequal ratios. Using a series of truncated and mutant proteins of hGBP-1, we identified a hydrophobic helix in the connecting region between the two domains that plays a critical role in dimerization and regulation of the GTPase activity. The fluorescence with 1-8-anilinonaphthalene sulfonate and circular dichroism measurements together suggest that in the absence of the substrate analog, the helix is masked inside the protein but becomes exposed through a substrate-induced conformational switch, and thus mediates dimerization. This is further supported by the intrinsic fluorescence experiment, where Leu(298) of this helix is replaced by a tryptophan. Remarkably, the enzyme exhibits differential GTPase activities depending on dimerization; a monomer produces only GDP, but a dimer gives both GDP and GMP with stimulation of the activity. An absolute dependence of GMP formation with dimerization demonstrates a cross talk between the monomers during the second hydrolysis. Similar to hGBP-1, hGBP-2 showed dimerization-related GTPase activity for GMP formation, indicating that this family of proteins follows a broadly similar mechanism for GTP hydrolysis.

  7. A Strategy for Complex Dimer Formation When Biomimicry Fails: Total Synthesis of Ten Coccinellid Alkaloids

    PubMed Central

    2015-01-01

    Although dimeric natural products can often be synthesized in the laboratory by directly merging advanced monomers, these approaches sometimes fail, leading instead to non-natural architectures via incorrect unions. Such a situation arose during our studies of the coccinellid alkaloids, when attempts to directly dimerize Nature’s presumed monomeric precursors in a putative biomimetic sequence afforded only a non-natural analogue through improper regiocontrol. Herein, we outline a unique strategy for dimer formation that obviates these difficulties, one which rapidly constructs the coccinellid dimers psylloborine A and isopsylloborine A through a terminating sequence of two reaction cascades that generate five bonds, five rings, and four stereocenters. In addition, a common synthetic intermediate is identified which allows for the rapid, asymmetric formal or complete total syntheses of eight monomeric members of the class. PMID:24959981

  8. A strategy for complex dimer formation when biomimicry fails: total synthesis of ten coccinellid alkaloids.

    PubMed

    Sherwood, Trevor C; Trotta, Adam H; Snyder, Scott A

    2014-07-09

    Although dimeric natural products can often be synthesized in the laboratory by directly merging advanced monomers, these approaches sometimes fail, leading instead to non-natural architectures via incorrect unions. Such a situation arose during our studies of the coccinellid alkaloids, when attempts to directly dimerize Nature's presumed monomeric precursors in a putative biomimetic sequence afforded only a non-natural analogue through improper regiocontrol. Herein, we outline a unique strategy for dimer formation that obviates these difficulties, one which rapidly constructs the coccinellid dimers psylloborine A and isopsylloborine A through a terminating sequence of two reaction cascades that generate five bonds, five rings, and four stereocenters. In addition, a common synthetic intermediate is identified which allows for the rapid, asymmetric formal or complete total syntheses of eight monomeric members of the class.

  9. Formation of covalent di-tyrosine dimers in recombinant α-synuclein

    PubMed Central

    van Maarschalkerweerd, A; Pedersen, MN; Peterson, H; Nilsson, M; Nguyen, TTT; Skamris, T; Rand, K; Vetri, V; Langkilde, AE; Vestergaard, B

    2015-01-01

    Parkinson's disease is associated with fibril deposition in the diseased brain. Misfolding events of the intrinsically disordered synaptic protein α-synuclein are suggested to lead to the formation of transient oligomeric and cytotoxic species. The etiology of Parkinson's disease is further associated with mitochondrial dysfunction and formation of reactive oxygen species. Oxidative stress causes chemical modification of native α-synuclein, plausibly further influencing misfolding events. Here, we present evidence for the spontaneous formation of covalent di-tyrosine α-synuclein dimers in standard recombinant protein preparations, induced without extrinsic oxidative or nitrative agents. The dimers exhibit no secondary structure but advanced SAXS studies reveal an increased structural definition, resulting in a more hydrophobic micro-environment than the highly disordered monomer. Accordingly, monomers and dimers follow distinct fibrillation pathways. PMID:28232892

  10. A new quadruple hydrogen-bonding module with a DDAA array: formation of a stable homodimer without competition from undesired hydrogen-bonded dimers.

    PubMed

    Hisamatsu, Yosuke; Shirai, Naohiro; Ikeda, Shin-ichi; Odashima, Kazunori

    2009-10-01

    A new DDAA hydrogen-bonding module (UImp-2), based on a ureidoimidazo[1,2-a]pyrimidine structure, forms a highly stable homodimer (K(dim) > 1.1 x 10(5) M(-1) in CDCl(3)) without competition from undesired hydrogen-bonded dimers.

  11. Computational investigations on covalent dimerization/oligomerization of polyacenes: is it relevant to soot formation?

    PubMed

    Koley, D; Arunan, E; Ramakrishnan, S

    2012-08-05

    We have postulated a novel pathway that could assist in the nucleation of soot particles through covalent dimerization and oligomerizations of a variety of PAHs. DFT calculations were performed with the objective of obtaining the relative thermal stabilities and formation probabilities of oligomeric species that exploit the facile dimerization that is known to occur in linear oligoacenes. We propose that the presence of small stretches of linear oligoacence (tetracene or longer) in extended PAH, either embedded or tethered, would be adequate for enabling the formation of such dimeric and oligomeric adducts; these could then serve as nuclei for the growth of soot particles. Our studies also reveal the importance of π-stacking interactions between extended aromatic frameworks in governing the relative stabilities of the oligomeric species that are formed.

  12. Homochiral Selectivity in RNA Synthesis: Montmorillonite-catalyzed Quaternary Reactions of D, L-Purine with D, L- Pyrimidine Nucleotides

    NASA Astrophysics Data System (ADS)

    Joshi, Prakash C.; Aldersley, Michael F.; Ferris, James P.

    2011-06-01

    Selective adsorption of D, L-ImpA with D, L-ImpU on the platelets of montmorillonite demonstrates an important reaction pathway for the origin of homochirality in RNA synthesis. Our earlier studies have shown that the individual reactions of D, L-ImpA or D, L-ImpU on montmorillonite catalyst produced oligomers which were only partially inhibited by the incorporation of both D- and L-enantiomers. Homochirality in these reactions was largely due to the formation of cyclic dimers that cannot elongate. We investigated the quaternary reactions of D, L-ImpA with D, L-ImpU on montmorillonite. The chain length of these oligomers increased from 9-mer to 11-mer as observed by HPLC, with a concominant increase in the yield of linear dimers and higher oligomers in the reactions involving D, L-ImpA with D, L-ImpU as compared to the similar reactions carried out with D-enantiomers only. The formation of cyclic dimers of U was completely inhibited in the quaternary reactions. The yield of cyclic dimers of A was reduced from 60% to 10% within the dimer fraction. 12 linear dimers and 3 cyclic dimers were isolated and characterized from the quaternary reaction. The homochirality and regioselectivity of dimers were 64.1% and 71.7%, respectively. Their sequence selectivity was shown by the formation of purine-pyrimidine (54-59%) linkages, followed by purine-purine (29-32%) linkages and pyrimidine-pyrimidine (9-13%) linkages. Of the 16 trimers detected, 10 were homochiral with an overall homochirality of 73-76%. In view of the greater homochirality, sequence- and regio- selectivity, the quaternary reactions on montmorillonite demonstrate an unexpectedly favorable route for the prebiotic synthesis of homochiral RNA compared with the separate reactions of enantiomeric activated mononucleotides.

  13. The RAD7 and RAD16 genes, which are essential for pyrimidine dimer removal from the silent mating type loci, are also required for repair of the nontranscribed strand of an active gene in Saccharomyces cerevisiae.

    PubMed Central

    Verhage, R; Zeeman, A M; de Groot, N; Gleig, F; Bang, D D; van de Putte, P; Brouwer, J

    1994-01-01

    The rad16 mutant of Saccharomyces cerevisiae was previously shown to be impaired in removal of UV-induced pyrimidine dimers from the silent mating-type loci (D. D. Bang, R. A. Verhage, N. Goosen, J. Brouwer, and P. van de Putte, Nucleic Acids Res. 20:3925-3931, 1992). Here we show that rad7 as well as rad7 rad16 double mutants have the same repair phenotype, indicating that the RAD7 and RAD16 gene products might operate in the same nucleotide excision repair subpathway. Dimer removal from the genome overall is essentially incomplete in these mutants, leaving about 20 to 30% of the DNA unrepaired. Repair analysis of the transcribed RPB2 gene shows that the nontranscribed strand is not repaired at all in rad7 and rad16 mutants, whereas the transcribed strand is repaired in these mutants at a fast rate similar to that in RAD+ cells. When the results obtained with the RPB2 gene can be generalized, the RAD7 and RAD16 proteins not only are essential for repair of silenced regions but also function in repair of nontranscribed strands of active genes in S. cerevisiae. The phenotype of rad7 and rad16 mutants closely resembles that of human xeroderma pigmentosum complementation group C (XP-C) cells, suggesting that RAD7 and RAD16 in S. cerevisiae function in the same pathway as the XPC gene in human cells. RAD4, which on the basis of sequence homology has been proposed to be the yeast XPC counterpart, seems to be involved in repair of both inactive and active yeast DNA, challenging the hypothesis that RAD4 and XPC are functional homologs. Images PMID:8065346

  14. Mutations that affect coenzyme binding and dimer formation of fungal 17beta-hydroxysteroid dehydrogenase.

    PubMed

    Brunskole, Mojca; Kristan, Katja; Stojan, Jure; Rizner, Tea Lanisnik

    2009-03-25

    The 17beta-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus (17beta-HSDcl) is an NADPH-dependent member of the short-chain dehydrogenase/reductase superfamily, and it functions as a dimer that is composed of two identical subunits. By constructing the appropriate mutants, we have examined the M204 residue that is situated in the coenzyme binding pocket, for its role in the binding of the coenzyme NADP(H). We have also studied the importance of hydrophobic interactions through F124, F132, F133 and F177 for 17beta-HSDcl dimer formation. The M204G substitution decreased the catalytic efficiency of 17beta-HSDcl, suggesting that M204 sterically coerces the nicotinamide moiety of the coenzyme into the appropriate position for further hydride transfer. Phenylalanine substitutions introduced at the dimer interface produced inactive aggregates and oligomers with high molecular masses, suggesting that these hydrophobic interactions have important roles in the formation of the active dimer.

  15. Surface Electrochemistry of Chloro(phthalocyaninato)rhodium(III) species, and Oxygen Reduction Electrocatalysis, Formation of a Dimeric Species

    DTIC Science & Technology

    1991-08-20

    rhodium(III) Species, and Oxygen Reduction Electrocatalysis , Formation of a Dimeric Species By Y.-H. Tse, P. Seymour, N. Kobayashi, H. Lam, C.C. Leznoff... Electrocatalysis , Formation of a Dimeric Species 12. PERSONAL AuTI𔃾OR(S)* Y.-H. Ise, P. Sey;mour, N. Kobayashi, H. Lam, C.C. Leznoff, and A.B.P. L...Oxygen Reduction Electrocatalysis . Formation of a Dimeric Species. Yu-Hong Tse, Penny Seymour, Nagao Kobayashi, 1 Herman Lam, Clifford C. Leznoff. and

  16. Peptide modification results in the formation of a dimer with a 60-fold enhanced antimicrobial activity

    PubMed Central

    Thamri, Amal; Létourneau, Myriam; Djoboulian, Alex; Chatenet, David; Déziel, Eric; Perreault, Jonathan

    2017-01-01

    Cationic antimicrobial peptides (CAMPs) occur naturally in numerous organisms and are considered as a class of antibiotics with promising potential against multi-resistant bacteria. Herein, we report a strategy that can lead to the discovery of novel small CAMPs with greatly enhanced antimicrobial activity and retained antibiofilm potential. We geared our efforts towards i) the N-terminal cysteine functionalization of a previously reported small synthetic cationic peptide (peptide 1037, KRFRIRVRV-NH2), ii) its dimerization through a disulfide bond, and iii) a preliminary antimicrobial activity assessment of the newly prepared dimer against Pseudomonas aeruginosa and Burkholderia cenocepacia, pathogens responsible for the formation of biofilms in lungs of individuals with cystic fibrosis. This dimer is of high interest as it does not only show greatly enhanced bacterial growth inhibition properties compared to its pep1037 precursor (up to 60 times), but importantly, also displays antibiofilm potential at sub-MICs. Our results suggest that the reported dimer holds promise for its use in future adjunctive therapy, in combination with clinically-relevant antibiotics. PMID:28296935

  17. Formation and occurrence of dimer esters of pinene oxidation products in atmospheric aerosols

    NASA Astrophysics Data System (ADS)

    Kristensen, K.; Enggrob, K. L.; King, S. M.; Worton, D. R.; Platt, S. M.; Mortensen, R.; Rosenoern, T.; Surratt, J. D.; Bilde, M.; Goldstein, A. H.; Glasius, M.

    2013-04-01

    The formation of carboxylic acids and dimer esters from α-pinene oxidation was investigated in a smog chamber and in ambient aerosol samples collected during the Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX). Chamber experiments of α-pinene ozonolysis in dry air and at low NOx concentrations demonstrated formation of two dimer esters, pinyl-diaterpenyl (MW 358) and pinonyl-pinyl dimer ester (MW 368), under both low- and high-temperature conditions. Concentration levels of the pinyl-diaterpenyl dimer ester were lower than the assumed first-generation oxidation products cis-pinic and terpenylic acids, but similar to the second-generation oxidation products 3-methyl-1,2,3-butane tricarboxylic acid (MBTCA) and diaterpenylic acid acetate (DTAA). Dimer esters were observed within the first 30 min, indicating rapid production simultaneous to their structural precursors. However, the sampling time resolution precluded conclusive evidence regarding formation from gas- or particle-phase processes. CCN activities of the particles formed in the smog chamber displayed a modest variation during the course of experiments, with κ values in the range 0.06-0.09 (derived at a supersaturation of 0.19%). The pinyl-diaterpenyl dimer ester was also observed in ambient aerosol samples collected above a ponderosa pine forest in the Sierra Nevada Mountains of California during two seasonally distinct field campaigns in September 2007 and July 2009. The pinonyl-pinyl ester was observed for the first time in ambient air during the 2009 campaign, and although present at much lower concentrations, it was correlated with the abundance of the pinyl-diaterpenyl ester, suggesting similarities in their formation. The maximum concentration of the pinyl-diaterpenyl ester was almost 10 times higher during the warmer 2009 campaign relative to 2007, while the concentration of cis-pinic acid was approximately the same during both periods, and lack of correlation with levels of

  18. Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane

    NASA Astrophysics Data System (ADS)

    Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

    2016-09-01

    Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.

  19. Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane

    PubMed Central

    Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

    2016-01-01

    Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail. PMID:27630059

  20. Sites of preferential induction of cyclobutane pyrimidine dimers in the nontranscribed strand of lacI correspond with sites of UV-induced mutation in Escherichia coli

    SciTech Connect

    Koehler, D.R.; Awadallah, S.S.; Glickman, B.W. )

    1991-06-25

    An approach utilizing fluorescence-activated DNA sequencing technology was used to study the position and frequency of UV-induced lesions in the lacI gene of Escherichia coli. The spectrum of sites of UV damage in the NC+ region of the gene was compared with a published spectrum of UV-induced mutation in lacI . On average, the frequency of UV-induced lesions in the nontranscribed strand was higher than that in the transcribed strand in the region analyzed. A large fraction of mutations occurs at sites of UV-induced lesions in the nontranscribed strand, but not in the transcribed strand. This bias is reduced in an excision repair deficient (UvrB-) strain. In addition, mutations occur overwhelmingly at sites where a dipyrimidine sequence is present in the nontranscribed strand. This bias is also markedly reduced in the UvrB- strain. In light of recent work Mellon and Hanawalt describing the preferential removal of cyclobutane dimers from the transcribed strand of the expressed lacZ gene in E. coli, our data suggest that preferential strand repair may have a significant effect on mutagenesis.

  1. Structural diversity of Alzheimer’s disease Aβ dimers and their role in oligomerization and fibril formation

    PubMed Central

    Tsigelny, Igor F.; Sharikov, Yuriy; Kouznetsova, Valentina L.; Greenberg, Jerry P.; Wrasidlo, Wolfgang; Gonzalez, Tania; Desplats, Paula; Michael, Sarah E.; Trejo-Morales, Margarita; Overk, Cassia R.; Masliah, Eliezer

    2015-01-01

    Alzheimer’s disease (AD) is associated with the formation of toxic Aβ42 oligomers and recent evidence supports a role for Aβ dimers as building blocks for oligomers. Molecular dynamics (MD) simulation studies have identified clans for the dominant conformations of Aβ42 forming dimers; however, it is unclear if a larger spectrum of dimers is involved and which set(s) of dimers might evolve to oligomers verse fibrils. Therefore, for this study we generated multiple structural conformations of Aβ42, using explicit all-atom MD, and then clustering the different structures based on key conformational similarities. Those matching a selection threshold were then used to model a process of oligomerization. Remarkably, we showed a greater diversity in Aβ dimers than previously described. Depending on the clan family, different types of Aβ dimers were obtained. While some had the tendency to evolve into oligomeric rings, others formed fibrils of diverse characteristics. Then we selected the dimers that would evolve to membranephilic annular oligomers. Nearly one third of the 28 evaluated annular oligomers had the dimer interfaces between the neighboring Aβ42 monomers with possible salt bridges between the residue K28 from one side and either residue E22 or D23 on the other. Based on these results, key amino acids were identified for point mutations that either enhanced or suppressed the formation and toxicity of oligomer rings. Our studies suggest a greater diversity of Aβ dimers. Understanding the structure of Aβ dimers might be important for the rationale design of small molecules that block formation of toxic oligomers. PMID:24240640

  2. Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin

    SciTech Connect

    Pehrson, J.R. )

    1989-12-01

    Photo-induced thymine dimer formation was used to probe nucleosome structure in nuclei. The distribution of thymine dimers in the nucleosome and recent studies of the structure of thymine dimer-containing DNA suggest that the rate of thymine dimer formation is affected by the direction and degree of DNA bending. This premise was used to construct a model of the path of DNA in the nucleosome, which has the following features. (i) There are four regions of sharp bending, two which have been seen previously by x-ray crystallography of the core particle. (ii) The DNA in H1-containing nucleosomes deviates from its superhelical path near the midpoint; this is not seen with H1-stripped chromatin. (iii) The internucleosomal (linker) DNA appears to be relatively straight.

  3. Reactivity of damaged pyrimidines: formation of a Schiff base intermediate at the glycosidic bond of saturated dihydrouridine.

    PubMed

    Jian, Yajun; Lin, Gengjie; Chomicz, Lidia; Li, Lei

    2015-03-11

    DNA glycosylases catalyze the first step of the base excision repair (BER) pathway. The chemistry used by these enzymes for deglycosylation has been largely considered as the chemistry of the oxocarbenium ion, e.g., direct rupture of the C1'-N1 bond resulting in an oxocarbenium ion intermediate. Here we present mechanistic studies revealing the 2'-deoxyribose isomerization and subsequent deglycosylation processes in two pyrimidine lesions: 5,6-dihydro-2'-deoxyuridine (dHdU) and 5,6-dihydrothymidine (dHT), formed via ionizing radiation damage to 2'-deoxycytidine and thymidine, respectively, under anoxic conditions. Acid or heat treatment of these two lesions leads to the production of two pairs of C1' epimers containing a pyranose and a furanose, respectively, indicating that both lesions favor the rupture of the C1'-O4' bond, resulting in a Schiff base intermediate at the N-glycosidic bond. Such a Schiff base intermediate was trapped and characterized by either Pd-catalyzed hydrogenation or thiol-mediated addition reaction. In contrast, in undamaged 2'-deoxyuridine and thymidine, reactions at elevated temperatures lead to the release of nucleobases most likely via the traditional oxocarbenium ion pathway. DFT calculations further support the experimental findings, suggesting that the oxocarbenium ion intermediate is responsible for the deglycosylation process if the integrity of the pyrimidine ring is maintained, while the Schiff base intermediate is preferred if the C5═C6 bond is saturated. Currently, the oxocarbenium ion pathway is indicated to be solely responsible for the deglycosylation in BER enzymes, however our results suggest an alternative Schiff base mechanism which may be responsible for the repair of saturated pyrimidine damages.

  4. Host cell reactivation of gene expression for an adenovirus-encoded reporter gene reflects the repair of UVC-induced cyclobutane pyrimidine dimers and methylene blue plus visible light-induced 8-oxoguanine.

    PubMed

    Leach, Derrik M; Zacal, Natalie J; Rainbow, Andrew J

    2013-09-01

    Previously, we have reported the use of a recombinant adenovirus (Ad)-based host cell reactivation (HCR) assay to examine nucleotide excision repair (NER) of UVC-induced DNA lesions in several mammalian cell types. The recombinant non-replicating Ad expresses the Escherichia coli β-galactosidase (β-gal) reporter gene under control of the cytomegalovirus immediate-early enhancer region. We have also used methylene blue plus visible light (MB + VL) to induce the major oxidative lesion 7,8-dihydro-8-oxoguanine (8-oxoG) in the recombinant Ad-encoded reporter gene in order to study base excision repair (BER). The reported variability regarding 8-oxoG's potential to block transcription by RNA polymerase II and data demonstrating that a number of factors play a role in transcriptional bypass of the lesion led us to examine the repair of 8-oxoG in the Ad reporter and its relationship to HCR for expression of the reporter gene. We have used Southern blotting to examine removal of UVC- and MB + VL-induced DNA damage by loss of endonuclease-sensitive sites from the Ad-encoded β-gal reporter gene in human and rodent cells. We show that repair of MB + VL-induced 8-oxoG via BER and UVC-induced cyclobutane pyrimidine dimers (CPDs) via NER is substantially greater in human SV40-transformed GM637F skin fibroblasts compared to hamster CHO-AA8 cells. We also show that HCR for expression of the MB + VL-damaged and the UVC-damaged reporter gene is substantially greater in human SV40-transformed GM637F skin fibroblasts compared to hamster CHO-AA8 cells. The difference between the human and rodent cells in the removal of both 8-oxoG and CPDs from the damaged reporter gene was comparable to the difference in HCR for expression of the damaged reporter gene. These results suggest that the major factor for HCR of the MB + VL-treated reporter gene in mammalian cells is DNA repair in the Ad rather than lesion bypass.

  5. Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation.

    PubMed

    Shore, Sabrina; Henderson, Jordana M; Lebedev, Alexandre; Salcedo, Michelle P; Zon, Gerald; McCaffrey, Anton P; Paul, Natasha; Hogrefe, Richard I

    2016-01-01

    For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.

  6. Sulfur dimers adsorbed on Au(111) as building blocks for sulfur octomers formation: A density functional study

    SciTech Connect

    Hernandez-Tamargo, Carlos E.; Montero-Alejo, Ana Lilian; Pujals, Daniel Codorniu; Mikosch, Hans

    2014-07-28

    Experimental scanning tunneling microscopy (STM) studies have shown for more than two decades rectangular formations when sulfur atoms are deposited on Au(111) surfaces. The precursors have ranged from simple molecules or ions, such as SO{sub 2} gas or sulfide anions, to more complex organosulfur compounds. We investigated, within the framework of the Density Functional Theory, the structure of these rectangular patterns assuming them entirely composed of sulfur atoms as the experimental evidence suggests. The sulfur coverage at which the simulations were carried out (0.67 ML or higher) provoked that the sulfur-sulfur association had to be taken into account for achieving a good agreement between the sets of simulated and experimental STM images. A combination of four sulfur dimers per rectangular formation properly explained the trends obtained by the experimental STM analysis which were related with the rectangles' size and shape fluctuations together with sulfur-sulfur distances within these rectangles. Finally, a projected density of states analysis showed that the dimers were capable of altering the Au(5d) electronic states at the same level as atomic sulfur adsorbed at low coverage. Besides, sulfur dimers states were perfectly distinguished, whose presence near and above the Fermi level can explain both: sulfur-sulfur bond elongation and dimers stability when they stayed adsorbed on the surface at high coverage.

  7. A molecular beam mass spectrometric study of the formation and photolysis of C(lc)lO dimer

    NASA Technical Reports Server (NTRS)

    Greene, Frank T.; Robaugh, David A.

    1992-01-01

    A study of the chlorine oxides present at temperatures and pressures typical of the Antarctic stratosphere was carried out. A series of low temperature flow reactors was constructed and used in conjunction with molecular beam mass spectrometric techniques to identify species and characterize their kinetic behavior at temperatures of -20 to -70 C and pressures of from 30 to 130 Torr. It was found that the gas phase chlorine-oxygen system was quite complex at low temperatures. ClO dimer was identified and found to be thermodynamically very stable under stratospheric conditions. It was also found that any system which contained ClO also contained a larger oxide. The oxide was identified as Cl2O3. A survey of possible higher oxides, which have been postulated as possible chlorine sinks in the stratosphere, was also carried out. The rate of formation of ClO dimer was measured as a function of temperature and pressure. Measurements were made of both the decay of ClO and the formation of the dimer. By comparing these rates it was determined that virtually all of the ClO was converted to the dimer under stratospheric conditions, and that the other ClO reactions were not important under these conditions.

  8. New strategies for the synthesis of pyrimidine derivatives.

    PubMed

    Hill, Matthew D; Movassaghi, Mohammad

    2008-01-01

    Recent advances in pyrimidine synthesis are described. Modification of conventional strategies involving N-C-N fragment condensation with 1,3-dicarbonyl derivatives remains a common theme in current literature. Other methods, including N-C fragment condensation strategies, provide reactive intermediates capable of intramolecular cyclization and formation of pyrimidine derivatives. These recently developed methodologies offer a valuable addendum to azaheterocycle synthesis.

  9. Occurrence and formation kinetics of pyranomalvidin-procyanidin dimer pigment in Merlot red wine: impact of acidity and oxygen concentrations.

    PubMed

    Pechamat, Laurent; Zeng, Liming; Jourdes, Michael; Ghidossi, Rémy; Teissedre, Pierre-Louis

    2014-02-19

    Once released from red grape skins, anthocyanins undergo various chemical reactions leading to the formation of more stable pigments such as pyranoanthocyanin, as well as other derivatives. Among these pigments, pyranoanthocyanins linked directly to flavanol dimers have been detected and identified in aged Port wine but not in dry red wine. These pigments are very important with regard to the wine color evolution since they are involved in wine color evolution and stabilization. During this investigation, the occurrence in dry red wine of two pyranomalvidin-procyanidin dimer has been established by low and high resolution HPLC-UV-MS analysis. Moreover, the impact of acidity and oxygen levels on their formation in red wine has been estimated. After four months of evolution, the results showed that, for the same pH, the quantity of this pigment was correlated with oxygen concentrations. Moreover, for the same quantity of oxygen, the concentration of this pigment was related to the acidity level.

  10. C...H...N Hydrogen Bond Formation in Trimethylamine Dimer upon One-Photon Ionization

    NASA Astrophysics Data System (ADS)

    Nakayama, Yuichiro; Matsuda, Yoshiyuki; Fujii, Asuka

    2011-06-01

    Structures of trimethylamine dimer cluster cations which are generated by the vacuum-ultraviolet photoionization are investigated by a combination of infrared spectroscopic methods and theoretical reaction-pass calculations. In the trimethylamine dimer cluster cation, a proton of a methyl group is shared with the N atom of the other trimethylamine moiety. This is evidence that the methyl group acts as a proton donor in the cation state.

  11. Distribution of ions around thymine dimer containing DNA: A possible recognition element for endonuclease V

    SciTech Connect

    Osman, R.; Luo, N.; Miaskiewicz, K.; Miller, J.

    1995-10-01

    The molecular link between sunlight exposure and skin cancer can be traced to the formation of cyclobutane pyrimidine dimers together with (6-4) photoadducts of pyrimidines in DNA upon exposure to UV radiation. The mutagenicity of these lesions is frequently explained by miscoding during DNA replication due to perturbations of base-pairing interactions. However the mutagenicity of UV photoproducts depends of their sequence context, suggesting that more global structural changes in DNA contribute to mutation induction. One of the most effective protections against the deleterious effects of cyclobutane pyrimidine dimers is the wide range of repair of this lesion by different enzymatic pathways. This paper presents the results of a 200 ps molecular dynamics simulation on the dodecarner d(CGCGAATTCGCG){sub 2} containing a cis, syn-cyclobutane thymine dimer, explicit water and counterions. The averaged structure calculated from the simulation shows good agreement with the available NMR data. The distribution of counterions around the damaged DNA is different from that around a non damaged DNA and suggests a possible mechanism of damage recognition by the enzyme.

  12. Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation

    PubMed Central

    Henderson, Jordana M.; Lebedev, Alexandre; Salcedo, Michelle P.; Zon, Gerald; McCaffrey, Anton P.; Paul, Natasha; Hogrefe, Richard I.

    2016-01-01

    For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol. PMID:27875576

  13. Base pairing enhances fluorescence and favors cyclobutane dimer formation induced upon absorption of UVA radiation by DNA.

    PubMed

    Banyasz, Akos; Vayá, Ignacio; Changenet-Barret, Pascale; Gustavsson, Thomas; Douki, Thierry; Markovitsi, Dimitra

    2011-04-13

    The photochemical properties of the DNA duplex (dA)(20)·(dT)(20) are compared with those of the parent single strands. It is shown that base pairing increases the probability of absorbing UVA photons, probably due to the formation of charge-transfer states. UVA excitation induces fluorescence peaking at ∼420 nm and decaying on the nanosecond time scale. The fluorescence quantum yield, the fluorescence lifetime, and the quantum yield for cyclobutane dimer formation increase upon base pairing. Such behavior contrasts with that of the UVC-induced processes.

  14. Formation of H-type liquid crystal dimer at air-water interface

    SciTech Connect

    Karthik, C. Gupta, Adbhut Joshi, Aditya Manjuladevi, V. Gupta, Raj Kumar; Varia, Mahesh C.; Kumar, Sandeep

    2014-04-24

    We have formed the Langmuir monolayer of H-shaped Azo linked liquid crystal dimer molecule at the air-water interface. Isocycles of the molecule showed hysteresis suggesting the ir-reversible nature of the monolayer formed. The thin film deposited on the silicon wafer was characterized using Atomic Force Microscopy (AFM) and Field Emission Scanning Electron Microscopy (FESEM). The images showed uniform domains of the dimer molecule. We propose that these molecules tend to take book shelf configuration in the liquid phase.

  15. Strongly frustrated triangular spin lattice emerging from triplet dimer formation in honeycomb Li2IrO3

    PubMed Central

    Nishimoto, Satoshi; Katukuri, Vamshi M.; Yushankhai, Viktor; Stoll, Hermann; Rößler, Ulrich K.; Hozoi, Liviu; Rousochatzakis, Ioannis; van den Brink, Jeroen

    2016-01-01

    Iridium oxides with a honeycomb lattice have been identified as platforms for the much anticipated Kitaev topological spin liquid: the spin-orbit entangled states of Ir4+ in principle generate precisely the required type of anisotropic exchange. However, other magnetic couplings can drive the system away from the spin-liquid phase. With this in mind, here we disentangle the different magnetic interactions in Li2IrO3, a honeycomb iridate with two crystallographically inequivalent sets of adjacent Ir sites. Our ab initio many-body calculations show that, while both Heisenberg and Kitaev nearest-neighbour couplings are present, on one set of Ir–Ir bonds the former dominates, resulting in the formation of spin-triplet dimers. The triplet dimers frame a strongly frustrated triangular lattice and by exact cluster diagonalization we show that they remain protected in a wide region of the phase diagram. PMID:26776664

  16. Driving the formation of the RbCs dimer by a laser pulse: A nonlinear-dynamics approach

    NASA Astrophysics Data System (ADS)

    Chandre, C.; Mahecha, Jorge; Salas, J. Pablo

    2017-03-01

    We study the formation of the RbCs molecule by an intense laser pulse using nonlinear dynamics. Under the Born-Oppenheimer approximation, the system is modeled by a two-degree-of-freedom rovibrational Hamiltonian, which includes the ground electronic potential energy curve of the diatomic molecule and the interaction of the molecular polarizability with the electric field of the laser. As the laser intensity increases, we observe that the formation probability first increases and then decreases after reaching a maximum. We show that the analysis can be simplified to the investigation of the long-range interaction between the two atoms. We conclude that the formation is due to a very small change in the radial momentum of the dimer induced by the laser pulse. From this observation, we build a reduced one-dimensional model which allows us to derive an approximate expression of the formation probability as a function of the laser intensity.

  17. Electronic excited states responsible for dimer formation upon UV absorption directly by thymine strands: joint experimental and theoretical study.

    PubMed

    Banyasz, Akos; Douki, Thierry; Improta, Roberto; Gustavsson, Thomas; Onidas, Delphine; Vayá, Ignacio; Perron, Marion; Markovitsi, Dimitra

    2012-09-12

    The study addresses interconnected issues related to two major types of cycloadditions between adjacent thymines in DNA leading to cyclobutane dimers (T<>Ts) and (6-4) adducts. Experimental results are obtained for the single strand (dT)(20) by steady-state and time-resolved optical spectroscopy, as well as by HPLC coupled to mass spectrometry. Calculations are carried out for the dinucleoside monophosphate in water using the TD-M052X method and including the polarizable continuum model; the reliability of TD-M052X is checked against CASPT2 calculations regarding the behavior of two stacked thymines in the gas phase. It is shown that irradiation at the main absorption band leads to cyclobutane dimers (T<>Ts) and (6-4) adducts via different electronic excited states. T<>Ts are formed via (1)ππ* excitons; [2 + 2] dimerization proceeds along a barrierless path, in line with the constant quantum yield (0.05) with the irradiation wavelength, the contribution of the (3)ππ* state to this reaction being less than 10%. The formation of oxetane, the reaction intermediate leading to (6-4) adducts, occurs via charge transfer excited states involving two stacked thymines, whose fingerprint is detected in the fluorescence spectra; it involves an energy barrier explaining the important decrease in the quantum yield of (6-4) adducts with the irradiation wavelength.

  18. Electrical conductivity and luminescence in coordination polymers based on copper(I)-halides and sulfur-pyrimidine ligands.

    PubMed

    Gallego, Almudena; Castillo, Oscar; Gómez-García, Carlos J; Zamora, Félix; Delgado, Salome

    2012-01-02

    The solvothermal reactions between pyrimidinedisulfide (pym(2)S(2)) and CuI or CuBr(2) in CH(2)Cl(2):CH(3)CN lead to the formation of [Cu(11)I(7)(pymS)(4)](n) (pymSH = pyrimidine-2(1H)-thione) (1) and the dimer [Cu(II)(μ-Br)(Br)L](2) (L = 2-(pyrimidin-2-ylamino)-1,3-thiazole-4-carbaldehyde) (2). In the later reaction, there is an in situ S-S, S-C(sp(2)), and C(sp(2))-N multiple bond cleavage of the pyrimidinedisulfide resulting in the formation of 2-(pyrimidin-2-ylamino)-1,3-thiazole-4-carbaldehyde. Interestingly, similar reactions carried out just with a change in the solvent (H(2)O:CH(3)CN instead of CH(2)Cl(2):CH(3)CN) give rise to the formation of coordination polymers with rather different architectures. Thus, the reaction between pym(2)S(2) and CuI leads to the formation of [Cu(3)I(pymS)(2)](n) (3) and [CuI(pym(2)S(3))] (pym(2)S(3) = pyrimidiltrisulfide) (4), while [Cu(3)Br(pymS)(2)](n) (5) is isolated in the reaction with CuBr(2). Finally, the solvothermal reactions between CuI and pyrimidine-2-thione (pymSH) in CH(2)Cl(2):CH(3)CN at different ratios, 1:1 or 2:1, give the polymers [Cu(2)I(2)(pymSH)(2)](n) (6) and [Cu(2)I(2)(pymSH)](n) (7), respectively. The structure of the new compounds has been determined by X-ray diffraction. The studies of the physical properties of the novel coordination polymers reveal that compounds 3 and 5 present excellent electrical conductivity values at room temperature, while compounds 1, 3, and 5-7 show luminescent strong red emission at room temperature.

  19. Fibroblast Growth Factor 2 Dimer with Superagonist In Vitro Activity Improves Granulation Tissue Formation During Wound Healing

    PubMed Central

    Decker, Caitlin G.; Wang, Yu; Paluck, Samantha J.; Shen, Lu; Loo, Joseph A.; Levine, Alex J.; Miller, Lloyd S.; Maynard, Heather D.

    2015-01-01

    Site-specific chemical dimerization of fibroblast growth factor 2 (FGF2) with the optimal linker length resulted in a FGF2 homodimer with improved granulation tissue formation and blood vessel formation at exceptionally low concentrations. Homodimers of FGF2 were synthesized through site-specific linkages to both ends of different molecular weight poly(ethylene glycols) (PEGs). The optimal linker length was determined by screening dimer-induced metabolic activity of human dermal fibroblasts and found to be that closest to the inter-cysteine distance, 70 Å, corresponding to 2 kDa PEG. A straightforward analysis of the kinetics of second ligand binding as a function of tether length showed that, as the polymerization index (the number of monomer repeat units in the polymer, N) of the tether decreases, the mean time for second ligand capture decreases as ~N3/2, leading to an enhancement of the number of doubly bound ligands in steady-state for a given (tethered) ligand concentration. FGF2-PEG2k-FGF2 induced greater fibroblast metabolic activity than FGF2 alone, all other dimers, and all monoconjugates, at each concentration tested, with the greatest difference observed at low (0.1 ng/mL) concentration. FGF2-PEG2k-FGF2 further exhibited superior activity compared to FGF2 for both metabolic activity and migration in human umbilical vein endothelial cells, as well as improved angiogenesis in a coculture model in vitro. Efficacy in an in vivo wound healing model was assessed in diabetic mice. FGF2-PEG2k-FGF2 increased granulation tissue and blood vessel density in the wound bed compared to FGF2. The results suggest that this rationally designed construct may be useful for improving the fibroblast matrix formation and angiogenesis in chronic wound healing. PMID:26731578

  20. Fibroblast growth factor 2 dimer with superagonist in vitro activity improves granulation tissue formation during wound healing.

    PubMed

    Decker, Caitlin G; Wang, Yu; Paluck, Samantha J; Shen, Lu; Loo, Joseph A; Levine, Alex J; Miller, Lloyd S; Maynard, Heather D

    2016-03-01

    Site-specific chemical dimerization of fibroblast growth factor 2 (FGF2) with the optimal linker length resulted in a FGF2 homodimer with improved granulation tissue formation and blood vessel formation at exceptionally low concentrations. Homodimers of FGF2 were synthesized through site-specific linkages to both ends of different molecular weight poly(ethylene glycols) (PEGs). The optimal linker length was determined by screening dimer-induced metabolic activity of human dermal fibroblasts and found to be that closest to the inter-cysteine distance, 70 Å, corresponding to 2 kDa PEG. A straightforward analysis of the kinetics of second ligand binding as a function of tether length showed that, as the polymerization index (the number of monomer repeat units in the polymer, N) of the tether decreases, the mean time for second ligand capture decreases as ∼N(3/2), leading to an enhancement of the number of doubly bound ligands in steady-state for a given (tethered) ligand concentration. FGF2-PEG2k-FGF2 induced greater fibroblast metabolic activity than FGF2 alone, all other dimers, and all monoconjugates, at each concentration tested, with the greatest difference observed at low (0.1 ng/mL) concentration. FGF2-PEG2k-FGF2 further exhibited superior activity compared to FGF2 for both metabolic activity and migration in human umbilical vein endothelial cells, as well as improved angiogenesis in a coculture model in vitro. Efficacy in an in vivo wound healing model was assessed in diabetic mice. FGF2-PEG2k-FGF2 increased granulation tissue and blood vessel density in the wound bed compared to FGF2. The results suggest that this rationally designed construct may be useful for improving the fibroblast matrix formation and angiogenesis in chronic wound healing.

  1. Dimer formation and conformational flexibility ensure cytoplasmic stability and nuclear accumulation of Elk-1.

    PubMed

    Evans, Emma L; Saxton, Janice; Shelton, Samuel J; Begitt, Andreas; Holliday, Nicholas D; Hipskind, Robert A; Shaw, Peter E

    2011-08-01

    The ETS (E26) protein Elk-1 serves as a paradigm for mitogen-responsive transcription factors. It is multiply phosphorylated by mitogen-activated protein kinases (MAPKs), which it recruits into pre-initiation complexes on target gene promoters. However, events preparatory to Elk-1 phosphorylation are less well understood. Here, we identify two novel, functional elements in Elk-1 that determine its stability and nuclear accumulation. One element corresponds to a dimerization interface in the ETS domain and the second is a cryptic degron adjacent to the serum response factor (SRF)-interaction domain that marks dimerization-defective Elk-1 for rapid degradation by the ubiquitin-proteasome system. Dimerization appears to be crucial for Elk-1 stability only in the cytoplasm, as latent Elk-1 accumulates in the nucleus and interacts dynamically with DNA as a monomer. These findings define a novel role for the ETS domain of Elk-1 and demonstrate that nuclear accumulation of Elk-1 involves conformational flexibility prior to its phosphorylation by MAPKs.

  2. Functionalization with C-terminal cysteine enhances transfection efficiency of cell-penetrating peptides through dimer formation

    SciTech Connect

    Amand, Helene L.

    2012-02-17

    Highlights: Black-Right-Pointing-Pointer Reversible CPP dimerisation is a simple yet efficient strategy to improve delivery. Black-Right-Pointing-Pointer Dimer formation enhances peptiplex stability, resulting in increased transfection. Black-Right-Pointing-Pointer By dimerisation, the CPP EB1 even gain endosomal escape properties while lowering cytotoxicity. -- Abstract: Cell-penetrating peptides have the ability to stimulate uptake of macromolecular cargo in mammalian cells in a non-toxic manner and therefore hold promise as efficient and well tolerated gene delivery vectors. Non-covalent peptide-DNA complexes ('peptiplexes') enter cells via endocytosis, but poor peptiplex stability and endosomal entrapment are considered as main barriers to peptide-mediated delivery. We explore a simple, yet highly efficient, strategy to improve the function of peptide-based vectors, by adding one terminal cysteine residue. This allows the peptide to dimerize by disulfide bond formation, increasing its affinity for nucleic acids by the 'chelate effect' and, when the bond is reduced intracellularly, letting the complex dissociate to deliver the nucleic acid. By introducing a single C-terminal cysteine in the classical CPP penetratin and the penetratin analogs PenArg and EB1, we show that this minor modification greatly enhances the transfection capacity for plasmid DNA in HEK293T cells. We conclude that this effect is mainly due to enhanced thermodynamic stability of the peptiplexes as endosome-disruptive chloroquine is still required for transfection and the effect is more pronounced for peptides with lower inherent DNA condensation capacity. Interestingly, for EB1, addition of one cysteine makes the peptide able to mediate transfection in absence of chloroquine, indicating that dimerisation can also improve endosomal escape properties. Further, the cytotoxicity of EB1 peptiplexes is considerably reduced, possibly due to lower concentration of free peptide dimer resulting from

  3. Synthetic control to achieve lanthanide(III)/pyrimidine-4,6-dicarboxylate compounds by preventing oxalate formation: structural, magnetic, and luminescent properties.

    PubMed

    Cepeda, Javier; Balda, Rolindes; Beobide, Garikoitz; Castillo, Oscar; Fernández, Joaquín; Luque, Antonio; Pérez-Yáñez, Sonia; Román, Pascual

    2012-07-16

    Control over the synthetic conditions in many metal/diazinedicarboxylato systems is crucial to prevent oxalate formation, since dicarboxylato ligands easily undergo degradation in the presence of metal salts. We report here an efficient route to obtain oxalato-free compounds for the lanthanide/pyrimidine-4,6-dicarboxylato (pmdc) system on the basis of the reaction temperature and nonacidic pH or oxygen free atmosphere. Two different crystal architectures have been obtained: {[Ln(μ-pmdc)(1.5)(H(2)O)(3)]·xH(2)O}(n) (1-Ln) and {[Ln(2)(μ(4)-pmdc)(2)(μ-pmdc)(H(2)O)(2)]·H(2)O}(n) (2-Ln) with Ln(III) = La-Yb, except Pm. Both crystal structures are built from distorted two-dimensional honeycomb networks based on the recurrent double chelating mode established by the pmdc. In compounds 1-Ln, the tricapped trigonal prismatic coordination environment of the lanthanides is completed by three water molecules, precluding a further increase in the dimensionality. Crystallization water molecules are arranged in the interlamellar space, giving rise to highly flexible supramolecular clusters that are responsible for the modulation found in compound 1-Gd. Two of the coordinated water molecules are replaced by nonchelating carboxylate oxygen atoms of pmdc ligands in compounds 2-Ln, joining the metal-organic layers together and thus providing a compact three-dimensional network. The crystal structure of the compounds is governed by the competition between two opposing factors: the ionic size and the reaction temperature. The lanthanide contraction rejects the sterically hindered coordination geometries whereas high-temperature entropy driven desolvation pathway favors the release of solvent molecules leading to more compact frameworks. The characteristic luminescence of the Nd, Eu, and Tb centers is improved when moving from 1-Ln to 2-Ln compounds as a consequence of the decrease of the O-H oscillators. The magnetic properties of the compounds are dominated by the spin

  4. A short sequence motif in the 5' leader of the HIV-1 genome modulates extended RNA dimer formation and virus replication.

    PubMed

    van Bel, Nikki; Das, Atze T; Cornelissen, Marion; Abbink, Truus E M; Berkhout, Ben

    2014-12-19

    The 5' leader of the HIV-1 RNA genome encodes signals that control various steps in the replication cycle, including the dimerization initiation signal (DIS) that triggers RNA dimerization. The DIS folds a hairpin structure with a palindromic sequence in the loop that allows RNA dimerization via intermolecular kissing loop (KL) base pairing. The KL dimer can be stabilized by including the DIS stem nucleotides in the intermolecular base pairing, forming an extended dimer (ED). The role of the ED RNA dimer in HIV-1 replication has hardly been addressed because of technical challenges. We analyzed a set of leader mutants with a stabilized DIS hairpin for in vitro RNA dimerization and virus replication in T cells. In agreement with previous observations, DIS hairpin stability modulated KL and ED dimerization. An unexpected previous finding was that mutation of three nucleotides immediately upstream of the DIS hairpin significantly reduced in vitro ED formation. In this study, we tested such mutants in vivo for the importance of the ED in HIV-1 biology. Mutants with a stabilized DIS hairpin replicated less efficiently than WT HIV-1. This defect was most severe when the upstream sequence motif was altered. Virus evolution experiments with the defective mutants yielded fast replicating HIV-1 variants with second site mutations that (partially) restored the WT hairpin stability. Characterization of the mutant and revertant RNA molecules and the corresponding viruses confirmed the correlation between in vitro ED RNA dimer formation and efficient virus replication, thus indicating that the ED structure is important for HIV-1 replication.

  5. Orbital-selective singlet dimer formation and suppression of double exchange in 4d and 5d systems

    NASA Astrophysics Data System (ADS)

    Streltsov, Sergey; Cao, Gang; Khomskii, Daniel

    One of the main mechanisms of ferromagnetic ordering in conducting materials is the double exchange (DE). It is usually supposed in DE model that the Hund's coupling JH is much larger than electron hopping t; in this case one stabilizes the state with maximum spin per pair of ions, which finally leads to ferromagnetism in bulk systems. We show that in the dimerized 4 d / 5 d transition metal oxides for which JH is reduced and t is in contrast enhanced, another situation is possible, when formation of the spin-singlets on delocalized orbitals is more favorable. This leads to suppression of the DE and to a strong decrease of the total spin. The model calculations using the dynamical mean-field theory show that this effect survives even in the extended systems, not only for dimers. Such a situation is realized, e.g., in Y5Mo2O12, CrO2 under pressure and in many other 4 d / 5 d based materials. Another mechanism, which may suppress DE and which is also typical for 4 d / 5 d compounds is the spin-orbit coupling (SOC). We show on the example of Ba5AlIr2O11, that in this system it is the combination of molecular-orbital formation and SOC that strongly decreases magnetic moment on Ir. Civil Research and Development Foundation via FSCX-14-61025-0.

  6. Localized dimerization and nucleoid binding drive gradient formation by the bacterial cell division inhibitor MipZ.

    PubMed

    Kiekebusch, Daniela; Michie, Katharine A; Essen, Lars-Oliver; Löwe, Jan; Thanbichler, Martin

    2012-05-11

    Protein gradients play a central role in the spatial organization of cells, but the mechanisms of their formation are incompletely understood. This study analyzes the determinants responsible for establishing bipolar gradients of the ATPase MipZ, a key regulator of division site placement in Caulobacter crescentus. We have solved the crystal structure of MipZ in different nucleotide states, dissected its ATPase cycle, and investigated its interaction with FtsZ, ParB, and the nucleoid. Our results suggest that the polar ParB complexes locally stimulate the formation of ATP-bound MipZ dimers, which are then retained near the cell poles through association with chromosomal DNA. Due to their intrinsic ATPase activity, dimers eventually dissociate into freely diffusible monomers that undergo spontaneous nucleotide exchange and are recaptured by ParB. These findings clarify the molecular function of a conserved gradient-forming system and reveal mechanistic principles that might be commonly used to sustain protein gradients within cells.

  7. Formation of macrocyclic lactones in the Paternò-Büchi dimerization reaction.

    PubMed

    Arimura, Junya; Mizuta, Tsutomu; Hiraga, Yoshikazu; Abe, Manabu

    2011-02-28

    Furan-2-ylmethyl 2-oxoacetates 1a,b, in which the furan ring and the carbonyl moiety were embedded intramolecularly, were synthesized from commercially available furan-2-ylmethanol and their photochemical reaction (hν > 290 nm) was investigated. Twelve-membered macrocyclic lactones 2a,b with C(i) symmetry including two oxetane-rings, which are the Paternò-Büchi dimerization products, were isolated in ca. 20% yield. The intramolecular cyclization products, such as 3-alkoxyoxetane and 2,7-dioxabicyclo[2.2.1]hept-5-ene derivatives, were not detected in the photolysate.

  8. Formation of the Antarctic ozone hole by the ClO dimer mechanism

    NASA Technical Reports Server (NTRS)

    Barrett, J. W.; Solomon, P. M.; De Zafra, R. L.; Jaramillo, M.; Emmons, L.

    1988-01-01

    New measurements of the low-altitude ClO profile, made during September 1987, are presented along with detailed observations of ozone depletion over McMurdo Station, Antarctica during the same period. The results show that both the rate and altitude range of ozone depletion can be quantitatively accounted for by a mechanism in which the ClO dimer is the important intermediary in the catalytic destruction of ozone. An alternative bromine mechanism appears capable of contributing only 5-15 percent to the ozone loss rate.

  9. On the adsorption and formation of Pt dimers on the CeO2(111) surface.

    PubMed

    Bruix, Albert; Nazari, Fariba; Neyman, Konstantin M; Illas, Francesc

    2011-12-28

    The direct adsorption of Pt(2) dimers on CeO(2)(111) and their formation from isolated adsorbed Pt atoms have been studied using periodic slab model calculations based on density functional theory and including the so-called on-site Hubbard parameter (GGA + U). In the most stable configuration Pt(2) is found to be almost parallel to the surface; the electronic ground state is closed shell and there is no evidence of charge transfer towards or from the surface. The formation of Pt(2) from two single adsorbed Pt atoms involves a rather small energy barrier of ~0.10 eV only. On the contrary, dissociation of adsorbed Pt(2) requires to overcome a considerable barrier of ~1.43 eV. This indicates that once Pt(2) is formed it will remain on the surface, thus likely triggering the growth of larger supported Pt particles.

  10. Equilibrium constants from spectrophotometric data: dimer formation in gaseous Br2.

    PubMed

    Tellinghuisen, Joel

    2008-07-03

    The equilibrium constant for the dimerization reaction, 2Br 2(g) right arrow over left arrow Br 4(g), is estimated using the classic spectrophotometric method with precise data and a multiwavelength fitting approach. The analysis is very sensitive to small errors in the data, requiring that parameters for the baseline absorption be included at each wavelength. To that end spectra for 18 Br 2 pressures in the range 6-119 Torr are augmented by six baseline scans to facilitate estimation of three baseline constants and two molar absorptivities at each wavelength, yielding K c = 2.5 +/- 0.4 L/mol at 22 degrees C. This value is more than double the only previous estimate, which was based on analysis of PVT data. With adoption of a literature estimate of Delta H degrees = -9.5 kJ/mol, the new K implies Delta S degrees = -51 J mol (-1) K (-1) (ideal gas, 1 bar reference). The spectra for monomer absorption (peak 227 nm) and dimer absorption (205 nm) are obtained with unprecedented precision.

  11. Crystal structure of N'-hy-droxy-pyrimidine-2-carboximidamide.

    PubMed

    Jasmine, Nithianantham Jeeva; Muthiah, Packianathan Thomas; Stanley, Nithianantham

    2014-10-01

    The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)° between the planes of the pyrimidine ring and the non-H atoms of the carboximidamide unit. The mol-ecule adopts an E configuration about the C=N double bond. In the crystal, adjacent mol-ecules are linked by pairs of N-H⋯O hydrogen bonds, forming inversion dimers with an R 2 (2)(10) ring motif. The dimers are further linked via N-H⋯N and O-H⋯N hydrogen bonds into a sheet structure parallel to the ac plane. The crystal structure also features N-H⋯O and weak C-H⋯O hydrogen bonds and offset π-π stacking inter-actions between adjacent pyrimidine rings [centroid-centroid distance = 3.622 (1) Å].

  12. Computational study of the hydration of sulfuric acid dimers: implications for acid dissociation and aerosol formation.

    PubMed

    Temelso, Berhane; Phan, Thuong Ngoc; Shields, George C

    2012-10-04

    We have investigated the thermodynamics of sulfuric acid dimer hydration using ab initio quantum mechanical methods. For (H(2)SO(4))(2)(H(2)O)(n) where n = 0-6, we employed high-level ab initio calculations to locate the most stable minima for each cluster size. The results presented herein yield a detailed understanding of the first deprotonation of sulfuric acid as a function of temperature for a system consisting of two sulfuric acid molecules and up to six waters. At 0 K, a cluster of two sulfuric acid molecules and one water remains undissociated. Addition of a second water begins the deprotonation of the first sulfuric acid leading to the di-ionic species (the bisulfate anion HSO(4)(-), the hydronium cation H(3)O(+), an undissociated sulfuric acid molecule, and a water). Upon the addition of a third water molecule, the second sulfuric acid molecule begins to dissociate. For the (H(2)SO(4))(2)(H(2)O)(3) cluster, the di-ionic cluster is a few kcal mol(-1) more stable than the neutral cluster, which is just slightly more stable than the tetra-ionic cluster (two bisulfate anions, two hydronium cations, and one water). With four water molecules, the tetra-ionic cluster, (HSO(4)(-))(2)(H(3)O(+))(2)(H(2)O)(2), becomes as favorable as the di-ionic cluster H(2)SO(4)(HSO(4)(-))(H(3)O(+))(H(2)O)(3) at 0 K. Increasing the temperature favors the undissociated clusters, and at room temperature we predict that the di-ionic species is slightly more favorable than the neutral cluster once three waters have been added to the cluster. The tetra-ionic species competes with the di-ionic species once five waters have been added to the cluster. The thermodynamics of stepwise hydration of sulfuric acid dimer is similar to that of the monomer; it is favorable up to n = 4-5 at 298 K. A much more thermodynamically favorable pathway forming sulfuric acid dimer hydrates is through the combination of sulfuric acid monomer hydrates, but the low concentration of sulfuric acid relative to

  13. The acrylonitrile dimer ion

    NASA Astrophysics Data System (ADS)

    Ervasti, Henri K.; Jobst, Karl J.; Burgers, Peter C.; Ruttink, Paul J. Ae; Terlouw, Johan K.

    2007-04-01

    Large energy barriers prohibit the rearrangement of solitary acrylonitrile ions, CH2CHCN+, into their more stable hydrogen-shift isomers CH2CCNH+ or CHCH-CNH+. This prompted us to examine if these isomerizations occur by self-catalysis in acrylonitrile dimer ions. Such ions, generated by chemical ionization experiments of acrylonitrile with an excess of carbon dioxide, undergo five dissociations in the [mu]s time frame, as witnessed by peaks at m/z 53, 54, 79, 80 and 105 in their metastable ion mass spectrum. Collision experiments on these product ions, deuterium labeling, and a detailed computational analysis using the CBS-QB3 model chemistry lead to the following conclusions: (i) the m/z 54 ions are ions CH2CHCNH+ generated by self-protonation in ion-dipole stabilized hydrogen-bridged dimer ions [CH2CHCN...H-C(CN)CH2]+ and [CH2CHCN...H-C(H)C(H)CN]+; the proton shifts in these ions are associated with a small reverse barrier; (ii) dissociation of the H-bridged ions into CH2CCNH+ or CHCH-CNH+ by self-catalysis is energetically feasible but kinetically improbable: experiment shows that the m/z 53 ions are CH2CHCN+ ions, generated by back dissociation; (iii) the peaks at m/z 79, 80 and 105 correspond with the losses of HCN, C2H2 and H, respectively. The calculations indicate that these ions are generated from dimer ions that have adopted the (much more stable) covalently bound "head-to-tail" structure [CH2CHCN-C(H2)C(H)CN]+; experiments indicate that the m/z 79 (C5H5N) and m/z 105 (C6H6N2) ions have linear structures but the m/z 80 (C4H4N2) ions consist of ionized pyrimidine in admixture with its stable pyrimidine-2-ylidene isomer. Acrylonitrile is a confirmed species in interstellar space and our study provides experimental and computational evidence that its dimer radical cation yields the ionized prebiotic pyrimidine molecule.

  14. Elucidation of the Dexter-Type Energy Transfer in DNA by Thymine-Thymine Dimer Formation Using Photosensitizers as Artificial Nucleosides.

    PubMed

    Antusch, Linda; Gaß, Nadine; Wagenknecht, Hans-Achim

    2017-01-24

    C-nucleosides of 4-methylbenzophenone, 4-methoxybenzophenone, and 2'-methoxyacetophenone were synthetically incorporated as internal photosensitizers into DNA double strands. This structurally new approach makes it possible to study the distance dependence of thymidine dimer formation because the site of photoinduced triplet energy transfer injection is clearly defined. The counterstrands to these modified strands lacked the phosphodiester bond between the two adjacent thymidines that are supposed to react with each other. Their dimerization could be evidenced by gel electrophoresis because the covalent connection by cyclobutane formation between the two thymidines changes the mobility. A shallow exponential distance dependence for the formation of thymidine dimers over up to 10 A-T base pairs was observed that agrees with a Dexter-type triplet-triplet energy transfer mechanism. Concomitantly, a significant amount of photoinduced DNA crosslinking was observed.

  15. Evidence for Watson-Crick and not Hoogsteen or wobble base pairing in the selection of nucleotides for insertion opposite pyrimidines and a thymine dimer by yeast DNA pol eta.

    PubMed

    Hwang, Hanshin; Taylor, John-Stephen

    2005-03-29

    We have recently reported that pyrene nucleotide is preferentially inserted opposite an abasic site, the 3'-T of a thymine dimer, and most undamaged bases by yeast DNA polymerase eta (pol eta). Because pyrene is a nonpolar molecule with no H-bonding ability, the unusually high efficiencies of dPMP insertion are ascribed to its superior base stacking ability, and underscore the importance of base stacking in the selection of nucleotides by pol eta. To investigate the role of H-bonding and base pair geometry in the selection of nucleotides by pol eta, we determined the insertion efficiencies of the base-modified nucleotides 2,6-diaminopurine, 2-aminopurine, 6-chloropurine, and inosine which would make a different number of H-bonds with the template base depending on base pair geometry. Watson-Crick base pairing appears to play an important role in the selection of nucleotide analogues for insertion opposite C and T as evidenced by the decrease in the relative insertion efficiencies with a decrease in the number of Watson-Crick H-bonds and an increase in the number of donor-donor and acceptor-acceptor interactions. The selectivity of nucleotide insertion is greater opposite the 5'-T than the 3'-T of the thymine dimer, in accord with previous work suggesting that the 5'-T is held more rigidly than the 3'-T. Furthermore, insertion of A opposite both Ts of the dimer appears to be mediated by Watson-Crick base pairing and not by Hoogsteen base pairing based on the almost identical insertion efficiencies of A and 7-deaza-A, the latter of which lacks H-bonding capability at N7. The relative efficiencies for insertion of nucleotides that can form Watson-Crick base pairs parallel those for the Klenow fragment, whereas the Klenow fragment more strongly discriminates against mismatches, in accord with its greater shape selectivity. These results underscore the importance of H-bonding and Watson-Crick base pair geometry in the selection of nucleotides by both pol eta and the

  16. Distinct sensory pathways in Vibrio cholerae El Tor and classical biotypes modulate cyclic dimeric GMP levels to control biofilm formation.

    PubMed

    Hammer, Brian K; Bassler, Bonnie L

    2009-01-01

    Quorum sensing (QS), or cell-cell communication in bacteria, is achieved through the production and subsequent response to the accumulation of extracellular signal molecules called autoinducers (AIs). To identify AI-regulated target genes in Vibrio cholerae El Tor (V. cholerae(El)), the strain responsible for the current cholera pandemic, luciferase expression was assayed in an AI(-) strain carrying a random lux transcriptional reporter library in the presence and absence of exogenously added AIs. Twenty-three genes were identified and shown to require the QS transcription factor, HapR, for their regulation. Several of the QS-dependent target genes, annotated as encoding hypothetical proteins, in fact encode HD-GYP proteins, phosphodiesterases that degrade the intracellular second messenger cyclic dimeric GMP (c-di-GMP), which is important for controlling biofilm formation. Indeed, overexpression of a representative QS-activated HD-GYP protein in V. cholerae(El) reduced the intracellular concentration of c-di-GMP, which in turn decreased exopolysaccharide production and biofilm formation. The V. cholerae classical biotype (V. cholerae(Cl)), which caused previous cholera pandemics and is HapR(-), controls c-di-GMP levels and biofilm formation by the VieA signaling pathway. We show that the VieA pathway is dispensable for biofilm formation in V. cholerae(El) but that restoring HapR in V. cholerae(Cl) reestablishes QS-dependent repression of exopolysaccharide production. Thus, different pandemic strains of V. cholerae modulate c-di-GMP levels and control biofilm formation in response to distinct sensory pathways.

  17. Prebiotic syntheses of purines and pyrimidines.

    PubMed

    Basile, B; Lazcano, A; Oró, J

    1984-01-01

    The work done in many laboratories during the last two decades has confirmed that hydrogen cyanide and cyanoacetylene are the two major precursors for the prebiotic synthesis of purines and pyrimidines, respectively. Although several different pathways for the synthesis of purines have been described, they are all variations of the initial mechanism proposed by Oró and Kimball, where hydrogen cyanide leads first to the formation of a 4,5-di-substituted imidazole derivative, and then to the closing of the purine ring with a C1 compound. A number of experiments have shown that purines and pyrimidines can also be obtained from methane, ammonia (nitrogen), and water mixtures, provided an activating source of energy (radiation, electric discharges, etc.) is available. However, in this case the yields are lower by about two orders of magnitude because of the intermediate formation of hydrogen cyanide and cyanoacetylene. The latter two compounds have been found in interstellar space, Titan and other bodies of the solar system. They were probably present in the primordial parent bodies from the solar nebula in concentrations of 10(-2) to 10(-3) M as inferred from recent calculations by Miller and coworkers obtained for the Murchison meteorite. These concentrations should have been sufficient to generate relatively large amounts of purine and pyrimidine bases on the primitive Earth.

  18. Thiamin Pyrimidine Biosynthesis in Candida albicans: A Remarkable Reaction between Histidine and Pyridoxal Phosphate

    SciTech Connect

    Lai, Rung-Yi; Huang, Siyu; Fenwick, Michael K.; Hazra, Amrita; Zhang, Yang; Rajashankar, Kanagalaghatta; Philmus, Benjamin; Kinsland, Cynthia; Sanders, Jennie Mansell; Ealick, Steven E.; Begley, Tadhg P.

    2012-06-26

    In Saccharomyces cerevisiae, thiamin pyrimidine is formed from histidine and pyridoxal phosphate (PLP). The origin of all of the pyrimidine atoms has been previously determined using labeling studies and suggests that the pyrimidine is formed using remarkable chemistry that is without chemical or biochemical precedent. Here we report the overexpression of the closely related Candida albicans pyrimidine synthase (THI5p) and the reconstitution and preliminary characterization of the enzymatic activity. A structure of the C. albicans THI5p shows PLP bound at the active site via an imine with Lys62 and His66 in close proximity to the PLP. Our data suggest that His66 of the THI5 protein is the histidine source for pyrimidine formation and that the pyrimidine synthase is a single-turnover enzyme.

  19. Dimers in nucleating vapors

    NASA Astrophysics Data System (ADS)

    Lushnikov, A. A.; Kulmala, M.

    1998-09-01

    The dimer stage of nucleation may affect considerably the rate of the nucleation process at high supersaturation of the nucleating vapor. Assuming that the dimer formation limits the nucleation rate, the kinetics of the particle formation-growth process is studied starting with the definition of dimers as bound states of two associating molecules. The partition function of dimer states is calculated by summing the Boltzmann factor over all classical bound states, and the equilibrium population of dimers is found for two types of intermolecular forces: the Lennard-Jones (LJ) and rectangular well+hard core (RW) potentials. The principle of detailed balance is used for calculating the evaporation rate of dimers. The kinetics of the particle formation-growth process is then investigated under the assumption that the trimers are stable with respect to evaporation and that the condensation rate is a power function of the particle mass. If the power exponent λ=n/(n+1) (n is a non-negative integer), the kinetics of the process is described by a finite set of moments of particle mass distribution. When the characteristic time of the particle formation by nucleation is much shorter than that of the condensational growth, n+2 universal functions of a nondimensional time define the kinetic process. These functions are calculated for λ=2/3 (gas-to-particle conversion in the free molecular regime) and λ=1/2 (formation of islands on surfaces).

  20. Nature and possible mechanisms of formation of potential mutations arising at emerging of thymine dimers after irradiation of double-stranded DNA by ultraviolet light

    NASA Astrophysics Data System (ADS)

    Grebneva, H. A.

    2003-01-01

    The mutagenesis under ultraviolet (UV)-irradiation is discussed. It is assumed, that the basic damages resulting in transitions, transversions, mutations of the frameshift and complex mutations are changes of the tautomeric state of the bases. The bases may be a part of dimers or may be not the dimer components. We consider such rare tautomeric states, which may influence the character of base pairing. A model of the formation of the above rare tautomeric forms of nucleotide bases under the UV-irradiation of the DNA is proposed. In the case of a radiation deexcitation of the DNA, which has absorbed the UV-quantum of the triplet energy level, there occur strong forced oscillations. They may result in changes of the lengths of hydrogen bonds between DNA bases. As a result, at H-bond shortening, the hydrogen atom may be almost in the center of H-bond. In the case of H-bond elongation, it may remain near the partner atom. Because of the H-bond breaking, during the formation of dimers, rare tautomeric forms of bases influencing the character of pairing can be realized. If a pair of the bases is not a part of dimer, then the only new stable configuration of the hydrogen atoms is the one that occurred at double-proton phototautomerism. It is shown that only those dimers are mutational, in which the change of a tautomeric state of the DNA bases have taken place. This is one of the differences between the proposed model and the standard one. The latter assumes, that from the point of view of ability of forming the mutations all the dimers are identical, and the DNA-polymerase is sometimes mistaken, incidentally building uncomplementary bases in. The consideration is only of qualitative character, it needs experimental verification, subsequent study by methods of quantum chemistry and theoretical physics. A list of problems to be studied in this respect is given.

  1. Dimer formation in radiation-irradiated aqueous solution of lysozyme studied by light-scattering-intensity measurement.

    PubMed

    Hashimoto, S; Seki, H; Masuda, T; Imamura, M; Kondo, M

    1981-07-01

    The reaction of lysozyme with OH., Br.-2 and e-aq, produced in an aqueous solution by pulsed electrons and gamma-rays, were investigated. Irradiated enzymes showed an increase in the light scattering intensity (LSI) which is proportional to the absorbed dose. Results obtained from SDS gel electrophoresis confirm dimerization of lysozyme, which is considered to be responsible for the increase in LSI. It was found that the rate constant of the dimerization of protein radicals produced in the reaction with OH. is 2K=(1.0 +/- 0.3) X 10(6)M-1 s-1 and the yield of the dimerization is 0.6 in G. The enzymatic activity of the dimer is shown to be reduced to about 30 per cent of that of the intact enzyme. It is concluded that the radiation-induced inactivation of lysozyme is largely due to dimerization.

  2. A deoxyribozyme that harnesses light to repair thymine dimers in DNA.

    PubMed

    Chinnapen, Daniel J-F; Sen, Dipankar

    2004-01-06

    In vitro selection was used to investigate whether nucleic acid enzymes are capable of catalyzing photochemical reactions. The reaction chosen was photoreactivation of thymine cyclobutane dimers in DNA by using serotonin as cofactor and light of wavelengths longer than the absorption spectrum of DNA. Curiously, the dominant single-stranded DNA sequence selected, UV1A, was found to repair its internal thymine dimer substrate efficiently even in the absence of serotonin or any other cofactor. UV1C, a 42-nucleotide fragment of UV1A, repaired the thymine dimer substrate in trans (k(cat)/k(uncat) = 2.5 x 10(4)), showing optimal activity with 305 nm light and thus resembling naturally occurring photolyase enzymes. Mechanistic investigation of UV1C indicated that its catalytic role likely exceeded the mere positioning of the substrate in a conformation favorable for photoreactivation. A higher-order structure, likely a quadruplex, formed by specific guanine bases within the deoxyribozyme, was implicated as serving as a light-harvesting antenna, with photoreactivation of the thymine dimer proceeding possibly via electron donation from an excited guanine base. In a primordial "RNA world," self-replicating nucleic acid populations may have been vulnerable to deactivation via UV light-mediated pyrimidine dimer formation. Photolyase nucleic acid enzymes such as the one described here could thus have played a role in preserving the integrity of such an RNA world.

  3. Dimerization Mechanism of Alzheimer Aβ40 Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation.

    PubMed

    Nguyen, Phuong H; Sterpone, Fabio; Pouplana, Ramon; Derreumaux, Philippe; Campanera, Josep M

    2016-12-01

    Amyloid beta (Aβ) oligomerization is associated with the origin and progression of Alzheimer's disease (AD). While the A2V mutation enhances aggregation kinetics and toxicity, mixtures of wild-type (WT) and A2V, and also WT and A2T, peptides retard fibril formation and protect against AD. In this study, we simulate the equilibrium ensemble of WT:A2T Aβ40 dimer by means of extensive atomistic replica exchange molecular dynamics and compare our results with previous equivalent simulations of A2V:A2V, WT:WT, and WT:A2V Aβ40 dimers for a total time scale of nearly 0.1 ms. Qualitative comparison of the resulting thermodynamic properties, such as the relative binding free energies, with the reported experimental kinetic and thermodynamic data affords us important insight into the conversion from slow-pathway to fast-pathway dimer conformations. The crucial reaction coordinate or driving force of such transformation turns out to be related to hydrophobic interpeptide interactions. Analysis of the equilibrium ensembles shows that the fast-pathway conformations contain interpeptide out-of-register antiparallel β-sheet structures at short interpeptide distances. In contrast, the slow-pathway conformations are formed by the association of peptides at large interpeptide distances and high intrapeptide compactness, such as conformations containing intramolecular three-stranded β-sheets which sharply distinguish fast (A2V:A2V and WT:WT) and slow (WT:A2T and WT:A2V) amyloid-forming sequences. Also, this analysis leads us to predict that a molecule stabilizing the intramolecular three-stranded β-sheet or inhibiting the formation of an interpeptide β-sheet spanning residues 17-20 and 31-37 would further reduce fibril formation and probably the cytotoxicity of Aβ species.

  4. The impact of thermal treatment on the stability of freeze dried amorphous pharmaceuticals: I. Dimer formation in sodium ethacrynate.

    PubMed

    Wang, Bingquan; Pikal, Michael J

    2010-02-01

    The objective of this study was to investigate the impact of heat treatment (annealing) on the molecular mobility and chemical stability of dried sodium ethacrynate (ECA). ECA was lyophilized with sucrose or trehalose, and some samples were held as control while others were annealed at temperatures below T(g). Enthalpy recovery was studied with DSC and free volume was estimated based on density measurements. Global mobility was measured by the thermal activity monitor (TAM), and fast local mobility was studied with neutron backscattering. Formation of ECA dimer was measured by reverse phase HPLC. Maximum enthalpy recovery and minimum fictive temperature were observed at about T(g)-15 degrees C for both ECA/saccharide formulations. Annealing ECA in amorphous solids improved chemical stability, as shown by the decrease in degradation rate constant relative to the control. Annealed samples exhibited larger structural relaxation time than the control, and thus annealing decreased global mobility in the system. However, annealing does not significantly impact the local mobility. Chemical stability correlates with structural relaxation time, fictive temperature, and free volume, which suggests that improved stability is mainly a result of the reduced global mobility upon annealing.

  5. Formation of trans-2-[4-(Dimethylamino)Styryl]-3-Ethyl-1,3-Benzothiazolium Perchlorate Dimers in the Presence of Sodium Polystyrene Sulfonate

    NASA Astrophysics Data System (ADS)

    Lavysh, A. V.; Maskevich, A. A.; Lugovskii, A. A.; Voropai, E. S.; Sulatskaya, A. I.; Kuznetsova, I. M.; Turoverov, K. K.

    2017-01-01

    The spectral properties of a novel thioflavin T derivative, trans-2-[4-(dimethylamino)styryl]-3-ethyl-1,3-benzothiazolium perchlorate (DMASEBT), were studied in aqueous solutions in the presence of sodium polystyrene sulfonate (SPS). It was shown that SPS either could interact with dye monomers or initiate the formation of non-fluorescent dye dimers depending on the concentration ratio of dye and polyelectrolyte. DMASEBT dimer formation in the presence of SPS produced a hypsochromic shift by 40 nm in the absorption spectrum and quenched fluorescence. A bathochromic shift of the absorption spectrum and an increase of the fluorescence intensity by an order of magnitude were observed if DMASEBT monomers interacted with SPS. Quantum-chemical analysis found that sandwich dimers (H-aggregates) were most stable. A comparison of DMASEBT spectra in the presence of SPS and amyloid fibrils showed that DMASEBT molecules were incorporated into amyloid fibrils as monomers. The spectral changes associated with this incorporation could not be explained by the formation of dye aggregates.

  6. One-electron oxidation pathway of thiols by peroxynitrite in biological fluids: bicarbonate and ascorbate promote the formation of albumin disulphide dimers in human blood plasma.

    PubMed Central

    Scorza, G; Minetti, M

    1998-01-01

    Recent studies have shown that peroxynitrite oxidizes thiol groups through competing one- and two-electron pathways. The two-electron pathway is mediated by the peroxynitrite anion and prevails quantitatively over the one-electron pathway, which is mediated by peroxynitrous acid or a reactive species derived from it. In CO2-containing fluids the oxidation of thiols might follow a different mechanism owing to the rapid formation of a different oxidant, the nitrosoperoxycarbonate anion (ONOOCO2(-)). Here we present evidence that in blood plasma peroxynitrite induces the formation of a disulphide cross-linked protein identified by immunological (anti-albumin antibodies) and biochemical criteria (peptide mapping) as a dimer of serum albumin. The albumin dimer did not form in plasma devoid of CO2 and its formation was enhanced by ascorbate. However, analysis of thiol groups showed that reconstituting dialysed plasma with NaHCO3 protected protein thiols against the oxidation mediated by peroxynitrite and that the simultaneouspresence of ascorbate provided further protection. Ascorbate alone did not protect thiol groups from peroxynitrite-mediated oxidation. ESR spin-trapping studies with N-t-butyl-alpha-phenylnitrone (PBN) revealed that peroxynitrite induced the formation of protein thiyl radicals and their intensity was markedly decreased by plasma dialysis and restored by reconstitution with NaHCO3. PBN completely inhibited the formation of albumin dimer. Moreover, the addition of iron-diethyldithiocarbamate to plasma demonstrated that peroxynitrite induced the formation of protein S-nitrosothiols and/or S-nitrothiols. Our results are consistent with the hypothesis that NaHCO3 favours the one-electron oxidation of thiols by peroxynitrite with formation of thiyl radicals, ;NO2, and RSNOx. Thiyl radicals, in turn, are involved in chain reactions by which thiols are oxidized to disulphides. PMID:9425126

  7. Formation of a new copper(II) dimer through heterocyclic ligand ring opening reaction: Supramolecular features and magnetic properties

    NASA Astrophysics Data System (ADS)

    Gonçalves, Bruna Lisboa; Gervini, Vanessa Carratu; Flores, Alex Fabiani Claro; Junior, Jorge Luiz Pimentel; Bortoluzzi, Adailton João; Burrow, Robert Alan; Duarte, Rafael; da Silva, Robson Ricardo; Vicenti, Juliano Rosa de Menezes

    2017-01-01

    Two new compounds were synthesized and characterized in this work: the heterocycle (Z)-1-(4-(hydroxyimino)-3,5-dimethyl-1-(methylcarbamothioyl)-4,5-dihydro-1H-pyrazol-5-yl)-4-methylthiosemicarbazide and a copper(II) thiosemicarbazonato dimeric complex. Green prismatic single crystals of the dimer were obtained by the reaction of the heterocycle with copper(II) chloride dihydrate. Both compounds were essentially characterized by spectroscopic methods and X-ray diffraction crystallography. The crystal structures revealed molecules connected through supramolecular hydrogen bond interactions and copper(II) centers in a slightly distorted square-pyramidal environment. SQUID magnetometry performed for the dimer revealed both ferromagnetic and antiferromagnetic interactions in the studied complex, presenting a critical temperature of 19 K.

  8. 2-Acylamino- and 2,4-bis(acylamino)pyrimidines as supramolecular synthons analyzed by multiple noncovalent interactions. DFT, X-ray diffraction, and NMR spectral studies.

    PubMed

    Ośmiałowski, Borys; Kolehmainen, Erkki; Ikonen, Satu; Valkonen, Arto; Kwiatkowski, Adam; Grela, Izabela; Haapaniemi, Esa

    2012-11-02

    Intermolecular interactions of ten 2-acylamino and 2,4-bis(acylamino)pyrimidines (7 of which are previously unknown) have been investigated by X-ray structural, quantum chemical (DFT), and NMR spectral methods. Especially the concentration dependencies of the (1)H NMR chemical shifts and titrations with other molecules capable of multiple hydrogen bonding provided useful information regarding their association via triple or quadruple hydrogen bonding, which is controlled by the conformational preferences of 2-acylamino- and 2,4-bis(acylamino)pyrimidines. On comparison of the properties of 2-acylamino- and 2,4-bis(acylamino)pyrimidines with the corresponding pyridines, an additional nitrogen in the heterocyclic ring is the crucial factor in explaining the stability of various conformers and dimers of pyrimidines. Computational modeling of their dimerization (self-association) and heteroassociation supports the experimental findings. The substituent effects in 2-acylamino- and 2,4-bis(acylamino)pyrimidines are discussed via inter- and intramolecular terms. The subtle balance between several structural factors and their influence on the aggregation of studied pyrimidines was confirmed also by variable-temperature NMR and NOE experiments. X-ray structures of 2-methyl- and 2-adamantyl-CONH-pyrimidines revealed very different intermolecular interactions, showing the importance of the substituent size on the self-assembly process. As a whole NMR spectral, X-ray structural, and computational data of 2-acylamino- and 2,4-bis(acylamino)pyrimidines can be interpreted in terms of multiple intra-/intermolecular interactions.

  9. High sensitivity detection of cancer in vivo using a dual-controlled activation fluorescent imaging probe based on H-dimer formation and pH activation.

    PubMed

    Ogawa, Mikako; Kosaka, Nobuyuki; Regino, Celeste A S; Mitsunaga, Makoto; Choyke, Peter L; Kobayashi, Hisataka

    2010-05-01

    The key to improving the sensitivity of in vivo molecular imaging is to increase the target-to-background signal ratio (TBR). Optical imaging has a distinct advantage over other molecular imaging methods in that the fluorescent signal can be activated at the target thus reducing background signal. Previously, we found that H-dimer formation quenches fluorescence of xanthene fluorophores, and among these, TAMRA had the highest quenching ratio. Another approach to lowering background signal is to employ pH activation based on the photon-induced electron transfer (PeT) theory. We hypothesized that combining these two strategies could lead to greater quenching capacity than was possible with either probe alone. A pH-sensitive fluorophore, pHrodo or TAMRA was conjugated to the cancer targeting molecules, avidin (Av) and trastuzumab (Tra). As expected, both pHrodo and TAMRA formed H-dimers when conjugated to avidin or antibody and the dimerization resulted in efficient fluorescence quenching. In addition, pHrodo conjugated probes showed pH-dependent fluorescence activation. When the probes were used in an in vivo animal model, fluorescence endoscopy with Av-pHrodo depicted tumors with high TBR 1 h and 2 h after injection. Av-TAMRA also visualized tumors 1 h and 2 h after the injection, however, TBR was lower due to the background signal from non-specific binding 1 h after the injection as well as background fluorescence from the unbound agent. Thus, we demonstrate that a dual-controlled activatable optical probe based on the combination of H-dimer formation and pH activation can achieve high TBR at early time points during in vivo molecular imaging.

  10. Multiple spectroscopic and magnetic techniques show that chloroquine induces formation of the μ-oxo dimer of ferriprotoporphyrin IX.

    PubMed

    Kuter, David; Benjamin, Stefan J; Egan, Timothy J

    2014-04-01

    Interaction of the antimalarial chloroquine (CQ) with ferriprotoporphyrin IX, Fe(III)PPIX, was investigated in aqueous solution (pH7.4) and as a precipitate from aqueous medium at pH5.0. In solution, spectrophotometric titrations indicated strong association (logKobs 13.3±0.2) and a Job plot gave a stoichiometry of 1:2 CQ:Fe(III)PPIX. UV-visible absorbance and magnetic circular dichroism spectra of the complex were compared to various Fe(III)PPIX species. Close similarity to the spectra of the μ-oxo dimer, μ-[Fe(III)PPIX]2O, was revealed. The induction of this species by CQ was confirmed by magnetic susceptibility measurements using the Evans NMR method. The observed low-magnetic moment (2.25±0.02 μB) could only be attributed to antiferromagnetically coupled Fe(III) centers. The value was comparable to that of μ-[Fe(III)PPIX]2O (2.0±0.1 μB). In the solid-state, mass spectrometry confirmed the presence of CQ in the complex. Dissolution of this solid in aqueous solution (pH7.4) resulted in a solution with a UV-visible spectrum consistent with the same 1:2 stoichiometry observed in the Job plot. Magnetic susceptibility measurements made on the solid using an Evans balance produced a magnetic moment (2.3±0.1 μB) consistent with that in solution. Diffusion coefficients of CQ and its complex with Fe(III)PPIX were measured in aqueous solution (3.3±0.3 and 0.6±0.2×10(-10) m(2)·s(-1), respectively). The latter was used in conjunction with an empirical relationship between diffusion coefficient and molar volume to estimate the degree of aggregation. The findings suggest the formation of a 2:4 CQ:Fe(III)PPIX complex in aqueous solution at pH7.4.

  11. Studies on the Effect of Sub-zero Temperatures on the Formation of Extremely Low Volatility Dimer Esters in Secondary Organic Aerosol from Alpha-Pinene

    NASA Astrophysics Data System (ADS)

    Kristensen, Kasper; Normann Jensen, Louise; Bilde, Merete

    2016-04-01

    The oxidation of volatile organic compounds (VOC) is considered a major source of secondary organic aerosols (SOA) in the atmosphere. Recently, extremely low volatility organic compounds, or ELVOC, formed from the oxidation of VOCs have been shown to play a crucial role in new particle formation (Ehn et al., 2014). In addition, higher molecular weight dimer esters originating from the oxidation of the biogenic VOC alpha-pinene have been observed in both laboratory-generated and ambient SOA (Kristensen et al., 2013). The low volatility of the dimer esters along with an observed rapid formation makes these high molecular weight compounds likely candidates involved in new particle formation from the oxidation of alpha-pinene. Furthermore, laboratory experiments show that the dimer esters only form in the presence of ozone, thus may be used as tracers for the ozone-initiated oxidation of alpha-pinene, and are therefore indicative of enhanced anthropogenic activities. In this work, we present the results of a series of oxidation experiments performed in the newly constructed cold-room smog chamber at Aarhus University. This unique and state-of-the-art Teflon chamber allows for atmospheric simulations of the oxidation VOCs and subsequent SOA formation at temperatures down to -16 °C. In this study, ozonolysis and photochemical oxidations of alpha-pinene are performed at temperatures ranging from +20 to -16 °C. Chemical characterization of the formed SOA is performed using liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. The results show significant differences in the chemical composition related to the experiment temperature. In particularly, the concentration of the high molecular weight dimer esters showed to be highly affected by temperature. Interestingly, preliminary results show higher formation of dimer esters related to increased SOA formation rate, thus indicating that these particle-phase ELVOCs may be linked with new particle

  12. Quantifying Dimer and Trimer Formation of Tri-n-butyl Phosphates in Different Alkane Diluents: FTIR Study.

    PubMed

    Vo, Quynh N; Unangst, Jaclynn L; Nguyen, Hung D; Nilsson, Mikael

    2016-07-21

    Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous metal-ion-extracting reagents, is an important ligand used in solvent extraction processes for the recovery of uranium and plutonium from spent nuclear fuel, as well as other non-nuclear applications. Ligand-ligand and organic solvent-ligand interactions play an important role in these processes. The self-association behavior of TBP in various alkane diluents of different chain lengths (8, 12, and 16 carbons) and a branched alkane (iso-octane) was investigated by Fourier transform infrared spectroscopic measurements. By careful deconvolution of the spectra into multiple peaks, our results indicate that TBP self-associates to form not only dimers, as previous studies showed, but also trimers in the practical concentration range. Using a mathematical fitting procedure, the dimerization and trimerization constants were determined. As expected, these equilibrium constants are dependent on the solvent used. As the alkane chain for linear hydrocarbon solvents becomes longer, dimerization decreases whereas trimerization increases. For the more branched hydrocarbon, we observe a significantly higher dimerization constant. These effects are most likely due to the intermolecular van der Waals interactions between the butyl tails of each TBP molecule and the diluent hydrocarbon chain as all solvents in this study are relatively nonpolar.

  13. Ligand-free highly effective iron/copper co-catalyzed formation of dimeric aryl ethers or sulfides.

    PubMed

    Qu, Xiaoming; Li, Tingyi; Zhu, Yan; Sun, Peng; Yang, Hailong; Mao, Jincheng

    2011-07-21

    Highly selective coupling of diiodoarenes with phenols or phenthiols can be performed by using a low-cost, benign character and readily available Fe/Cu catalytic system in the absence of ligands. It is noteworthy that the desired dimeric aryl ethers or sulfides could be obtained in high yields by coupling between diiodoarenes and phenols, or diphenols with aryl iodides.

  14. Hypermutation of DPYD Deregulates Pyrimidine Metabolism and Promotes Malignant Progression

    PubMed Central

    Edwards, Lauren; Gupta, Rohit; Filipp, Fabian V.

    2016-01-01

    New strategies are needed to diagnose and target human melanoma. To this end, genomic analyses was performed to assess somatic mutations and gene expression signatures using a large cohort of human skin cutaneous melanoma (SKCM) patients from The Cancer Genome Atlas (TCGA) project to identify critical differences between primary and metastatic tumors. Interestingly, pyrimidine metabolism is one of the major pathways to be significantly enriched and deregulated at the transcriptional level in melanoma progression. In addition, dihydropyrimidine dehydrogenase (DPYD) and other important pyrimidine-related genes: DPYS, AK9, CAD, CANT1, ENTPD1, NME6, NT5C1A, POLE, POLQ, POLR3B, PRIM2, REV3L, and UPP2 are significantly enriched in somatic mutations relative to the background mutation rate. Structural analysis of the DPYD protein dimer reveals a potential hotspot of recurring somatic mutations in the ligand binding sites as well as the interfaces of protein domains that mediated electron transfer. Somatic mutations of DPYD are associated with upregulation of pyrimidine degradation, nucleotide synthesis, and nucleic acid processing while salvage and nucleotide conversion is downregulated in TCGA SKCM. PMID:26609109

  15. 6-Chloro-N 4,N 4-dimethyl­pyrimidine-2,4-diamine

    PubMed Central

    Pang, Yuan-Yuan; Yu, Kai; Sun, Bin; Guo, Dian-Shun

    2012-01-01

    The asymmetric unit of the title compound, C6H9ClN4, contains four independent mol­ecules (A, B, C and D). Their main difference is the torsion angles, ranging from 1.6 (5) to 5.9 (5)°, between the methyl group and the pyrimidine plane. A pair of inter­molecular N—H⋯N hydrogen bonds link mol­ecules A and C into a twisted dimer with a dihedral angle of 32.9 (1)° between the two pyrimidine rings, creating an R 2 2(8) motif. In the packing, each two mol­ecules of B, C and D form centrosymmetric dimers through two inter­molecular N—H⋯N hydrogen bonds, locally creating R 2 2(8) motifs. The dimers of C and D are alternately bridged by A into an infinite zigzag strip, locally creating two different R 2 2(8) motifs with dihedral angles of 32.9 (1) and 63.4 (1)° between the pyrimidine rings. Finally, these strips together with the dimers of B associate into a complicated three-dimensional framework. PMID:22590204

  16. A helical bundle in the N-terminal domain of the BLM helicase mediates dimer and potentially hexamer formation.

    PubMed

    Shi, Jing; Chen, Wei-Fei; Zhang, Bo; Fan, San-Hong; Ai, Xia; Liu, Na-Nv; Rety, Stephane; Xi, Xu-Guang

    2017-04-07

    Helicases play a critical role in processes such as replication or recombination by unwinding double-stranded DNA; mutations of these genes can therefore have devastating biological consequences. In humans, mutations in genes of three members of the RecQ family helicases (blm, wrn, and recq4) give rise to three strikingly distinctive clinical phenotypes: Bloom syndrome, Werner syndrome, and Rothmund-Thomson syndrome, respectively. However, the molecular basis for these varying phenotypic outcomes is unclear, in part because a full mechanistic description of helicase activity is lacking. Because the helicase core domains are highly conserved, it has been postulated that functional differences among family members might be explained by significant differences in the N-terminal domains, but these domains are poorly characterized. To help fill this gap, we now describe bioinformatics, biochemical, and structural data for three vertebrate BLM proteins. We pair high resolution crystal structures with SAXS analysis to describe an internal, highly conserved sequence we term the dimerization helical bundle in N-terminal domain (DHBN). We show that, despite the N-terminal domain being loosely structured and potentially lacking a defined three-dimensional structure in general, the DHBN exists as a dimeric structure required for higher order oligomer assembly. Interestingly, the unwinding amplitude and rate decrease as BLM is assembled from dimer into hexamer, and also, the stable DHBN dimer can be dissociated upon ATP hydrolysis. Thus, the structural and biochemical characterizations of N-terminal domains will provide new insights into how the N-terminal domain affects the structural and functional organization of the full BLM molecule.

  17. Metabolism of Pyrimidines and Pyrimidine Nucleosides by Salmonella typhimurium

    PubMed Central

    Beck, Christoph F.; Ingraham, John L.; Neuhard, Jan; Thomassen, Elisabeth

    1972-01-01

    The pathways by which uracil, cytosine, uridine, cytidine, deoxyuridine, and deoxycytidine are metabolized by Salmonella typhimurium are established. The various 5-fluoropyrimidine analogues are shown to exert their toxic effects only after having been converted to the nucleotide level, and these conversions are shown to be catalyzed by the same enzymes which similarly convert the natural substrates. Methods for isolating mutant strains blocked in various steps of metabolism of pyrimidine bases and nucleosides are described. PMID:4259664

  18. Characterization of mAb dimers reveals predominant dimer forms common in therapeutic mAbs

    PubMed Central

    Plath, Friederike; Ringler, Philippe; Graff-Meyer, Alexandra; Stahlberg, Henning; Lauer, Matthias E.; Rufer, Arne C.; Graewert, Melissa A.; Svergun, Dmitri; Gellermann, Gerald; Finkler, Christof; Stracke, Jan O.; Koulov, Atanas; Schnaible, Volker

    2016-01-01

    ABSTRACT The formation of undesired high molecular weight species such as dimers is an important quality attribute for therapeutic monoclonal antibody formulations. Therefore, the thorough understanding of mAb dimerization and the detailed characterization mAb dimers is of great interest for future pharmaceutical development of therapeutic antibodies. In this work, we focused on the analyses of different mAb dimers regarding size, surface properties, chemical identity, overall structure and localization of possible dimerization sites. Dimer fractions of different mAbs were isolated to a satisfactory purity from bulk material and revealed 2 predominant overall structures, namely elongated and compact dimer forms. The elongated dimers displayed one dimerization site involving the tip of the Fab domain. Depending on the stress applied, these elongated dimers are connected either covalently or non-covalently. In contrast, the compact dimers exhibited non-covalent association. Several interaction points were detected for the compact dimers involving the hinge region or the base of the Fab domain. These results indicate that mAb dimer fractions are rather complex and may contain more than one kind of dimer. Nevertheless, the overall appearance of mAb dimers suggests the existence of 2 predominant dimeric structures, elongated and compact, which are commonly present in preparations of therapeutic mAbs. PMID:27031922

  19. Quantifying Dimer and Trimer Formation by Tri-n-butyl Phosphates in n-Dodecane: Molecular Dynamics Simulations.

    PubMed

    Vo, Quynh N; Dang, Liem X; Nilsson, Mikael; Nguyen, Hung D

    2016-07-21

    Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous ligands, is an important extractant used in the solvent extraction process for the recovery of uranium and plutonium from spent nuclear fuel. Microscopic pictures of TBP isomerism and its behavior in n-dodecane diluent were investigated utilizing MD simulations with previously optimized force field parameters for TBP and n-dodecane. Potential mean force (PMF) calculations on a single TBP molecule show seven probable TBP isomers. Radial distribution functions (RDFs) of TBP suggest the existence of TBP trimers at high TBP concentrations in addition to dimers. 2D PMF calculations were performed to determine the angle and distance criteria for TBP trimers. The dimerization and trimerization constants of TBP in n-dodecane were obtained and match our own experimental values using the FTIR technique. The new insights into the conformational behaviors of the TBP molecule as a monomer and as part of an aggregate could greatly aid in the understanding of the complexation between TBP and metal ions in a solvent extraction system.

  20. An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telomeres

    PubMed Central

    Aihara, Hideki; Huang, Wai Mun; Ellenberger, Tom

    2007-01-01

    Summary The termini of linear chromosomes are protected by specialized DNA structures known as telomeres that also facilitate the complete replication of DNA ends. The simplest type of telomere is a covalently closed DNA hairpin structure found in linear chromosomes of prokaryotes and viruses. Bidirectional replication of a chromosome with hairpin telomeres produces a catenated circular dimer that is subsequently resolved into unit-length chromosomes by a dedicated DNA cleavage-rejoining enzyme known as a hairpin telomere resolvase (protelomerase). Here we report a crystal structure of the protelomerase TelK from Klebseilla oxytoca phage φKO2, in complex with the palindromic target DNA. The structure shows the TelK dimer destabilizes base pairing interactions to promote the refolding of cleaved DNA ends into two hairpin ends. We propose that the hairpinning reaction is made effectively irreversible by a unique protein-induced distortion of the DNA substrate that prevents re-ligation of the cleaved DNA substrate. PMID:17889664

  1. Influence of exogenous silicon on UV-B radiation-induced cyclobutane pyrimidine dimmers in soybean leaves and its alleviation mechanism.

    PubMed

    Chen, Jiana; Zhang, Mingcai; Eneji, A Egrinya; Li, Jianmin

    2016-06-01

    The DNA is particularly sensitive to UV-B radiation and can readily be damaged by UV-B stress, resulting to the formation of photoproducts like cyclobutane pyrimidine dimers (CPDs). Silicon has multifarious benefits to plants, especially under biotic and abiotic stress. In this study, we used soybean seedlings to determine whether silicon could alleviate damage to DNA caused by UV-B stress. Silicon significantly reduced the accumulation of CPDs, lessening the damage of UV-B stress to the seedlings by the following three mechanisms: (1) increasing the concentration of UV-B absorbing compounds to reduce damage; (2) strengthening the antioxidant capacity of plants represented by higher levels of non-enzymatic antioxidants and (3) increasing the photolyase gene expression, thus accelerating photorepair.

  2. Molecular approach to the mechanisms of C-C bond formation and cleavage on metal surfaces: Hydrogenolysis, homologation, and dimerization of ethylene over Ru/SiO sub 2 catalysts

    SciTech Connect

    Rodriguez, E.; Leconte, M.; Basset, J.M.; Tanaka, K. )

    1989-09-01

    At temperatures above ca. 50 C, over Ru/SiO{sub 2} catalysts and in the presence of hydrogen, ethylene undergoes hydrogenation, hydrogenolysis, homologation, and dimerization reactions. The influence of contact times and reaction temperatures on conversions and selectivities has been examined. At low temperatures (dimerization reaction. With increasing temperature, hydrogenolysis of ethylene to methane and homologation to propene increase. Hydrogenolysis and homologation seem to be mechanistically related in terms of elementary steps of C-C bond cleavage and formation; two mechanisms are proposed which involve either metallocarbene insertion-elimination reactions or formation and decomposition of dimetallacyclic intermediates. Several mechanisms are envisioned for dimerization of ethylene; experimental data seem to support a mechanism which involves formation and coupling of two ethylidene species.

  3. C-N bond formation under Cu-catalysis: synthesis and in vitro evaluation of N-aryl substituted thieno[2,3-d]pyrimidin-4(3H)-ones against chorismate mutase.

    PubMed

    Adepu, Raju; Shiva Kumar, K; Sandra, Sandhya; Rambabu, D; Rama Krishna, G; Malla Reddy, C; Kandale, Ajit; Misra, Parimal; Pal, Manojit

    2012-09-01

    A series of novel N-aryl substituted thieno[2,3-d]pyrimidin-4(3H)-ones were designed and synthesized as potential inhibitors of chorismate mutase. Synthesis of this class of compounds was carried out by using Cu-mediated C-N bond forming reaction between thieno[2,3-d]pyrimidin-4(3H)-ones and aryl boronic acids. The reaction can be performed in an open flask as the conversion was found to be not sensitive to the presence of air or atmospheric moisture. A range of compounds were prepared by using this method and single crystal X-ray diffraction study was performed using a representative compound. In vitro pharmacological data of some of the compounds synthesized along with dose response studies using active molecules are presented. In silico interactions of these molecules with chorismate mutase are also presented.

  4. Ultraviolet irradiation of DNA complexed with. alpha. /. beta. -type small, acid-soluble proteins from spores of Bacillus or Clostridium species makes spore photoproduct but not thymine dimers

    SciTech Connect

    Nicholson, W.L.; Setlow, B.; Setlow, P. )

    1991-10-01

    UV irradiation of complexes of DNA and an {alpha}/{beta}-type small, acid-soluble protein (SASP) from Bacillus subtilis spores gave decreasing amounts of pyrimidine dimers and increasing amounts of spore photoproduct as the SASP/DNA ratio was increased. The yields of pyrimidine dimers and spore photoproduct were < 0.2% and 8% of total thymine, respectively, when DNA saturated with SASP was irradiated at 254 nm with 30 kJ/m{sup 2}; in the absence of SASP the yields were reversed - 4.5% and 0.3%, respectively. Complexes of DNA with {alpha}/{beta}-type SASP from Bacillus cereus, Bacillus megaterium, or Clostridium bifermentans spores also gave spore photoproduct upon UV irradiation. However, incubation of these SASPs with DNA under conditions preventing complex formation or use of mutant SASPs that do not form complexes did not affect the photoproducts formed in vitro. These results suggest that the UV photochemistry of bacterial spore DNA in vivo is due to the binding of {alpha}/{beta}-type SASP, a binding that is known to cause a change in DNA conformation in vitro from the B form to the A form. The yields of spore photoproduct in vitro were significantly lower than in vivo, perhaps because of the presence of substances other than SASP in spores. It is suggested that as these factors diffuse out in the first minutes of spore germination, spore photoproduct yields become similar to those observed for irradiation of SASP/DNA complexes in vitro.

  5. Interruption of electronically excited Xe dimer formation by the photoassociation of Xe(6s[3/2]2)-Xe(5p6 1S0) thermal collision pairs

    NASA Astrophysics Data System (ADS)

    Galvin, T. C.; Wagner, C. J.; Eden, J. G.

    2016-06-01

    The diatomic collisional intermediate responsible for the formation of an electronically excited molecule by teratomic recombination has been observed in both the spectral and temporal domains by laser spectroscopy. We report experiments demonstrating thermal Xe(6s[3/2]2)-Xe(5p6 1S0) atomic collision pairs to be the immediate precursor to the formation of Xe 2∗ ( a 3 Σu + , A 1 Σu +) by the three body process: Xe∗(6s) + 2Xe ⟶ Xe 2∗ + Xe, where the asterisk denotes an excited electronic state. Photoassociating Xe(6s)-Xe atomic pairs by free ⟵ free transitions of the collision complex interrupts the production of the electronically excited Xe dimer, thereby suppressing Xe2 spontaneous emission in the vacuum ultraviolet (VUV, λ ˜ 172 nm, A 1 Σu + → X 1 Σg +). Intercepting Xe(6s)-Xe pairs before the complex is stabilized by the arrival of the third atom in the teratomic collision process selectively depletes the pair population in a specific Franck-Condon region determined by the probe laser wavelength (λ). Measurements of the variation of VUV emission suppression with λ provide a spectral signature of the [Xe(6s[3/2]2) - Xe(1S0)]∗ complex and map the probe laser wavelength onto the thermal energy (ɛ″) of the incoming collision pairs.

  6. Interruption of electronically excited Xe dimer formation by the photoassociation of Xe(6s[3/2]2)-Xe(5p(6) (1)S0) thermal collision pairs.

    PubMed

    Galvin, T C; Wagner, C J; Eden, J G

    2016-06-28

    The diatomic collisional intermediate responsible for the formation of an electronically excited molecule by teratomic recombination has been observed in both the spectral and temporal domains by laser spectroscopy. We report experiments demonstrating thermal Xe(6s[3/2]2)-Xe(5p(6) (1)S0) atomic collision pairs to be the immediate precursor to the formation of Xe2 (∗)(a(3)Σu (+),A(1)Σu (+)) by the three body process: Xe(∗)(6s) + 2Xe ⟶ Xe2 (∗) + Xe, where the asterisk denotes an excited electronic state. Photoassociating Xe(6s)-Xe atomic pairs by free ⟵ free transitions of the collision complex interrupts the production of the electronically excited Xe dimer, thereby suppressing Xe2 spontaneous emission in the vacuum ultraviolet (VUV, λ ∼ 172 nm, A(1)Σu (+)→X(1)Σg (+)). Intercepting Xe(6s)-Xe pairs before the complex is stabilized by the arrival of the third atom in the teratomic collision process selectively depletes the pair population in a specific Franck-Condon region determined by the probe laser wavelength (λ). Measurements of the variation of VUV emission suppression with λ provide a spectral signature of the [Xe(6s[3/2]2) - Xe((1)S0)](∗) complex and map the probe laser wavelength onto the thermal energy (ϵ″) of the incoming collision pairs.

  7. Formation of cyclobutane dimers and (6-4) photoproducts upon far-UV photolysis of 5-methylcytosine-containing dinucleotide monophosphates.

    PubMed

    Douki, T; Cadet, J

    1994-10-04

    The far-UV photochemistry of 5-methylcytosine, a minor DNA base, was studied in three dinucleoside monophosphates, including m5dCpT, Tpm5dC, and m5dCpdC. The model compounds were exposed to 254-nm radiation, and the resulting photoproducts were isolated by reverse-phase HPLC and characterized as cyclobutane dimers, (6-4) adducts, and the related Dewar valence isomers by UV, mass, and 1H NMR spectroscopies. The rate of formation of the different photoproducts was compared with those obtained by photolysis of TpT and the corresponding cytosine dinucleoside monophosphates, including dCpT, TpdC, and dCpdC. The formation of deaminated m5dC-containing photoproducts was observed in each of the far-UV irradiated solution of m5dCpT, Tpm5dC, and m5dCpdC. They were shown to be generated mainly through a photochemical process since methylation of the C5 atom of the cytosine ring appeared to dramatically decrease the deamination rate of the C5-C6 saturated photoproducts.

  8. Tracking Rh Atoms in Zeolite HY: First Steps of Metal Cluster Formation and Influence of Metal Nuclearity on Catalysis of Ethylene Hydrogenation and Ethylene Dimerization

    SciTech Connect

    Yang, Dong; Xu, Pinghong; Browning, Nigel D.; Gates, Bruce C.

    2016-07-07

    The initial steps of rhodium cluster formation from zeolite-supported mononuclear Rh(C2H4)2 complexes in H2 at 373 K and 1 bar were investigated by infrared and extended X-ray absorption fine structure spectroscopies and scanning transmission electron microscopy (STEM). The data show that ethylene ligands on the rhodium react with H2 to give supported rhodium hydrides and trigger the formation of rhodium clusters. STEM provided the first images of the smallest rhodium clusters (Rh2) and their further conversion into larger clusters. The samples were investigated in a plug-flow reactor as catalysts for the conversion of ethylene + H2 in a molar ratio of 4:1 at 1 bar and 298 K, with the results showing how the changes in catalyst structure affect the activity and selectivity; the rhodium clusters are more active for hydrogenation of ethylene than the single-site complexes, which are more selective for dimerization of ethylene to give butenes

  9. Dimerization of Human Growth Hormone by Zinc

    NASA Astrophysics Data System (ADS)

    Cunningham, Brian C.; Mulkerrin, Michael G.; Wells, James A.

    1991-08-01

    Size-exclusion chromatography and sedimentation equilibrium studies demonstrated that zinc ion (Zn2+) induced the dimerization of human growth hormone (hGH). Scatchard analysis of 65Zn2+ binding to hGH showed that two Zn2+ ions associate per dimer of hGH in a cooperative fashion. Cobalt (II) can substitute for Zn2+ in the hormone dimer and gives a visible spectrum characteristic of cobalt coordinated in a tetrahedral fashion by oxygen- and nitrogen-containing ligands. Replacement of potential Zn2+ ligands (His18, His21, and Glu174) in hGH with alanine weakened both Zn2+ binding and hGH dimer formation. The Zn2+-hGH dimer was more stable than monomeric hGH to denaturation in guanidine-HCl. Formation of a Zn2+-hGH dimeric complex may be important for storage of hGH in secretory granules.

  10. Role of Human DNA Polymerase kappa in Extension Opposite from a cis-syn Thymine Dimer

    SciTech Connect

    R Vasquez-Del Carpio; T Silverstein; S Lone; R Johnson; L Prakash; S Prakash; A Aggarwal

    2011-12-31

    Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase {Kappa} (Pol{Kappa}), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Pol{Kappa} in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Pol{Kappa} in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.

  11. Accumulation of the Cyclobutane Thymine Dimer in Defined Sequences of Free and Nucleosomal DNA

    DTIC Science & Technology

    2013-08-01

    luteus , Nature, 1980, 285, 634–641. 15 F. Bourre, G. Renault, P. C. Seawell and A. Sarasin, Distri- bution of ultraviolet-induced lesions in Simian...40, 2495–2501. 54 L. K. Gordon and W. A. Haseltine, Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4 and Micrococcus luteus UV

  12. Mechanism of Clathrate Formation through Binding Nature of Si-X and Ge-X dimers: ab initio Study

    NASA Astrophysics Data System (ADS)

    Tsumuraya, Kazuo; Eguchi, Haruki; Takenaka, Hiroyuki; Suzuki, Akihiko

    2003-03-01

    The Si-clathrates have been synthesized when alkaline or alkaline-earth atoms are coexisted with the host Si atoms, which is also the case for the Ge-clathrates. The I-encapsulating Si-clathrates have been also synthesized recently. In the case of the hydrate clathrates, the formation has been controlled by both the sizes and the hydrophobic interactions of the endohedral molecules.[1] We study the mechanism of the clathrate formation through the binding nature of the Si-X and Ge-X dimmers, where X is selected elements in the periodic table. We calculate the charge transfers (population analysis), the binding energies, and the bonding distances using the ab-initio molecular dynamics method with planewaves and pseudo-potentials. We discuss the mechanism of the formation comparing with that of hydrate clathrates and evaluate the stability of clathrates predicted by the present study. [1]E.Dendy Sloan,Jr, Clathrate Hydrates of Natural Gasses, Marcel Dekker, 1998.

  13. Potassium Hexacyanoferrate (III)-Catalyzed Dimerization of Hydroxystilbene: Biomimetic Synthesis of Indane Stilbene Dimers.

    PubMed

    Xie, Jing-Shan; Wen, Jin; Wang, Xian-Fen; Zhang, Jian-Qiao; Zhang, Ji-Fa; Kang, Yu-Long; Hui, You-Wei; Zheng, Wen-Sheng; Yao, Chun-Suo

    2015-12-18

    Using potassium hexacyanoferrate (III)-sodium acetate as oxidant, the oxidative coupling reaction of isorhapontigenin and resveratrol in aqueous acetone resulted in the isolation of three new indane dimers 4, 6, and 7, together with six known stilbene dimers. Indane dimer 5 was obtained for the first time by direct transformation from isorhapontigenin. The structures and relative configurations of the dimers were elucidated using spectral analysis, and their possible formation mechanisms were discussed. The results indicate that this reaction could be used as a convenient method for the semi-synthesis of indane dimers because of the mild conditions and simple reaction products.

  14. Oxidative cyclization, 1,4-benzothiazine formation and dimerization of 2-bromo-3-(glutathion-S-yl)hydroquinone.

    PubMed

    Monks, T J; Highet, R J; Lau, S S

    1990-07-01

    Several lines of evidence suggest that the renal-specific toxicity of quinol-linked GSH conjugates is probably a result of their metabolism by gamma-glutamyl transpeptidase and selective accumulation by proximal tubular cells. Transport of the resultant quinol-cysteine and/or cystein-S-ylglycine conjugate followed by oxidation to the quinone may be important steps in the mechanism of toxicity of these compounds. Factors modulating the intracellular and/or intralumenal concentration of the cystein-S-yl and cystein-S-ylglycine conjugate will, therefore, be important determinants of toxicity. We have now studied the gamma-glutamyl transpeptidase-mediated metabolism of 2-bromo-3-(glutathion-S-yl)hydroquinone. The product of this reaction, 2-bromo-3-(cystein-S-ylglycyl)hydroquinone, undergoes an intramolecular cyclization to yield a 1,4-benzothiazine derivative that retains the glycine residue. A similar cyclization reaction occurs with 2-bromo-3-(cystein-S-yl)hydroquinone, which is unstable in aqueous solutions and undergoes a pH-dependent rearrangement that requires initial oxidation to the quinone. UV spectroscopy revealed that, at neutral pH, further reaction results in the formation of a chromophore, consistent with 1,4-benzothiazine formation. This product arises via cyclization of the cysteine residue via an intramolecular 1,4 Michael addition. Further reaction results in the precipitation of a pigment that exhibits properties of a pH indicator. The pigment undergoes a marked pH-dependent bathochromic shift (approximately 100 nm); it is red in alkali (lambda max, 480 nm) and violet in acid (lambda max, 578 nm). These properties are similar to those of the trichochrome polymers that are formed during melanin biosynthesis from S-(3,4-dihydroxyphenylalanine)-L-cysteine. Because the intramolecular cyclization reactions remove the reactive quinone moiety from the molecules, they may be regarded as detoxication reactions. 1,4-Benzothiazine formation represents a novel

  15. The dimers of cyanamide

    NASA Astrophysics Data System (ADS)

    Moffat, J. B.

    Ab initio calculations have been performed on various dimeric forms of cyanamide. The "nondissociative" dimerization of cyanamide leads to cyclic molecules all of which are unstable with respect to cyanamide. However, the molecules produced by "dissociative" dimerization are stable relative to cyanamide. Dicyandiamide is found to be the most stable of nine dimeric configurations.

  16. Determination of pK(a)'s for thymol blue in aqueous medium: evidence of dimer formation.

    PubMed

    Balderas-Hernández, P; Ramírez, M T; Rojas-Hernández, A; Gutiérrez, A

    1998-08-01

    Formation constants for recrystallized thymol blue were determined in water, using the SQUAD and SUPERQUAD programs. The best model correlating spectrophotometric, potentiometric and conductimetric data was fitted with the dissociation of HL(-)=L(2-)+H(+)-log K=8.918+/-0.070 and H(3)L(2)(-)=2L(2-)+3H(+)-log K=29.806+/-0.133 with the SUPERQUAD program at variable low ionic strength (1.5x10(-4)-3.0x10(-4) M); and HL=L(2-)+H(+)-log K=8.9+/-0.000, H(3)L(2)(-) =2L(2-)+3H(+)-log K=30.730+/-0.032, H(4)L(2)=2L(2-)+4H(+)-log K=32.106+/-0.033 with SQUAD at 1.1 M ionic strength.

  17. Structural Basis for Dimer Formation of Human Condensin Structural Maintenance of Chromosome Proteins and Its Implications for Single-stranded DNA Recognition*

    PubMed Central

    Uchiyama, Susumu; Kawahara, Kazuki; Hosokawa, Yuki; Fukakusa, Shunsuke; Oki, Hiroya; Nakamura, Shota; Kojima, Yukiko; Noda, Masanori; Takino, Rie; Miyahara, Yuya; Maruno, Takahiro; Kobayashi, Yuji; Ohkubo, Tadayasu; Fukui, Kiichi

    2015-01-01

    Eukaryotic structural maintenance of chromosome proteins (SMC) are major components of cohesin and condensins that regulate chromosome structure and dynamics during cell cycle. We here determine the crystal structure of human condensin SMC hinge heterodimer with ∼30 residues of coiled coils. The structure, in conjunction with the hydrogen exchange mass spectrometry analyses, revealed the structural basis for the specific heterodimer formation of eukaryotic SMC and that the coiled coils from two different hinges protrude in the same direction, providing a unique binding surface conducive for binding to single-stranded DNA. The characteristic hydrogen exchange profiles of peptides constituted regions especially across the hinge-hinge dimerization interface, further suggesting the structural alterations upon single-stranded DNA binding and the presence of a half-opened state of hinge heterodimer. This structural change potentially relates to the DNA loading mechanism of SMC, in which the hinge domain functions as an entrance gate as previously proposed for cohesin. Our results, however, indicated that this is not the case for condensins based on the fact that the coiled coils are still interacting with each other, even when DNA binding induces structural changes in the hinge region, suggesting the functional differences of SMC hinge domain between condensins and cohesin in DNA recognition. PMID:26491021

  18. RNA Dimerization Promotes PKR Dimerization and Activation

    PubMed Central

    Heinicke, Laurie A.; Wong, C. Jason; Lary, Jeffrey; Nallagatla, Subba Rao; Diegelman-Parente, Amy; Zheng, Xiaofeng; Cole, James L.; Bevilacqua, Philip C.

    2009-01-01

    The double-stranded RNA (dsRNA)-activated protein kinase (PKR) plays a major role in the innate immune response in humans. PKR binds dsRNA non-sequence specifically and requires a minimum of 15 bp dsRNA for one protein to bind and 30 bp dsRNA to induce protein dimerization and activation by autophosphorylation. PKR phosphorylates eIF2α, a translation initiation factor, resulting in the inhibition of protein synthesis. We investigated the mechanism of PKR activation by an RNA hairpin with a number of base pairs intermediate between these 15 to 30 bp limits: HIV-I TAR RNA, a 23 bp hairpin with three bulges that is known to dimerize. To test whether RNA dimerization affects PKR dimerization and activation, TAR monomers and dimers were isolated from native gels and assayed for RNA and protein dimerization. To modulate the extent of dimerization, we included TAR mutants with different secondary features. Native gel mixing experiments and analytical ultracentrifugation indicate that TAR monomers bind one PKR monomer and that TAR dimers bind two or three PKRs, demonstrating that RNA dimerization drives the binding of multiple PKR molecules. Consistent with functional dimerization of PKR, TAR dimers activated PKR while TAR monomers did not, and RNA dimers with fewer asymmetrical secondary structure defects, as determined by enzymatic structure mapping, were more potent activators. Thus, the secondary structure defects in the TAR RNA stem function as antideterminants to PKR binding and activation. Our studies support that dimerization of a 15–30 bp hairpin RNA, which effectively doubles its length, is a key step in driving activation of PKR and provide a model for how RNA folding can be related to human disease. PMID:19445956

  19. D-Dimer elevation and adverse outcomes.

    PubMed

    Halaby, Rim; Popma, Christopher J; Cohen, Ander; Chi, Gerald; Zacarkim, Marcelo Rodrigues; Romero, Gonzalo; Goldhaber, Samuel Z; Hull, Russell; Hernandez, Adrian; Mentz, Robert; Harrington, Robert; Lip, Gregory; Peacock, Frank; Welker, James; Martin-Loeches, Ignacio; Daaboul, Yazan; Korjian, Serge; Gibson, C Michael

    2015-01-01

    D-Dimer is a biomarker of fibrin formation and degradation. While a D-dimer within normal limits is used to rule out the diagnosis of deep venous thrombosis and pulmonary embolism among patients with a low clinical probability of venous thromboembolism (VTE), the prognostic association of an elevated D-dimer with adverse outcomes has received far less emphasis. An elevated D-dimer is independently associated with an increased risk for incident VTE, recurrent VTE, and mortality. An elevated D-dimer is an independent correlate of increased mortality and subsequent VTE across a broad variety of disease states. Therefore, medically ill subjects in whom the D-dimer is elevated constitute a high risk subgroup in which the prospective evaluation of the efficacy and safety of antithrombotic therapy is warranted.

  20. The catalytic effect of water, water dimers and water trimers on H2S + (3)O2 formation by the HO2 + HS reaction under tropospheric conditions.

    PubMed

    Zhang, Tianlei; Yang, Chen; Feng, Xukai; Kang, Jiaxin; Song, Liang; Lu, Yousong; Wang, Zhiyin; Xu, Qiong; Wang, Wenliang; Wang, Zhuqing

    2016-06-29

    In this article, the reaction mechanisms of H2S + (3)O2 formation by the HO2 + HS reaction without and with catalyst X (X = H2O, (H2O)2 and (H2O)3) have been investigated theoretically at the CCSD(T)/6-311++G(3df,2pd)//B3LYP/6-311+G(2df,2p) level of theory, coupled with rate constant calculations by using conventional transition state theory. Our results show that in the presence of catalyst X (X = H2O, (H2O)2 and (H2O)3) into the channel of H2S + (3)O2 formation, the reactions between the SH radical and HO2(H2O)n (n = 1-3) complexes are more favorable than the corresponding reactions of the HO2 radical with HS(H2O)n (n = 1-3) complexes due to the lower barrier of the former reactions and the higher concentrations of HO2(H2O)n (n = 1-3) complexes. Meanwhile, the catalytic effect of water, water dimers and water trimers is mainly taken from the contribution of a single water vapor molecule, since the total effective rate constant of HO2H2O + HS and H2OHO2 + HS reactions was, respectively, larger by 7-9 and 9-12 orders of magnitude than that of SH + HO2(H2O)2 and SH + HO2(H2O)3 reactions. Besides, the enhancement factor of water vapor is only 0.37% at 240 K, while at high temperatures, such as 425 K, the positive water vapor effect is enhanced up to 38.00%, indicating that at high temperatures the positive water effect is obvious under atmospheric conditions. Overall, these results show how water and water clusters catalyze the gas phase reactions under atmospheric conditions.

  1. Universal four-Boson states in ultracold molecular gases: resonant effects in dimer-dimer collisions.

    PubMed

    D'Incao, J P; von Stecher, J; Greene, Chris H

    2009-07-17

    We study the manifestations of universal four-body physics in ultracold dimer-dimer collisions. We show that resonant features associated with three-body Efimov physics and dimer-dimer scattering lengths are universally related. The emergence of universal four-boson states allows for the tunability of the dimer-dimer interaction, thus enabling the future study of ultracold molecular gases with both attractive and repulsive interactions. Moreover, our study of the interconversion between dimers and Efimov trimers shows that B2+B2-->B3+B rearrangement reactions can provide an efficient trimer formation mechanism. Our analysis of the temperature dependence of this reaction provides an interpretation of the available experimental data and sheds light on the possible experimental realization of rearrangement processes in ultracold gases.

  2. Nucleobases and other Prebiotic Species from the Ultraviolet Irradiation of Pyrimidine in Astrophysical Ices

    NASA Technical Reports Server (NTRS)

    Sandford, S. A.; Nuevo, M.; Materese, C. K.; Milam, S. N.

    2012-01-01

    Nucleobases are N-heterocycles that are the informational subunits of DNA and RNA, and are divided into two families: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites and their extraterrestrial origin confirmed by isotope measurement. Although no Nheterocycles have ever been observed in the ISM, the positions of the 6.2-m interstellar emission features suggest a population of such molecules is likely to be present. In this work we study the formation of pyrimidine-based molecules, including nucleobases, as well as other species of prebiotic interest, from the ultraviolet (UV) irradiation of pyrimidine in combinations of H2O, NH3, CH3OH, and CH4 ices at low temperature, in order to simulate the astrophysical conditions under which prebiotic species may be formed in the interstellar medium and icy bodies of the Solar System. Experimental: Gas mixtures are prepared in a glass mixing line (background pressure approx. 10(exp -6)-10(exp -5) mbar). Relative proportions between mixture components are determined by their partial pressures. Gas mixtures are then deposited on an aluminum foil attached to a cold finger (15-20 K) and simultaneously irradiated with an H2 lamp emitting UV photons (Lyman and a continuum at approx.160 nm). After irradiation samples are warmed to room temperature, at which time the remaining residues are recovered to be analyzed with liquid and gas chromatographies. Results: These experiments showed that the UV irradiation of pyrimidine mixed in these ices at low temperature leads to the formation of several photoproducts derived from pyrimidine, including the nucleobases uracil and cytosine, as well as their precursors 4(3H)-pyrimidone and 4-aminopyrimidine (Fig. 1). Theoretical quantum calculations on the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in pure H2O ices are in agreement with their experimental formation pathways. In

  3. Nucleobases and Other Prebiotic Species from the UV Irradiation of Pyrimidine in Astrophysical Ices

    NASA Technical Reports Server (NTRS)

    Sandford, Scott; Materese, Christopher; Nuevo, Michel

    2012-01-01

    Nucleobases are aromatic N-heterocycles that constitute the informational subunits of DNA and RNA and are divided into two families: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites and their extraterrestrial origin confirmed by isotope measurement. Although no N-heterocycles have been individually identified in the ISM, the 6.2-micron interstellar emission feature seen towards many astronomical objects suggests a population of such molecules is likely present. We report on a study of the formation of pyrimidine-based molecules, including nucleobases and other species of prebiotic interest, from the ultraviolet (UV) irradiation of pyrimidine in low temperature ices containing H2O, NH3, C3OH, and CH4, to simulate the astrophysical conditions under which prebiotic species may be formed in the Solar System.

  4. Significant change of alignment effect by dimer formation in the dissociative energy transfer reaction of Ar(3P2)+(N2O)n and (H2O)n

    NASA Astrophysics Data System (ADS)

    Watanabe, D.; Ohoyama, H.; Matsumura, T.; Kasai, T.

    2006-12-01

    An alignment effect in the dissociative energy transfer reaction of Ar(P23)+(X2O)n(X=N,H) was directly measured using an oriented Ar(P23,MJ=2) beam. The chemiluminescence intensity of N2(B,Πg3) for (N2O)n and OH(A,Σ+2) for (H2O)n was measured as a function of the magnetic orientation field direction in the collision frame. The relative reaction cross section for each magnetic substate in the collision frame, σMJ', was determined. In both the reaction systems, it is observed that the dimer formation significantly enhances the alignment effect and decreases the reactivity, especially for σ∣1∣ and σ∣2∣. A significant contribution of rank 4 moment is recognized in the dimer reaction.

  5. Regioselectivity and competition of the Paternò-Büchi reaction and triplet-triplet energy transfer between triplet benzophenones and pyrimidines: control by triplet energy levels.

    PubMed

    Liu, Xiu-Ling; Wang, Jian-Bo; Tong, Yao; Song, Qin-Hua

    2013-09-23

    The photochemical reaction of a pyrimidine and a ketone occurs either as a Paternò-Büchi (PB) reaction or as energy transfer (ET) from the triplet ketone to the pyrimidine. It is rare for the two types of reactions to occur concurrently, and their competitive mechanism remains unknown. In this work, two classes of products, regioisomeric oxetane(s) (2, 3) from a PB reaction and three isomeric dimers of 5-fluoro-1,3-dimethyl uracil (FDMU) (4-6) from a photosensitized dimerization of FDMU, are obtained through the UV irradiation of FDMU with various benzophenones (BPs). The ratio of the two products (oxetanes to dimers) reveals that the two competitive reactions depend strongly on the triplet energy levels (ET ) of the BPs. The BPs with higher ET values lead to higher proportions of dimers, whereas those with lower ET values give higher proportions of oxetane(s), with the generation of just two regioisomeric oxetanes for the BP with the lowest ET of the eight BPs investigated. The ratio of the two oxetanes (2:3) decreases with the BP ET value. The competitive mechanism for the two types of photochemical reactions is demonstrated through quenching experiments and investigation of temperature effects. Kinetic analysis shows that the rate constants of the two [2+2] photocycloadditions are comparable. Furthermore, in combination with the results of previous studies, we have gained insight into the dependence of the photochemical type and the regioselectivity in the PB reaction on the triplet energy gaps (ΔE) between the pyrimidines and ketones. For ketones with higher ET values than the pyrimidines, the photochemical reaction is a photosensitized dimerization of the pyrimidine. In the opposite case, a PB reaction occurs, and the lower the ET of the ketones, the lower the ratio of oxetanes (2:3). When the ET of values of the ketones are close to those of the pyrimidines, the two reactions occur concurrently, and the higher the ET of the ketones, the higher the

  6. Enzymology of Pyrimidine Metabolism and Neurodegeneration.

    PubMed

    Vincenzetti, Silvia; Polzonetti, Valeria; Micozzi, Daniela; Pucciarelli, Stefania

    2016-01-01

    It is well known that disorders of pyrimidine pathways may lead to neurological, hematological, immunological diseases, renal impairments, and association with malignancies. Nucleotide homeostasis depends on the three stages of pyrimidine metabolism: de novo synthesis, catabolism and recycling of these metabolites. Cytidine and uridine, in addition to be used as substrates for pyrimidine nucleotide salvaging, also act as the precursors of cytidine triphosphate used in the biosynthetic pathway of both brain's phosphatidylcholine and phosphatidylethanolamine via the Kennedy cycle. The synthesis in the brain of phosphatidylcholine and other membrane phosphatides can utilize, in addition to glucose, three compounds present in the blood stream: choline, uridine, and a polyunsaturated fatty acids like docosahexaenoic acid. Some authors, using rat models, found that oral administration of two phospholipid precursors such as uridine and omega-3 fatty acids, along with choline from the diet, can increase the amount of synaptic membrane generated by surviving striatal neurons in rats with induced Parkinson's disease. Other authors found that in hypertensive rat fed with uridine and choline, cognitive deficit resulted improved. Uridine has also been recently considered as a neuroactive molecule, because of its involvement in important neurological functions by improving memory, sleep disorders, anti-epileptic effects, as well as neuronal plasticity. Cytidine and uridine are uptaken by the brain via specific receptors and successively salvaged to the corresponding nucleotides. The present review is devoted to the enzymology of pyrimidine pathways whose importance has attracted the attention of several researchers investigating on the mechanisms underlying the physiopathology of brain.

  7. Synthesis, structure and spectral and redox properties of new mixed ligand monomeric and dimeric Ru(II) complexes: predominant formation of the "cis-alpha" diastereoisomer and unusual 3MC emission by dimeric complexes.

    PubMed

    Murali, Mariappan; Palaniandavar, Mallayan

    2006-02-07

    The tetradentate ligands 1,8-bis(pyrid-2-yl)-3,6-dithiaoctane (pdto) and 1,8-bis(benzimidazol-2-yl)-3,6-dithiaoctane (bbdo) form the complexes [Ru(pdto)(mu-Cl)](2)(ClO(4))(2) 1 and [Ru(bbdo)(mu-Cl)](2)(ClO(4))(2) 2 respectively. The new di-mu-chloro dimers 1 and 2 undergo facile symmetrical bridge cleavage reactions with the diimine ligands 2,2'-bipyridine (bpy) and dipyridylamine (dpa) to form the six-coordinate complexes [Ru(pdto)(bpy)](ClO(4))(2) 3, [Ru(bbdo)(bpy)](ClO(4))(2) 4, [Ru(pdto)(dpa)](ClO(4))(2) 5 and [Ru(bbdo)(dpa)](ClO(4))(2) 6 and with the triimine ligand 2,2':6,2''-terpyridine (terpy) to form the unusual seven-coordinate complexes [Ru(pdto)(terpy)](ClO(4))(2) 7 and [Ru(bbdo)(terpy)](ClO(4))(2) 8. In 1 the dimeric cation [Ru(pdto)(mu-Cl)](2)(2+) is made up of two approximately octahedrally coordinated Ru(II) centers bridged by two chloride ions, which constitute a common edge between the two Ru(II) octahedra. Each ruthenium is coordinated also to two pyridine nitrogen and two thioether sulfur atoms of the tetradentate ligand. The ligand pdto is folded around Ru(II) as a result of the cis-dichloro coordination, which corresponds to a "cis-alpha" configuration [DeltaDelta/LambdaLambda(rac) diastereoisomer] supporting the possibility of some attractive pi-stacking interactions between the parallel py rings at each ruthenium atom. The ruthenium atom in the complex cations 3a and 4 exhibit a distorted octahedral coordination geometry composed of two nitrogen atoms of the bpy and the two thioether sulfur and two py/bzim nitrogen atoms of the pdto/bbdo ligand, which is actually folded around Ru(II) to give a "cis-alpha" isomer. The molecule of complex 5 contains a six-coordinated ruthenium atom chelated by pdto and dpa ligands in the expected distorted octahedral fashion. The (1)H and (13)C NMR spectral data of the complexes throw light on the nature of metal-ligand bonding and the conformations of the chelate rings, which indicates that the dithioether

  8. The cytoplasmic PASC domain of the sensor kinase DcuS of Escherichia coli: role in signal transduction, dimer formation, and DctA interaction

    PubMed Central

    Monzel, Christian; Degreif-Dünnwald, Pia; Gröpper, Christina; Griesinger, Christian; Unden, Gottfried

    2013-01-01

    The cytoplasmic PASC domain of the fumarate responsive sensor kinase DcuS of Escherichia coli links the transmembrane to the kinase domain. PASC is also required for interaction with the transporter DctA serving as a cosensor of DcuS. Earlier studies suggested that PASC functions as a hinge and transmits the signal to the kinase. Reorganizing the PASC dimer interaction and, independently, removal of DctA, converts DcuS to the constitutive ON state (active without fumarate stimulation). ON mutants were categorized with respect to these two biophysical interactions and the functional state of DcuS: type I-ON mutations grossly reorganize the homodimer, and decrease interaction with DctA. Type IIA-ON mutations create the ON state without grossly reorganizing the homodimer, whereas interaction with DctA is decreased. The type IIB-ON mutations were neither in PASC/PASC, nor in DctA/DcuS interaction affected, similar to fumarate activated wild-typic DcuS. OFF mutations never affected dimer stability. The ON mutations provide novel mechanistic insight: PASC dimerization is essential to silence the kinase. Reorganizing the homodimer and its interaction with DctA activate the kinase. The study suggests a novel ON homo-dimer conformation (type IIB) and an OFF conformation for PASC. Type IIB-ON corresponds to the fumarate induced wild-type conformation, representing an interesting target for structural biology. PMID:24039243

  9. Glycal Formation in Crystals of Uridine Phosphorylase

    SciTech Connect

    Paul, Debamita; O’Leary, Sen E.; Rajashankar, Kanagalaghatta; Bu, Weiming; Toms, Angela; Settembre, Ethan C.; Sanders, Jennie M.; Begley, Tadhg P.; Ealick, Steven E.

    2010-06-22

    Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2{prime}-deoxyuridine to 2{prime}-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2{prime}-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate, and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2{prime}. Crystals of bovine uridine phosphorylase treated with 2{prime}-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds.

  10. Differential DNA lesion formation and repair in heterochromatin and euchromatin

    PubMed Central

    Han, Chunhua; Srivastava, Amit Kumar; Cui, Tiantian; Wang, Qi-En; Wani, Altaf A.

    2016-01-01

    Discretely orchestrated chromatin condensation is important for chromosome protection from DNA damage. However, it is still unclear how different chromatin states affect the formation and repair of nucleotide excision repair (NER) substrates, e.g. ultraviolet (UV)-induced cyclobutane pyrimidine dimers (CPD) and the pyrimidine (6-4) pyrimidone photoproducts (6-4PP), as well as cisplatin-induced intrastrand crosslinks (Pt-GG). Here, by using immunofluorescence and chromatin immunoprecipitation assays, we have demonstrated that CPD, which cause minor distortion of DNA double helix, can be detected in both euchromatic and heterochromatic regions, while 6-4PP and Pt-GG, which cause major distortion of DNA helix, can exclusively be detected in euchromatin, indicating that the condensed chromatin environment specifically interferes with the formation of these DNA lesions. Mechanistic investigation revealed that the class III histone deacetylase SIRT1 is responsible for restricting the formation of 6-4PP and Pt-GG in cells, probably by facilitating the maintenance of highly condensed heterochromatin. In addition, we also showed that the repair of CPD in heterochromatin is slower than that in euchromatin, and DNA damage binding protein 2 (DDB2) can promote the removal of CPD from heterochromatic region. In summary, our data provide evidence for differential formation and repair of DNA lesions that are substrates of NER. Both the sensitivity of DNA to damage and the kinetics of repair can be affected by the underlying level of chromatin compaction. PMID:26717995

  11. The Photochemistry of Pyrimidine in Realistic Astrophysical Ices and the Production of Nucleobases

    NASA Astrophysics Data System (ADS)

    Nuevo, Michel; Materese, Christopher K.; Sandford, Scott A.

    2014-10-01

    Nucleobases, together with deoxyribose/ribose and phosphoric acid, are the building blocks of DNA and RNA for all known life. The presence of nucleobase-like compounds in carbonaceous chondrites delivered to the Earth raises the question of an extraterrestrial origin for the molecules that triggered life on our planet. Whether these molecules are formed in interstellar/protostellar environments, in small parent bodies in the solar system, or both, is currently unclear. Recent experiments show that the UV irradiation of pyrimidine (C4H4N2) in H2O-rich ice mixtures that contain NH3, CH3OH, or CH4 leads to the formation of the pyrimidine-based nucleobases uracil, cytosine, and thymine. In this work, we discuss the low-temperature UV irradiation of pyrimidine in realistic astrophysical ice mixtures containing H2O, CH3OH, and NH3, with or without CH4, to search for the production of nucleobases and other prebiotic compounds. These experiments show the presence of uracil, urea, glycerol, hexamethylenetetramine, small amino acids, and small carboxylic acids in all samples. Cytosine was only found in one sample produced from ices irradiated with a higher UV dose, while thymine was not found in any sample, even after irradiation with a higher UV dose. Results are discussed to evaluate the role of the photochemistry of pyrimidine in the inventory of organic molecules detected in meteorites and their astrophysical/astrobiological implications.

  12. The pyrimidine nucleotide biosynthetic pathway modulates production of biofilm determinants in Escherichia coli.

    PubMed

    Garavaglia, Marco; Rossi, Elio; Landini, Paolo

    2012-01-01

    Bacteria are often found in multicellular communities known as biofilms, which constitute a resistance form against environmental stresses. Extracellular adhesion and cell aggregation factors, responsible for bacterial biofilm formation and maintenance, are tightly regulated in response to physiological and environmental cues. We show that, in Escherichia coli, inactivation of genes belonging to the de novo uridine monophosphate (UMP) biosynthetic pathway impairs production of curli fibers and cellulose, important components of the bacterial biofilm matrix, by inhibiting transcription of the csgDEFG operon, thus preventing production of the biofilm master regulator CsgD protein. Supplementing growth media with exogenous uracil, which can be converted to UMP through the pyrimidine nucleotide salvage pathway, restores csgDEFG transcription and curli production. In addition, however, exogenous uracil triggers cellulose production, particularly in strains defective in either carB or pyrB genes, which encode enzymes catalyzing the first steps of de novo UMP biosynthesis. Our results indicate the existence of tight and complex links between pyrimidine metabolism and curli/cellulose production: transcription of the csgDEFG operon responds to pyrimidine nucleotide availability, while cellulose production is triggered by exogenous uracil in the absence of active de novo UMP biosynthesis. We speculate that perturbations in the UMP biosynthetic pathways allow the bacterial cell to sense signals such as starvation, nucleic acids degradation, and availability of exogenous pyrimidines, and to adapt the production of the extracellular matrix to the changing environmental conditions.

  13. Steric and electronic control over the reactivity of a thiolate-ligated Fe(II) complex with dioxygen and superoxide: reversible mu-oxo dimer formation.

    PubMed

    Theisen, Roslyn M; Shearer, Jason; Kaminsky, Werner; Kovacs, Julie A

    2004-11-29

    The reactivity between a thiolate-ligated five-coordinate complex [FeII(SMe2N4(tren))]+ (1) and dioxygen is examined in order to determine if O2 activation, resembling that of the metalloenzyme cytochrome P450, can be promoted even when O2 binds cis, as opposed to trans, to a thiolate. Previous work in our group showed that [FeII(SMe2N4(tren))]+ (1) reacts readily with superoxide (O2-) in the presence of a proton source to afford H2O2 via an Fe(III)-OOH intermediate, thus providing a biomimetic model for the metalloenzyme superoxide reductase (SOR). Addition of O2 to 1 affords binuclear mu-oxo-bridged [FeIII(SMe2N4(tren))]2(mu2-O)(PF6)2.3MeCN (3). At low temperatures, in protic solvents, an intermediate is detected, the details of which will be the subject of a separate paper. Although the thiolate ligand does not appear to perturb the metrical parameters of the unsupported mu-oxo bridge (Fe-O= 1.807(8) A, and Fe-O-Fe= 155.3(5) degrees fall in the usual range), it decreases the magnetic coupling between the irons (J=-28 cm(-1)) and creates a rather basic oxo site. Protonation of this oxo using strong (HBF4, HCl) or weak (HOAc, NH4PF6, LutNHCl) acids results in bridge cleavage to cleanly afford the corresponding monomeric anion-ligated (OAc- (6), or Cl- (7)) or solvent-ligated (MeCN (4)) derivatives. Addition of OH- converts [FeIII(SMe2N4(tren))(MeCN2+ (4) back to mu-oxo 3. Thus, mu-oxo bridge cleavage is reversible. The protonated mu-hydroxo-bridged intermediate is not observed. In an attempt to prevent mu-oxo dimer formation, and facilitate the observation of O2-bound intermediates, a bulkier tertiary amine ligand, tren-Et4= N-(2-amino-ethyl)-N-(2-diethylamino-ethyl)-N',N'-diethyl-ethane-1,2-diamine, and the corresponding [FeII(SMe2N4(tren-Et4))]+ (5) complex was synthesized and structurally characterized. Steric repulsive interactions create unusually long FeII-N(3,4) amine bonds in 5 (mean distance=2.219(1) A). The [(tren-Et4)N4SMe2]1- ligand is unable to

  14. Chemical evolution. XXIX - Pyrimidines from hydrogen cyanide

    NASA Technical Reports Server (NTRS)

    Ferris, J. P.; Joshi, P. C.; Lawless, J. G.

    1978-01-01

    Compounds obtained by hydrolysis of HCN oligomers formed by allowing pH 9.2, 0.1 M cyanide to stand at room temperature for 4 to 12 months were analyzed. Hydrolysis of HCN oligomers yielded 4,5-dihydroxypyrimidine and 5-hydroxyuracil; orotic acid was detected after hydrolysis at pH 8.5. A unified pathway from diaminofumaronitrile to the pyrimidines observed is suggested. As purines, pyrimidines and amino acids are released by hydrolysis of HCN oligomers in either acidic or mildly basic aqueous solutions, they could have been formed on the primitive earth in spite of fluctuations in pH. 4,5-dihydroxypyrimidines appear to be likely candidates for incorporation into primitive nucleic acids, as they should undergo Watson-Crick hydrogen bonding with adenine.

  15. Pyrimidine derivatives as potential agents acting on central nervous system.

    PubMed

    Kumar, Sanjiv; Deep, Aakash; Narasimhan, Balasubramanian

    2015-01-01

    Pyrimidine and its derivatives are present in many of the bioactive aromatic compounds that are of wide interest because of their diverse biological and clinical applications. The utility of pyrimidines as synthon for various biologically active compounds has given impetus to these studies. The review article aims to review the work reported on pharmacological activities of central nervous system (CNS) such as anticonvulsant and antidepressant, which created interest among researchers to synthesize variety of pyrimidine and their derivatives. The present study shows, objective of the work can be summarized as pyrimidine derivative constitute an important class of compounds for new drug development. These observations have been given novel idea for the development of new pyrimidine derivative that possess varied biological activities. This article aims to review the recent works on pyrimidine moiety together with the biological potential during the past year.

  16. Synthesis and spectral characterization of new bis(2-(pyrimidin-2-yl)ethoxy)alkanes and their pharmacological activity.

    PubMed

    Rani, Vangavaragu Jhansi; Aminedi, Raghavendra; Polireddy, Kishore; Jagadeeswarareddy, Kanala

    2012-08-01

    The pyrimidine nucleus is an important component of nucleic acids (DNA and RNA) and vitamins (B(2) and folic acid). It is evident from the literature that pyrimidine derivatives possess a wide spectrum of biological activities such as antioxidant, anticancer, antibacterial, and anti-inflammatory activities. On the basis of diverse biological activities, we attempted to synthesize a series of novel bis(2-(pyrimidin-2-yl)ethoxy)alkanes 5a-j in four steps with good yields. 2-Chloropyrimidine (1) was reacted with diethyl malonate in the presence of sodium hydride in dry dimethyl formamide to yield the intermediate diethyl 2-(pyrimidin-2-yl)malonate (2), which on further reaction with sodium chloride and dimethyl sulfoxide yielded ethyl 2-(pyrimidin-2-yl)ethanoate (3). Reduction with sodium borohydride (NaBH(4) ) resulted in the formation of 2-(pyrimidin-2-yl)ethanol (4). This was further reacted with various dibromoalkanes to obtain the title compounds 5a-j. In this current study, we evaluated the antioxidant properties of the title compounds using four in vitro test systems: the 2,2-diphenyl-2-picrylhydrazyl radical-, superoxide radical-, and hydroxyl radical-scavenging assays, and the anti-lipid peroxidation activity test. The title compounds showed promising antioxidant activity when compared to butylated hydroxytoluene. The potency of their antioxidant activity was mainly influenced by the alkyl fragment attached to 2-(pyrimidin-2-yl)ethanol. The ethyl and butyl fragments linked to oxygen led to increased antioxidant activity of the title compounds (i.e., 5b and 5d) in all our in vitro assays.

  17. Isoflavonoid Formation as an Indicator of UV Stress in Bean (Phaseolus vulgaris L.) Leaves 1

    PubMed Central

    Beggs, Christopher J.; Stolzer-Jehle, Andrea; Wellmann, Eckard

    1985-01-01

    Induction of the isoflavonoid pigment, coumestrol (3,9-dihydroxy-6H-benzofuro-[3,2-c][1] benzopyran-6-one), in primary leaves of beans (Phaseolus vulgaris L. var Saxa) by ultraviolet (UV) radiation was used as a quantifiable marker for UV damage to a plant system. Coumestrol was induced only by wavelengths below 300 nanometers and its formation could be reversed by treatment with white, but not red light after the UV irradiation period. Formation of coumestrol by UV could also be prevented over a period of 14 hours by simultaneous irradiation with blue light provided that the blue fluence rate was high enough. The results suggest that coumestrol formation is mediated via UV-induced pyrimidine dimer formation in the plant DNA and the photorepair properties of blue light are discussed with respect to possible increases in solar UV due to stratospheric ozone depletion. PMID:16664463

  18. Isoflavonoid formation as an indicator of UV stress in bean (Phaseolus vulgaris L. ) leaves

    SciTech Connect

    Beggs, C.J.; Stolzer-Jehle, A.; Wellmann, E.

    1985-11-01

    Induction of the isoflavonoid pigment, coumestrol (3,9-dihydroxy-6H-benzofuro-(3,2-c)(1) benzopyran-6-one), in primary leaves of beans (Phaseolus vulgaris L. var Saxa) by ultraviolet (UV) radiation was used as a quantifiable marker for UV damage to a plant system. Coumestrol was induced only by wavelengths below 300 nanometers and its formation could be reversed by treatment with white, but not red light after the UV irradiation period. Formation of coumestrol by UV could also be prevented over a period of 14 hours by simultaneous irradiation with blue light provided that the blue fluence rate was high enough. The results suggest that coumestrol formation is mediated via UV-induced pyrimidine dimer formation in the plant DNA and the photorepair properties of blue light are discussed with respect to possible increases in solar UV due to stratospheric ozone depletion.

  19. Photochemical dimerization of organic compounds

    DOEpatents

    Crabtree, Robert H.; Brown, Stephen H.; Muedas, Cesar A.; Ferguson, Richard R.

    1992-01-01

    At least one of selectivity and reaction rate of photosensitized vapor phase dimerizations, including dehydrodimerizations, hydrodimerizations and cross-dimerizations of saturated and unsaturated organic compounds is improved by conducting the dimerization in the presence of hydrogen or nitrous oxide.

  20. Isolation and characterization of pyrimidine-psoralen-pyrimidine photodiadducts from DNA. [Ultraviolet radiation

    SciTech Connect

    Kanne, D.; Straub, K.; Hearst, J.E.; Rapoport, H.

    1982-12-01

    The isolation and characterization of pyrimidine-psoralen-pyrimidine photodiadducts from DNA are reported for the first time. For each of the four psoralens studied, a single pair of diastereomeric thymidine-psoralen-thymidine photodiadducts, each with cis-syn stereochemistry, was found to account for > 90% of the diadducts formed. Additionally, pulse-chase experiments that establish that these photo cross-links are formed by cycloaddition of a second thymidine residue to the 3,4 double bond (pyrone side) of an initially formed 4',5' (furan-side) psoralen-thymidine photomonoadduct have been carried out.

  1. Unusual transformation of substituted-3-formylchromones to pyrimidine analogues: synthesis and antimicrobial activities of 5-(o-hydroxyaroyl)pyrimidines.

    PubMed

    Raj, Tilak; Singh, Narinder; Ishar, M P S

    2013-11-15

    Substituted-3-formylchromones (4a-e) on reaction with 1,3-bis-dimethylaminomethylene-thiourea (5) in refluxing toluene solution give novel substituted 5-(o-hydroxyaroyl)pyrimidines (6a-e) in high yields. A mechanistic rationalization of the formation of products (6a-e) is proffered. Antimicrobial activities of all the synthesized compounds (6a-e) were evaluated against various fungal and bacterial strains. Compound 6d display significant antifungal activity (MIC 15) against Geotrichum candidum in comparison fluconazole used as positive control. Some of the compounds also display good antibacterial activity. Cytotoxic profile of compound 6d against HeLa cells indicates that at concentration (20 μM) no significant cell death (~2%) was observed.

  2. Discovery tactics to mitigate toxicity risks due to reactive metabolite formation with 2-(2-hydroxyaryl)-5-(trifluoromethyl)pyrido[4,3-d]pyrimidin-4(3h)-one derivatives, potent calcium-sensing receptor antagonists and clinical candidate(s) for the treatment of osteoporosis.

    PubMed

    Kalgutkar, Amit S; Griffith, David A; Ryder, Tim; Sun, Hao; Miao, Zhuang; Bauman, Jonathan N; Didiuk, Mary T; Frederick, Kosea S; Zhao, Sabrina X; Prakash, Chandra; Soglia, John R; Bagley, Scott W; Bechle, Bruce M; Kelley, Ryan M; Dirico, Kenneth; Zawistoski, Michael; Li, Jianke; Oliver, Robert; Guzman-Perez, Angel; Liu, Kevin K C; Walker, Daniel P; Benbow, John W; Morris, Joel

    2010-06-21

    The synthesis and structure-activity relationship studies on 5-trifluoromethylpyrido[4,3-d]pyrimidin-4(3H)-ones as antagonists of the human calcium receptor (CaSR) have been recently disclosed [ Didiuk et al. ( 2009 ) Bioorg. Med. Chem. Lett. 19 , 4555 - 4559 ). On the basis of its pharmacology and disposition attributes, (R)-2-(2-hydroxyphenyl)-3-(1-phenylpropan-2-yl)-5-(trifluoromethyl)pyrido[4,3-d]pyrimidin-4(3H)-one (1) was considered for rapid advancement to first-in-human (FIH) trials to mitigate uncertainty surrounding the pharmacokinetic/pharmacodynamic (PK/PD) predictions for a short-acting bone anabolic agent. During the course of metabolic profiling, however, glutathione (GSH) conjugates of 1 were detected in human liver microsomes in an NADPH-dependent fashion. Characterization of the GSH conjugate structures allowed insight(s) into the bioactivation pathway, which involved CYP3A4-mediated phenol ring oxidation to the catechol, followed by further oxidation to the electrophilic ortho-quinone species. While the reactive metabolite (RM) liability raised concerns around the likelihood of a potential toxicological outcome, a more immediate program goal was establishing confidence in human PK predictions in the FIH study. Furthermore, the availability of a clinical biomarker (serum parathyroid hormone) meant that PD could be assessed side by side with PK, an ideal scenario for a relatively unprecedented pharmacologic target. Consequently, progressing 1 into the clinic was given a high priority, provided the compound demonstrated an adequate safety profile to support FIH studies. Despite forming identical RMs in rat liver microsomes, no clinical or histopathological signs prototypical of target organ toxicity were observed with 1 in in vivo safety assessments in rats. Compound 1 was also devoid of metabolism-based mutagenicity in in vitro (e.g., Salmonella Ames) and in vivo assessments (micronuclei induction in bone marrow) in rats. Likewise, metabolism

  3. DNA photochemistry: geometrically unconstrained pyrimidine (6-4) pyrimidone photoproducts do photoisomerize.

    PubMed

    Douki, Thierry; Rebelo-Moreira, Silvestre; Hamon, Nadège; Bayle, Pierre-Alain

    2015-01-16

    Structural features are of major importance for the formation of mutagenic photoproducts in DNA. It was recently reported that lack of constraints between two adjacent nucleosidic units prevents the conversion of pyrimidine (6-4) pyrimidone photoproducts into their Dewar valence isomers. We here report that this is not the case for the thymidine photoproducts which, although unconstrained, are quantitatively converted into photolysis products identified as Dewar valence isomers by mass spectrometry and NMR and infrared spectroscopies.

  4. Coexistence of spin ordering on ladders and spin dimer formation in a new-structure-type compound Sr2Co3S2O3

    NASA Astrophysics Data System (ADS)

    Lai, Kwing To; Valldor, Martin

    2017-03-01

    We report on the syntheses and characterizations of single crystalline and polycrystalline Sr2Co3S2O3 with a novel crystal structure type. It contains Co–O 2-leg rectangular ladders and necklace ladders. The two ladders share common legs and construct a hybrid spin ladder. A rare meridional heteroleptic octahedral coordination is found for the Co2+ ions in the 2-leg ladder. Within the necklace ladders, the Co2+ ions are in trans-octahedral coordination. An antiferromagnetic order is observed at TN ~ 267 K, while a broad maximum in magnetic susceptibility is found below TN. This relatively high ordering temperature among Co-based ladder compounds is related to the highly anisotropic mer-coordination of the Co2+ ions. The trans-octahedrally coordinated Co2+ ions, on the other hand, corresponds to the possible short-range magnetic correlations through dimers with an effective . This results in a rare situation that spin ordering and spin dimers coexist down to 2 K.

  5. Quantifying Dimer and Trimer Formation by Tri- n -butyl Phosphates in n -Dodecane: Molecular Dynamics Simulations

    SciTech Connect

    Vo, Quynh N.; Dang, Liem X.; Nilsson, Mikael; Nguyen, Hung D.

    2016-07-21

    Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous ligands, is an important extractant used in solvent extraction process for the recovery of uranium and plutonium from spent nuclear fuel. Microscopic pictures of TBP isomerism and its behavior in n-dodecane diluent were investigated utilizing MD simulations with previously optimized force field parameters for TBP and n-dodecane. Potential Mean Force (PMF) calculations on a single TBP molecule show seven probable TBP isomers. Radial Distribution Functions (RDF) of TBP suggests the existence of TBP trimers at high TBP concentrations in addition to dimers. 2D PMF calculations were performed to determine the angle and distance criteria for TBP trimers. The dimerization and trimerization constants of TBP in n-dodecane were obtained and match our own experimental values using FTIR technique. The new insights into the conformational behaviors of TBP molecule as a monomer and as part of an aggregate could greatly aid the understanding of the complexation between TBP and metal ions in solvent extraction system. The U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences funded the work performed by LXD.

  6. Coexistence of spin ordering on ladders and spin dimer formation in a new-structure-type compound Sr2Co3S2O3

    PubMed Central

    Lai, Kwing To; Valldor, Martin

    2017-01-01

    We report on the syntheses and characterizations of single crystalline and polycrystalline Sr2Co3S2O3 with a novel crystal structure type. It contains Co–O 2-leg rectangular ladders and necklace ladders. The two ladders share common legs and construct a hybrid spin ladder. A rare meridional heteroleptic octahedral coordination is found for the Co2+ ions in the 2-leg ladder. Within the necklace ladders, the Co2+ ions are in trans-octahedral coordination. An antiferromagnetic order is observed at TN ~ 267 K, while a broad maximum in magnetic susceptibility is found below TN. This relatively high ordering temperature among Co-based ladder compounds is related to the highly anisotropic mer-coordination of the Co2+ ions. The trans-octahedrally coordinated Co2+ ions, on the other hand, corresponds to the possible short-range magnetic correlations through dimers with an effective . This results in a rare situation that spin ordering and spin dimers coexist down to 2 K. PMID:28256576

  7. Crystal structure of 4-allyl­sulfanyl-1H-pyrazolo­[3,4-d]pyrimidine

    PubMed Central

    El Fal, Mohammed; Ramli, Youssef; Essassi, El Mokhtar; Saadi, Mohamed; El Ammari, Lahcen

    2014-01-01

    In the title compound, C8H8N4S, the pyrazolo­[3,4-d]pyrimidine ring system is essentially planar, with a maximum deviation from the mean plane of 0.025 (3) Å. The allyl group is disordered over two sites in a 0.512 (6):0.488 (6) ratio. In the crystal, mol­ecules are linked by pairs of N—H⋯N hydrogen bonds, forming inversion dimers with an R 2 2(8) graph-set motif. PMID:25309213

  8. Chemistry of isoflavone heterocyclic analogs. 10. Synthesis of pyrimidines by recyclization of isoflavones and their heterocyclic analogs

    SciTech Connect

    Khilya, V.P.; Kornilov, M.Yu.; Gorbulenko, N.V.; Golubushina, G.M.; Kovtun, E.N.; Kolotusha, N.V.; Panasenko, G.V.

    1986-05-01

    Isoflavones and their thiazole and pyrazole analogs are recyclized into the corresponding 4-(2-hydroxyphenyl)-pyrimidine derivatives under the effect of amidines. Their PMR spectra were studied. The effects related to the formation and strength of the intramolecular hydrogen bond were examined.

  9. Dimerization of thymol blue in solution: Theoretical evidence.

    PubMed

    Balderas-Hernández, Patricia; Vargas, Rubicelia; Rojas-Hernández, Alberto; Ramírez-Silva, Ma Teresa; Galván, Marcelo

    2007-02-28

    The possibility of dimerization of thymol blue was addressed by ab initio and force field calculations. In agreement with experimental information, a dimer forming symmetrical chemical environments for hydrogen bond formation was determined. This dimer is stable in vacuum and aqueous media and corresponds to the same protonated state proposed by the experiment. A comparison of the CVFF and MM3 force fields and ab initio results shows the suitability of CVFF to qualitatively describe this system.

  10. Crystal structures of 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(naphthalen-1-yl)acetamide and 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(4-fluoro­phen­yl)acetamide

    PubMed Central

    Subasri, S.; Kumar, Timiri Ajay; Sinha, Barij Nayan; Jayaprakash, Venkatesan; Viswanathan, Vijayan; Velmurugan, Devadasan

    2017-01-01

    The title compounds, C16H15N5OS, (I), and C12H12FN5OS, (II), are [(di­amino­pyrimidine)­sulfan­yl]acetamide derivatives. In (I), the pyrimidine ring is inclined to the naphthalene ring system by 55.5 (1)°, while in (II), the pyrimidine ring is inclined to the benzene ring by 58.93 (8)°. In (II), there is an intra­molecular N—H⋯N hydrogen bond and a short C—H⋯O contact. In the crystals of (I) and (II), mol­ecules are linked by pairs of N—H⋯N hydrogen bonds, forming inversion dimers with R 2 2(8) ring motifs. In the crystal of (I), the dimers are linked by bifurcated N—H⋯(O,O) and C—H⋯O hydrogen bonds, forming layers parallel to (100). In the crystal of (II), the dimers are linked by N—H⋯O hydrogen bonds, also forming layers parallel to (100). The layers are linked by C—H⋯F hydrogen bonds, forming a three-dimensional architecture. PMID:28217364

  11. The effect of purine and pyrimidine analogues and virazole on adenovirus replication.

    PubMed

    Scheffler, P; Haghchenas, D; Wigand, R

    1975-04-01

    The multiplication of adenovirus 19 in HeLa cells was inhibited by various purine and pyrimidine analogues and by virazole. The formation of infectious virus and of capsid proteins (haemagglutin, group-specific complement-fixing antigen) was inhibited to the same degree, while the viral cytopathic effect (CPE) was not inhibited. The reversibility of the inhibition after removal of the substances was more complete for purine than for pyrimidine analogues. The inhibition was counteracted by simulataneous addition of the corresponding nucleosides. Adenosine was more effected than guanosine against purine analogues; both were partially effective against virazole, but none of them against arabinofuranosyladenine. The time-dependence of inhibition, the ensuing eclipse period after removal of the inhibitors, and the successive application of two inhibitors led to the conclusion that most of them affect the viral multiplication mainly by inhibition of DNA synthesis. Azacytidine inhibits the synthesis of structural proteins as well.

  12. Assembly of Drosophila centromeric nucleosomes requires CID dimerization.

    PubMed

    Zhang, Weiguo; Colmenares, Serafin U; Karpen, Gary H

    2012-01-27

    Centromeres are essential chromosomal regions required for kinetochore assembly and chromosome segregation. The composition and organization of centromeric nucleosomes containing the essential histone H3 variant CENP-A (CID in Drosophila) is a fundamental, unresolved issue. Using immunoprecipitation of CID mononucleosomes and cysteine crosslinking, we demonstrate that centromeric nucleosomes contain CID dimers in vivo. Furthermore, CID dimerization and centromeric targeting require a residue implicated in formation of the four-helix bundle, which mediates intranucleosomal H3 dimerization and nucleosome integrity. Taken together, our findings suggest that CID nucleosomes are octameric in vivo and that CID dimerization is essential for correct centromere assembly.

  13. Assembly of Drosophila Centromeric Nucleosomes Requires CID Dimerization

    PubMed Central

    Zhang, Weiguo; Colmenares, Serafin U.; Karpen, Gary H.

    2012-01-01

    SUMMARY Centromeres are essential chromosomal regions required for kinetochore assembly and chromosome segregation. The composition and organization of centromeric nucleosomes containing the essential histone H3 variant CENP-A (CID in Drosophila) is a fundamental, unresolved issue. Using immunoprecipitation of CID mononucleosomes and cysteine crosslinking, we demonstrate that centromeric nucleosomes contain CID dimers in vivo. Furthermore, CID dimerization and centromeric targeting require a residue implicated in formation of the four helix bundle, which mediates intra-nucleosomal H3 dimerization and nucleosome integrity. Taken together, our findings suggest that CID nucleosomes are octameric in vivo and that CID dimerization is essential for correct centromere assembly. PMID:22209075

  14. Allosteric Modulation of Purine and Pyrimidine Receptors

    PubMed Central

    Jacobson, Kenneth A.; Gao, Zhan-Guo; Göblyös, Anikó; IJzerman, Adriaan P.

    2011-01-01

    Among the purine and pyrimidine receptors, the discovery of small molecular allosteric modulators has been most highly advanced for the A1 and A3 ARs. These AR modulators have allosteric effects that are structurally separated from the orthosteric effects in SAR studies. The benzoylthiophene derivatives tend to act as allosteric agonists, as well as selective positive allosteric modulators (PAMs) of the A1 AR. A 2-amino-3-aroylthiophene derivative T-62 has been under development as a PAM of the A1 AR for the treatment of chronic pain. Several structurally distinct classes of allosteric modulators of the human A3 AR have been reported: 3-(2-pyridinyl)isoquinolines, 2,4-disubstituted quinolines, 1H-imidazo-[4,5-c]quinolin-4-amines, endocannabinoid 2-arachidonylglycerol and the food dye Brilliant Black BN. Site-directed mutagenesis of A1 and A3 ARs has identified residues associated with the allosteric effect, distinct from those that affect orthosteric binding. A few small molecular allosteric modulators have been reported for several of the P2X ligand-gated ion channels and the G protein-coupled P2Y receptor nucleotides. Metal ion modulation of the P2X receptors has been extensively explored. The allosteric approach to modulation of purine and pyrimidine receptors looks promising for development of drugs that are event-specific and site-specific in action. PMID:21586360

  15. Influence of Exciplex formation on the electroluminescent properties of dimeric Zn (II) bis-2-(2'-hydroxyphenyl) benzoxazole complex and monomeric Zn (II) 2-(1'-hydroxynaphthyl) benzothiazole complex

    NASA Astrophysics Data System (ADS)

    Prakash, Sattey; Anand, R. S.; Manoharan, S. Sundar

    2011-10-01

    In this paper we present the factors affecting electroluminescent properties of Zinc complexes of oxazole & thiazole derivatives. Electroluminescent spectra of the Zinc (II) complex of bis-[2-(2'-hydroxyphenyl) benzoxazole], [Zn (HPBO)2]2 and 2-(1'-hydroxynaphthyl) benzothiazole [Zn (HNBT)2] show unusual broadening and shows structural and photophysical similarity with [Zn (HPBT)2]2, a dimeric complex. The [Zn (HPBO)2]2 complex as an emissive layer in the device structure ITO /PEDOT:PSS /TPD (30nm) /[Zn (HPBO)2]2 (60nm) /BCP (6nm) /Ca (3nm) /Al (200nm) shows a broad bluish green emission, with a full width at half maxima (FWHM1˜70nm). The EL spectra is much broader compared to the PL spectra because of exciplex formation at the interfacial region between the emissive layer (EML) & hole transport layer (HTL). We also show the device performance of Zinc 2-(1'-hydroxynaphthyl) benzothiazole [Zn (HNBT)2] complex as emissive layer. Distinctly this device shows a broad greenish yellow emission with a peak maxima at 535nm and 690nm, owing to the exciplex formation between electron transport layer (ETL) and emissive layer (EML), which is in sharp contrast to the exciplex formation across the HTL-EML interface observed for the [Zn (HPBO)2]2 complex.

  16. Collective motion of dimers.

    PubMed

    Penington, Catherine J; Korvasová, Karolína; Hughes, Barry D; Landman, Kerry A

    2012-11-01

    We consider a discrete agent-based model on a one-dimensional lattice and a two-dimensional square lattice, where each agent is a dimer occupying two sites. Agents move by vacating one occupied site in favor of a nearest-neighbor site and obey either a strict simple exclusion rule or a weaker constraint that permits partial overlaps between dimers. Using indicator variables and careful probability arguments, a discrete-time master equation for these processes is derived systematically within a mean-field approximation. In the continuum limit, nonlinear diffusion equations that describe the average agent occupancy of the dimer population are obtained. In addition, we show that multiple species of interacting subpopulations give rise to advection-diffusion equations. Averaged discrete simulation data compares very well with the solution to the continuum partial differential equation models. Since many cell types are elongated rather than circular, this work offers insight into population-level behavior of collective cellular motion.

  17. The photochemistry of pyrimidine in realistic astrophysical ices and the production of nucleobases

    SciTech Connect

    Nuevo, Michel; Materese, Christopher K.; Sandford, Scott A.

    2014-10-01

    Nucleobases, together with deoxyribose/ribose and phosphoric acid, are the building blocks of DNA and RNA for all known life. The presence of nucleobase-like compounds in carbonaceous chondrites delivered to the Earth raises the question of an extraterrestrial origin for the molecules that triggered life on our planet. Whether these molecules are formed in interstellar/protostellar environments, in small parent bodies in the solar system, or both, is currently unclear. Recent experiments show that the UV irradiation of pyrimidine (C{sub 4}H{sub 4}N{sub 2}) in H{sub 2}O-rich ice mixtures that contain NH{sub 3}, CH{sub 3}OH, or CH{sub 4} leads to the formation of the pyrimidine-based nucleobases uracil, cytosine, and thymine. In this work, we discuss the low-temperature UV irradiation of pyrimidine in realistic astrophysical ice mixtures containing H{sub 2}O, CH{sub 3}OH, and NH{sub 3}, with or without CH{sub 4}, to search for the production of nucleobases and other prebiotic compounds. These experiments show the presence of uracil, urea, glycerol, hexamethylenetetramine, small amino acids, and small carboxylic acids in all samples. Cytosine was only found in one sample produced from ices irradiated with a higher UV dose, while thymine was not found in any sample, even after irradiation with a higher UV dose. Results are discussed to evaluate the role of the photochemistry of pyrimidine in the inventory of organic molecules detected in meteorites and their astrophysical/astrobiological implications.

  18. Partition-DFT on the water dimer.

    PubMed

    Gómez, Sara; Nafziger, Jonathan; Restrepo, Albeiro; Wasserman, Adam

    2017-02-21

    As is well known, the ground-state symmetry group of the water dimer switches from its equilibrium Cs-character to C2h-character as the distance between the two oxygen atoms of the dimer decreases below RO-O∼2.5 Å. For a range of RO-O between 1 and 5 Å, and for both symmetries, we apply Partition Density Functional Theory (PDFT) to find the unique monomer densities that sum to the correct dimer densities while minimizing the sum of the monomer energies. We calculate the work involved in deforming the isolated monomer densities and find that it is slightly larger for the Cs geometry for all RO-O. We discuss how the PDFT densities and the corresponding partition potentials support the orbital-interaction picture of hydrogen-bond formation.

  19. A 14-3-3γ dimer-based scaffold bridges CtBP1-S/BARS to PI(4)KIIIβ to regulate post-Golgi carrier formation.

    PubMed

    Valente, Carmen; Turacchio, Gabriele; Mariggiò, Stefania; Pagliuso, Alessandro; Gaibisso, Renato; Di Tullio, Giuseppe; Santoro, Michele; Formiggini, Fabio; Spanò, Stefania; Piccini, Daniele; Polishchuk, Roman S; Colanzi, Antonino; Luini, Alberto; Corda, Daniela

    2012-02-26

    Large pleiomorphic carriers leave the Golgi complex for the plasma membrane by en bloc extrusion of specialized tubular domains, which then undergo fission. Several components of the underlying molecular machinery have been identified, including those involved in the budding/initiation of tubular carrier precursors (for example, the phosphoinositide kinase PI(4)KIIIβ, the GTPase ARF, and FAPP2), and in the fission of these precursors (for example, PKD, CtBP1-S/BARS). However, how these proteins interact to bring about carrier formation is poorly understood. Here, we describe a protein complex that mediates carrier formation and contains budding and fission molecules, as well as other molecules, such as the adaptor protein 14-3-3γ. Specifically, we show that 14-3-3γ dimers bridge CtBP1-S/BARS with PI(4)KIIIβ, and that the resulting complex is stabilized by phosphorylation by PKD and PAK. Disrupting the association of these proteins inhibits the fission of elongating carrier precursors, indicating that this complex couples the carrier budding and fission processes.

  20. Synthesis and crystal structure of N-(4-chloro­phen­yl)-5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidin-2-amine

    PubMed Central

    Repich, Hlib; Orysyk, Svitlana; Savytskyi, Pavlo; Pekhnyo, Vasyl

    2017-01-01

    The title compound, C13H12ClN5, was synthesized by the cyclization of 1-(4,6-di­methyl­pyrimidin-2-yl)-4-phenyl­thio­semicarbazide in the presence of Ni(NO3)2. The mol­ecular structure of the compound is essentially planar. In the crystal, mol­ecules form dimers via pairs of N—H⋯N hydrogen bonds between the H atom of the exocyclic amino group and the N atom at the 4-position of the triazole ring. The resulting dimers are packed into layers which are connected by π-stacking inter­actions between the aromatic systems of the pyrimidine and benzene nuclei, and between the triazole cores. PMID:28083130

  1. Titanium(IV) isopropoxide mediated synthesis of pyrimidin-4-ones.

    PubMed

    Ramanjulu, Joshi M; Demartino, Michael P; Lan, Yunfeng; Marquis, Robert

    2010-05-21

    A novel, one-step method for the synthesis of tri- and tetrasubstituted pyrimidin-4-ones is reported. This method involves a titanium(IV)-mediated cyclization involving two sequential condensations of primary and beta-ketoamides. The reaction is operationally facile, readily scalable, and offers rapid entry into differentially substituted pyrimidin-4-one scaffolds. The high functional group compatibility allows for substantial diversification in the products generated from this transformation.

  2. Structure-Activity Relationship of Indole-Tethered Pyrimidine Derivatives that Concurrently Inhibit Epidermal Growth Factor Receptor and Other Angiokinases

    PubMed Central

    Song, Jiho; Yoo, Jakyung; Kwon, Ara; Kim, Doran; Nguyen, Hong Khanh; Lee, Bong-Yong; Suh, Wonhee; Min, Kyung Hoon

    2015-01-01

    Antiangiogenic agents have been widely investigated in combination with standard chemotherapy or targeted cancer agents for better management of advanced cancers. Therapeutic agents that concurrently inhibit epidermal growth factor receptor and other angiokinases could be useful alternatives to combination therapies for epidermal growth factor receptor-dependent cancers. Here, we report the synthesis of an indole derivative of pazopanib using a bioisosteric replacement strategy, which was designated MKP101. MKP101 inhibited not only the epidermal growth factor receptor with an IC50 value of 43 nM but also inhibited angiokinases as potently as pazopanib. In addition, MKP101 effectively inhibited vascular endothelial growth factor-induced endothelial proliferation, tube formation, migration of human umbilical vein endothelial cells and proliferation of HCC827, an epidermal growth factor receptor-addicted cancer cell line. A docking model of MKP101 and the kinase domain of the epidermal growth factor receptor was generated to predict its binding mode, and validated by synthesizing and evaluating MKP101 derivatives. Additionally, a study of structure-activity relationships of indolylamino or indolyloxy pyrimidine analogues derived from MKP101 demonstrated that selectivity for epidermal growth factor receptor and other angiokinases, especially vascular endothelial growth factor receptor 2 depends on the position of substituents on pyrimidine and the type of link between pyrimidine and the indole moiety. We believe that this study could provide a basis for developing angiokinase inhibitors having high affinity for the epidermal growth factor receptor, from the pyrimidine scaffold. PMID:26401847

  3. Quantum Dimer Model: Phase Diagrams

    NASA Astrophysics Data System (ADS)

    Goldstein, Garry; Chamon, Claudio; Castelnovo, Claudio

    We present new theoretical analysis of the Quantum Dimer Model. We study dimer models on square, cubic and triangular lattices and we reproduce their phase diagrams (which were previously known only numerically). We show that there are several types of dimer liquids and solids. We present preliminary analysis of several other models including doped dimers and planar spin ice, and some results on the Kagome and hexagonal lattices.

  4. Evidence for dimerization of dimers in K+ channel assembly.

    PubMed Central

    Tu, L; Deutsch, C

    1999-01-01

    Voltage-gated K+ channels are tetrameric, but how the four subunits assemble is not known. We analyzed inactivation kinetics and peak current levels elicited for a variety of wild-type and mutant Kv1.3 subunits, expressed singly, in combination, and as tandem constructs, to show that 1) the dominant pathway involves a dimerization of dimers, and 2) dimer-dimer interaction may involve interaction sites that differ from those involved in monomer-monomer association. Moreover, using nondenaturing gel electrophoresis, we detected dimers and tetramers, but not trimers, in the translation reaction of Kv1.3 monomers. PMID:10096897

  5. Discovery of Macrocyclic Pyrimidines as MerTK-Specific Inhibitors.

    PubMed

    McIver, Andrew L; Zhang, Weihe; Liu, Qingyang; Jiang, Xinpeng; Stashko, Michael A; Nichols, James; Miley, Michael J; Norris-Drouin, Jacqueline; Machius, Mischa; DeRyckere, Deborah; Wood, Edgar; Graham, Douglas K; Earp, H Shelton; Kireev, Dmitri; Frye, Stephen V; Wang, Xiaodong

    2017-02-03

    Macrocycles have attracted significant attention in drug discovery recently. In fact, a few de novo designed macrocyclic kinase inhibitors are currently in clinical trials with good potency and selectivity for their intended target. In this study, we successfully engaged a structure-based drug design approach to discover macrocyclic pyrimidines as potent Mer tyrosine kinase (MerTK)-specific inhibitors. An enzyme-linked immunosorbent assay (ELISA) in 384-well format was employed to evaluate the inhibitory activity of macrocycles in a cell-based assay assessing tyrosine phosphorylation of MerTK. Through structure-activity relationship (SAR) studies, analogue 11 [UNC2541; (S)-7-amino-N-(4-fluorobenzyl)-8-oxo-2,9,16-triaza-1(2,4)-pyrimidinacyclohexadecaphane-1-carboxamide] was identified as a potent and MerTK-specific inhibitor that exhibits sub-micromolar inhibitory activity in the cell-based ELISA. In addition, an X-ray structure of MerTK protein in complex with 11 was resolved to show that these macrocycles bind in the MerTK ATP pocket.

  6. Acceleration of 5-Methylcytosine Deamination in Cyclobutane Dimers by G and its Implications for UV-induced C to T Mutation Hotspots

    PubMed Central

    Cannistraro, Vincent J.; Taylor, John-Stephen

    2010-01-01

    Sunlight-induced C→T mutation hotspots occur most frequently at methylated CpG sites in tumor suppressor genes and thought to arise from trans-lesion synthesis past deaminated cyclobutane pyrimidine dimers (CPDs). While it is known that methylation enhances CPD formation in sunlight, little is known about the effect of methylation and sequence context on the deamination of 5-methyl C (mC) and its contribution to mutagenesis at these hotspots. Using an enzymatic method we have determined the yields and deamination rates of C and mC in CPDs and find that the frequency of UVB-induced CPDs correlates with the oxidation potential of the flanking bases. We also found that the deamination of TmC and mCT CPDs is about 25-fold faster when flanked by G’s than by A’s, C’s or T’s in duplex DNA and appears to involve catalysis by the O6 group of guanine. In contrast, the first deamination of either C or mC in ACmCG with a flanking G was much slower (t ½ >250 h) and rate limiting, while the second deamination was much faster. The observation that CmCG dimers deaminate very slowly but at the same time correlate with C→T mutation hotspots suggests that their repair must be slow enough to allow sufficient time for deamination. There are, however, a greater number of single C→T mutations than CC→TT mutations at CmCG sites even though the second deamination is very fast, which could reflect faster repair of doubly deaminated dimers. PMID:19631218

  7. Thermolysis of vic-dihydroxybacteriochlorins: effect of the nature of substrates in directing the formation of chlorin-chlorin dimers with fixed and flexible orientations and their preliminary in vitro photosensitizing efficacy.

    PubMed

    Li, Guolin; Dobhal, Mahabeer P; Graham, Andrew; Shibata, Masayuki; Zheng, Gang; Kozyrev, Andrei; Pandey, Ravindra K

    2003-05-16

    The thermolysis products obtained by refluxing a series of vic-dihydroxychlorins in o-dichlorobenzene are characterized. Depending on the nature of substrates, this methodology provides an access for novel carbon-carbon linked chlorin-chlorin dimers and chlorin-porphyrin dimers with fixed and flexible orientations. The configuration of the linkers in the symmetrical and unsymmetrical dimers was confirmed by extensive NMR (COSY, ROESY) and molecular modeling studies. The molecular modeling studies of the energy-optimized dimers with flexible orientation confirmed that one of the chlorin units of the dimeric structure is tilted toward the opposite ring as evident by the shielding effect in the resonances of some of the protons in the (1)H NMR spectroscopy. Among the dimers with fixed orientation, compared to the free-base analogues, the related mono- and di-Zn(II) complexes produced a decreased fluorescence intensity, suggesting a possibility of the faster energy transfer via intersystem crossing (ISC) in the metalated derivatives than the corresponding free-base analogues to produce the corresponding excited triplet states. The photosensitizing efficacy of the monomers and the related dimers was also compared in radiation-induced fibrosarcoma (RIF) tumor cells at variable drug/light doses. In preliminary screening, compared to monomers, the corresponding carbon-carbon linked dimers produced enhanced photosensitizing efficacy.

  8. Dimer excision in Escherichia coli in the presence of caffeine

    SciTech Connect

    Rothman, R.H.

    1980-07-01

    The observation that polA1 and recL152 mutations result in both slow pyrimidine dimer excision and large repair patch size leads to the hypothesis that patch size is directly related to the rate of excision. In this study caffeine, a known inhibitor of excision repair, was used to examine the extent of correlation between excision rate and patch size by measuring patch size in the presence of several concentrations of caffeine. Both the rate of excision and the resistance to ultraviolet radiation were reduced with increasing concentrations of caffeine after irradiation. Caffeine also inhibited the rate at which incisions were made and prolonged the time required to rejoin the discontinuities. Patch size, however, was unaffected by caffeine treatment.

  9. Glycal Formation in Crystals of Uridine Phosphorylase †‖‡

    PubMed Central

    Paul, Debamita; O'Leary, Seán E.; Rajashankar, Kanagalaghatta; Bu, Weiming; Toms, Angela; Settembre, Ethan C.; Sanders, Jennie M.; Begley, Tadhg P.; Ealick, Steven E.

    2010-01-01

    Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2′-deoxyuridine to 2′-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2′-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2′. Crystals of bovine uridine phosphorylase treated with 2′-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously-unencountered motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds. PMID:20364833

  10. Low-energy positron scattering by pyrimidine

    SciTech Connect

    Barbosa, Alessandra Souza; Pastega, Diego F.; Bettega, Márcio H. F.

    2015-12-28

    This work reports elastic integral and differential cross sections for positron collisions with pyrimidine, for energies up to 20 eV. The cross sections were computed with the Schwinger multichannel method in the static plus polarization approximation. We also employed the Born closure procedure to account for the long range potential due to the permanent dipole moment of the molecule. Our results are compared with the experimental total cross section of Zecca et al. [J. Phys. B 43, 215204 (2010)], the experimental grand-total, quasi-elastic integral and differential cross section of Palihawadana et al. [Phys. Rev. A 88, 12717 (2013)]. We also compare our results with theoretical integral and differential cross sections obtained by Sanz et al. [Phys. Rev. A 88, 62704 (2013)] with the R-matrix and the independent atom model with screening-corrected additivity rule methods, and with the results computed by Franz and Gianturco [Phys. Rev. A 88, 042711 (2013)] using model correlation-polarization potentials. The agreement between the theory and the experiment is encouraging.

  11. Clay catalysis of oligonucleotide formation: kinetics of the reaction of the 5'-phosphorimidazolides of nucleotides with the non-basic heterocycles uracil and hypoxanthine

    NASA Technical Reports Server (NTRS)

    Kawamura, K.; Ferris, J. P.

    1999-01-01

    The montmorillonite clay catalyzed condensation of activated monocleotides to oligomers of RNA is a possible first step in the formation of the proposed RNA world. The rate constants for the condensation of the phosphorimidazolide of adenosine were measured previously and these studies have been extended to the phosphorimidazolides of inosine and uridine in the present work to determine of substitution of neutral heterocycles for the basic adenine ring changes the reaction rate or regioselectivity. The oligomerization reactions of the 5'-phosphoromidazolides of uridine (ImpU) and inosine (ImpI) on montmorillonite yield oligo(U)s and oligo(I)s as long as heptamers. The rate constants for oligonucleotide formation were determined by measuring the rates of formation of the oligomers by HPLC. Both the apparent rate constants in the reaction mixture and the rate constants on the clay surface were calculated using the partition coefficients of the oligomers between the aqueous and clay phases. The rate constants for trimer formation are much greater than those dimer synthesis but there was little difference in the rate constants for the formation of trimers and higher oligomers. The overall rates of oligomerization of the phosphorimidazolides of purine and pyrimidine nucleosides in the presence of montmorillonite clay are the same suggesting that RNA formed on the primitive Earth could have contained a variety of heterocyclic bases. The rate constants for oligomerization of pyrimidine nucleotides on the clay surface are significantly higher than those of purine nucleotides since the pyrimidine nucleotides bind less strongly to the clay than do the purine nucleotides. The differences in the binding is probably due to Van der Waals interactions between the purine bases and the clay surface. Differences in the basicity of the heterocyclic ring in the nucleotide have little effect on the oligomerization process.

  12. Threshold electron attachment and electron impact ionization involving oxygen dimers

    NASA Astrophysics Data System (ADS)

    Kreil, J.; Ruf, M.-W.; Hotop, H.; Ettischer, I.; Buck, U.

    1998-12-01

    Using two different crossed-beams machines we have carried out the first quantitative study of threshold electron attachment and electron impact-induced ionization and fragmentation involving oxygen dimers (O 2) 2. In the electron attachment experiment we study electron transfer from state-selected Ar **(20d) Rydberg atoms to O 2 molecules and dimers in a skimmed supersonic beam at variable nozzle temperatures ( T0) and stagnation pressures ( p0). The relative dimer density is determined through measurements of Penning ionization by metastable Ne *(3s 3P2,0) atoms and used to estimate the absolute cross-section for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 dimers to be nearly 10 -17 m 2, almost four orders of magnitude larger than that for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 monomers. The fragmentation of the oxygen cluster beam is quantitatively characterized by the transverse helium beam scattering method which allows us to spatially separate different clusters. It is shown that in 70 eV electron impact of (O 2) 2 only 3.6(4)% of the dimers are detected as dimer ions (O 2) 2+. In additional experiments involving SF 6 clusters we show that SF 6 dimers fragment nearly completely upon 70 eV electron impact, yielding SF 5+ ions (probability for (SF 6)·SF 5+ production at most 0.3%).

  13. Adsorption of dimeric surfactants in lamellar silicates

    NASA Astrophysics Data System (ADS)

    Balcerzak, Mateusz; Pietralik, Zuzanna; Domka, Ludwik; Skrzypczak, Andrzej; Kozak, Maciej

    2015-12-01

    The adsorption of different types of cationic surfactants in lamellar silicates changes their surface character from hydrophilic to hydrophobic. This study was undertaken to obtain lamellar silicates modified by a series of novel dimeric (gemini) surfactants of different length alkyl chains and to characterise these organophilised materials. Synthetic sodium montmorillonite SOMASIF® ME 100 (M) and enriched bentonite of natural origin (Nanoclay - hydrophilic bentonite®) were organophilised with dimeric (gemini) surfactants (1,1‧-(1,4-butanediyl)bis(alkoxymethyl)imidazolium dichlorides). As a result of surfactant molecule adsorption in interlamellar space, the d-spacing (d001) increased from 0.97 nm (for the anhydrous structure) to 2.04 nm. A Fourier transform infrared spectroscopy (FTIR) analysis of the modified systems reveals bands assigned to the stretching vibrations of the CH2 and CH3 groups and the scissoring vibrations of the NH group from the structure of the dimeric surfactants. Thermogravimetric (TG) and derivative thermogravimetric (DTG) studies imply a four-stage process of surfactant decomposition. Scanning electron microscopy (SEM) images provide information on the influence of dimeric surfactant intercalation into the silicate structures. Particles of the modified systems show a tendency toward the formation of irregularly shaped agglomerates.

  14. Functional Asymmetry in Kinesin and Dynein Dimers

    PubMed Central

    Rank, Katherine C.; Rayment, Ivan

    2012-01-01

    Active transport along the microtubule lattice is a complex process that involves both the Kinesin and Dynein superfamily of motors. Transportation requires sophisticated regulation much of which occurs through the motor’s tail domain. However, a significant portion of this regulation also occurs through structural changes that arise in the motor and the microtubule upon binding. The most obvious structural change being the manifestation of asymmetry. To a first approximation in solution, kinesin dimers exhibit two-fold symmetry, and microtubules, helical symmetry. The higher symmetries of both the kinesin dimers and microtubule lattice are lost on formation of the kinesin-microtubule complex. Loss of symmetry has functional consequences such as an asymmetric hand-over-hand mechanism in plus-end directed kinesins, asymmetric microtubule binding in the Kinesin-14 family, spatially biased stepping in dynein, and cooperative binding of additional motors to the microtubule. This review focuses on how the consequences of asymmetry affect regulation of motor heads within a dimer, dimers within an ensemble of motors, and suggests how these asymmetries may affect regulation of active transport within the cell. PMID:23066835

  15. Electric and magnetic hotspots in dielectric nanowire dimers

    NASA Astrophysics Data System (ADS)

    Mirzaei, Ali; Miroshnichenko, Andrey E.

    2015-03-01

    We study the formation of the electric and magnetic near-field hotspots in dielectric cylindrical dimers. We compare dielectric and metallic dimers by using experimental data for all materials and consider both TM and TE polarizations of light. We demonstrate that dielectric dimers allow us to simultaneously achieve pure magnetic and electric near-field hotspots for both polarizations in contrast to plasmonic structures. This offers new approaches for near-field engineering such as sensing, control of spontaneous emission, and enhanced Raman scattering.

  16. Dynamical dimer-dimer correlation functions from exact diagonalization

    SciTech Connect

    Werner, Ralph

    2001-05-01

    A regularization method is presented to deduce dynamic correlation functions from exact diagonalization calculations. It is applied to dimer-dimer correlation functions in quantum spin chains relevant for the description of spin-Peierls systems. Exact results for the XY model are presented. The analysis draws into doubt that the dimer-dimer correlation functions show the same scale invariance as spin-spin correlation functions. The results are applied to describe the quasielastic scattering in CuGeO{sub 3} and the hardening of the Peierls-active phonons.

  17. Significance and Biological Importance of Pyrimidine in the Microbial World

    PubMed Central

    Sharma, Vinita; Agarwal, Ajay Kumar

    2014-01-01

    Microbes are unique creatures that adapt to varying lifestyles and environment resistance in extreme or adverse conditions. The genetic architecture of microbe may bear a significant signature not only in the sequences position, but also in the lifestyle to which it is adapted. It becomes a challenge for the society to find new chemical entities which can treat microbial infections. The present review aims to focus on account of important chemical moiety, that is, pyrimidine and its various derivatives as antimicrobial agents. In the current studies we represent more than 200 pyrimidines as antimicrobial agents with different mono-, di-, tri-, and tetrasubstituted classes along with in vitro antimicrobial activities of pyrimidines derivatives which can facilitate the development of more potent and effective antimicrobial agents. PMID:25383216

  18. D Dimer in acute care

    PubMed Central

    Sathe, Prachee M.; Patwa, Urvil D.

    2014-01-01

    Pulmonary embolism, Deep Vein Thrombosis (DVT) and Disseminated intravascular coagulation (DIC) are important sources of mortality and morbidity in intensive care unit (ICU). And every time D-dimer remains the the commonest investigation. Many times D-dimer is erroneously considered as a diagnostic test in above mentioned conditions. Its interpretation requires cautions. To circumvent this source of error it is necessary to understand D-dimer test and its significance in various disorder. This article review some basic details of D-dimer, condition associated with its increased level and some prognostic value in intracranial hemorrhage and gastrointestinal (GI) bleed. PMID:25337485

  19. Synthesis of L-enantiomers of 4'-thioarabinofuranosyl pyrimidine nucleosides.

    PubMed

    Satoh, H; Yoshimura, Y; Sakata, S; Miura, S; Machida, H; Matsuda, A

    1998-05-05

    L-Enantiomers of 4'-thioarabinofuranosyl pyrimidine nucleosides were synthesized from D-xylose. Methyl 2,3,5-tri-O-benzyl-D-xylofuranoside 6 was converted to the corresponding xylitol 7, which was treated with MsCl and then Na2S to give 1,4-anhydro-L-4-thioarabitol 8. As previously reported, Pummerer rearrangement of 8 followed by glycosylation with a silylated thymine and N4-acetylcytosine derivative and deprotection gave the corresponding alpha- and beta-L-4'-thioarabinofuranosyl pyrimidine nucleosides.

  20. Mechanism of host-guest complex formation and identification of intermediates through NMR titration and diffusion NMR spectroscopy.

    PubMed

    Lamm, Jan-Hendrik; Niermeier, Philipp; Mix, Andreas; Chmiel, Jasmin; Neumann, Beate; Stammler, Hans-Georg; Mitzel, Norbert W

    2014-07-21

    The formation of host-guest (H-G) complexes between 1,8-bis[(diethylgallanyl)ethynyl]anthracene (H) and the N-heterocycles pyridine and pyrimidine (G) was studied in solution using a combination of NMR titration and diffusion NMR experiments. For the latter, diffusion coefficients of potential host-guest structures in solution were compared with those of tailor-made reference compounds of similar shape (synthesized and characterized by NMR, HRMS, and in part XRD). Highly dynamic behavior was observed in both cases, but with different host-guest species and equilibria. With increasing concentrations of the pyridine guest, the equilibrium H2⇄H2κ(1)-G1⇄HG2 is observed (in the second step a host dimer coordinates one guest molecule); for pyrimidine the equilibrium H2→H1κ(2)-G1⇄HG2 is observed (the formation of a 1:1 aggregate is the second step).

  1. Irradiation of pyrimidine in pure H2O ice with high-energy ultraviolet photons.

    PubMed

    Nuevo, Michel; Chen, Yu-Jung; Hu, Wei-Jie; Qiu, Jun-Ming; Wu, Shang-Ruei; Fung, Hok-Sum; Chu, Ching-Chi; Yih, Tai-Sone; Ip, Wing-Huen; Wu, C-Y Robert

    2014-02-01

    The detection of nucleobases, the informational subunits of DNA and RNA, in several meteorites suggests that these compounds of biological interest were formed via astrophysical, abiotic processes. This hypothesis is in agreement with recent laboratory studies of irradiation of pyrimidine in H2O-rich ices with vacuum UV photons emitted by an H2-discharge lamp in the 6.9-11.3 eV (110-180 nm) range at low temperature, shown to lead to the abiotic formation of several compounds including the nucleobases uracil, cytosine, and thymine. In this work, we irradiated H2O:pyrimidine ice mixtures under astrophysically relevant conditions (14 K, ≤10(-9) torr) with high-energy UV photons provided by a synchrotron source in three different ranges: the 0(th) order light (4.1-49.6 eV, 25-300 nm), the He i line (21.2 eV, 58.4 nm), and the He ii line (40.8 eV, 30.4 nm). The photodestruction of pyrimidine was monitored with IR spectroscopy, and the samples recovered at room temperature were analyzed with liquid and gas chromatographies. Uracil and its precursor 4(3H)-pyrimidone were found in all samples, with absolute and relative abundances varying significantly from one sample to another. These results support a scenario in which compounds of biological interest can be formed and survive in environments subjected to high-energy UV radiation fields.

  2. Irradiation of Pyrimidine in Pure H2O Ice with High-Energy Ultraviolet Photons

    PubMed Central

    Chen, Yu-Jung; Hu, Wei-Jie; Qiu, Jun-Ming; Wu, Shang-Ruei; Fung, Hok-Sum; Chu, Ching-Chi; Yih, Tai-Sone; Ip, Wing-Huen; Wu, C.-Y. Robert

    2014-01-01

    Abstract The detection of nucleobases, the informational subunits of DNA and RNA, in several meteorites suggests that these compounds of biological interest were formed via astrophysical, abiotic processes. This hypothesis is in agreement with recent laboratory studies of irradiation of pyrimidine in H2O-rich ices with vacuum UV photons emitted by an H2-discharge lamp in the 6.9–11.3 eV (110–180 nm) range at low temperature, shown to lead to the abiotic formation of several compounds including the nucleobases uracil, cytosine, and thymine. In this work, we irradiated H2O:pyrimidine ice mixtures under astrophysically relevant conditions (14 K, ≤10−9 torr) with high-energy UV photons provided by a synchrotron source in three different ranges: the 0th order light (4.1–49.6 eV, 25–300 nm), the He i line (21.2 eV, 58.4 nm), and the He ii line (40.8 eV, 30.4 nm). The photodestruction of pyrimidine was monitored with IR spectroscopy, and the samples recovered at room temperature were analyzed with liquid and gas chromatographies. Uracil and its precursor 4(3H)-pyrimidone were found in all samples, with absolute and relative abundances varying significantly from one sample to another. These results support a scenario in which compounds of biological interest can be formed and survive in environments subjected to high-energy UV radiation fields. Key Words: Pyrimidine—Nucleobases—Interstellar ices—Cometary ices—High-energy photons—Molecular processes—Prebiotic chemistry. Astrobiology 14, 119–131. PMID:24512484

  3. A model for triplet mutation formation based on error-prone translesional DNA synthesis opposite UV photolesions.

    PubMed

    Ikehata, Hironobu; Ono, Tetsuya; Tanaka, Kiyoji; Todo, Takeshi

    2007-05-01

    A triplet mutation is defined as multiple base substitutions or frameshifts within a three-nucleotide sequence which includes a dipyrimidine sequence. Triplet mutations have recently been identified as a new type of UV-specific mutation, although the mechanism of their formation is unknown. A total of 163 triplet mutations were identified through an extensive search of previously published data on UV-induced mutations, including mutations from skin, skin cancer, and cultured mammalian cells. Seven common patterns of sequence changes were found: Type I, NTC-->TTT; Type IIa, NCC-->PyTT or PyCT (Py, pyrimidine); Type IIb, TCC-->PuTT or PuCT (Pu, purine); Type III, NCC-->NAT or NTA; Type IV, NTT-->AAT; Type Va, NCT-->NTX; and Type Vb, PuCT-->XTT (N and X, independent anonymous bases). Furthermore, it is suggested that the type of UV lesion responsible for each of these triplet mutation classes are (a) pyrimidine(6-4)pyrimidone photoproducts for Types I, IIb, III, IV and Vb, (b) cyclobutane pyrimidine dimers for Type Va, and (c) Dewar valence isomers for Types IIa and IIb. These estimations are based primarily on results from previous studies using photolyases specific for each type of UV lesion. A model is proposed to explain the formation of each type of triplet mutation, based on error-prone translesional DNA synthesis opposite UV-specific photolesions. The model is largely consistent with the 'A-rule', and predicts error-prone insertions not only opposite photolesions but also opposite the undamaged template base one-nucleotide downstream from the lesions.

  4. 7-Amino-5-methyl-2-phenyl-6-(phenyldiazenyl)pyrazolo[1,5-a]pyrimidine crystallizes with Z' = 2: pseudosymmetry and the formation of complex sheets built from N-H...N and C-H...pi(arene) hydrogen bonds.

    PubMed

    Portilla, Jaime; Estupiñan, Diego; Cobo, Justo; Glidewell, Christopher

    2010-03-01

    The title compound, C(19)H(16)N(6), crystallizes with Z' = 2 in the space group P2(1)/n. The two molecules in the selected asymmetric unit are approximate mirror images of one another; most corresponding pairs of atoms are related by an approximate half-cell translation along [100]. Each molecule contains an intramolecular N-H...N hydrogen bond and the molecules are linked into complex sheets by a combination of two intermolecular N-H...N and four C-H...pi(arene) hydrogen bonds. Comparisons are made with some other 7-aminopyrazolo[1,5-a]pyrimidines.

  5. Final report on the amended safety assessment of diisopropyl dimer dilinoleate, dicetearyl dimer dilinoleate, diisostearyl dimer dilinoleate, dioctyl dimer dilinoleate, dioctyldodecyl dimer dilinoleate, and ditridecyl dimer dilinoleate.

    PubMed

    Fiume, Monice Zondlo

    2003-01-01

    Diisopropyl Dimer Dilinoleate, Dicetearyl Dimer Dilinoleate, Diisostearyl Dimer Dilinoleate, Dioctyl Dimer Dilinoleate, Dioctyldodecyl Dimer Dilinoleate, and Ditridecyl Dimer Dilinoleate are diesters of their respective alcohols and dilinoleic acid. They function as skin-conditioning agents in a variety of cosmetic products at concentrations around 10%, but may be used at concentrations up to 53% in lipsticks. These ingredients do not absorb radiation in the ultraviolet (UV) UVA or UVB range and the only impurities expected are <0.5% dilinoleic acid, <0.1% isopropyl alcohol or <1% isostearyl alcohol, and/or small amounts of dilinoleic acid and cetearyl alcohol or octyldodecanol, depending on which diester is used. The potential skin penetration of these ingredients was evaluated using an estimate of the octanol/water partition coefficient (logP of 17.7) based on the structure of Diisopropyl Dimer Dilinoleate. This is consistent with the insolubility of these ingredients in water. Safety test data on dilinoleic acid (no adverse effects) were considered relevant because dilinoleic acid is a component of these diesters and a likely breakdown product. The acute oral and dermal LD(50) values for rats of Diisopropyl, Diisostearyl, and Dioctyldodecyl Dimer Dilinoleate were >5.0 g/kg. In a subchronic feeding study, macrophage aggregation was seen in the mesenteric lymph node at the lowest dose level (0.1% in the diet). These ingredients did not produce skin or ocular irritation in animal tests, nor were they comedogenic. Ames testing, clastogenesis in human lymphocytes in culture, and L5178Y mouse lymphoma cell forward mutations were all negative, indicating no dilinoleic acid genotoxicity. No carcinogenicity or reproductive/developmental toxicity data were available; however, structural alerts that would suggest a mutagenic or carcinogenic risk are absent. Significant reproductive/developmental toxicity or other systemic toxicity is not expected with these ingredients

  6. Plaquette order in a dimerized frustrated spin ladder

    NASA Astrophysics Data System (ADS)

    Shlagman, Ofer; Shimshoni, Efrat

    2014-11-01

    We study the effect of dimerization (due to, e.g., spin-Peierls instability) on the phase diagram of a frustrated antiferromagnetic spin-1/2 ladder, with weak transverse and diagonal rung coupling. Our analysis focuses on a one-dimensional version of the model (i.e., a single two-leg ladder) where we consider two forms of dimerization on the legs: columnar dimers (CDs) and staggered dimers (SDs). We examine in particular the regime of parameters (corresponding to an intermediate X X Z anisotropy) in which the leg dimerization and the rung coupling terms are equally relevant. In both the CD and SD cases, we find that the effective field theory describing the system is a self-dual sine-Gordon model, which favors ordering and the opening of a gap to excitations. The order parameter, which reflects the interplay between the leg and rung dimerization interactions, represents a crystal of 4-spin plaquettes on which longitudinal and transverse dimers are in a coherent superposition. Depending on the leg dimerization mode, these plaquettes are closed or open, however both types spontaneously break reflection symmetry across the ladder. The closed plaquettes are stable, while the open plaquette order is relatively fragile and the corresponding gap may be tuned to zero under extreme conditions. We further find that a first-order transition occurs from the plaquette order to a valence bond crystal (VBC) of dimers on the legs. This suggests that in a higher-dimensional version of this system, this variety of distinct VBC states with comparable energies leads to the formation of domains. Effectively one-dimensional gapless spinon modes on domain boundaries may account for the experimental observation of spin-liquid behavior in a physical realization of the model.

  7. Effect of carbon source on pyrimidine biosynthesis in Pseudomonas alcaligenes ATCC 14909.

    PubMed

    Santiago, Manuel F; West, Thomas P

    2003-01-01

    The effect of carbon source on the regulation of the de novo pyrimidine biosynthetic enzymes in Pseudomonas alcaligenes ATCC 14909 was investigated. The de novo pyrimidine biosynthetic enzymes were measured in extracts of P. alcaligenes ATCC 14909 cells and of cells from an auxotroph deficient for orotate phosphoribosyltransferase activity. Pyrimidine biosynthetic enzyme activities in ATCC 14909 were influenced by pyrimidine supplementation to the culture medium but not by the carbon source present. Pyrimidine limitation of the auxotroph elevated the de novo enzyme activities indicating that this pathway may be controlled at the transcriptional level by a pyrimidine-related compound. Its regulation seemed to be subject to less transcriptional control by a pyrimidine-related compound than what was observed in the closely related species Pseudomonas pseudoalcaligenes.

  8. 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.

  9. OCLI-023, a Novel Pyrimidine Compound, Suppresses Osteoclastogenesis In Vitro and Alveolar Bone Resorption In Vivo

    PubMed Central

    Kim, Ju Ang; Lee, Doohyun; Kim, Nam Doo; Shin, Hong-In; Bae, Yong Chul; Park, Eui Kyun

    2017-01-01

    An abnormal increase in osteoclast differentiation and activation results in various bone-resorptive diseases, including periodontitis, rheumatoid arthritis, and osteoporosis. Chemical compounds containing pyrimidine ring have been shown to regulate a variety of biological processes. Therefore, in order to identify an antiresorptive agent, we synthesized a series of pyrimidine ring-containing chemical compounds, and found that OCLI-023 suppressed the differentiation and activation of osteoclasts in vitro. OCLI-023 directly inhibited receptor activator of nuclear factor-κB ligand (RANKL)-induced differentiation of bone marrow macrophages into osteoclasts, without a cytotoxic response. OCLI-023 also downregulated the RANKL-induced mRNA expression of osteoclast markers as well as inhibited the formation of actin rings and resorption pits. OCLI-023 attenuated the RANKL-induced activation of c-Jun N-terminal kinase and nuclear factor kappa-light-chain-enhancer of activated B cell signaling pathways. In a mouse model of periodontitis, ligature induced an increase of distance between cementoenamel junction (CEJ) and alveolar bone crest (ABC) in the second molar, and OCLI-023 significantly reduced it. Histological analysis showed ligature-induced increase of osteoclast numbers was also significantly reduced by OCLI-023. These data demonstrated the inhibitory effect of OCLI-023 on osteoclast differentiation and activity of osteoclasts in vitro, as well as on ligature-induced bone loss in vivo, and OCLI-023 can be proposed as a novel anti-resorptive compound. PMID:28085946

  10. Separation of purine and pyrimidine bases and nucleosides by hydrophilic interaction chromatography.

    PubMed

    Marrubini, Giorgio; Mendoza, Bolivar Enrique Castillo; Massolini, Gabriella

    2010-03-01

    The separation of 12 model compounds chosen among purine and pyrimidine bases and nucleosides was studied by using hydrophilic interaction chromatography (HILIC). The compounds investigated were small molecules with relevant properties for biomedical and pharmaceutical studies. The mixture of pyrimidines and purines was applied on a ZIC-HILIC 150 x 2.1 mm, 5 microm, and two TSKgel Amide-80 150 x 2.0 mm, 5 microm and 3 microm particle size columns. The retention of the analytes was studied by varying ACN%, ammonium formate concentration, pH, and column temperature. The results obtained confirmed the elution order of nucleobases, nucleosides, and nucleotides based on their hydrophobicity. The retention mechanism of the columns was studied considering the models used for describing partitioning and surface adsorption. The influence on retention of chromatographic conditions (ACN%, salt concentration, pH, and temperature) was described and discussed for both columns. The optimization of the conditions studied allowed to assess a gradient method for the separation of the 12 analytes. The developed method is a valuable alternative to existing methods for the separation of the compounds concerned.

  11. Mechanisms for kinase-mediated dimerization of the epidermal growth factor receptor.

    PubMed

    Lu, Chafen; Mi, Li-Zhi; Schürpf, Thomas; Walz, Thomas; Springer, Timothy A

    2012-11-02

    We study a mechanism by which dimerization of the EGF receptor (EGFR) cytoplasmic domain is transmitted to the ectodomain. Therapeutic and other small molecule antagonists to the kinase domain that stabilize its active conformation, but not those that stabilize an inactive conformation, stabilize ectodomain dimerization. Inhibitor-induced dimerization requires an asymmetric kinase domain interface associated with activation. EGF and kinase inhibitors stimulate formation of identical dimer interfaces in the EGFR transmembrane domain, as shown by disulfide cross-linking. Disulfide cross-linking at an interface in domain IV in the ectodomain was also stimulated similarly; however, EGF but not inhibitors stimulated cross-linking in domain II. Inhibitors similarly induced noncovalent dimerization in nearly full-length, detergent-solubilized EGFR as shown by gel filtration. EGFR ectodomain deletion resulted in spontaneous dimerization, whereas deletion of exons 2-7, in which extracellular domains III and IV are retained, did not. In EM, kinase inhibitor-induced dimers lacked any well defined orientation between the ectodomain monomers. Fab of the therapeutic antibody cetuximab to domain III confirmed a variable position and orientation of this domain in inhibitor-induced dimers but suggested that the C termini of domain IV of the two monomers were in close proximity, consistent with dimerization in the transmembrane domains. The results provide insights into the relative energetics of intracellular and extracellular dimerization in EGFR and have significance for physiologic dimerization through the asymmetric kinase interface, bidirectional signal transmission in EGFR, and mechanism of action of therapeutics.

  12. Photochemical dimerization and functionalization of alkanes, ethers, primary alcohols and silanes

    DOEpatents

    Crabtree, R.H.; Brown, S.H.

    1988-02-16

    The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary alcohols and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

  13. Photochemical dimerization and functionalization of alkanes, ethers, primary alcohols and silanes

    DOEpatents

    Crabtree, Robert H.; Brown, Stephen H.

    1988-01-01

    The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary alcohols and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

  14. Detection of alpha-helical coiled-coil dimer formation by spin-labeled synthetic peptides: a model parallel coiled-coil peptide and the antiparallel coiled coil formed by a replica of the ProP C-terminus.

    PubMed

    Hillar, Alexander; Tripet, Brian; Zoetewey, David; Wood, Janet M; Hodges, Robert S; Boggs, Joan M

    2003-12-30

    Electron paramagnetic resonance spectroscopy was used to determine relative peptide orientation within homodimeric, alpha-helical coiled-coil structures. Introduction of cysteine (Cys) residues into peptides/proteins for spin labeling allows detection of their oligomerization from exchange broadening or dipolar interactions between residues within 25 A of each other. Two synthetic peptides containing Cys substitutions were used: a 35-residue model peptide and the 30-residue ProP peptide. The model peptide is known to form a stable, parallel homodimeric coiled coil, which is partially destabilized by Cys substitutions at heptad a and d positions (peptides C30a and C33d). The ProP peptide, a 30-residue synthetic peptide, corresponds to residues 468-497 of osmoregulatory transporter ProP from Escherichia coli. It forms a relatively unstable, homodimeric coiled coil that is predicted to be antiparallel in orientation. Cys was introduced in heptad g positions of the ProP peptide, near the N-terminus (K473C, creating peptide C473g) or closer to the center of the sequence (E480C, creating peptide C480g). In contrast to the destabilizing effect of Cys substitution at the core heptad a or d positions of model peptides C30a and C33d, circular dichroism spectroscopy showed that Cys substitutions at the heptad g positions of the ProP peptide had little or no effect on coiled-coil stability. Thermal denaturation analysis showed that spin labeling increased the stability of the coiled coil for all peptides. Strong exchange broadening was detected for both C30a and C33d, in agreement with a parallel structure. EPR spectra of C480g had a large hyperfine splitting of about 90 G, indicative of strong dipole-dipole interactions and a distance between spin-labeled residues of less than 9 A. Spin-spin interactions were much weaker for C473g. These results supported the hypothesis that the ProP peptide primarily formed an antiparallel coiled coil, since formation of a parallel dimer

  15. 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.

  16. Chemotaxis of Escherichia coli to pyrimidines: a new role for the signal transducer tap.

    PubMed

    Liu, Xianxian; Parales, Rebecca E

    2008-02-01

    Escherichia coli exhibits chemotactic responses to sugars, amino acids, and dipeptides, and the responses are mediated by methyl-accepting chemotaxis proteins (MCPs). Using capillary assays, we demonstrated that Escherichia coli RP437 is attracted to the pyrimidines thymine and uracil and the response was constitutively expressed under all tested growth conditions. All MCP mutants lacking the MCP Tap protein showed no response to pyrimidines, suggesting that Tap, which is known to mediate dipeptide chemotaxis, is required for pyrimidine chemotaxis. In order to confirm the role of Tap in pyrimidine chemotaxis, we constructed chimeric chemoreceptors (Tapsr and Tsrap), in which the periplasmic and cytoplasmic domains of Tap and Tsr were switched. When Tapsr and Tsrap were individually expressed in an E. coli strain lacking all four native MCPs, Tapsr mediated chemotaxis toward pyrimidines and dipeptides, but Tsrap did not complement the chemotaxis defect. The addition of the C-terminal 19 amino acids from Tsr to the C terminus of Tsrap resulted in a functional chemoreceptor that mediated chemotaxis to serine but not pyrimidines or dipeptides. These results indicate that the periplasmic domain of Tap is responsible for detecting pyrimidines and the Tsr signaling domain confers on Tapsr the ability to mediate efficient chemotaxis. A mutant lacking dipeptide binding protein (DBP) was wild type for pyrimidine taxis, indicating that DBP, which is the primary chemoreceptor for dipeptides, is not responsible for detecting pyrimidines. It is not yet known whether Tap detects pyrimidines directly or via an additional chemoreceptor protein.

  17. Regiospecific synthesis of 3-substituted imidazo[1,2-a]pyridines, imidazo[1,2-a]pyrimidines, and imidazo[1,2-c]pyrimidine.

    PubMed

    Katritzky, Alan R; Xu, Yong-Jiang; Tu, Hongbin

    2003-06-13

    3-Substituted imidazo[1,2-a]pyridines, imidazo[1,2-a]pyrimidines, and imidazo[1,2-c]pyrimidine were obtained regiospecifically in yields of 35-92% in one pot by reaction of 2-aminopyridines or 2-(or 4-)aminopyrimidines, respectively, with 1,2-bis(benzotriazolyl)-1,2-(dialkylamino)ethanes.

  18. Mechanism of dimerization of the human melanocortin 1 receptor

    SciTech Connect

    Zanna, Paola T.; Sanchez-Laorden, Berta L.; Perez-Oliva, Ana B.; Turpin, Maria C.; Herraiz, Cecilia; Jimenez-Cervantes, Celia; Garcia-Borron, Jose C.

    2008-04-04

    The melanocortin 1 receptor (MC1R) is a dimeric G protein-coupled receptor expressed in melanocytes, where it regulates the amount and type of melanins produced and determines the tanning response to ultraviolet radiation. We have studied the mechanisms of MC1R dimerization. Normal dimerization of a deleted mutant lacking the seventh transmembrane fragment and the C-terminal cytosolic extension excluded coiled-coil interactions as the basis of dimerization. Conversely, the electrophoretic pattern of wild type receptor and several Cys {yields} Ala mutants showed that four disulfide bonds are established between the monomers. Disruption of any of these bonds abolished MC1R function, but only the one involving Cys35 was essential for traffic to the plasma membrane. A quadruple Cys35-267-273-275Ala mutant migrating as a monomer in SDS-PAGE in the absence of reducing agents was able to dimerize with WT, suggesting that in addition to disulfide bond formation, dimerization involves non-covalent interactions, likely of domain swap type.

  19. Conformational stability of dimeric proteins: quantitative studies by equilibrium denaturation.

    PubMed Central

    Neet, K. E.; Timm, D. E.

    1994-01-01

    The conformational stability of dimeric globular proteins can be measured by equilibrium denaturation studies in solvents such as guanidine hydrochloride or urea. Many dimeric proteins denature with a 2-state equilibrium transition, whereas others have stable intermediates in the process. For those proteins showing a single transition of native dimer to denatured monomer, the conformational stabilities, delta Gu (H2O), range from 10 to 27 kcal/mol, which is significantly greater than the conformational stability found for monomeric proteins. The relative contribution of quaternary interactions to the overall stability of the dimer can be estimated by comparing delta Gu (H2O) from equilibrium denaturation studies to the free energy associated with simple dissociation in the absence of denaturant. In many cases the large stabilization energy of dimers is primarily due to the intersubunit interactions and thus gives a rationale for the formation of oligomers. The magnitude of the conformational stability is related to the size of the polypeptide in the subunit and depends upon the type of structure in the subunit interface. The practical use, interpretation, and utility of estimation of conformational stability of dimers by equilibrium denaturation methods are discussed. PMID:7756976

  20. Magneto-association near an atom-dimer resonance

    NASA Astrophysics Data System (ADS)

    Luo, D.; Nguyen, J. H. V.; Hulet, R. G.

    2015-05-01

    Over the past decade the universal scaling of Efimov trimers has been explored in various atomic species by measuring the three-body loss coefficient. An enhancement of the three-body loss at the atom-dimer resonance has been observed, but remains unexplained. It has been attributed to an ``avanlanche mechanism'' based on resonant atom-dimer scattering, yet the effectiveness of the hypothesis is under scrutiny. We present a new piece to the puzzle. In our work, Feshbach dimers and Efimov trimers are formed near the atom-dimer resonance by RF-association, from a Bose-Einstein condensate of 7Li atoms. The molecular binding energies are tunable by the broad Feshbach resonance of the atoms in the | 1 , 1 > state. We observe that the dimer formation rate is significantly enhanced at the atom-dimer resonance. The origin of this enhanement is unclear, but it may be closely related to the enhancement of the three-body loss rate. Work supported by the NSF, ARO, and the Welch Foundation.

  1. Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors.

    PubMed

    Kaczor, Agnieszka A; Guixà-González, Ramon; Carrió, Pau; Poso, Antti; Dove, Stefan; Pastor, Manuel; Selent, Jana

    2015-04-01

    In order to apply structure-based drug design techniques to GPCR complexes, it is essential to model their 3D structure. For this purpose, a multi-component protocol was derived based on protein-protein docking which generates populations of dimers compatible with membrane integration, considering all reasonable interfaces. At the next stage, we applied a scoring procedure based on up to eleven different parameters including shape or electrostatics complementarity. Two methods of consensus scoring were performed: (i) average scores of 100 best scored dimers with respect to each interface, and (ii) frequencies of interfaces among 100 best scored dimers. In general, our multi-component protocol gives correct indications for dimer interfaces that have been observed in X-ray crystal structures of GPCR dimers (opsin dimer, chemokine CXCR4 and CCR5 dimers, κ opioid receptor dimer, β1 adrenergic receptor dimer and smoothened receptor dimer) but also suggests alternative dimerization interfaces. Interestingly, at times these alternative interfaces are scored higher than the experimentally observed ones suggesting them to be also relevant in the life cycle of studied GPCR dimers. Further results indicate that GPCR dimer and higher-order oligomer formation may involve transmembrane helices (TMs) TM1-TM2-TM7, TM3-TM4-TM5 or TM4-TM5-TM6 but not TM1-TM2-TM3 or TM2-TM3-TM4 which is in general agreement with available experimental and computational data.

  2. The Renaissance of Metal-Pyrimidine Nucleobase Coordination Chemistry.

    PubMed

    Lippert, Bernhard; Sanz Miguel, Pablo J

    2016-08-16

    The significance of metal ions for the function and properties of DNA and RNA, long seen primarily under biological aspects and medicinal uses, has recently gained a renewed momentum. This is a consequence of the advent of novel applications in the fields of materials science, biotechnology, and analytical sensor chemistry that relate to the designed incorporation of transition metal ions into nucleic acid base pairs. Ag(+) and Hg(2+) ions, binding to pyrimidine (pym) nucleobases, represent major players in this development. Interestingly, these metal ions were the ones that some 60 years ago started the field! At the same time, the mentioned metal ions had demonstrated a "special relationship" with the pym nucleobases cytosine, thymine, and uracil! Parallel work conducted with oligonucleotides and model nucleobases fostered numerous significant details of these interactions, in particular when X-ray crystallography was involved, correcting earlier views occasionally. Our own activities during the past three to four decades have focused on, among others, the coordination chemistry of transition and main-group metal ions with pym model nucleobases, with an emphasis on Pt(II) and Pd(II). It has always been our goal to deduce, if possible, the potential relevance of our findings for biological processes. It is interesting to put our data, in particular for trans-a2Pt(II) (a = NH3 or amine), into perspective with those of other metal ions, notably Ag(+) and Hg(2+). Irrespective of major differences in kinetics and lability/inertness between d(8) and d(10) metal ions, there is also a lot of similarity in structural aspects as a result of the preferred linear coordination geometry of these species. Moreover, the apparent clustering of metal ions to the pym nucleobases, which is presumably essential for the formation of nanoclusters on oligonucleotide scaffolds, is impressively reflected in model systems, as are reasons for inter-nucleobase cross-links containing more

  3. Nucleobases and Prebiotic Molecules in Organic Residues Produced from the Ultraviolet Photo-Irradiation of Pyrimidine in NH3 and H2O+NH3 Ices

    NASA Technical Reports Server (NTRS)

    Nuevo, Michel; Milam, Stefanie N.; Sandford, Scott

    2012-01-01

    Although not yet identified in the interstellar medium (ISM), N-heterocycles including nucleobases the information subunits of DNA and RNA are present in carbonaceous chondrites, which indicates that molecules of biological interest can be formed in non-terrestrial environments via abiotic pathways. Recent laboratory experiments and ab-initio calculations have already shown that the irradiation of pyrimidine in pure H2O ices leads to the formation of a suite of oxidized pyrimidine derivatives, including the nucleobase uracil. In the present work, NH3:pyrimidine and H2O:NH3:pyrimidine ice mixtures with different relative proportions were irradiated with UV photons under astrophysically relevant conditions. Liquid- and gas-chromatography analysis of the resulting organic residues has led to the detection of the nucleobases uracil and cytosine, as well as other species of prebiotic interest such as urea and small amino acids. The presence of these molecules in organic residues formed under abiotic conditions supports scenarios in which extraterrestrial organics that formed in space and were subsequently delivered to telluric planets via comets and meteorites could have contributed to the inventory of molecules that triggered the first biological reactions on their surfaces.

  4. Prebiotic syntheses of purines and pyrimidines

    NASA Technical Reports Server (NTRS)

    Basile, B.; Oro, J.; Lazcano, A.

    1984-01-01

    The results of experimental and theoretical investigations of the prebiotic synthesis of purines and pyramidines are surveyed. Topics examined include the synthesis of purines from HCN via 4,5-disubstituted imidazole derivatives in aqueous solutions or liquid NH3, simultaneous formation of amino acids and purines by electron irradiation of CH4-NH3-H2O mixtures, synthesis of pyrimadines from cynoacetylene, energetics, formation of bases under anhydrous or concentrated conditions, formation of bases under dilute conditions, Fischer-Tropsch-type reactions, and the role of activated intermediates. It is pointed out that the precursor compounds have been detected in the interstellar medium, on Titan, and in other solar-system bodies, and that solar-nebula HCN concentrations of the order of 1-10 mM have been estimated on the basis of meteorite measurements.

  5. 7-Amino-5-methyl-2-phenyl-6-(phenyl­diazenyl)pyrazolo[1,5-a]pyrimidine crystallizes with Z′ = 2: pseudosymmetry and the formation of complex sheets built from N—H⋯N and C—H⋯π(arene) hydrogen bonds

    PubMed Central

    Portilla, Jaime; Estupiñan, Diego; Cobo, Justo; Glidewell, Christopher

    2010-01-01

    The title compound, C19H16N6, crystallizes with Z′ = 2 in the space group P21/n. The two mol­ecules in the selected asym­metric unit are approximate mirror images of one another; most corresponding pairs of atoms are related by an approximate half-cell translation along [100]. Each mol­ecule contains an intra­molecular N—H⋯N hydrogen bond and the mol­ecules are linked into complex sheets by a combination of two inter­molecular N—H⋯N and four C—H⋯π(arene) hydrogen bonds. Comparisons are made with some other 7-amino­pyrazolo[1,5-a]pyrimidines. PMID:20203410

  6. Pyrimidine nucleobase radical reactivity in DNA and RNA

    NASA Astrophysics Data System (ADS)

    Greenberg, Marc M.

    2016-11-01

    Nucleobase radicals are major products of the reactions between nucleic acids and hydroxyl radical, which is produced via the indirect effect of ionizing radiation. The nucleobase radicals also result from hydration of cation radicals that are produced via the direct effect of ionizing radiation. The role that nucleobase radicals play in strand scission has been investigated indirectly using ionizing radiation to generate them. More recently, the reactivity of nucleobase radicals resulting from formal hydrogen atom or hydroxyl radical addition to pyrimidines has been studied by independently generating the reactive intermediates via UV-photolysis of synthetic precursors. This approach has provided control over where the reactive intermediates are produced within biopolymers and facilitated studying their reactivity. The contributions to our understanding of pyrimidine nucleobase radical reactivity by this approach are summarized.

  7. 5-Benzothiazole substituted pyrimidine derivatives as HCV replication (replicase) inhibitors.

    PubMed

    Arasappan, Ashok; Bennett, Frank; Girijavallabhan, Vinay; Huang, Yuhua; Huelgas, Regina; Alvarez, Carmen; Chen, Lei; Gavalas, Stephen; Kim, Seong-Heon; Kosinski, Aneta; Pinto, Patrick; Rizvi, Razia; Rossman, Randall; Shankar, Bandarpalle; Tong, Ling; Velazquez, Francisco; Venkatraman, Srikanth; Verma, Vishal A; Kozlowski, Joseph; Shih, Neng-Yang; Piwinski, John J; MacCoss, Malcolm; Kwong, Cecil D; Clark, Jeremy L; Fowler, Anita T; Geng, Feng; Kezar, Hollis S; Roychowdhury, Abhijit; Reynolds, Robert C; Maddry, Joseph A; Ananthan, Subramaniam; Secrist, John A; Li, Cheng; Chase, Robert; Curry, Stephanie; Huang, Hsueh-Cheng; Tong, Xiao; Njoroge, F George

    2012-05-01

    Based on a previously identified HCV replication (replicase) inhibitor 1, SAR efforts were conducted around the pyrimidine core to improve the potency and pharmacokinetic profile of the inhibitors. A benzothiazole moiety was found to be the optimal substituent at the pyrimidine 5-position. Due to potential reactivity concern, the 4-chloro residue was replaced by a methyl group with some loss in potency and enhanced rat in vivo profile. Extensive investigations at the C-2 position resulted in identification of compound 16 that demonstrated very good replicon potency, selectivity and rodent plasma/target organ concentration. Inhibitor 16 also demonstrated good plasma levels and oral bioavailability in dogs, while monkey exposure was rather low. Chemistry optimization towards a practical route to install the benzothiazole moiety resulted in an efficient direct C-H arylation protocol.

  8. Infrared Spectroscopy of Charge Transfer Complexes of Purines and Pyrimidines

    SciTech Connect

    Rathod, Pravinsinh I.; Oza, A. T.

    2011-10-20

    The FTIR spectra of charge transfer complexes of purines and pyrimidines with organic acceptors such as TCNQ, TCNE, DDQ, chloranil and iodine are obtained and studied in the present work. Adenine, guanine, thymine, cytosine and uracil are the purines and pyrimidines which are found as constituent of DNA and RNA. Charge transfer induced hydrogen bonding is concluded on the basis of indirect transitions observed in the infrared range in these CTCs. Some CTCs show gaussian bands revealing delocalization of charge carriers. The CTCs show interband transition in three-dimensions rather than two-dimensions unlike CTCs of amino acids. There is no extended hydrogen bonded network spanning the whole crystal. This leads to indirect transition due to locally deformed lattice furnishing a phonon-assisted transition.

  9. Electron- and proton-induced ionization of pyrimidine

    SciTech Connect

    Champion, Christophe; Quinto, Michele; Weck, Philippe F

    2015-03-27

    This present work describes a quantum-mechanically based model of the electron- and proton-induced ionization of isolated pyrimidine molecules. The impact energies range from the target ionization threshold up to ~1 keV for electrons and from 10 keV up to 10 MeV for protons. The cross-section calculations are performed within the 1st Born approximation in which the ejected electron is described by a Coulomb wave whereas the incident and the scattered projectiles are both described by plane waves. The pyrimidine target is described using the Gaussian 09 software package. Furthermore, our theoretical predictions obtained are in good agreement with experimental absolute total cross sections, while large discrepancies are observed between existing semi-empirical models and the present calculations.

  10. Electron- and proton-induced ionization of pyrimidine

    DOE PAGES

    Champion, Christophe; Quinto, Michele; Weck, Philippe F

    2015-03-27

    This present work describes a quantum-mechanically based model of the electron- and proton-induced ionization of isolated pyrimidine molecules. The impact energies range from the target ionization threshold up to ~1 keV for electrons and from 10 keV up to 10 MeV for protons. The cross-section calculations are performed within the 1st Born approximation in which the ejected electron is described by a Coulomb wave whereas the incident and the scattered projectiles are both described by plane waves. The pyrimidine target is described using the Gaussian 09 software package. Furthermore, our theoretical predictions obtained are in good agreement with experimental absolutemore » total cross sections, while large discrepancies are observed between existing semi-empirical models and the present calculations.« less

  11. Infrared Spectroscopy of Charge Transfer Complexes of Purines and Pyrimidines

    NASA Astrophysics Data System (ADS)

    Rathod, Pravinsinh I.; Oza, A. T.

    2011-10-01

    The FTIR spectra of charge transfer complexes of purines and pyrimidines with organic acceptors such as TCNQ, TCNE, DDQ, chloranil and iodine are obtained and studied in the present work. Adenine, guanine, thymine, cytosine and uracil are the purines and pyrimidines which are found as constituent of DNA and RNA. Charge transfer induced hydrogen bonding is concluded on the basis of indirect transitions observed in the infrared range in these CTCs. Some CTCs show gaussian bands revealing delocalization of charge carriers. The CTCs show interband transition in three-dimensions rather than two-dimensions unlike CTCs of amino acids. There is no extended hydrogen bonded network spanning the whole crystal. This leads to indirect transition due to locally deformed lattice furnishing a phonon-assisted transition.

  12. Physico-chemical properties of molten dimer ascorbate oxidase.

    PubMed

    Nicolai, Eleonora; Di Venere, Almerinda; Rosato, Nicola; Rossi, Antonello; Finazzi Agro', Alessandro; Mei, Giampiero

    2006-11-01

    The possible presence of dimeric unfolding intermediates might offer a clue to understanding the relationship between tertiary and quaternary structure formation in dimers. Ascorbate oxidase is a large dimeric enzyme that displays such an intermediate along its unfolding pathway. In this study the combined effect of high pressure and denaturing agents gave new insight on this intermediate and on the mechanism of its formation. The transition from native dimer to the dimeric intermediate is characterized by the release of copper ions forming the tri-nuclear copper center located at the interface between domain 2 and 3 of each subunit. This transition, which is pH-dependent, is accompanied by a decrease in volume, probably associated to electrostriction due to the loosening of intra-subunit electrostatic interactions. The dimeric species is present even at 3 x 10(8) Pa, providing evidence that mechanically or chemically induced unfolding lead to a similar intermediate state. Instead, dissociation occurs with an extremely large and negative volume change (DeltaV approximately -200 mL.mol(-1)) by pressurization in the presence of moderate amounts of denaturant. This volume change can be ascribed to the elimination of voids at the subunit interface. Furthermore, the combination of guanidine and high pressure uncovers the presence of a marginally stable (DeltaG approximately 2 kcal.mol(-1)) monomeric species (which was not observed in previous equilibrium unfolding measurements) that might be populated in the early folding steps of ascorbate oxidase. These findings provide new aspects of the protein folding pathway, further supporting the important role of quaternary interactions in the folding strategy of large dimeric enzymes.

  13. Products and mechanism of acene dimerization. A computational study.

    PubMed

    Zade, Sanjio S; Zamoshchik, Natalia; Reddy, A Ravikumar; Fridman-Marueli, Galit; Sheberla, Dennis; Bendikov, Michael

    2011-07-20

    The high reactivity of acenes can reduce their potential applications in the field of molecular electronics. Although pentacene is an important material for use in organic field-effect transistors because of its high charge mobility, its reactivity is a major disadvantage hindering the development of pentacene applications. In this study, several reaction pathways for the thermal dimerization of acenes were considered computationally. The formation of acene dimers via a central benzene ring and the formation of acene-based polymers were found to be the preferred pathways, depending on the length of the monomer. Interestingly, starting from hexacene, acene dimers are thermodynamically disfavored products, and the reaction pathway is predicted to proceed instead via a double cycloaddition reaction (polymerization) to yield acene-based polymers. A concerted asynchronous reaction mechanism was found for benzene and naphthalene dimerization, while a stepwise biradical mechanism was predicted for the dimerization of anthracene, pentacene, and heptacene. The biradical mechanism for dimerization of anthracene and pentacene proceeds via syn or anti transition states and biradical minima through stepwise biradical pathways, while dimerization of heptacene proceeds via asynchronous ring closure of the complex formed by two heptacene molecules. The activation barriers for thermal dimerization decrease rapidly with increasing acene chain length and are calculated (at M06-2X/6-31G(d)+ZPVE) to be 77.9, 57.1, 33.3, -0.3, and -12.1 kcal/mol vs two isolated acene molecules for benzene, naphthalene, anthracene, pentacene, and heptacene, respectively. If activation energy is calculated vs the initially formed complex of two acene molecules, then the calculated barriers are 80.5, 63.2, 43.7, 16.7, and 12.3 kcal/mol. Dimerization is exothermic from anthracene onward, but it is endothermic at the terminal rings, even for heptacene. Phenyl substitution at the most reactive meso

  14. Novel pyrimidine-2,4-dione-1,2,3-triazole and furo[2,3-d]pyrimidine-2-one-1,2,3-triazole hybrids as potential anti-cancer agents: Synthesis, computational and X-ray analysis and biological evaluation.

    PubMed

    Gregorić, Tomislav; Sedić, Mirela; Grbčić, Petra; Tomljenović Paravić, Andrea; Kraljević Pavelić, Sandra; Cetina, Mario; Vianello, Robert; Raić-Malić, Silvana

    2017-01-05

    Regioselective 1,4-disubstituted 1,2,3-triazole tethered pyrimidine-2,4-dione derivatives (5-23) were successfully prepared by the copper(I)-catalyzed click chemistry. While known palladium/copper-cocatalyzed method based on Sonogashira cross-coupling followed by the intramolecular 5-endo-dig ring closure generated novel 6-alkylfuro[2,3-d]pyrimidine-2-one-1,2,3-triazole hybrids (24b-37b), a small library of their 5-alkylethynyl analogs (24a-37a) was synthesized and described for the first time by tandem terminal alkyne dimerization and subsequent 5-endo-trig cyclization, which was additionally corroborated with computational and X-ray crystal structure analyses. The nature of substituents on alkynes and thereof homocoupled 1,3-diynes predominantly influenced the ratio of the formed products in both pathways. In vitro antiproliferative activity of prepared compounds evaluated on five human cancer cell lines revealed that N,N-1,3-bis-(1,2,3-triazole)-5-bromouracil (5-7) and 5,6-disubstituted furo[2,3-d]pyrimidine-2-one-1,2,3-triazole 34a hybrids exhibited the most pronounced cytostatic acitivities against hepatocellular carcinoma (HepG2) and cervical carcinoma (HeLa) cells with higher potencies than the reference drug 5-fluorouracil. Cytostatic effect of pyrimidine-2,4-dione-1,2,3-triazole hybrid 7 in HepG2 cells could be attributed to the Wee-1 kinase inhibition and abolishment of sphingolipid signaling mediated by acid ceramidase and sphingosine kinase 1. Importantly, this compound proved to be a non-mitochondrial toxicant, which makes it a promising candidate for further lead optimization and development of a new and more efficient agent for the treatment of hepatocellular carcinoma.

  15. Altered Dimer Interface Decreases Stability in an Amyloidogenic Protein

    SciTech Connect

    Baden, Elizabeth M.; Owen, Barbara A.L.; Peterson, Francis C.; Volkman, Brian F.; Ramirez-Alvarado, Marina; Thompson, James R.

    2008-07-21

    Amyloidoses are devastating and currently incurable diseases in which the process of amyloid formation causes fatal cellular and organ damage. The molecular mechanisms underlying amyloidoses are not well known. In this study, we address the structural basis of immunoglobulin light chain amyloidosis, which results from deposition of light chains produced by clonal plasma cells. We compare light chain amyloidosis protein AL-09 to its wild-type counterpart, the kl O18/O8 light chain germline. Crystallographic studies indicate that both proteins form dimers. However, AL-09 has an altered dimer interface that is rotated 90 degrees from the kl O18/O8 dimer interface. The three non-conservative mutations in AL-09 are located within the dimer interface, consistent with their role in the decreased stability of this amyloidogenic protein. Moreover, AL-09 forms amyloid fibrils more quickly than kl O18/O8 in vitro. These results support the notion that the increased stability of the monomer and delayed fibril formation, together with a properly formed dimer, may be protective against amyloidogenesis. This could open a new direction into rational drug design for amyloidogenic proteins.

  16. Modulation of ceramide synthase activity via dimerization.

    PubMed

    Laviad, Elad L; Kelly, Samuel; Merrill, Alfred H; Futerman, Anthony H

    2012-06-15

    Ceramide, the backbone of all sphingolipids, is synthesized by a family of ceramide synthases (CerS) that each use acyl-CoAs of defined chain length for N-acylation of the sphingoid long chain base. CerS mRNA expression and enzymatic activity do not always correlate with the sphingolipid acyl chain composition of a particular tissue, suggesting post-translational mechanism(s) of regulation of CerS activity. We now demonstrate that CerS activity can be modulated by dimer formation. Under suitable conditions, high M(r) CerS complexes can be detected by Western blotting, and various CerS co-immunoprecipitate. CerS5 activity is inhibited in a dominant-negative fashion by co-expression with catalytically inactive CerS5, and CerS2 activity is enhanced by co-expression with a catalytically active form of CerS5 or CerS6. In a constitutive heterodimer comprising CerS5 and CerS2, the activity of CerS2 depends on the catalytic activity of CerS5. Finally, CerS dimers are formed upon rapid stimulation of ceramide synthesis by curcumin. Together, these data demonstrate that ceramide synthesis can be regulated by the formation of CerS dimers and suggest a novel way to generate the acyl chain composition of ceramide (and downstream sphingolipids), which may depend on the interaction of CerS with each other.

  17. Resolving Ultrafast Photoinduced Deactivations in Water-solvated Pyrimidine Nucleosides.

    PubMed

    Pepino, Ana J; Segarra-Martí, Javier; Nenov, Artur; Improta, Roberto; Garavelli, Marco

    2017-03-27

    For the first time, ultrafast deactivations of photo-excited water-solvated pyrimidine nucleosides are mapped employing hybrid QM(CASPT2)/MM(AMBER) optimizations that account for explicit solvation, sugar effects and dynamically correlated potential energy surfaces. Low energy S1/S0 ring-puckering and ring-opening conical intersections (CIs) are suggested to drive the ballistic coherent sub-ps (<200fs) decays observed in each pyrimidine, the energetics controlling this processes correlating with the lifetimes observed. A second bright 1π2π* state, promoting excited-state population branching and leading towards a third CI with the ground state, is proposed to be involved in the slower ultrafast decay component observed in Thd/Cyd. The transient spectroscopic signals of the competitive deactivation channels are computed for the first time. A general unified scheme for ultrafast deactivations, spanning the sub-to-few ps time domain, is eventually delivered, with computed data that matches the experiments and elucidates the intrinsic photo-protection mechanism in solvated pyrimidine nucleosides.

  18. Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei

    PubMed Central

    Rijo-Ferreira, Filipa; Kinch, Lisa N.; Grishin, Nick V.; Hu, Zeping; Phillips, Margaret A.

    2016-01-01

    The human pathogenic parasite Trypanosoma brucei possess both de novo and salvage routes for the biosynthesis of pyrimidine nucleotides. Consequently, they do not require salvageable pyrimidines for growth. Thymidine kinase (TK) catalyzes the formation of dTMP and dUMP and is one of several salvage enzymes that appear redundant to the de novo pathway. Surprisingly, we show through analysis of TK conditional null and RNAi cells that TK is essential for growth and for infectivity in a mouse model, and that a catalytically active enzyme is required for its function. Unlike humans, T. brucei and all other kinetoplastids lack dCMP deaminase (DCTD), which provides an alternative route to dUMP formation. Ectopic expression of human DCTD resulted in full rescue of the RNAi growth phenotype and allowed for selection of viable TK null cells. Metabolite profiling by LC-MS/MS revealed a buildup of deoxypyrimidine nucleosides in TK depleted cells. Knockout of cytidine deaminase (CDA), which converts deoxycytidine to deoxyuridine led to thymidine/deoxyuridine auxotrophy. These unexpected results suggested that T. brucei encodes an unidentified 5'-nucleotidase that converts deoxypyrimidine nucleotides to their corresponding nucleosides, leading to their dead-end buildup in TK depleted cells at the expense of dTTP pools. Bioinformatics analysis identified several potential candidate genes that could encode 5’-nucleotidase activity including an HD-domain protein that we show catalyzes dephosphorylation of deoxyribonucleotide 5’-monophosphates. We conclude that TK is essential for synthesis of thymine nucleotides regardless of whether the nucleoside precursors originate from the de novo pathway or through salvage. Reliance on TK in the absence of DCTD may be a shared vulnerability among trypanosomatids and may provide a unique opportunity to selectively target a diverse group of pathogenic single-celled eukaryotes with a single drug. PMID:27820863

  19. Dimer crystallization of chiral proteoids.

    PubMed

    Wang, Po-Yuan; Mason, Thomas G

    2017-03-08

    Proteins can self-assemble into a variety of exquisitely organized structures through hierarchical reaction pathways. To examine how different core shapes of proteins and entropy combine to influence self-assembly, we create systems of lithographically fabricated proteomimetic colloids, or 'proteoids', and explore how Brownian monolayers of mobile proteoids, which have hard interactions, self-assemble as they are slowly crowded. Remarkably, chiral C-shaped proteoids having circular heads on only one side form enantiopure lock-and-key chiral dimers; these dimers have corrugated, shape-complementary perimeters, so they, in turn, form lock-and-key arrangements into chiral dimer crystals. Time-lapse video microscopy reveals the expulsion of monomers from the growing dimer crystals through tautomerization translocation reactions which expedite the crystallization kinetics. By lithographically mutating proteoids, we also tune the types and structures of the resulting dimer crystals. Thus, rational design of sub-particle features in hard-core colloidal shapes can be used to sterically select desired self-assembly pathways without introducing any site-specific attractions, thereby generating a striking degree of hierarchical self-ordering, reminiscent of protein crystallization.

  20. Haldane relation for interacting dimers

    NASA Astrophysics Data System (ADS)

    Giuliani, Alessandro; Mastropietro, Vieri; Lucio Toninelli, Fabio

    2017-03-01

    We consider a model of weakly interacting close-packed dimers on the two-dimensional square lattice. In a previous paper, we computed both the multi-point dimer correlations, which display non-trivial critical exponents, continuously varying with the interaction strength; and the height fluctuations, which, after proper coarse graining and rescaling, converge to a massless Gaussian field with a suitable interaction-dependent pre-factor (‘amplitude’). In this paper, we prove the identity between the critical exponent of the two-point dimer correlation and the amplitude of this massless Gaussian field. This identity is the restatement, in the context of interacting dimers, of one of the Haldane universality relations, part of his Luttinger-liquid conjecture, originally formulated in the context of one-dimensional interacting Fermi systems. Its validity is a strong confirmation of the effective massless Gaussian field description of the interacting dimer model, which was proposed on the basis of formal bosonization arguments. We also conjecture that a certain discrete curve defined at the lattice level via the Temperley bijection converges in the scaling limit to an SLE κ process, with κ depending non-trivially on the interaction and related in a simple way to the amplitude of the limiting Gaussian field.

  1. One-pot synthesis of high molecular weight synthetic heteroprotein dimers driven by charge complementarity electrostatic interactions.

    PubMed

    Hvasanov, David; Nam, Ekaterina V; Peterson, Joshua R; Pornsaksit, Dithepon; Wiedenmann, Jörg; Marquis, Christopher P; Thordarson, Pall

    2014-10-17

    Despite the importance of protein dimers and dimerization in biology, the formation of protein dimers through synthetic covalent chemistry has not found widespread use. In the case of maleimide-cysteine-based dimerization of proteins, we show here that when the proteins have the same charge, dimerization appears to be inherently difficult with yields around 1% or less, regardless of the nature of the spacer used or whether homo- or heteroprotein dimers are targeted. In contrast, if the proteins have opposing (complementary) charges, the formation of heteroprotein dimers proceeds much more readily, and in the case of one high molecular weight (>80 kDa) synthetic dimer between cytochrome c and bovine serum albumin, a 30% yield of the purified, isolated dimer was achieved. This represents at least a 30-fold increase in yield for protein dimers formed from proteins with complementary charges, compared to when the proteins have the same charge, under otherwise similar conditions. These results illustrate the role of ionic supramolecular interactions in controlling the reactivity of proteins toward bis-functionalized spacers. The strategy here for effective synthetic dimerization of proteins could be very useful for developing novel approaches to study the important role of protein-protein interactions in chemical biology.

  2. Adventures in holographic dimer models

    NASA Astrophysics Data System (ADS)

    Kachru, Shamit; Karch, Andreas; Yaida, Sho

    2011-03-01

    We abstract the essential features of holographic dimer models, and develop several new applications of these models. Firstly, semi-holographically coupling free band fermions to holographic dimers, we uncover novel phase transitions between conventional Fermi liquids and non-Fermi liquids, accompanied by a change in the structure of the Fermi surface. Secondly, we make dimer vibrations propagate through the whole crystal by way of double trace deformations, obtaining nontrivial band structure. In a simple toy model, the topology of the band structure experiences an interesting reorganization as we vary the strength of the double trace deformations. Finally, we develop tools that would allow one to build, in a bottom-up fashion, a holographic avatar of the Hubbard model.

  3. Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Monomucleotides

    NASA Astrophysics Data System (ADS)

    Kanavarioti, Anastassia

    1997-08-01

    Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2-methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2+ in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MeImpU and 2-MeImpC produce about 65% of oligomers including 4% of the 3',5'-linked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of internucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MeImpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

  4. Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Mononucleotides

    NASA Technical Reports Server (NTRS)

    Kanavarioti, Anastassia

    1997-01-01

    Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2- methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2(+) in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MelmpU and 2-MelmpC produce about 65% of oligomers including 4% of the 3',5'-Iinked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of intemucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MelmpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

  5. Highly stable tetrathiafulvalene radical dimers in [3]catenanes

    SciTech Connect

    Spruell, Jason M.; Coskun, Ali; Friedman, Douglas C.; Forgan, Ross S.; Sarjeant, Amy A.; Trabolsi, Ali; Fahrenbach, Albert C.; Barin, Gokhan; Paxton, Walter F.; Dey, Sanjeev K.; Olson, Mark A.; Benítez, Diego; Tkatchouk, Ekaterina; Colvin, Michael T.; Carmielli, Raanan; Caldwell, Stuart T.; Rosair, Georgina M.; Hewage, Shanika Gunatilaka; Duclairoir, Florence; Seymour, Jennifer L.; Slawin, Alexandra M.Z.; Goddard, III, William A.; Wasielewski, Michael R.; Cooke, Graeme; Stoddart, J. Fraser

    2010-12-03

    Two [3]catenane 'molecular flasks' have been designed to create stabilized, redox-controlled tetrathiafulvalene (TTF) dimers, enabling their spectrophotometric and structural properties to be probed in detail. The mechanically interlocked framework of the [3]catenanes creates the ideal arrangement and ultrahigh local concentration for the encircled TTF units to form stable dimers associated with their discrete oxidation states. These dimerization events represent an affinity umpolung, wherein the inversion in electronic affinity replaces the traditional TTF-bipyridinium interaction, which is over-ridden by stabilizing mixed-valence (TTF){sub 2}{sup {sm_bullet}+} and radical-cation (TTF{sup {sm_bullet}+}){sub 2} states inside the 'molecular flasks.' The experimental data, collected in the solid state as well as in solution under ambient conditions, together with supporting quantum mechanical calculations, are consistent with the formation of stabilized paramagnetic mixed-valence dimers, and then diamagnetic radical-cation dimers following subsequent one-electron oxidations of the [3]catenanes.

  6. Covalent intermolecular interaction of the nitric oxide dimer (NO)2

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Zheng, Gui-Li; Lv, Gang; Geng, Yi-Zhao; Ji, Qing

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5

  7. Three-state kinetic folding mechanism of the H2A/H2B histone heterodimer: the N-terminal tails affect the transition state between a dimeric intermediate and the native dimer.

    PubMed

    Placek, Brandon J; Gloss, Lisa M

    2005-01-28

    The H2A/H2B heterodimer is a component of the nucleosome core particle, the fundamental repeating unit of chromatin in all eukaryotic cells. The kinetic folding mechanism for the H2A/H2B dimer has been determined from unfolding and refolding kinetics as a function of urea using stopped-flow, circular dichroism and fluorescence methods. The kinetic data are consistent with a three-state mechanism: two unfolded monomers associate to form a dimeric intermediate in the dead-time of the SF instrument (approximately 5 ms); this intermediate is then converted to the native dimer by a slower, first-order reaction. Analysis of the burst-phase amplitudes as a function of denaturant indicates that the dimeric kinetic intermediate possesses approximately 50% of the secondary structure and approximately 60% of the surface area burial of the native dimer. The stability of the dimeric intermediate is approximately 30% of that of the native dimer at the monomer concentrations employed in the SF experiments. Folding-to-unfolding double-jump experiments were performed to monitor the formation of the native dimer as a function of folding delay times. The double-jump data demonstrate that the dimeric intermediate is on-pathway and obligatory. Formation of a transient dimeric burst-phase intermediate has been observed in the kinetic mechanism of other intertwined, segment-swapped, alpha-helical, DNA-binding dimers, such as the H3-H4 histone dimer, Escherichia coli factor for inversion stimulation and E.coli Trp repressor. The common feature of a dimeric intermediate in these folding mechanisms suggests that this intermediate may accelerate protein folding, when compared to the folding of archael histones, which do not populate a transient dimeric species and fold more slowly.

  8. Kinetics of DNA tile dimerization.

    PubMed

    Jiang, Shuoxing; Yan, Hao; Liu, Yan

    2014-06-24

    Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

  9. Kinetics of DNA Tile Dimerization

    PubMed Central

    2015-01-01

    Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile–tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency. PMID:24794259

  10. Carbon-Carbon Bond Cleavage Reaction: Synthesis of Multisubstituted Pyrazolo[1,5-a]pyrimidines.

    PubMed

    Saikia, Pallabi; Gogoi, Sanjib; Boruah, Romesh C

    2015-07-02

    A new carbon-carbon bond cleavage reaction was developed for the efficient synthesis of multisubstituted pyrazolo[1,5-a]pyrimidines. This base induced reaction of 1,3,5-trisubstituted pentane-1,5-diones and substituted pyrazoles afforded good yields of the pyrazolo[1,5-a]pyrimidines.

  11. Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria

    PubMed Central

    Mühleip, Alexander W.; Joos, Friederike; Wigge, Christoph; Frangakis, Achilleas S.; Kühlbrandt, Werner; Davies, Karen M.

    2016-01-01

    F1Fo-ATP synthases are universal energy-converting membrane protein complexes that synthesize ATP from ADP and inorganic phosphate. In mitochondria of yeast and mammals, the ATP synthase forms V-shaped dimers, which assemble into rows along the highly curved ridges of lamellar cristae. Using electron cryotomography and subtomogram averaging, we have determined the in situ structure and organization of the mitochondrial ATP synthase dimer of the ciliate Paramecium tetraurelia. The ATP synthase forms U-shaped dimers with parallel monomers. Each complex has a prominent intracrista domain, which links the c-ring of one monomer to the peripheral stalk of the other. Close interaction of intracrista domains in adjacent dimers results in the formation of helical ATP synthase dimer arrays, which differ from the loose dimer rows in all other organisms observed so far. The parameters of the helical arrays match those of the cristae tubes, suggesting the unique features of the P. tetraurelia ATP synthase are directly responsible for generating the helical tubular cristae. We conclude that despite major structural differences between ATP synthase dimers of ciliates and other eukaryotes, the formation of ATP synthase dimer rows is a universal feature of mitochondria and a fundamental determinant of cristae morphology. PMID:27402755

  12. Enhancement of the therapeutic effectiveness of methotrexate and protection of normal proliferating tissues with purines and pyrimidines.

    PubMed

    Harrap, K R; Taylor, G A; Browman, G P

    1977-07-01

    Mice can be protected against the toxicity arising from lethal doses of methotrexate with purine and pyrimidine combinations, but not with pyrimidine alone. Furthermore, methotrexate treatment of tumour-bearing mice, conjunction with purine/pyrimidine protection, can be more effective than conventional metotrexate/folinic acid treatment.

  13. Cholesteric LC orientation in spherical capsules of LC composites containing pyrimidine additives

    NASA Astrophysics Data System (ADS)

    Vetrov, S.; Zharkova, G. M.; Khachaturyan, V. M.; Korets, A.; Sadreev, A.; Shabanov, V. F.

    1996-01-01

    The reflection spectra of cholesteric liquid crystals dispersed in polymer and comprising pyrimidine dopes are investigated in the entire temperature range of the mesophase existence. One or several oxyphenyl substituents in an ortho position implemented into a pyrimidine system induce the second reflection region. The reflection curves for different wavelengths corresponding to regions I and II merge with temperature. Thermodynamically equilibrium states of polymer-dispersed cholesterics under the influence of polar pyrimidine dopes are considered. The pyrimidine effect is modulated by the orientational near-surface potential. The existence of two space regions of a spherical droplet with different helix pitches is validated. The natural helix pitch is retained inside the droplet while a new pyrimidine-induced pitch is formed in a layer close to the droplet surface. The results obtained describe the existence of two reflection regions and the temperature behavior of the helix pitch.

  14. Synthesis and Applications of Non-spherical Dimer Colloids

    NASA Astrophysics Data System (ADS)

    Yoon, Kisun

    Colloids are promising building blocks in material synthesis because of their controllability of size and surface properties. The synthesis of chemically and/or geometrically anisotropic colloidal particles has received attentions with the expectation of building blocks for complex structures. However, the synthesis of anisotropic colloidal particles is by far more difficult than the synthesis of spherical colloidal particles. Lack of monodispersity and productivity of many anisotropic particles often limits their applications as a building block for complex structures. Thus, it is highly desirable to develop methods which can produce a large amount of monodisperse non-spherical particles with controllable asymmetric surface properties. This dissertation details the work for developing such a method. The major result of this dissertation is a synthetic method to produce monodisperse non-spherical colloids with anisotropic surface property in a large quantity. The anisotropic colloid, which we call it as Dimer particle, has two fused lobes like a dumbbell and each lobe's size can be independently controlled. We present a novel method to synthesize sub-micron size Dimer particles. This method can produce a large amount of submicron-sized Dimer particles with good monodispersity and well-controlled shape. Submicron-sized Dimer particles have been highly desired since they can be used as a building block for self assembly using Brownian motion, colloidal surfactant for Pickering emulsion, and photonic materials. To fully take advantage of the anisotropy of the particles, we develop a facile method to tailor the surface property of each lobe independently by asymmetrically coating the particles with gold nanoparticles. This method doesn't need the arrangement of particles onto any type of interfaces. Asymmetric coating of gold nanoparticles can be carried out simply by mixing Dimer particles with gold nanoparticles. The formation mechanism of the submicron-sized Dimer

  15. Hypochlorite-induced damage to nucleosides: formation of chloramines and nitrogen-centered radicals.

    PubMed

    Hawkins, C L; Davies, M J

    2001-08-01

    Stimulated monocytes and neutrophils generate hypochlorite (HOCl) via the release of the enzyme myeloperoxidase and hydrogen peroxide. HOCl is a key bactericidal agent, but can also damage host tissue. As there is a strong link between chronic inflammation and some cancers, we have investigated HOCl damage to DNA bases. We show that reaction of HOCl with the exocyclic -NH(2) groups of cytidine, adenosine, and guanosine, and the ring NH groups of all bases, yields chloramines (RNHCl/RR'NCl). These are the major initial products. Chloramine decay can be accelerated by UV light and metal ions, and these reactions, together with thermal decomposition, give rise to nucleoside-derived nitrogen-centered radicals. Evidence is presented for the rapid addition of pyrimidine-derived nitrogen-centered radicals to another parent molecule to give dimers. Experiments with nucleoside mixtures show that the propensity for radical formation is cytidine > adenosine = guanosine > uridine = thymidine. These data are inconsistent with the selectivity of HOCl attack and the stability of the resulting chloramines, but can be rationalized if chlorine transfer between bases is rapid and yields the most stable chloramine, with such transfer preceding radical formation. Thus, though thymidine is the major initial site of chloramine formation, rapid chlorine atom transfer generates cytidine and adenosine chloramines. These reactions rationalize the preferential formation of chlorinated cytidine and adenosine in DNA.

  16. Water dimer equilibrium constant of saturated vapor

    NASA Astrophysics Data System (ADS)

    Malomuzh, N. P.; Mahlaichuk, V. N.; Khrapatyi, S. V.

    2014-08-01

    The value and temperature dependence of the dimerization constant for saturated water vapor are determined. A general expression that links the second virial coefficient and the dimerization constant is obtained. It is shown that the attraction between water monomers and dimers is fundamental, especially at T > 350 K. The range of application for the obtained results is determined.

  17. First-principles prediction of the effects of temperature and solvent selection on the dimerization of benzoic acid.

    PubMed

    Pham, Hieu H; Taylor, Christopher D; Henson, Neil J

    2013-01-24

    We introduce a procedure of quantum chemical calculations (B3P86/6-31G**) to study carboxylic acid dimerization and its correlation with temperature and properties of the solvent. Benzoic acid is chosen as a model system for studying dimerization via hydrogen bonding. Organic solvents are simulated using the self-consistent reaction field (SCRF) method with the polarized continuum model (PCM). The cyclic dimer is the most stable structure both in gas phase and solution. Dimer mono- and dihydrates could be found in the gas phase if acid molecules are in contact with water vapor. However, the formation of these hydrated conformers is very limited and cyclic dimer is the principal conformer to coexist with monomer acid in solution. Solvation of the cyclic dimer is more favorable compared to other complexes, partially due to the diminishing of hydrogen bonding capability and annihilation of dipole moments. Solvents have a strong effect on inducing dimer dissociation and this dependence is more pronounced at low dielectric constants. By accounting for selected terms in the total free energy of solvation, the solvation entropy could be incorporated to predict the dimer behavior at elevated temperatures. The temperature dependence of benzoic acid dimerization obtained by this technique is in good agreement with available experimental measurements, in which a tendency of dimer to dissociate is observed with increased temperatures. In addition, dimer breakup is more sensitive to temperature in low dielectric environments rather than in solvents with a higher dielectric constant.

  18. Pyrimidine Salvage in Trypanosoma brucei Bloodstream Forms and the Trypanocidal Action of Halogenated Pyrimidiness

    PubMed Central

    Ali, Juma A. M.; Creek, Darren J.; Burgess, Karl; Allison, Harriet C.; Field, Mark C.; Mäser, Pascal; De Koning, Harry P.

    2016-01-01

    African trypanosomes are capable of both pyrimidine biosynthesis and salvage of preformed pyrimidines from the host. However, uptake of pyrimidines in bloodstream form trypanosomes has not been investigated, making it difficult to judge the relative importance of salvage and synthesis or to design a pyrimidine-based chemotherapy. Detailed characterization of pyrimidine transport activities in bloodstream form Trypanosoma brucei brucei found that these cells express a high-affinity uracil transporter (designated TbU3) that is clearly distinct from the procyclic pyrimidine transporters. This transporter had low affinity for uridine and 2′deoxyuridine and was the sole pyrimidine transporter expressed in these cells. In addition, thymidine was taken up inefficiently through a P1-type nucleoside transporter. Of importance, the anticancer drug 5-fluorouracil was an excellent substrate for TbU3, and several 5-fluoropyrimidine analogs were investigated for uptake and trypanocidal activity; 5F-orotic acid, 5F-2′deoxyuridine displayed activity in the low micromolar range. The metabolism and mode of action of these analogs was determined using metabolomic assessments of T. brucei clonal lines adapted to high levels of these pyrimidine analogs, and of the sensitive parental strains. The analysis showed that 5-fluorouracil is incorporated into a large number of metabolites but likely exerts toxicity through incorporation into RNA. 5F-2′dUrd and 5F-2′dCtd are not incorporated into nucleic acids but act as prodrugs by inhibiting thymidylate synthase as 5F-dUMP. We present the most complete model of pyrimidine salvage in T. brucei to date, supported by genome-wide profiling of the predicted pyrimidine biosynthesis and conversion enzymes. PMID:23188714

  19. 2, 4-Diamino-6- hydroxy pyrimidine inhibits NSAIDs induced nitrosyl-complex EPR signals and ulcer in rat jejunum

    PubMed Central

    Somasundaram, S; Simpson, R; Rafi, S; Shergill, JK; Bjarnason, I; Wrigglesworth, J

    2002-01-01

    Background It has been suggested that one aspect of non-steroidal anti-inflammatory drugs induced intestinal damage is due to either uncoupling of mitochondrial oxidative phosphorylation or inhibition of electron transport. We investigated the latter possibility using electron paramagnetic resonance spectroscopy. Results Electron paramagnetic studies of NSAIDS on sub-mitochondrial particles revealed that indomethacin, but not with nabumetone, bound to a site near to Complex I and ubiquinone to generate a radical species. Normal rats exhibited prominent [3Fe-4S]ox signals (g ~ 2.01) at 20 K. One hour after indomethacin there was a prominent, intense and broad absorption pattern at (g ~2.07) suggesting, appearance of radical species overlapping [3Fe-4S]ox and was unaffected by pretreatment with 2,4 diamino -6-hydroxy pyrimidine. At 24 hrs, when macroscopic ulcers were seen, there was a new signal due to a nitric oxide radical (NO•). In contrast, nabumetone and 2,4 diamino-6-hydroxy pyrimidine pre-treated animals receiving indomethacin exhibited electron paramagnetic resonance spectra identical to those of controls at 24 hrs and neither was associated with small intestinal ulcers. Indomethacin and 2,4 diamino hydroxy pyrimidine pre-treated rats, but not nabumetone, had increased intestinal permeability. Conclusion The results suggest that the in vivo effects of indomethacin modulate the mitochondrial respiratory chain directly at 1 h and 24 h through formation of nitric oxide. NO• appears to play an important role in the late pathogenic stages of NSAID enteropathy and may be the site for targeted treatment to reduce their toxicity. PMID:11960558

  20. UV-induced pyrimidine dimers and trimethylpsoralen cross-links do not alter chromatin folding in vitro

    SciTech Connect

    Gale, J.M.; Smerdon, M.J.

    1988-09-20

    We have examined the ability of intact and histone H1 depleted chromatin fibers to fold into higher ordered structures in vitro following DNA damage by two different agents: UV irradiation at 254 nm and trimethylpsoralen plus near-UV light. Both agents damage DNA specifically, yet cause different degrees of unwinding (and possibly bending) of the DNA helix. In addition, trimethylpsoralen forms interstrand DNA cross-links. The structural transitions of intact and histone H1 depleted chromatin fibers, induced by NaCl, were monitored by analytical ultracentrifugation, light scattering, and circular dichroism. Our results indicate that when chromatin fibers contain even large, nonphysiological amounts of DNA photodamage by either agent, the salt-induced folding of these fibers into higher ordered structures is unaffected. The compact 30-nm fiber must therefore be able to accommodate a large amount of DNA photodamage (greater than one UV-induced photoproduct or trimethylpsoralen interstrand cross-link per nucleosome) with little or no change in the overall size or compaction of this structure.

  1. Micellisation and immunoreactivities of dimeric beta-caseins.

    PubMed

    Yousefi, Reza; Gaudin, Jean-Charles; Chobert, Jean-Marc; Pourpak, Zahra; Moin, Mostafa; Moosavi-Movahedi, Ali Akbar; Haertle, Thomas

    2009-12-01

    Bovine beta-casein (beta-CN) is a highly amphiphilic micellising phospho-protein showing chaperone-like activity in vitro. Recently, existence of multiple sequential epitopes on beta-CN polypeptide chain in both hydrophilic-polar (psi) and hydrophobic-apolar domains (phi) has been evidenced. In order to clarify specific contribution of polar and apolar domains in micellisation process and in shaping immunoreactivity of beta-CN, its dimeric/bi-amphiphilic "quasi palindromic" forms covalently connected by a disulfide bond linking either N-terminal (C4 beta-CND) or C-terminal domain (C208 beta-CND) were produced and studied. Depending on the C- or N-terminal position of inserted cysteine, each dimeric beta-CN contains one polar/apolar region at the centre and two external hydrophobic/hydrophilic ends. Consequently, such casein dimers have radically different polarities/hydrophobicities on their outside surfaces. Dynamic light scattering (DLS) measurements indicate that these dimeric casein molecules form micelles of different sizes depending on arrangement of polar fragments of the beta-CN mutants in their constrained dimers. Non-aggregated dimers have different hydrodynamic diameters that could be explained by their different geometries. Measurements of fluorescence showed more hydrophobic environment of Trp residues of C208 beta-CND, while in similar experimental conditions Trp residues of C4 beta-CND and native beta-CN were more exposed to the polar medium. Both fluorescence and DLS studies showed greater propensity for micellisation of the dimeric beta-CNs, suggesting that the factors inducing the formation of micelles are stronger in the bi-amphiphilic dimers. 1-anilino-naphthalene-8-sulfonate (ANS) binding studies showed different binding of ANS by these dimers as well as different exposition of ANS binding (hydrophobic) regions in the micellar states. The differences in fluorescence resonance energy transfer (FRET) profiles of C4 beta-CND and C208 beta-CND can

  2. Inhibition of Arenavirus by A3, a Pyrimidine Biosynthesis Inhibitor

    PubMed Central

    Ortiz-Riaño, Emilio; Ngo, Nhi; Devito, Stefanie; Eggink, Dirk; Munger, Joshua; Shaw, Megan L.

    2014-01-01

    Arenaviruses merit significant interest as important human pathogens, since several of them cause severe hemorrhagic fever disease that is associated with high morbidity and significant mortality. Currently, there are no FDA-licensed arenavirus vaccines available, and current antiarenaviral therapy is limited to an off-labeled use of the nucleoside analog ribavirin, which has limited prophylactic efficacy. The pyrimidine biosynthesis inhibitor A3, which was identified in a high-throughput screen for compounds that blocked influenza virus replication, exhibits a broad-spectrum antiviral activity against negative- and positive-sense RNA viruses, retroviruses, and DNA viruses. In this study, we evaluated the antiviral activity of A3 against representative Old World (lymphocytic choriomeningitis virus) and New World (Junin virus) arenaviruses in rodent, monkey, and human cell lines. We show that A3 is significantly more efficient than ribavirin in controlling arenavirus multiplication and that the A3 inhibitory effect is in part due to its ability to interfere with viral RNA replication and transcription. We document an additive antiarenavirus effect of A3 and ribavirin, supporting the potential combination therapy of ribavirin and pyrimidine biosynthesis inhibitors for the treatment of arenavirus infections. PMID:24198417

  3. Inhibition of arenavirus by A3, a pyrimidine biosynthesis inhibitor.

    PubMed

    Ortiz-Riaño, Emilio; Ngo, Nhi; Devito, Stefanie; Eggink, Dirk; Munger, Joshua; Shaw, Megan L; de la Torre, Juan Carlos; Martínez-Sobrido, Luis

    2014-01-01

    Arenaviruses merit significant interest as important human pathogens, since several of them cause severe hemorrhagic fever disease that is associated with high morbidity and significant mortality. Currently, there are no FDA-licensed arenavirus vaccines available, and current antiarenaviral therapy is limited to an off-labeled use of the nucleoside analog ribavirin, which has limited prophylactic efficacy. The pyrimidine biosynthesis inhibitor A3, which was identified in a high-throughput screen for compounds that blocked influenza virus replication, exhibits a broad-spectrum antiviral activity against negative- and positive-sense RNA viruses, retroviruses, and DNA viruses. In this study, we evaluated the antiviral activity of A3 against representative Old World (lymphocytic choriomeningitis virus) and New World (Junin virus) arenaviruses in rodent, monkey, and human cell lines. We show that A3 is significantly more efficient than ribavirin in controlling arenavirus multiplication and that the A3 inhibitory effect is in part due to its ability to interfere with viral RNA replication and transcription. We document an additive antiarenavirus effect of A3 and ribavirin, supporting the potential combination therapy of ribavirin and pyrimidine biosynthesis inhibitors for the treatment of arenavirus infections.

  4. Isolation of Purines and Pyrimidines from the Murchison Meteorite

    NASA Technical Reports Server (NTRS)

    Glavin, D. P.; Bada, J. K.

    2003-01-01

    The origin of life on Earth, and possibly on other planets such as Mars, would have required the presence of liquid water and a continuous supply of prebiotic organic compounds. The delivery of organic matter by asteroids, comets, and carbonaceous meteorites could have contributed to the early Earth's prebiotic inventory by seeding the planet with biologically important organic compounds. A wide variety of prebiotic organic compounds have previously been detected in the Murchison CM type carbonaceous chondrite including amino acids, purines and pyrimidines'. These compounds play a major role in terrestrial biochemistry and are integral components of proteins, DNA and RNA. In this study we developed a new extraction technique using sublimation in order to isolate purines and pyrimidines from Murchison2, which is cleaner and more time efficient that traditional methods3. Several purines including adenine, guanine, hypoxanthine and xanthine were positively identified by high performance liquid chromatography and ultraviolet absorption detection in our Murchison extracts. The purines detected in Murchison do not correlate with the distribution of nucleobases found in geological environments on Earth4. Moreover, the abundance of extraterrestrial amino acids and the low level of terrestrial amino acid contaminants found in Murchison', support the idea that the purines in t h s meteorite are extraterrestrial in origin.

  5. Electron- and proton-induced ionization of pyrimidine

    NASA Astrophysics Data System (ADS)

    Champion, Christophe; Quinto, Michele A.; Weck, Philippe F.

    2015-05-01

    The present work describes a quantum-mechanically based model of the electron- and proton-induced ionization of isolated pyrimidine molecules. The impact energies range from the target ionization threshold up to ~1 keV for electrons and from 10 keV up to 10 MeV for protons. The cross-section calculations are performed within the 1st Born approximation in which the ejected electron is described by a Coulomb wave whereas the incident and the scattered projectiles are both described by plane waves. The pyrimidine target is described using the Gaussian 09 software package. The theoretical predictions obtained are in good agreement with experimental absolute total cross sections, while large discrepancies are observed between existing semi-empirical models and the present calculations. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

  6. Assembly Pathway of Hepatitis B Core Virus-like Particles from Genetically Fused Dimers*

    PubMed Central

    Holmes, Kris; Shepherd, Dale A.; Ashcroft, Alison E.; Whelan, Mike; Rowlands, David J.; Stonehouse, Nicola J.

    2015-01-01

    Macromolecular complexes are responsible for many key biological processes. However, in most cases details of the assembly/disassembly of such complexes are unknown at the molecular level, as the low abundance and transient nature of assembly intermediates make analysis challenging. The assembly of virus capsids is an example of such a process. The hepatitis B virus capsid (core) can be composed of either 90 or 120 dimers of coat protein. Previous studies have proposed a trimer of dimers as an important intermediate species in assembly, acting to nucleate further assembly by dimer addition. Using novel genetically-fused coat protein dimers, we have been able to trap higher-order assembly intermediates and to demonstrate for the first time that both dimeric and trimeric complexes are on pathway to virus-like particle (capsid) formation. PMID:25953902

  7. Magneto-association of atoms near an atom-dimer resonance

    NASA Astrophysics Data System (ADS)

    Nguyen, Jason H. V.; Luo, De; Hulet, Randall G.

    2015-05-01

    Ultracold atomic gases provide an environment to study few body physics in a regime where universal properties, such as the scaling laws of Efimov trimers, can be explored. In our work, Efimov trimers and Feshbach dimers are created in a condensate of 7Li atoms by RF-field modulation. The molecular binding energies are tunable using the broad Feshbach resonance for atoms in the | 1 , 1 > state. We find that the rate of dimer formation is sharply peaked at the atom-dimer resonance, where the trimer merges with the dimer plus free-atom continuum. The origins of this enhancement are unclear, but may be related to our previous observation of enhanced three-body loss at the atom-dimer resonance. Work supported by NSF, ARO, and the Welch Foundation.

  8. Fiber optic D dimer biosensor

    DOEpatents

    Glass, R.S.; Grant, S.A.

    1999-08-17

    A fiber optic sensor for D dimer (a fibrinolytic product) can be used in vivo (e.g., in catheter-based procedures) for the diagnosis and treatment of stroke-related conditions in humans. Stroke is the third leading cause of death in the United States. It has been estimated that strokes and stroke-related disorders cost Americans between $15-30 billion annually. Relatively recently, new medical procedures have been developed for the treatment of stroke. These endovascular procedures rely upon the use of microcatheters. These procedures could be facilitated with this sensor for D dimer integrated with a microcatheter for the diagnosis of clot type, and as an indicator of the effectiveness, or end-point of thrombolytic therapy. 4 figs.

  9. Fiber optic D dimer biosensor

    DOEpatents

    Glass, Robert S.; Grant, Sheila A.

    1999-01-01

    A fiber optic sensor for D dimer (a fibrinolytic product) can be used in vivo (e.g., in catheter-based procedures) for the diagnosis and treatment of stroke-related conditions in humans. Stroke is the third leading cause of death in the United States. It has been estimated that strokes and stroke-related disorders cost Americans between $15-30 billion annually. Relatively recently, new medical procedures have been developed for the treatment of stroke. These endovascular procedures rely upon the use of microcatheters. These procedures could be facilitated with this sensor for D dimer integrated with a microcatheter for the diagnosis of clot type, and as an indicator of the effectiveness, or end-point of thrombolytic therapy.

  10. Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV.

    PubMed

    Thiagarajan, Viruthachalam; Byrdin, Martin; Eker, André P M; Müller, Pavel; Brettel, Klaus

    2011-06-07

    CPD photolyase uses light to repair cyclobutane pyrimidine dimers (CPDs) formed between adjacent pyrimidines in UV-irradiated DNA. The enzyme harbors an FAD cofactor in fully reduced state (FADH(-)). The CPD repair mechanism involves electron transfer from photoexcited FADH(-) to the CPD, splitting of its intradimer bonds, and electron return to restore catalytically active FADH(-). The two electron transfer processes occur on time scales of 10(-10) and 10(-9) s, respectively. Until now, CPD splitting itself has only been poorly characterized by experiments. Using a previously unreported transient absorption setup, we succeeded in monitoring cyclobutane thymine dimer repair in the main UV absorption band of intact thymine at 266 nm. Flavin transitions that overlay DNA-based absorption changes at 266 nm were monitored independently in the visible and subtracted to obtain the true repair kinetics. Restoration of intact thymine showed a short lag and a biexponential rise with time constants of 0.2 and 1.5 ns. We assign these two time constants to splitting of the intradimer bonds (creating one intact thymine and one thymine anion radical T(∘-)) and electron return from T(∘-) to the FAD cofactor with recovery of the second thymine, respectively. Previous model studies and computer simulations yielded various CPD splitting times between < 1 ps and < 100 ns. Our experimental results should serve as a benchmark for future efforts to model enzymatic photorepair. The technique and methods developed here may be applied to monitor other photoreactions involving DNA.

  11. Mechanism of FGF receptor dimerization and activation

    NASA Astrophysics Data System (ADS)

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-01-01

    Fibroblast growth factors (fgfs) are widely believed to activate their receptors by mediating receptor dimerization. Here we show, however, that the FGF receptors form dimers in the absence of ligand, and that these unliganded dimers are phosphorylated. We further show that ligand binding triggers structural changes in the FGFR dimers, which increase FGFR phosphorylation. The observed effects due to the ligands fgf1 and fgf2 are very different. The fgf2-bound dimer structure ensures the smallest separation between the transmembrane (TM) domains and the highest possible phosphorylation, a conclusion that is supported by a strong correlation between TM helix separation in the dimer and kinase phosphorylation. The pathogenic A391E mutation in FGFR3 TM domain emulates the action of fgf2, trapping the FGFR3 dimer in its most active state. This study establishes the existence of multiple active ligand-bound states, and uncovers a novel molecular mechanism through which FGFR-linked pathologies can arise.

  12. Functional Roles of the Dimer-Interface Residues in Human Ornithine Decarboxylase

    PubMed Central

    Lee, Chien-Yun; Liu, Yi-Liang; Lin, Chih-Li; Liu, Guang-Yaw; Hung, Hui-Chih

    2014-01-01

    Ornithine decarboxylase (ODC) catalyzes the decarboxylation of ornithine to putrescine and is the rate-limiting enzyme in the polyamine biosynthesis pathway. ODC is a dimeric enzyme, and the active sites of this enzyme reside at the dimer interface. Once the enzyme dissociates, the enzyme activity is lost. In this paper, we investigated the roles of amino acid residues at the dimer interface regarding the dimerization, protein stability and/or enzyme activity of ODC. A multiple sequence alignment of ODC and its homologous protein antizyme inhibitor revealed that 5 of 9 residues (residues 165, 277, 331, 332 and 389) are divergent, whereas 4 (134, 169, 294 and 322) are conserved. Analytical ultracentrifugation analysis suggested that some dimer-interface amino acid residues contribute to formation of the dimer of ODC and that this dimerization results from the cooperativity of these interface residues. The quaternary structure of the sextuple mutant Y331S/Y389D/R277S/D332E/V322D/D134A was changed to a monomer rather than a dimer, and the Kd value of the mutant was 52.8 µM, which is over 500-fold greater than that of the wild-type ODC (ODC_WT). In addition, most interface mutants showed low but detectable or negligible enzyme activity. Therefore, the protein stability of these interface mutants was measured by differential scanning calorimetry. These results indicate that these dimer-interface residues are important for dimer formation and, as a consequence, are critical for enzyme catalysis. PMID:25140796

  13. Dimerization of postsynaptic neuroligin drives synaptic assembly via transsynaptic clustering of neurexin.

    PubMed

    Shipman, Seth L; Nicoll, Roger A

    2012-11-20

    The transsynaptic complex of neuroligin (NLGN) and neurexin forms a physical connection between pre- and postsynaptic neurons that occurs early in the course of new synapse assembly. Both neuroligin and neurexin have, indeed, been proposed to exhibit active, instructive roles in the formation of synapses. However, the process by which these instructive roles play out during synaptogenesis is not well understood. Here, we examine one aspect of postsynaptic neuroligin with regard to its synaptogenic properties: its basal state as a constitutive dimer. We show that dimerization is required for the synaptogenic properties of neuroligin and likely serves to induce presynaptic differentiation via a transsynaptic clustering of neurexin. Further, we introduce chemically inducible, exogenous dimerization domains to the neuroligin molecule, effectively bestowing chemical control of neuroligin dimerization. This allows us to identify the acute requirements of neuroligin dimerization by chemically manipulating the monomeric-to-dimeric conversion of neuroligin. Based on the results of the inducible dimerization experiments, we propose a model in which dimerized neuroligin induces the mechanical clustering of presynaptic molecules as part of a requisite step in the coordinated assembly of a chemical synapse.

  14. Evidence for the dimerization-mediated catalysis of methionine sulfoxide reductase A from Clostridium oremlandii.

    PubMed

    Lee, Eun Hye; Lee, Kitaik; Kwak, Geun-Hee; Park, Yeon Seung; Lee, Kong-Joo; Hwang, Kwang Yeon; Kim, Hwa-Young

    2015-01-01

    Clostridium oremlandii MsrA (CoMsrA) is a natively selenocysteine-containing methionine-S-sulfoxide reductase and classified into a 1-Cys type MsrA. CoMsrA exists as a monomer in solution. Herein, we report evidence that CoMsrA can undergo homodimerization during catalysis. The monomeric CoMsrA dimerizes in the presence of its substrate methionine sulfoxide via an intermolecular disulfide bond between catalytic Cys16 residues. The dimeric CoMsrA is resolved by the reductant glutaredoxin, suggesting the relevance of dimerization in catalysis. The dimerization reaction occurs in a concentration- and time-dependent manner. In addition, the occurrence of homodimer formation in the native selenoprotein CoMsrA is confirmed. We also determine the crystal structure of the dimeric CoMsrA, having the dimer interface around the two catalytic Cys16 residues. A central cone-shaped hole is present in the surface model of dimeric structure, and the two Cys16 residues constitute the base of the hole. Collectively, our biochemical and structural analyses suggest a novel dimerization-mediated mechanism for CoMsrA catalysis that is additionally involved in CoMsrA regeneration by glutaredoxin.

  15. Synchronized oscillations of dimers in biphasic charged fd-virus suspensions

    NASA Astrophysics Data System (ADS)

    Kang, K.; Piao, S. H.; Choi, H. J.

    2016-08-01

    Micron-sized colloidal spheres that are dispersed in an isotropic-nematic biphasic host suspension of charged rods (fd-virus particles) are shown to spontaneously form dimers, which exhibit a synchronized oscillatory motion. Dimer formation is not observed in the monophase of isotropic and nematic suspensions. The synchronized oscillations of dimers are connected to the inhomogeneous state of the host suspension of charged rods (fd viruses) where nematic domains are in coexistence with isotropic regions. The synchronization of oscillations occurs in bulk states, in the absence of an external field. With a low field strength of an applied electric field, the synchronization is rather reduced, but it recovers again when the field is turned off. In this Rapid Communication, we report this observation as an example of the strange attractor, occurring in the mixture of PS (polystyrene) dimers in an isotropic-nematic coexistence biphasic fd-virus network. Furthermore, we highlight that the synchronization of PS-dimer oscillations is the result of a global bifurcation diagram, driven by a delicate balance between the short-attractive "twisted" interaction of PS dimers and long-ranged electrostatic repulsive interactions of charged fd rods. The interest is then in the local enhancement of "twist-nematic" elasticity in reorientation of the dimer oscillations. An analysis of image-time correlations is provided with the data movies and Fourier transforms of averaged orientations for the synchronized oscillations of dimers in the biphasic I -N coexistence concentration of charged fd-virus suspensions.

  16. Methoxymethyl (MOM) group nitrogen protection of pyrimidines bearing C-6 acyclic side-chains.

    PubMed

    Kraljević, Tatjana Gazivoda; Petrović, Martina; Krištafor, Svjetlana; Makuc, Damjan; Plavec, Janez; Ross, Tobias L; Ametamey, Simon M; Raić-Malić, Silvana

    2011-06-20

    Novel N-methoxymethylated (MOM) pyrimidine (4-13) and pyrimidine-2,4-diones (15-17) nucleoside mimetics in which an isobutyl side-chain is attached at the C-6 position of the pyrimidine moiety were synthesized. Synthetic methods via O-persilylated or N-anionic uracil derivatives have been evaluated for the synthesis of N-1- and/or N-3-MOM pyrimidine derivatives with C-6 acyclic side-chains. A synthetic approach using an activated N-anionic pyrimidine derivative afforded the desired N,N-1,3-diMOM and N-1-MOM pyrimidines 4 and 5 in good yield. Introduction of fluorine into the side-chain was performed with DAST as the fluorinating reagent to give a N,N-1,3-diMOM pyrimidine 13 with a 1-fluoro-3-hydroxyisobutyl moiety at C-6. Conformational study of the monotritylated N-1-MOM pyrimidine 12 by the use of the NOE experiments revealed the predominant conformation of the compound to be one where the hydroxymethyl group in the C-6 side-chain is close to the N-1-MOM moiety, while the OMTr is in proximity to the CH(3)-5 group. Contrary to this no NOE enhancements between the N-1-MOM group and hydroxymethyl or fluoromethyl protons in 13 were observed, which suggested a nonrestricted rotation along the C-6 side-chain. Fluorinated N,N-1,3-diMOM pyrimidine 13 emerged as a model compound for development of tracer molecules for non-invasive imaging of gene expression using positron emission tomography (PET).

  17. Absorption and intermediary metabolism of purines and pyrimidines in lactating dairy cows.

    PubMed

    Stentoft, Charlotte; Røjen, Betina Amdisen; Jensen, Søren Krogh; Kristensen, Niels B; Vestergaard, Mogens; Larsen, Mogens

    2015-02-28

    About 20 % of ruminal microbial N in dairy cows derives from purines and pyrimidines; however, their intermediary metabolism and contribution to the overall N metabolism has sparsely been described. In the present study, the postprandial patterns of net portal-drained viscera (PDV) and hepatic metabolism were assessed to evaluate purine and pyrimidine N in dairy cows. Blood was sampled simultaneously from four veins with eight hourly samples from four multi-catheterised Holstein cows. Quantification of twenty purines and pyrimidines was performed with HPLC-MS/MS, and net fluxes were estimated across the PDV, hepatic tissue and total splanchnic tissue (TSP). Concentration differences between veins of fifteen purine and pyrimidine nucleosides (NS), bases (BS) and degradation products (DP) were different from zero (P≤ 0·05), resulting in the net PDV releases of purine NS (0·33-1·3 mmol/h), purine BS (0·0023-0·018 mmol/h), purine DP (7·0-7·8 mmol/h), pyrimidine NS (0·30-2·8 mmol/h) and pyrimidine DP (0·047-0·77 mmol/h). The hepatic removal of purine and pyrimidine was almost equivalent to the net PDV release, resulting in no net TSP release. One exception was uric acid (7·9 mmol/h) from which a large net TSP release originated from the degradation of purine NS and BS. A small net TSP release of the pyrimidine DP β-alanine and β-aminoisobutyric acid (-0·032 to 0·37 mmol/h) demonstrated an outlet of N into the circulating N pool. No effect of time relative to feeding was observed (P>0·05). These data indicate that considerable amounts of N are lost in the dairy cow due to prominent intermediary degradation of purines, but that pyrimidine N is reusable to a larger extent.

  18. Structure and function of nucleoside hydrolases from Physcomitrella patens and maize catalyzing the hydrolysis of purine, pyrimidine, and cytokinin ribosides.

    PubMed

    Kopecná, Martina; Blaschke, Hanna; Kopecny, David; Vigouroux, Armelle; Koncitíková, Radka; Novák, Ondrej; Kotland, Ondrej; Strnad, Miroslav; Moréra, Solange; von Schwartzenberg, Klaus

    2013-12-01

    We present a comprehensive characterization of the nucleoside N-ribohydrolase (NRH) family in two model plants, Physcomitrella patens (PpNRH) and maize (Zea mays; ZmNRH), using in vitro and in planta approaches. We identified two NRH subclasses in the plant kingdom; one preferentially targets the purine ribosides inosine and xanthosine, while the other is more active toward uridine and xanthosine. Both subclasses can hydrolyze plant hormones such as cytokinin ribosides. We also solved the crystal structures of two purine NRHs, PpNRH1 and ZmNRH3. Structural analyses, site-directed mutagenesis experiments, and phylogenetic studies were conducted to identify the residues responsible for the observed differences in substrate specificity between the NRH isoforms. The presence of a tyrosine at position 249 (PpNRH1 numbering) confers high hydrolase activity for purine ribosides, while an aspartate residue in this position confers high activity for uridine. Bud formation is delayed by knocking out single NRH genes in P. patens, and under conditions of nitrogen shortage, PpNRH1-deficient plants cannot salvage adenosine-bound nitrogen. All PpNRH knockout plants display elevated levels of certain purine and pyrimidine ribosides and cytokinins that reflect the substrate preferences of the knocked out enzymes. NRH enzymes thus have functions in cytokinin conversion and activation as well as in purine and pyrimidine metabolism.

  19. [Microsequencing, analysis of molecular weight and amino acid composition for pyrimidine 5'-nucleotidase I of human erythrocytes].

    PubMed

    Pan, Zhu-Lin; Li, Jin-Ying; Min, Bi-He; Ying, Kang; Zhou, Hong; Xu, Xiao-Ping; Shong, Xian-Min; Han, Feng-Lai; Zhang, Wei-Ping; Zhang, Xian

    2003-02-01

    To further explore the mechanism of congenital pyrimidine 5'-nuleotidase I (P5'N-I) deficiency, on the basis of purification of the protein, the molecular weight and amino acid composition were analysed by mass-spectrograph and amino-acid analyzer, microsequencing and bioinformation analysis of P5'N-I were performed after it was hydrolysed by trypsin. The results showed that three fractions were found in the purified P5'N-I and their molecular weights were 26,952.9, 55,476 and 110,938, respectively. The sequence from one of the peptide fragments was I-E-G-P-T-I-R-Q-I-E. The homologous sequence was not found after comparision with the ten-amino-acid sequence in GenBank by blast procedure. Amino acid analysis indicated that P5'N-I was composed of 18 amino acids at least, and 243 amino acid residues. In conclusion, the enzyme might be an allosteric enzyme, there might be homologous dimer or tetramer in physiological status of normal human erythrocyte, the microsequence could be designed as the probe for fishing the genes of interest. The composition of amino acid might be an important information in determination of its protein primary structure.

  20. 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

  1. Stopping power for electrons in pyrimidine in the energy range 20-3000 eV.

    PubMed

    Colmenares, R; Sanz, A G; Fuss, M C; Blanco, F; García, G

    2014-01-01

    In this work, we present new experimental electron energy loss distribution functions for pyrimidine (C4H4N2) measured for the incident energy range 30-2000 eV. Theoretical total and elastic cross sections for electron scattering from pyrimidine were calculated using the screening-corrected additivity rule (IAM-SCAR) method. Based on the mean energy loss observed in the experiment and the theoretical integral inelastic cross section, the stopping power for electrons in pyrimidine is calculated in the energy range 20-3000 eV.

  2. Measurement of oxidative damage at pyrimidine bases in gamma-irradiated DNA.

    PubMed

    Douki, T; Delatour, T; Paganon, F; Cadet, J

    1996-01-01

    Oxidized nucleobases represent one of the main classes of damage induced in DNA by ionizing radiation. Emphasis was placed in this work on the measurement of four oxidized pyrimidine bases, including 5-(hydroxymethyl)uracil (5-HMUra), 5-formyluracil (5-ForUra), 5-hydroxycytosine (5-OHCyt), and 5-hydroxyuracil (5-OHUra), in isolated DNA upon exposure to gamma radiation in aerated aqueous solution. For this purpose, both high performance liquid chromatography associated with electrochemical detection (HPLC-EC) and gas chromatography coupled to mass spectrometry (GC-MS) were used. Conditions of hydrolysis of the N-glycosidic bond were carefully checked in order to achieve a quantitative release of the lesions. We showed that 60% formic acid treatment leads to the decomposition of the four lesions studied. On the other hand, hydrolysis based on the use of either 88% formic acid or 70% hydrogen fluoride in pyridine (HF/Pyr) allowed the quantitative release of the modified bases, with the exception of 5-HMUra when the latter reagent was utilized. A dose course study of the radiation-induced formation of 5-HMUra and 5-ForUra in DNA by using the GC-MS assay showed that the latter lesion was produced in a 2.1-fold higher yield than the former one. HF/Pyr and 88% formic acid hydrolysis provided similar results for 5-ForUra, indicating the reliability of both techniques for the measurement of this lesion. For 5-OHUra and 5-OHCyt, the level of modification determined by GC-MS analysis was higher after 88% formic acid treatment than upon HF/Pyr hydrolysis. When DNA was enzymatically digested and analyzed by HPLC-EC for 5-OHdCyd and 5-OHdUrd, the results were very close to those obtained by GC-MS following HF/Pyr treatment. It was concluded that additional amounts of both 5-OHUra and 5-OHCyt are produced during the 88% formic acid treatment from radiation-induced 5,6-saturated pyrimidine precursors. It is likely that cytosine and uracil diols are involved in this reaction. The

  3. Photochemical dimerization and functionalization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and silanes

    DOEpatents

    Crabtree, R.H.; Brown, S.H.

    1989-10-17

    The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and primary, secondary and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

  4. Photochemical dimerization and functionalization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and silanes

    DOEpatents

    Crabtree, Robert H.; Brown, Stephen H.

    1989-01-01

    The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and primary, secondary and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

  5. Relative stabilities and the spectral signatures of stacked and hydrogen-bonded dimers of serotonin

    NASA Astrophysics Data System (ADS)

    Dev, S.; Giri, K.; Majumder, M.; Sathyamurthy, N.

    2015-10-01

    The O-HṡṡṡN hydrogen-bonded dimer of serotonin is shown to be more stable than the stacked dimer in its ground electronic state, by using the Møller-Plesset second-order perturbation theory (MP2) and the 6-31g** basis set. The vertical excitation energy for the lowest π → π* transition for the monomer as well as the dimer is predicted by time-dependent density functional theory. The experimentally observed red shift of excitation wavelength on oligomerisation is explained in terms of the change in the HOMO-LUMO energy gap due to complex formation. The impact of dimer formation on the proton magnetic resonance spectrum of serotonin monomer is also examined.

  6. Electron Scattering from Pyrazine compared with Pyrimidine and Benzene

    NASA Astrophysics Data System (ADS)

    Palihawadana, P. D.; Sullivan, J. P.; Buckman, S. J.; Brunger, M. J.; Winstead, C.; McKoy, V.; Garcia, G.; Blanco, F.

    2012-10-01

    Pyrazine (C4H4N2) is a model molecule for studying electron interactions with nucleases. Also pyrazine is an ideal target, due to its high symmetry (D2h), for theoreticians to investigate electron collisions with complex DNA/RNA bases. In this work we present absolute elastic differential cross sections and elastic excitation functions for scattering of low-energy electrons by pyrazine measured using a crossed electron-target beam apparatus at the Australian National University. A comparison is also made between pyrazine cross sections with previously measured pyrimidine and benzene cross sections. Since all those molecules are similar in structure and considered as analogues to nucleobases, we intend to discuss similarities and differences in electron scattering results between three molecules.

  7. Trisubstituted Pyrimidines as Efficacious and Fast-Acting Antimalarials

    PubMed Central

    2016-01-01

    In this paper we describe the optimization of a phenotypic hit against Plasmodium falciparum, based on a trisubstituted pyrimidine scaffold. This led to compounds with good pharmacokinetics and oral activity in a P. berghei mouse model of malaria. The most promising compound (13) showed a reduction in parasitemia of 96% when dosed at 30 mg/kg orally once a day for 4 days in the P. berghei mouse model of malaria. It also demonstrated a rapid rate of clearance of the erythrocytic stage of P. falciparum in the SCID mouse model with an ED90 of 11.7 mg/kg when dosed orally. Unfortunately, the compound is a potent inhibitor of cytochrome P450 enzymes, probably due to a 4-pyridyl substituent. Nevertheless, this is a lead molecule with a potentially useful antimalarial profile, which could either be further optimized or be used for target hunting. PMID:27314305

  8. Solitary waves in dimer binary collision model

    NASA Astrophysics Data System (ADS)

    Ahsan, Zaid; Jayaprakash, K. R.

    2017-01-01

    Solitary wave propagation in nonlinear diatomic (dimer) chains is a very interesting topic of research in the study of nonlinear lattices. Such waves were recently found to be supported by the essentially nonlinear granular lattice and Toda lattice. An interesting aspect of this discovery is attributed to the realization of a spectrum of the mass ratio (the only system parameter governing the dynamics) that supports the propagation of such waves corresponding to the considered interaction potential. The objective of this exposition is to explore solitary wave propagation in the dimer binary collision (BC) model. Interestingly, the dimer BC model supports solitary wave propagation at a discrete spectrum of mass ratios similar to those observed in granular and Toda dimers. Further, we report a qualitative and one-to-one correspondence between the spectrum of the mass ratio corresponding to the dimer BC model and those corresponding to granular and Toda dimer chains.

  9. Dimerization of Matrix Protein Is Required for Budding of Respiratory Syncytial Virus

    PubMed Central

    Förster, Andreas; Maertens, Goedele N.; Farrell, Paul J.

    2015-01-01

    mechanism of RSV assembly is still poorly understood. Here we show that the RSV matrix protein forms dimers in solution and in crystals; the dimer is essential for formation of higher-order oligomers. Destabilizing the dimer interface resulted in the loss of RSV filament formation and a lack of budding of virus-like particles. Importantly, our findings can potentially lead to new structure-based RSV inhibitors targeting the assembly process. PMID:25673702

  10. Monomer-dimer problem on some networks

    NASA Astrophysics Data System (ADS)

    Wu, Ruijuan; Yan, Weigen

    2016-09-01

    Zhang et al. (2012) obtained the exact formula for the number of all possible monomer-dimer arrangements and the asymptotic growth constant on a scale-free small-world network. In this note, we generalize this result and obtain the exact solution on the monomer-dimer model on many networks. Particularly, we prove that these networks have the same asymptotic growth constant of the number of monomer-dimer arrangements.

  11. Thermalization of a dimerized antiferromagnetic spin chain.

    PubMed

    Konstantinidis, N P

    2016-01-20

    Thermalization is investigated for the one-dimensional anisotropic antiferromagnetic Heisenberg model with dimerized nearest-neighbor interactions that break integrability. For this purpose the time evolution of local operator expectation values after an interacting quench is calculated directly with the Chebyshev polynomial expansion, and the deviation of the diagonal from the canonical thermal ensemble value is calculated for increasing system size for these operators. The spatial and spin symmetries of the Hamiltonian are taken into account to divide it into symmetry subsectors. The rate of thermalization is found to weaken with the dimerization parameter as the Hamiltonian evolves between two integrable limits, the non-dimerized and the fully dimerized where the chain breaks up into isolated dimers. This conclusion is supported by the distribution of the local operator off-diagonal elements between the eigenstates of the Hamiltonian with respect to their energy difference, which determines the strength of temporal fluctuations. The off-diagonal elements have a low-energy peak for small dimerization which facilitates thermalization, and originates in the reduction of spatial symmetry with respect to the non-dimerized limit. For increasing dimerization their distribution changes and develops a single low-energy maximum that relates to the fully dimerized limit and slows down thermalization.

  12. The 3-ureidopropionase of Caenorhabditis elegans, an enzyme involved in pyrimidine degradation.

    PubMed

    Janowitz, Tim; Ajonina, Irene; Perbandt, Markus; Woltersdorf, Christian; Hertel, Patrick; Liebau, Eva; Gigengack, Ulrike

    2010-10-01

    Pyrimidines are important metabolites in all cells. Levels of cellular pyrimidines are controlled by multiple mechanisms, with one of these comprising the reductive degradation pathway. In the model invertebrate Caenorhabditis elegans, two of the three enzymes of reductive pyrimidine degradation have previously been characterized. The enzyme catalysing the final step of pyrimidine breakdown, 3-ureidopropionase (β-alanine synthase), had only been identified based on homology. We therefore cloned and functionally expressed the 3-ureidopropionase of C. elegans as hexahistidine fusion protein. The purified recombinant enzyme readily converted the two pyrimidine degradation products: 3-ureidopropionate and 2-methyl-3-ureidopropionate. The enzyme showed a broad pH optimum between pH 7.0 and 8.0. Activity was highest at approximately 40 °C, although the half-life of activity was only 65 s at that temperature. The enzyme showed clear Michaelis-Menten kinetics, with a K(m) of 147 ± 26 μM and a V(max) of 1.1 ± 0.1 U·mg protein(-1). The quaternary structure of the recombinant enzyme was shown to correspond to a dodecamer by 'blue native' gel electrophoresis and gel filtration. The organ specific and subcellular localization of the enzyme was determined using a translational fusion to green fluorescent protein and high expression was observed in striated muscle cells. With the characterization of the 3-ureidopropionase, the reductive pyrimidine degradation pathway in C. elegans has been functionally characterized.

  13. Probing the excited state relaxation dynamics of pyrimidine nucleosides in chloroform solution.

    PubMed

    Röttger, Katharina; Marroux, Hugo J B; Böhnke, Hendrik; Morris, David T J; Voice, Angus T; Temps, Friedrich; Roberts, Gareth M; Orr-Ewing, Andrew J

    2016-12-16

    Ultrafast transient electronic and vibrational absorption spectroscopy (TEAS and TVAS) of 2'-deoxy-cytidine (dC) and 2'-deoxy-thymidine (dT) dissolved in chloroform examines their excited-state dynamics and the recovery of ground electronic state molecules following absorption of ultraviolet light. The chloroform serves as a weakly interacting solvent, allowing comparisons to be drawn with prior experimental studies of the photodynamics of these nucleosides in the gas phase and in polar solvents such as water. The pyrimidine base nucleosides have some propensity to dimerize in aprotic solvents, but the monomer photochemistry can be resolved clearly and is the focus of this study. UV absorption at a wavelength of 260 nm excites a (1)ππ* ← S0 transition, but prompt crossing of a significant fraction (50% in dC, 17% in dT) of the (1)ππ* population into a nearby (1)nπ* state is too fast for the experiments to resolve. The remaining flux on the (1)ππ* state leaves the vertical Franck-Condon region and encounters a conical intersection with the ground electronic state of ethylenic twist character. In dC, the (1)ππ* state decays to the ground state with a time constant of 1.1 ± 0.1 ps. The lifetime of the (1)nπ* state is much longer in the canonical forms of both molecules: recovery of the ground state population from these states occurs with time constants of 18.6 ± 1.1 ps in amino-oxo dC and ∼114 ps in dT, indicating potential energy barriers to the (1)nπ*/S0 conical intersections. The small fraction of the imino-oxo tautomer of dC present in solution has a longer-lived (1)nπ* state with a lifetime for ground state recovery of 193 ± 55 ps. No evidence is found for photo-induced tautomerization of amino-oxo dC to the imino-oxo form, or for population of low lying triplet states of this nucleoside. In contrast, ∼8% of the UV-excited dT molecules access the long-lived T1 ((3)ππ*) state through the (1)nπ* state. The primary influence of the solvent

  14. Pyrimidine non-nucleoside analogs: A direct synthesis of a novel class of N-substituted amino and N-sulfonamide derivatives of pyrimidines.

    PubMed

    Elgemeie, Galal H; Salah, Ali M; Abbas, Nermeen S; Hussein, Hoda A; Mohamed, Reham A

    2017-03-04

    A convenient method for the regioselective synthesis of pyrimidine non-nucleoside analogs was developed. This study reports a novel and efficient method for the synthesis of a new type of N-substituted amino methylsulfanylpyrimidines and the corresponding pyrazolo[3,4-d]pyrimidines. This series of compounds was designed through the reaction of dimethyl N-cyanodithioiminocarbonate with 2-cyano-N'-(thiophen-2-yl-, furan-2-yl- and pyridin-4-ylmethylene)acetohydrazide and N'-(2-cyanoacetyl)arylsulfonohydrazides. The scope and limitation of the method are demonstrated. The antibacterial and antifungal activities of the synthesized compounds were also evaluated.

  15. Solution-phase parallel synthesis of acyclic nucleoside libraries of purine, pyrimidine, and triazole acetamides.

    PubMed

    Pathak, Ashish K; Pathak, Vibha; Reynolds, Robert C

    2014-09-08

    Molecular diversity plays a pivotal role in modern drug discovery against phenotypic or enzyme-based targets using high throughput screening technology. Under the auspices of the Pilot Scale Library Program of the NIH Roadmap Initiative, we produced and report herein a diverse library of 181 purine, pyrimidine, and 1,2,4-triazole-N-acetamide analogues which were prepared in a parallel high throughput solution-phase reaction format. A set of assorted amines were reacted with several nucleic acid N-acetic acids utilizing HATU as the coupling reagent to produce diverse acyclic nucleoside N-acetamide analogues. These reactions were performed using 24 well reaction blocks and an automatic reagent-dispensing platform under inert atmosphere. The targeted compounds were purified on an automated purification system using solid sample loading prepacked cartridges and prepacked silica gel columns. All compounds were characterized by NMR and HRMS, and were analyzed for purity by HPLC before submission to the Molecular Libraries Small Molecule Repository (MLSMR) at NIH. Initial screening through the Molecular Libraries Probe Production Centers Network (MLPCN) program, indicates that several analogues showed diverse and interesting biological activities.

  16. Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage

    PubMed Central

    Knips, Alexander; Zacharias, Martin

    2017-01-01

    The photo-induced cis-syn-cyclobutane pyrimidine (CPD) dimer is a frequent DNA lesion. In bacteria photolyases efficiently repair dimers employing a light-driven reaction after flipping out the CPD damage to the active site. How the repair enzyme identifies a damaged site and how the damage is flipped out without external energy is still unclear. Employing molecular dynamics free energy calculations, the CPD flipping process was systematically compared to flipping undamaged nucleotides in various DNA global states and bound to photolyase enzyme. The global DNA deformation alone (without protein) significantly reduces the flipping penalty and induces a partially looped out state of the damage but not undamaged nucleotides. Bound enzyme further lowers the penalty for CPD damage flipping with a lower free energy of the flipped nucleotides in the active site compared to intra-helical state (not for undamaged DNA). Both the reduced penalty and partial looping by global DNA deformation contribute to a significantly shorter mean first passage time for CPD flipping compared to regular nucleotides which increases the repair likelihood upon short time encounter between repair enzyme and DNA. PMID:28128222

  17. Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage

    NASA Astrophysics Data System (ADS)

    Knips, Alexander; Zacharias, Martin

    2017-01-01

    The photo-induced cis-syn-cyclobutane pyrimidine (CPD) dimer is a frequent DNA lesion. In bacteria photolyases efficiently repair dimers employing a light-driven reaction after flipping out the CPD damage to the active site. How the repair enzyme identifies a damaged site and how the damage is flipped out without external energy is still unclear. Employing molecular dynamics free energy calculations, the CPD flipping process was systematically compared to flipping undamaged nucleotides in various DNA global states and bound to photolyase enzyme. The global DNA deformation alone (without protein) significantly reduces the flipping penalty and induces a partially looped out state of the damage but not undamaged nucleotides. Bound enzyme further lowers the penalty for CPD damage flipping with a lower free energy of the flipped nucleotides in the active site compared to intra-helical state (not for undamaged DNA). Both the reduced penalty and partial looping by global DNA deformation contribute to a significantly shorter mean first passage time for CPD flipping compared to regular nucleotides which increases the repair likelihood upon short time encounter between repair enzyme and DNA.

  18. pH-Stimulated Reconfiguration and Structural Isomerization of Origami Dimer and Trimer Systems.

    PubMed

    Wu, Na; Willner, Itamar

    2016-10-12

    Reversible pH-responsive dimer or trimer origami structures are assembled by bridging origami frames with pH-responsive units. The cyclic pH-stimulated separation and reassembly of dimer origami structures is demonstrated using i-motif or Hoogsteen-type (C-G·C(+) or T-A·T) interactions. The duplex-bridged dimer T1-T2 is separated by the pH-induced formation of an i-motif structure (pH = 4.5), and the dimer is reassembled at pH = 7.0. The duplex-bridged dimer, T3-T4, is separated at pH = 4.5 through the formation of C-G·C(+) triplex structures and is reassembled to the dimer at pH = 7.0. Similarly, the T-A·T triplex-bridged dimer, T5-T6, is separated at pH = 9.5 and is reassembled at neutral pH. Finally, a trimer, T3-T7-T6, that includes C-G·C(+) and T-A·T pH-responsive bridges reveals pH-programmed cleavage to selectively yield the dimers T3-T7 or T7-T6, which reassemble to the trimer at pH = 7.0. A linear three-frame origami structure bridged by duplexes including caged i-motif units undergoes pH-stimulated isomerization to a bent structure (pH = 4.5) through the formation of i-motif complex and bridging T-A·T triplex units.

  19. IgG dimers in multidonor-derived immunoglobulins: aspects of generation and function.

    PubMed

    Gronski, P

    2006-01-01

    Immunoglobulin G (IgG) concentrates for therapeutic purposes, like passive immunotherapy, supplementation in inherited or acquired deficiencies or immunomodulation, are prepared from multidonor-derived plasma pools. They usually contain varying amounts of dimeric IgG. The essential factor influencing dimer formation is the pool size; in addition, molecular properties of IgG and a variety of production process- and formulation-specific parameters are important. Numerous experimental findings suggest that dimers are predominantly generated by interactions of idiotypic and anti-idiotypic antibodies (Ids, anti-Ids). Ab-inherent crossreactivity, frequency distribution of both the affinities for particular Id-anti-Id interactions and the corresponding dimer concentrations still have to be elucidated. All these parameters influencing molecular features and functional activity of IgG dimers hamper the assay-dependent measurement of biological efficacy and correlation of total IgG content. A more detailed understanding may help to better control the dual nature of dimer-dependent biological activity comprising both undesirable (e.g., hypotension) and desirable effects of dimeric IgG (blockade of the reticuloendothelial system, RES, in immune thrombocytopenic purpura, ITP). These effects are detectable in in vitro and in vivo models and are thought to be of relevance for humans.

  20. Mechanism for Controlling the Dimer-Monomer Switch and Coupling Dimerization to Catalysis of the Severe Acute Respiratory Syndrome Coronavirus 3C-Like Protease

    SciTech Connect

    Shi,J.; Sivaraman, J.; Song, J.

    2008-01-01

    Unlike 3C protease, the severe acute respiratory syndrome coronavirus (SARS-CoV) 3C-like protease (3CLpro) is only enzymatically active as a homodimer and its catalysis is under extensive regulation by the unique extra domain. Despite intense studies, two puzzles still remain: (i) how the dimer-monomer switch is controlled and (ii) why dimerization is absolutely required for catalysis. Here we report the monomeric crystal structure of the SARS-CoV 3CLpro mutant R298A at a resolution of 1.75 Angstroms . Detailed analysis reveals that Arg298 serves as a key component for maintaining dimerization, and consequently, its mutation will trigger a cooperative switch from a dimer to a monomer. The monomeric enzyme is irreversibly inactivated because its catalytic machinery is frozen in the collapsed state, characteristic of the formation of a short 310-helix from an active-site loop. Remarkably, dimerization appears to be coupled to catalysis in 3CLpro through the use of overlapped residues for two networks, one for dimerization and another for the catalysis.

  1. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization.

    PubMed

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-Van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-10-18

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.

  2. Single nucleotide polymorphism analysis using different colored dye dimer probes

    NASA Astrophysics Data System (ADS)

    Marmé, Nicole; Friedrich, Achim; Denapaite, Dalia; Hakenbeck, Regine; Knemeyer, Jens-Peter

    2006-09-01

    Fluorescence quenching by dye dimer formation has been utilized to develop hairpin-structured DNA probes for the detection of a single nucleotide polymorphism (SNP) in the penicillin target gene pbp2x, which is implicated in the penicillin resistance of Streptococcus pneumoniae. We designed two specific DNA probes for the identification of the pbp2x genes from a penicillin susceptible strain R6 and a resistant strain Streptococcus mitis 661 using green-fluorescent tetramethylrhodamine (TMR) and red-fluorescent DY-636, respectively. Hybridization of each of the probes to its respective target DNA sequence opened the DNA hairpin probes, consequently breaking the nonfluorescent dye dimers into fluorescent species. This hybridization of the target with the hairpin probe achieved single nucleotide specific detection at nanomolar concentrations via increased fluorescence.

  3. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    NASA Astrophysics Data System (ADS)

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-10-01

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.

  4. Self-assembly of dimeric tetraurea calix[4]pyrrole capsules

    PubMed Central

    Ballester, Pablo; Gil-Ramírez, Guzmán

    2009-01-01

    Calix[4]pyrroles having extended aromatic cavities have been functionalized with 4 ureas in the para position of their meso phenyl substituents. This elaboration of the upper rim was completed in 2 synthetic steps starting from the α,α,α,α-tetranitro isomer of the calix[4]pyrrole obtained in the acid catalyzed condensation of p-nitrophenyl methyl ketone and pyrrole. In dichloromethane solution and in the presence of 4,4′-bipyridine N-N′-dioxide the tetraurea calix[4]pyrrole dimerizes reversibly forming a cyclic array of 16 hydrogen bonds and encapsulating 1 molecule of bis-N-oxide. The encapsulated guest is bound in the cavity by hydrogen bonding to the 2 endohedral calix[4]pyrrole centers. Further evidence for dimerization of the tetraurea calix[4]pyrroles is provided by 1H-NMR experiments and by the formation of mixed capsules. PMID:19261848

  5. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    PubMed Central

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-Van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-01-01

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development. PMID:27752093

  6. Glutamine-dependent carbamoyl-phosphate synthetase and other enzyme activities related to the pyrimidine pathway in spleen of Squalus acanthias (spiny dogfish).

    PubMed

    Anderson, P M

    1989-07-15

    The first two steps of urea synthesis in liver of marine elasmobranchs involve formation of glutamine from ammonia and of carbamoyl phosphate from glutamine, catalysed by glutamine synthetase and carbamoyl-phosphate synthetase, respectively [Anderson & Casey (1984) J. Biol. Chem. 259, 456-462]; both of these enzymes are localized exclusively in the mitochondrial matrix. The objective of this study was to establish the enzymology of carbamoyl phosphate formation and utilization for pyrimidine nucleotide biosynthesis in Squalus acanthias (spiny dogfish), a representative elasmobranch. Aspartate carbamoyltransferase could not be detected in liver of dogfish. Spleen extracts, however, had glutamine-dependent carbamoyl-phosphate synthetase, aspartate carbamoyltransferase, dihydro-orotase, and glutamine synthetase activities, all localized in the cytosol; dihydro-orotate dehydrogenase, orotate phosphoribosyltransferase, and orotidine-5'-decarboxylase activities were also present. Except for glutamine synthetase, the levels of all activities were very low. The carbamoyl-phosphate synthetase activity is inhibited by UTP and is activated by 5-phosphoribosyl 1-pyrophosphate. The first three enzyme activities of the pyrimidine pathway were eluted in distinctly different positions during gel filtration chromatography under a number of different conditions; although complete proteolysis of inter-domain regions of a multifunctional complex during extraction cannot be excluded, the evidence suggests that in dogfish, in contrast to mammalian species, these three enzymes of the pyrimidine pathway exist as individual polypeptide chains. These results: (1) establish that dogfish express two different glutamine-dependent carbamoyl-phosphate synthetase activities, (2) confirm the report [Smith, Ritter & Campbell (1987) J. Biol. Chem. 262, 198-202] that dogfish express two different glutamine synthetases, and (3) provide indirect evidence that glutamine may not be available in liver for

  7. Electronic transitions of palladium dimer

    SciTech Connect

    Qian, Yue; Ng, Y. W.; Chen, Zhihua; Cheung, A. S.-C.

    2013-11-21

    The laser induced fluorescence spectrum of palladium dimer (Pd{sub 2}) in the visible region between 480 and 700 nm has been observed and analyzed. The gas-phase Pd{sub 2} molecule was produced by laser ablation of palladium metal rod. Eleven vibrational bands were observed and assigned to the [17.1] {sup 3}II{sub g} - X{sup 3}Σ{sub u}{sup +} transition system. The bond length (r{sub o}) and vibrational frequency (ΔG{sub 1/2}) of the ground X{sup 3}Σ{sub u}{sup +} state were determined to be 2.47(4) Å and 211.4(5) cm{sup −1}, respectively. A molecular orbital energy level diagram was used to understand the observed ground and excited electronic states. This is the first gas-phase experimental investigation of the electronic transitions of Pd{sub 2}.

  8. Structural characterization of dimeric murine aminoacylase III.

    PubMed

    Ryazantsev, Sergey; Abuladze, Natalia; Newman, Debra; Bondar, Galyna; Kurtz, Ira; Pushkin, Alexander

    2007-05-01

    Aminoacylase III (AAIII) plays an important role in deacetylation of acetylated amino acids and N-acetylated S-cysteine conjugates of halogenated alkenes and alkanes. AAIII, recently cloned from mouse kidney and partially characterized, is a mixture of tetramers and dimers. In the present work, AAIII dimers were purified and shown to be enzymatically active. Limited trypsinolysis showed two domains of approximately 9 and 25 kDa. The three-dimensional structure of the dimer was studied by electron microscopy of negative stained samples and by single-particle reconstruction. A 16A resolution model of the AAIII dimer was created. It has an unusual, cage-like, structure. A realistic AAIII tetramer model was built from two dimers.

  9. Surface-enhanced Raman scattering spectroscopy of topotecan-DNA complexes: Binding to DNA induces topotecan dimerization

    NASA Astrophysics Data System (ADS)

    Mochalov, K. E.; Strel'Tsov, S. A.; Ermishov, M. A.; Grokhovskii, S. L.; Zhuze, A. L.; Ustinova, O. A.; Sukhanova, A. V.; Nabiev, I. R.; Oleinikov, V. A.

    2002-09-01

    The interaction of topotecan (TPT), antitumor inhibitor of human DNA topoisomerase I, with calf thymus DNA was studied by surface-enhanced Raman scattering (SERS) spectroscopy. The SERS spectra of TPT are found to depend on its concentration in solution, which is associated with the dimerization of TPT. The spectral signatures of dimerization are identified. It is shown that binding to DNA induces the formation of TPT dimers. The formation of DNA-TPT-TPT-DNA complexes is considered as one of the possible mechanisms of human DNA topoisomerase I inhibition.

  10. CtIP Protein Dimerization Is Critical for Its Recruitment to Chromosomal DNA Double-stranded Breaks*

    PubMed Central

    Wang, Hailong; Shao, Zhengping; Shi, Linda Z.; Hwang, Patty Yi-Hwa; Truong, Lan N.; Berns, Michael W.; Chen, David J.; Wu, Xiaohua

    2012-01-01

    CtIP (CtBP-interacting protein) associates with BRCA1 and the Mre11-Rad50-Nbs1 (MRN) complex and plays an essential role in homologous recombination (HR)-mediated DNA double-stranded break (DSB) repair. It has been described that CtIP forms dimers in mammalian cells, but the biological significance is not clear. In this study, we identified a conserved motif in the N terminus of CtIP, which is required for dimer formation. We further showed that CtIP mutants impaired in forming dimers are strongly defective in HR, end resection, and activation of the ataxia telangiectasia and Rad3-related pathway, without notable change of CtIP interactions with BRCA1 or Nbs1. In addition to HR, CtIP dimerization is also required for microhomology-mediated end joining. Live cell imaging of enhanced GFP-tagged CtIP demonstrates that the CtIP dimerization mutant fails to be localized to DSBs, whereas placing a heterologous dimerization motif to the dimerization mutant restores CtIP recruitment to DSBs. These studies suggest that CtIP dimer formation is essential for its recruitment to DSBs on chromatin upon DNA damage. Furthermore, DNA damage-induced phosphorylation of CtIP is significantly reduced in the CtIP dimerization mutants. Therefore, in addition to the C-terminal conserved domains critical for CtIP function, the dimerization motif on the N terminus of CtIP is also conserved and essential for its function in DNA damage responses. The severe repair defects of CtIP dimerization mutants are likely due to the failure in localization to chromosomal DSBs upon DNA damage. PMID:22544744

  11. Dimerization of Plant Defensin NaD1 Enhances Its Antifungal Activity*

    PubMed Central

    Lay, Fung T.; Mills, Grant D.; Poon, Ivan K. H.; Cowieson, Nathan P.; Kirby, Nigel; Baxter, Amy A.; van der Weerden, Nicole L.; Dogovski, Con; Perugini, Matthew A.; Anderson, Marilyn A.; Kvansakul, Marc; Hulett, Mark D.

    2012-01-01

    The plant defensin, NaD1, from the flowers of Nicotiana alata, is a member of a family of cationic peptides that displays growth inhibitory activity against several filamentous fungi, including Fusarium oxysporum. The antifungal activity of NaD1 has been attributed to its ability to permeabilize membranes; however, the molecular basis of this function remains poorly defined. In this study, we have solved the structure of NaD1 from two crystal forms to high resolution (1.4 and 1.58 Å, respectively), both of which contain NaD1 in a dimeric configuration. Using protein cross-linking experiments as well as small angle x-ray scattering analysis and analytical ultracentrifugation, we show that NaD1 forms dimers in solution. The structural studies identified Lys4 as critical in formation of the NaD1 dimer. This was confirmed by site-directed mutagenesis of Lys4 that resulted in substantially reduced dimer formation. Significantly, the reduced ability of the Lys4 mutant to dimerize correlated with diminished antifungal activity. These data demonstrate the importance of dimerization in NaD1 function and have implications for the use of defensins in agribiotechnology applications such as enhancing plant crop protection against fungal pathogens. PMID:22511788

  12. An improved reversibly dimerizing mutant of the FK506-binding protein FKBP

    PubMed Central

    Barrero, Juan J.; Papanikou, Effrosyni; Casler, Jason C.; Day, Kasey J.; Glick, Benjamin S.

    2016-01-01

    ABSTRACT FK506-binding protein (FKBP) is a monomer that binds to FK506, rapamycin, and related ligands. The F36M substitution, in which Phe36 in the ligand-binding pocket is changed to Met, leads to formation of antiparallel FKBP dimers, which can be dissociated into monomers by ligand binding. This FKBP(M) mutant has been employed in the mammalian secretory pathway to generate aggregates that can be dissolved by ligand addition to create cargo waves. However, when testing this approach in yeast, we found that dissolution of FKBP(M) aggregates was inefficient. An improved reversibly dimerizing FKBP formed aggregates that dissolved more readily. This FKBP(L,V) mutant carries the F36L mutation, which increases the affinity of ligand binding, and the I90V mutation, which accelerates ligand-induced dissociation of the dimers. The FKBP(L,V) mutant expands the utility of reversibly dimerizing FKBP. PMID:27738551

  13. Hexafluoroisopropyl alcohol mediated synthesis of 2,3-dihydro-4H-pyrido[1,2-a]pyrimidin-4-ones

    PubMed Central

    Alam, Mohammad A.; Alsharif, Zakeyah; Alkhattabi, Hessa; Jones, Derika; Delancey, Evan; Gottsponer, Adam; Yang, Tianhong

    2016-01-01

    An efficient synthesis of novel 2,3-dihydro-4H-pyrido[1,2-a]pyrimidin-4-ones has been reported. Inexpensive and readily available substrates, environmentally benign reaction condition, and product formation up to quantitative yield are the key features of this methodology. Products are formed by the aza-Michael addition followed by intramolecular acyl substitution in a domino process. The polar nature and strong hydrogen bond donor capability of 1,1,1,3,3,3-hexafluoropropan-2-ol is pivotal in this cascade protocol. PMID:27805054

  14. Hexafluoroisopropyl alcohol mediated synthesis of 2,3-dihydro-4H-pyrido[1,2-a]pyrimidin-4-ones

    NASA Astrophysics Data System (ADS)

    Alam, Mohammad A.; Alsharif, Zakeyah; Alkhattabi, Hessa; Jones, Derika; Delancey, Evan; Gottsponer, Adam; Yang, Tianhong

    2016-11-01

    An efficient synthesis of novel 2,3-dihydro-4H-pyrido[1,2-a]pyrimidin-4-ones has been reported. Inexpensive and readily available substrates, environmentally benign reaction condition, and product formation up to quantitative yield are the key features of this methodology. Products are formed by the aza-Michael addition followed by intramolecular acyl substitution in a domino process. The polar nature and strong hydrogen bond donor capability of 1,1,1,3,3,3-hexafluoropropan-2-ol is pivotal in this cascade protocol.

  15. Hydrogen bond induced HF elimination from photoionized fluorophenol dimers in the gas phase

    NASA Astrophysics Data System (ADS)

    Chatterjee, Piyali; Ghosh, Arup K.; Chakraborty, Tapas

    2017-02-01

    In this paper, we report finding of a remarkable chemical effect of hydrogen bonding, elimination of hydrogen fluoride (HF) from the hydrogen bonded dimers of 2-fluorophenol (2-FP) and 3-fluorophenol (3-FP), in a supersonic jet expansion upon multi-photon ionization using 4th harmonic wavelength (266 nm) of a Q-switched Nd:YAG laser, and the reaction has been probed by time-of-flight mass spectrometry. No HF elimination is observed to occur by such means from the monomer of 3-FP, but it occurs with a small yield from the monomer of 2-FP. On the other hand, upon dimerization the reaction is triggered on for 3-FP, and for 2-FP it becomes so facile that no intact dimer cation survives and only the HF eliminated product ion appears in the mass spectra. Electronic structure calculation shows that in the cationic ground (D0) state, although the reaction for 2-FP dimer is exothermic, the associated barrier is significantly high (2.75 eV) and for its occurrence, absorption of three photons (2+1 type) is required. However, the reaction is predicted barrierless in the intermediate S1 state of this dimer, and HF loss dimer cation mass peak could appear in the mass spectrum due to an effective two-photon (1+1) ionization process. In the case of 3-FP dimer, the energy barriers both in S1 (neutral) and D0 (ionic) states are high, and it is suggested that for occurrence of HF elimination, dimer cation needs to absorb an additional photon. For facilitation of HF loss from this dimer cation, a rearrangement of the geometry and formation of an intermediate adduct have been suggested, and it is argued that the latter could be produced by nucleophilic attack of the neutral moiety at the ortho site of the cationic counterpart.

  16. Hydrogen bond induced HF elimination from photoionized fluorophenol dimers in the gas phase.

    PubMed

    Chatterjee, Piyali; Ghosh, Arup K; Chakraborty, Tapas

    2017-02-28

    In this paper, we report finding of a remarkable chemical effect of hydrogen bonding, elimination of hydrogen fluoride (HF) from the hydrogen bonded dimers of 2-fluorophenol (2-FP) and 3-fluorophenol (3-FP), in a supersonic jet expansion upon multi-photon ionization using 4th harmonic wavelength (266 nm) of a Q-switched Nd:YAG laser, and the reaction has been probed by time-of-flight mass spectrometry. No HF elimination is observed to occur by such means from the monomer of 3-FP, but it occurs with a small yield from the monomer of 2-FP. On the other hand, upon dimerization the reaction is triggered on for 3-FP, and for 2-FP it becomes so facile that no intact dimer cation survives and only the HF eliminated product ion appears in the mass spectra. Electronic structure calculation shows that in the cationic ground (D0) state, although the reaction for 2-FP dimer is exothermic, the associated barrier is significantly high (2.75 eV) and for its occurrence, absorption of three photons (2+1 type) is required. However, the reaction is predicted barrierless in the intermediate S1 state of this dimer, and HF loss dimer cation mass peak could appear in the mass spectrum due to an effective two-photon (1+1) ionization process. In the case of 3-FP dimer, the energy barriers both in S1 (neutral) and D0 (ionic) states are high, and it is suggested that for occurrence of HF elimination, dimer cation needs to absorb an additional photon. For facilitation of HF loss from this dimer cation, a rearrangement of the geometry and formation of an intermediate adduct have been suggested, and it is argued that the latter could be produced by nucleophilic attack of the neutral moiety at the ortho site of the cationic counterpart.

  17. Approach for in vivo protein binding of 5-n-butyl-pyrazolo[1,5-a]pyrimidine bioactivated in chimeric mice with humanized liver by two-dimensional electrophoresis with accelerator mass spectrometry.

    PubMed

    Yamazaki, Hiroshi; Kuribayashi, Shunji; Inoue, Tae; Tateno, Chise; Nishikura, Yasufumi; Oofusa, Ken; Harada, Daisuke; Naito, Shinsaku; Horie, Toru; Ohta, Shigeru

    2010-01-01

    Drug development of a potential analgesic agent 5-n-butyl-7-(3,4,5-trimethoxybenzoylamino)pyrazolo[1,5-a]pyrimidine was withdrawn because of its limited hepatotoxic effects in humans that could not be predicted from regulatory animal or in vitro studies. In vivo formation of glutathione conjugates and covalent binding of a model compound 5-n-butyl-pyrazolo[1,5-a]pyrimidine were investigated in the present study after intravenous administration to chimeric mice with a human or rat liver because of an interesting capability of human cytochrome P450 1A2 in forming a covalently bound metabolite in vitro. Rapid distribution and elimination of radiolabeled 5-n-butyl-pyrazolo[1,5-a]pyrimidine in plasma or liver fractions were seen in chimeric mice after intravenous administration. However, similar covalent binding in liver was detected over 0.17-24 h after intravenous administration. Radio-LC analyses revealed that the chimeric mice with humanized liver preferentially gave the 3-hydroxylated metabolite and its glutathione conjugate in the plasma and liver. On the contrary, chimeric mice with a rat liver had some rat-specific metabolites in vivo. Analyses by electrophoresis with accelerator mass spectrometry of in vivo radiolabeled liver proteins in chimeric mice revealed that bioactivated 5-n-butyl-pyrazolo[1,5-a]pyrimidine bound nonspecifically to a variety of microsomal proteins including human P450 1A2 as well as cytosolic proteins in the livers from chimeric mice with humanized liver. These results suggest that the hepatotoxic model compound 5-n-butyl-pyrazolo[1,5-a]pyrimidine was activated by human liver microsomal P450 1A2 to reactive intermediate(s) in vivo in humanized chimeric mice and could relatively nonspecifically bind to biomolecules such as P450 1A2 and other proteins.

  18. Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers.

    PubMed

    Jang, Hyunbum; Muratcioglu, Serena; Gursoy, Attila; Keskin, Ozlem; Nussinov, Ruth

    2016-06-15

    Are the dimer structures of active Ras isoforms similar? This question is significant since Ras can activate its effectors as a monomer; however, as a dimer, it promotes Raf's activation and MAPK (mitogen-activated protein kinase) cell signalling. In the present study, we model possible catalytic domain dimer interfaces of membrane-anchored GTP-bound K-Ras4B and H-Ras, and compare their conformations. The active helical dimers formed by the allosteric lobe are isoform-specific: K-Ras4B-GTP favours the α3 and α4 interface; H-Ras-GTP favours α4 and α5. Both isoforms also populate a stable β-sheet dimer interface formed by the effector lobe; a less stable β-sandwich interface is sustained by salt bridges of the β-sheet side chains. Raf's high-affinity β-sheet interaction is promoted by the active helical interface. Collectively, Ras isoforms' dimer conformations are not uniform; instead, the isoform-specific dimers reflect the favoured interactions of the HVRs (hypervariable regions) with cell membrane microdomains, biasing the effector-binding site orientations, thus isoform binding selectivity.

  19. De novo pyrimidine biosynthesis in the oomycete plant pathogen Phytophthora infestans.

    PubMed

    García-Bayona, Leonor; Garavito, Manuel F; Lozano, Gabriel L; Vasquez, Juan J; Myers, Kevin; Fry, William E; Bernal, Adriana; Zimmermann, Barbara H; Restrepo, Silvia

    2014-03-10

    The oomycete Phytophthora infestans, causal agent of the tomato and potato late blight, generates important economic and environmental losses worldwide. As current control strategies are becoming less effective, there is a need for studies on oomycete metabolism to help identify promising and more effective targets for chemical control. The pyrimidine pathways are attractive metabolic targets to combat tumors, virus and parasitic diseases but have not yet been studied in Phytophthora. Pyrimidines are involved in several critical cellular processes and play structural, metabolic and regulatory functions. Here, we used genomic and transcriptomic information to survey the pyrimidine metabolism during the P. infestans life cycle. After assessing the putative gene machinery for pyrimidine salvage and de novo synthesis, we inferred genealogies for each enzymatic domain in the latter pathway, which displayed a mosaic origin. The last two enzymes of the pathway, orotate phosphoribosyltransferase and orotidine-5-monophosphate decarboxylase, are fused in a multi-domain enzyme and are duplicated in some P. infestans strains. Two splice variants of the third gene (dihydroorotase) were identified, one of them encoding a premature stop codon generating a non-functional truncated protein. Relative expression profiles of pyrimidine biosynthesis genes were evaluated by qRT-PCR during infection in Solanum phureja. The third and fifth genes involved in this pathway showed high up-regulation during biotrophic stages and down-regulation during necrotrophy, whereas the uracil phosphoribosyl transferase gene involved in pyrimidine salvage showed the inverse behavior. These findings suggest the importance of de novo pyrimidine biosynthesis during the fast replicative early infection stages and highlight the dynamics of the metabolism associated with the hemibiotrophic life style of pathogen.

  20. trans-Acting Inhibition of Genomic RNA Dimerization by Rous Sarcoma Virus Matrix Mutants

    PubMed Central

    Garbitt, Rachel A.; Albert, Jessica A.; Kessler, Michelle D.; Parent, Leslie J.

    2001-01-01

    The genomic RNA of retroviruses exists within the virion as a noncovalently linked dimer. Previously, we identified a mutant of the viral matrix (MA) protein of Rous sarcoma virus that disrupts viral RNA dimerization. This mutant, Myr1E, is modified at the N terminus of MA by the addition of 10 amino acids from the Src protein, resulting in the production of particles containing monomeric RNA. Dimerization is reestablished by a single amino acid substitution that abolishes myristylation (Myr1E−). To distinguish between cis and trans effects involving Myr1E, additional mutations were generated. In Myr1E.cc and Myr1E−.cc, different nucleotides were utilized to encode the same protein as Myr1E and Myr1E−, respectively. The alterations in RNA sequence did not change the properties of the viral mutants. Myr1E.ATG− was constructed so that translation began at the gag AUG, resulting in synthesis of the wild-type Gag protein but maintenance of the src RNA sequence. This mutant had normal infectivity and dimeric RNA, indicating that the src sequence did not prevent dimer formation. All of the src-containing RNA sequences formed dimers in vitro. Examination of MA-green fluorescent protein fusion proteins revealed that the wild-type and mutant MA proteins Myr1E.ATG−, Myr1E−, and Myr1E−.cc had distinctly different patterns of subcellular localization compared with Myr1E and Myr1E.cc MA proteins. This finding suggests that proper localization of the MA protein may be required for RNA dimer formation and infectivity. Taken together, these results provide compelling evidence that the genomic RNA dimerization defect is due to a trans-acting effect of the mutant MA proteins. PMID:11119596

  1. Smectic Phase Formed by DNA Dimers

    NASA Astrophysics Data System (ADS)

    Salamonczyk, Miroslaw; Gleeson, James; Jakli, Antal; Sprunt, Samuel; Dhont, Jan; Stiakakis, Emmanuel

    The rapidly expanding bio market is driving the development and characterization of new multifunctional materials. In particular, nucleic acids are under intense study for gene therapy, drug delivery and other bio-safe applications [1,2,3]. DNA is well-known to form a cholesteric nematic liquid crystal in its native form; however, much recent research has focused on self-assembly and mesomorphic behavior in concentrated solutions of short DNA helices [4]. Our work focuses on DNA dimers, consisting of 48 base-pair double-stranded helices connected by a 5 to 20 base flexible single strand, and suspended in a natural buffer. Depending on temperature, concentration and length of the flexible spacer, polarizing optical microscopy and small angle x-ray scattering reveal cholesteric nematic and, remarkably, smectic liquid crystalline phases. A model for smectic phase formation in this system will be presented. 1] J.-L. Lim et al., Int. J. of. Pharm. 490 (2015) 2652] D.-H. Kim et al., Nature Biotech. 23 (2005) 2223] K. Liu et al., Chem. Eur. J. 21 (2015) 48984] M. Nakata et al., Science 318 (2007) 1276 NSF DMR 1307674.

  2. Assembly of Dimer-Based Photonic Crystals

    NASA Astrophysics Data System (ADS)

    Liddell Watson, Chekesha M.

    2011-03-01

    Recent advances in colloid synthesis to prepare monodisperse shape anisotropic particles provide the opportunity to address challenges related to structural diversity in ordered colloidal solids. In particular, computational simulations and mechanical models suggest that upon system densification nonspherical dimer colloids undergo disorder-order and order-order phase transitions to unconventional solid structures including, base-centered monoclinic crystals, degenerate aperiodic crystals, plastic crystal or rotator, etc. based on free energy minimization. The particle systems have notable analogy to molecular systems, where the shape of molecules and their packing density has been shown to critically influence structural phase behavior and lead to a rich variety of structures, both natural and synthetic. The materials engineering challenges have been in attaining sufficiently monodisperse (size uniformity) colloidal building blocks, as well as the lack of understanding and control of self-assembly processes for non-spherical colloids. This talk highlights our investigations of how particle shape programs the self-organization of colloidal structures. Methods including evaporation mediated assembly and confinement provide a platform to understand the formation of complex colloidal structures from non-spherical building blocks (silica-coated iron oxide, polystyrene, hollow silica shell). Optical property simulations for unconventional 2D and 3D structures with nonspherical particle bases will also be discussed.

  3. N-(4-Meth-oxy-phen-yl)-6-methyl-2-phenyl-5-{[4-(tri-fluoro-meth-yl)anilino]meth-yl}pyrimidin-4-amine.

    PubMed

    Cieplik, Jerzy; Pluta, Janusz; Bryndal, Iwona; Lis, Tadeusz

    2013-11-27

    The title compound, C26H23F3N4O, crystallizes with two symmetry-independent mol-ecules in the asymmetric unit, denoted A and B, which differ mainly in the rotation of the meth-oxy-phenyl ring. The -CF3 group of mol-ecule B is disordered by rotation, with the F atoms split over two sets of sites; the occupancy factor for the major component is 0.853 (4). The dihedral angles between the pyrimidine ring and the attached phenyl, meth-oxy-phenyl and tri-fluoro-methyl-phenyl rings are 8.1 (2), 37.5 (2) and 70.7 (2)°, respectively, in mol-ecule A, and 9.3 (2), 5.3 (2) and 79.7 (2)° in mol-ecule B. An intra-molecular N-H⋯N hydrogen bond occurs in each mol-ecule. In the crystal, two crystallographically independent mol-ecules associate into a dimer via a pair of N-H⋯N hydrogen bonds, with a resulting R 2 (2)(12) ring motif and π-π stacking inter-actions [centroid-centroid distance = 3.517 (4) Å] between the pyrimidine rings. For the A mol-ecules, there are inter-molecular C-H⋯O hydrogen bonds between an aryl C atom of meth-oxy-phenyl ring and a meth-oxy O atom of an adjacent mol-ecule. A similar inter-action is lacking in the B mol-ecules.

  4. Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers

    PubMed Central

    Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Cho, Kwang-Jin; Dolino, Drew M.; Chen, Wei; Li, Hongyang; Grant, Barry J.; Hancock, John F.; Gorfe, Alemayehu A.

    2017-01-01

    Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers. For validation we used mutagenesis, electron microscopy and biochemical assays under non-denaturing conditions. We show that partial disruption of a predicted interface through charge reversal mutation of apposed residues reduces oligomerization while introduction of cysteines at these positions enhanced dimerization likely through the formation of an intermolecular disulfide bond. Free energy calculations indicated that K-Ras dimerization involves direct but weak protein-protein interactions in solution, consistent with the notion that dimerization is facilitated by membrane binding. Taken together, our atomically detailed analyses provide unique mechanistic insights into K-Ras dimer formation and membrane organization as well as the conformational fluctuations and equilibrium thermodynamics underlying these processes. PMID:28067274

  5. Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers

    NASA Astrophysics Data System (ADS)

    Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Cho, Kwang-Jin; Dolino, Drew M.; Chen, Wei; Li, Hongyang; Grant, Barry J.; Hancock, John F.; Gorfe, Alemayehu A.

    2017-01-01

    Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers. For validation we used mutagenesis, electron microscopy and biochemical assays under non-denaturing conditions. We show that partial disruption of a predicted interface through charge reversal mutation of apposed residues reduces oligomerization while introduction of cysteines at these positions enhanced dimerization likely through the formation of an intermolecular disulfide bond. Free energy calculations indicated that K-Ras dimerization involves direct but weak protein-protein interactions in solution, consistent with the notion that dimerization is facilitated by membrane binding. Taken together, our atomically detailed analyses provide unique mechanistic insights into K-Ras dimer formation and membrane organization as well as the conformational fluctuations and equilibrium thermodynamics underlying these processes.

  6. Dimerization of HCN in the gas phase: A theoretical mechanistic study

    NASA Astrophysics Data System (ADS)

    Yim, Min Kyoung; Choe, Joong Chul

    2012-06-01

    Potential energy surfaces for the formation of covalently bound HCN dimers from two molecules of HCN or HNC were determined from CBS-QB3/APNO calculations. Several novel pathways, with and without the aid of protons, were found for the formation of iminoacetonitrile (HNdbnd CHCN), an intermediate in adenine synthesis from HCN by oligomerization. Covalent C-C or C-N bonds between the two monomers were formed after rearrangement of bimolecular complex intermediates. Energetic and kinetic analyses suggest that the proton-catalyzed dimerizations substantially lower reaction barriers but cannot occur efficiently under interstellar conditions.

  7. Synthesis, anticonvulsant and neurotoxicity evaluation of some new pyrimidine-5-carbonitrile derivatives

    PubMed Central

    Shaquiquzzaman, Mohammad; Khan, Suroor Ahmad; Amir, Mohammad; Alam, Mohammad Mumtaz

    2011-01-01

    A series of 2-[2-(substituted benzylidene) hydrazinyl]-4-(4-methoxyphenyl)-6-oxo-1,6-dihydro-pyrimidine-5-carbonitrile (3–16) were synthesized by refluxing 2-hydrazino-4-(4-methoxy-phenyl)-6-oxo-1,6-dihydro-pyrimidine-5-carbonitrile (2) with different substituted aromatic aldehydes in glacial acetic acid and absolute alcohol mixture (8:2). The compounds were evaluated for their anticonvulsant and neurotoxicity effect. In MES test compounds 2-[2-(4-bromo-benzylidene)-hydrazinyl]-4-(4-methoxyphenyl)-6-oxo-1,6-dihydro-pyrimidine-5-carbonitrile (5), 2-[2-(4-hydroxy-benzylidene)-hydrazinyl]-4-(4-methoxyphenyl)-6-oxo-1,6-dihydro-pyrimidine-5-carbonitrile (9), and 2-[2-(3-fluoro-benzylidene)-hydrazinyl]-4-(4-methoxyphenyl)-6-oxo-1,6-dihydro-pyrimidine-5-carbonitrile (16) were found to be highly active at a dose level of 30 mgkg−1 at 0.5 h time interval, indicating their ability to prevent seizure spread at a relatively low dose. PMID:23960786

  8. Synthesis, crystal structure, characterization and antifungal activity of pyrazolo[1,5-a]pyrimidines derivatives

    NASA Astrophysics Data System (ADS)

    Zhang, Jin; Peng, Ju-Fang; Wang, Tao; Wang, Ping; Zhang, Zun-Ting

    2016-09-01

    Under microwave radiation, isomers 2-(pyrazolo[1,5-a]pyrimidin-5-yl)phenols (3) and 2-(pyrazolo[1,5-a]pyrimidin-7-yl)phenols (4) were simultaneously obtained by the condensation of chromones and 3-aminopyrazoles. These two isomers were fully characterized by IR, 1H NMR, 13C NMR and HRMS. In addition, a representative product 5-chloro-2-(2-methyl-pyrazolo[1,5-a] pyrimidin-5-yl)phenol (3e) was further conformed by the single crystal X-ray diffraction. The antifungal abilities of the obtained products 3 and 4 were evaluated against five phytopathogenic fungi (Cytospora sp., Colletotrichum gloeosporioides, Botrytis cinerea, Alternaria solani and Fusarium solani). The results revealed that 2-(pyrazolo[1,5-a]pyrimidin-5-yl)phenol (3a) and 4-chloro-2-(2-methylpyrazolo[1,5-a]pyrimidin-7-yl)phenol (4e) exhibited good antifungal abilities against Colletotrichum gloeosporioides with the IC50 values of 24.90 and 28.28 μg/mL, respectively.

  9. Vibrationally resolved emission of thiophosgene dimer

    NASA Astrophysics Data System (ADS)

    Berrios, Eduardo; Hui, Ho Yee; Gruebele, Martin

    2010-09-01

    During a study of thiophosgene electronic spectra, Fujiwara and co-workers observed a broad electronic transition peaked at 37 000 cm -1, attributed to thiophosgene dimer. Our dispersed fluorescence spectra of a thiophosgene molecular beam excited at 36 000 cm -1 reveal several vibrational modes too low in frequency for thiophosgene. We assign them to modes of thiophosgene dimer or their combination bands. MP2 calculations support the vibrational assignment. TD-DFT, CASSCF, and coupled cluster calculations suggest that the bright electronic state of thiophosgene dimer is the B 2u symmetry fifth excited singlet state. Two additional transitions are assigned to a thiophosgene synthesis impurity, trichloromethanesulfenyl chloride.

  10. Quantum dimer model for the pseudogap metal

    PubMed Central

    Punk, Matthias; Allais, Andrea; Sachdev, Subir

    2015-01-01

    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S=1/2, charge +e fermionic dimers. The model realizes a “fractionalized Fermi liquid” with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8×8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments. PMID:26195771

  11. Quantum dimer model for the pseudogap metal.

    PubMed

    Punk, Matthias; Allais, Andrea; Sachdev, Subir

    2015-08-04

    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S = 1/2, charge +e fermionic dimers. The model realizes a "fractionalized Fermi liquid" with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8 × 8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments.

  12. Synthesis and structures of Se analogues of the antithyroid drug 6-n-propyl-2-thiouracil and its alkyl derivatives: formation of dimeric Se-Se compounds and deselenation reactions of charge-transfer adducts of diiodine.

    PubMed

    Antoniadis, Constantinos D; Hadjikakou, Sotiris K; Hadjiliadis, Nick; Papakyriakou, Athanasios; Baril, Martin; Butler, Ian S

    2006-09-06

    Four selenium analogues of the antithyroid drug 6-n-propyl-2-thiouracil (PTU), of formulae RSeU, (R = methyl (Me) (1), ethyl (Et) (2), n-propyl (nPr) (3), and isopropyl (iPr) 4), have been synthesized. Reaction of 1-4 with diiodine in a 1:1 molar ratio in dichloromethane results in the formation of [(RSeU)I(2)] (R = methyl (5), ethyl (6), n-propyl (7) and isopropyl (8)). All compounds have been characterized by elemental analysis, FT-Raman, FT-IR, UV/Vis, (1)H-, (13)C-, (77)Se-1D and -2D NMR spectroscopy, and ESI-MS spectrometric techniques. Recrystallization of 4 from dichloromethane afforded (4CH(2)Cl(2)). Crystals of [(nPrSeU)I(2)] (7), a charge-transfer complex, were obtained from chloroform solutions, while crystallization of 6 and 7 from acetone afforded the diselenides [N-(6-Et-4-pyrimidone)(6-EtSeU)(2)] (92 H(2)O) and [N-(6-nPr-4-pyrimidone)(6-nPrSeU)(2)] (10) as oxidation products. Recrystallization of 7 from methanol/acetonitrile solutions led to deselenation with the formation of 6-n-propyl-2-uracil (nPrU) (11). [(nPrSeU)I(2)] (7) was found to be a charge-transfer complex with a Se--I bond. These results are discussed in relation to the mechanism of action of antithyroid drugs.

  13. Effects of Cd{sup 2+} on cis-dimer structure of E-cadherin in living cells

    SciTech Connect

    Takeda, Hiroshi

    2014-02-21

    Highlights: • The effects of Cd on the dimer of cadherin in living cells was analyzed. • Cd induced cadherin dimer formation was not detected in living cell with low Ca. • Ca mediated structural cooperativity and allostery in the native cadherin. • Ca concentration-dependent competitive displacement of Cd from cadherin is proposed. - Abstract: E-cadherin, a calcium (Ca{sup 2+})-dependent cell–cell adhesion molecule, plays a key role in the maintenance of tissue integrity. We have previously demonstrated that E-cadherin functions in vivo as a cis-dimer through chemical cross-linking reagents. Ca{sup 2+} plays an important role in the cis-dimer formation of cadherin. However, the molecular mechanisms by which Ca{sup 2+} interacts with the binding sites that regulate cis-dimer structures have not been completely elucidated. As expected for a Ca{sup 2+} antagonist, cadmium (Cd{sup 2+}) disrupts cadherin function by displacing Ca{sup 2+} from its binding sites on the cadherin molecules. We used Cd{sup 2+} as a probe for investigating the role of Ca{sup 2+} in the dynamics of the E-cadherin extracellular region that involve cis-dimer formation and adhesion. While cell–cell adhesion assembly was completely disrupted in the presence of Cd{sup 2+}, the amount of cis-dimers of E-cadherin that formed at the cell surface was not affected. In our “Cd{sup 2+}-switch” experiments, we did not find that Cd{sup 2+}-induced E-cadherin cis-dimer formation in EL cells when they were incubated in low-Ca{sup 2+} medium. In the present study, we demonstrated for the first time the effects of Cd{sup 2+} on the cis-dimer structure of E-cadherin in living cells using a chemical cross-link analysis.

  14. The multiple forms of bovine seminal ribonuclease: structure and stability of a C-terminal swapped dimer.

    PubMed

    Sica, Filomena; Pica, Andrea; Merlino, Antonello; Russo Krauss, Irene; Ercole, Carmine; Picone, Delia

    2013-11-29

    Bovine seminal ribonuclease (BS-RNase) acquires an interesting anti-tumor activity associated with the swapping on the N-terminal. The first direct experimental evidence on the formation of a C-terminal swapped dimer (C-dimer) obtained from the monomeric derivative of BS-RNase, although under non-native conditions, is here reported. The X-ray model of this dimer reveals a quaternary structure different from that of the C-dimer of RNase A, due to the presence of three mutations in the hinge peptide 111-116. The mutations increase the hinge peptide flexibility and decrease the stability of the C-dimer against dissociation. The biological implications of the structural data are also discussed.

  15. Rare-earth silylamide-catalyzed selective dimerization of terminal alkynes and subsequent hydrophosphination in one pot.

    PubMed

    Komeyama, Kimihiro; Kawabata, Tomonori; Takehira, Katsuomi; Takaki, Ken

    2005-09-02

    [reaction: see text] Rare-earth silylamides, Ln[N(SiMe3)2]3 (Ln = Y, La, Sm), catalyzed regio- and stereoselective dimerization of terminal alkynes in the presence of amine additives to give conjugated enynes in high yields. The additives played a crucial role to depress the oligomerization and to control the regio- and stereochemistry of the dimerization. Thus, the selectivity for (Z)-head-to-head enynes was increased in the order of tertiary < secondary < primary amine additives. On the other hand, the reversed order was observed for the formation of head-to-tail dimers. When alpha,omega-diynes were subjected to the dimerization, very novel cyclic bisenyne compounds were given through double-dimerization in satisfactory yields. In addition, an application of the system allowed subsequent hydrophosphination of the enynes generated in situ with diphenylphosphine, giving rise to 1-phosphinyl-1,3-dienes as the sole products in excellent yields after oxidative workup.

  16. Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily.

    PubMed

    Ohnishi, Satoshi; Tochio, Naoya; Tomizawa, Tadashi; Akasaka, Ryogo; Harada, Takushi; Seki, Eiko; Sato, Manami; Watanabe, Satoru; Fujikura, Yukiko; Koshiba, Seizo; Terada, Takaho; Shirouzu, Mikako; Tanaka, Akiko; Kigawa, Takanori; Yokoyama, Shigeyuki

    2008-09-01

    The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a beta-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) (MAGI1 WW2) shares high sequence similarity with SAV1 WW2, suggesting comparable dimerization. However, an analytical ultracentrifugation study revealed that MAGI1 WW2 (Leu355-Pro390) chiefly exists as a monomer at low protein concentrations, with an association constant of 1.3 x 10(2) M(-1). We determined its solution structure, and a structural comparison with the dimeric SAV1 WW2 suggested that an Asp residue is crucial for the inhibition of the dimerization. The substitution of this acidic residue with Ser resulted in the dimerization of MAGI1 WW2. The spin-relaxation data suggested that the MAGI1 WW2 undergoes a dynamic process of transient dimerization that is limited by the charge repulsion. Additionally, we characterized a longer construct of this WW domain with a C-terminal extension (Leu355-Glu401), as the formation of an extra alpha-helix was predicted. An NMR structural determination confirmed the formation of an alpha-helix in the extended C-terminal region, which appears to be independent from the dimerization regulation. A thermal denaturation study revealed that the dimerized MAGI1 WW2 with the Asp-to-Ser mutation gained apparent stability in a protein concentration-dependent manner. A structural comparison between the two constructs with different lengths suggested that the formation of the C-terminal alpha-helix stabilized the global fold by facilitating contacts between the N-terminal linker region and the main body of the WW domain.

  17. Visualization of Myc/Max/Mad family dimers and the competition for dimerization in living cells.

    PubMed

    Grinberg, Asya V; Hu, Chang-Deng; Kerppola, Tom K

    2004-05-01

    Myc and Mad family proteins play opposing roles in the control of cell growth and proliferation. We have visualized the subcellular locations of complexes formed by Myc/Max/Mad family proteins using bimolecular fluorescence complementation (BiFC) analysis. Max was recruited to different subnuclear locations by interactions with Myc versus Mad family members. Complexes formed by Max with Mxi1, Mad3, or Mad4 were enriched in nuclear foci, whereas complexes formed with Myc were more uniformly distributed in the nucleoplasm. Mad4 was localized to the cytoplasm when it was expressed separately, and Mad4 was recruited to the nucleus through dimerization with Max. The cytoplasmic localization of Mad4 was determined by a CRM1-dependent nuclear export signal located near the amino terminus. We compared the relative efficiencies of complex formation among Myc, Max, and Mad family proteins in living cells using multicolor BiFC analysis. Max formed heterodimers with the basic helix-loop-helix leucine zipper (bHLHZIP) domain of Myc (bMyc) more efficiently than it formed homodimers. Replacement of two amino acid residues in the leucine zipper of Max reversed the relative efficiencies of homo- and heterodimerization in cells. Surprisingly, Mad3 formed complexes with Max less efficiently than bMyc, whereas Mad4 formed complexes with Max more efficiently than bMyc. The distinct subcellular locations and the differences between the efficiencies of dimerization with Max indicate that Mad3 and Mad4 are likely to modulate transcription activation by Myc at least in part through distinct mechanisms.

  18. Visualization of Myc/Max/Mad Family Dimers and the Competition for Dimerization in Living Cells†

    PubMed Central

    Grinberg, Asya V.; Hu, Chang-Deng; Kerppola, Tom K.

    2004-01-01

    Myc and Mad family proteins play opposing roles in the control of cell growth and proliferation. We have visualized the subcellular locations of complexes formed by Myc/Max/Mad family proteins using bimolecular fluorescence complementation (BiFC) analysis. Max was recruited to different subnuclear locations by interactions with Myc versus Mad family members. Complexes formed by Max with Mxi1, Mad3, or Mad4 were enriched in nuclear foci, whereas complexes formed with Myc were more uniformly distributed in the nucleoplasm. Mad4 was localized to the cytoplasm when it was expressed separately, and Mad4 was recruited to the nucleus through dimerization with Max. The cytoplasmic localization of Mad4 was determined by a CRM1-dependent nuclear export signal located near the amino terminus. We compared the relative efficiencies of complex formation among Myc, Max, and Mad family proteins in living cells using multicolor BiFC analysis. Max formed heterodimers with the basic helix-loop-helix leucine zipper (bHLHZIP) domain of Myc (bMyc) more efficiently than it formed homodimers. Replacement of two amino acid residues in the leucine zipper of Max reversed the relative efficiencies of homo- and heterodimerization in cells. Surprisingly, Mad3 formed complexes with Max less efficiently than bMyc, whereas Mad4 formed complexes with Max more efficiently than bMyc. The distinct subcellular locations and the differences between the efficiencies of dimerization with Max indicate that Mad3 and Mad4 are likely to modulate transcription activation by Myc at least in part through distinct mechanisms. PMID:15121849

  19. Molecular interaction of the first 3 enzymes of the de novo pyrimidine biosynthetic pathway of Trypanosoma cruzi

    SciTech Connect

    Nara, Takeshi; Hashimoto, Muneaki; Hirawake, Hiroko; Liao, Chien-Wei; Fukai, Yoshihisa; Suzuki, Shigeo; Tsubouchi, Akiko; Morales, Jorge; Takamiya, Shinzaburo; Fujimura, Tsutomu; Taka, Hikari; Mineki, Reiko; Fan, Chia-Kwung; Inaoka, Daniel Ken; Inoue, Masayuki; Tanaka, Akiko; Harada, Shigeharu; Kita, Kiyoshi; and others

    2012-02-03

    Highlights: Black-Right-Pointing-Pointer An Escherichia coli strain co-expressing CPSII, ATC, and DHO of Trypanosoma cruzi was constructed. Black-Right-Pointing-Pointer Molecular interactions between CPSII, ATC, and DHO of T. cruzi were demonstrated. Black-Right-Pointing-Pointer CPSII bound with both ATC and DHO. Black-Right-Pointing-Pointer ATC bound with both CPSII and DHO. Black-Right-Pointing-Pointer A functional tri-enzyme complex might precede the establishment of the fused enzyme. -- Abstract: The first 3 reaction steps of the de novo pyrimidine biosynthetic pathway are catalyzed by carbamoyl-phosphate synthetase II (CPSII), aspartate transcarbamoylase (ATC), and dihydroorotase (DHO), respectively. In eukaryotes, these enzymes are structurally classified into 2 types: (1) a CPSII-DHO-ATC fusion enzyme (CAD) found in animals, fungi, and amoebozoa, and (2) stand-alone enzymes found in plants and the protist groups. In the present study, we demonstrate direct intermolecular interactions between CPSII, ATC, and DHO of the parasitic protist Trypanosoma cruzi, which is the causative agent of Chagas disease. The 3 enzymes were expressed in a bacterial expression system and their interactions were examined. Immunoprecipitation using an antibody specific for each enzyme coupled with Western blotting-based detection using antibodies for the counterpart enzymes showed co-precipitation of all 3 enzymes. From an evolutionary viewpoint, the formation of a functional tri-enzyme complex may have preceded-and led to-gene fusion to produce the CAD protein. This is the first report to demonstrate the structural basis of these 3 enzymes as a model of CAD. Moreover, in conjunction with the essentiality of de novo pyrimidine biosynthesis in the parasite, our findings provide a rationale for new strategies for developing drugs for Chagas disease, which target the intermolecular interactions of these 3 enzymes.

  20. High Molecular Weight Dimer Esters in α-Pinene Secondary Organic Aerosol

    NASA Astrophysics Data System (ADS)

    Kristensen, Kasper; Cui, Tianqu; Zhang, Haofei; Gold, Avram; Glasius, Marianne; Surratt, Jason D.

    2014-05-01

    Monoterpenes, such as α-pinene, constitute an important group of biogenic volatile organic compounds (BVOC). Once emitted into the atmosphere α-pinene is removed by oxidization by the hydroxyl radical (OH), reactions with ozone (O3), and with nitrate radicals (NO3) resulting in the formation of first-generation oxidation products, such as semi-volatile carboxylic acids. In addition, higher molecular weight dimer esters originating from the oxidation of α-pinene have been observed in both laboratory-generated and ambient secondary organic aerosols (SOA). While recent studies suggest that the dimers are formed through esterification between carboxylic acids in the particle phase, the formation mechanism of the dimer esters is still ambiguous. In this work, we present the results of a series of smog chamber experiments to assess the formation of dimer esters formed from the oxidation of α-pinene. Experiments were conducted in the University of North Carolina (UNC) dual outdoor smog chamber facility to investigate the effect of oxidant species (OH versus O3), relative humidity (RH), and seed aerosol acidity in order to obtain a better understanding of the conditions leading to the formation of the dimer esters and how these parameters may affect the formation and chemical composition of SOA. The chemical composition of α-pinene SOA was investigated by ultra-performance liquid chromatography/electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry (UPLC/ESI-HR-Q-TOFMS), and a total of eight carboxylic acids and four dimer esters were identified, constituting between 8 and 12 % of the total α-pinene SOA mass.

  1. Ultraviolet-induced mutations in Cockayne syndrome cells are primarily caused by cyclobutane dimer photoproducts while repair of other photoproducts is normal

    SciTech Connect

    Parris, C.N.; Kraemer, K.H. )

    1993-08-01

    The authors compared the contribution to mutagenesis on Cockayne syndrome (CS) cells of the major class of UV photoproducts, the cyclobutane pyrimidine dimer, to that of other DNA photoproducts by using the mutagenesis shuttle vector pZ189. Lymphoblastoid cell lines from the DNA repair-deficient disorders CS and xeroderma pigmentosum (XP) and a normal line were transfected with UV-treated pZ189. Cyclobutane dimers were selectively removed before transfection by photoreactivation (PR), leaving nondimer photoproducts intact. After UV exposure and replication in CS and XP cells, plasmid survival was abnormally elevated. After PR, plasmid survival increased and mutation frequency in CS cells decreased to normal levels but remained abnormal in XP cells. Sequence analysis of >200 mutant plasmids showed that with CS cells a major mutational hot spot was caused by unrepaired cyclobutane dimers. These data indicate that with both CS and XP cyclobutane dimers are major photoproducts generating reduced plasmid survival and increased mutation frequency. However, unlike XP, CS cells are proficient in repair of nondimer photoproducts. Since XP but not CS patients have a high frequency of UV-induced skin cancers, the data suggest that prevention of UV-induced skin cancers is associated with proficient repair of nondimer photoproducts. 38 refs., 3 figs., 2 tabs.

  2. Generalized Fibonacci Numbers and Dimer Statistics

    NASA Astrophysics Data System (ADS)

    Lu, W. T.; Wu, F. Y.

    2003-04-01

    We establish new product identities involving the q-analogue of the Fibonacci numbers. We show that the identities lead to alternate expressions of generating functions for close-packed dimers on non-orientable surfaces.

  3. Generalized Fibonacci Numbers and Dimer Statistics

    NASA Astrophysics Data System (ADS)

    Lu, W. T.; Wu, F. Y.

    We establish new product identities involving the q-analogue of the Fibonacci numbers. We show that the identities lead to alternate expressions of generating functions for close-packed dimers on non-orientable surfaces.

  4. Thymine and other prebiotic molecules produced from the ultraviolet photo-irradiation of pyrimidine in simple astrophysical ice analogs.

    PubMed

    Materese, Christopher K; Nuevo, Michel; Bera, Partha P; Lee, Timothy J; Sandford, Scott A

    2013-10-01

    The informational subunits of RNA or DNA consist of substituted N-heterocyclic compounds that fall into two groups: those based on purine (C₅H₄N₄) (adenine and guanine) and those based on pyrimidine (C₄H₄N₂) (uracil, cytosine, and thymine). Although not yet detected in the interstellar medium, N-heterocycles, including the nucleobase uracil, have been reported in carbonaceous chondrites. Recent laboratory experiments and ab initio calculations have shown that the irradiation of pyrimidine in ices containing H₂O, NH₃, or both leads to the abiotic production of substituted pyrimidines, including the nucleobases uracil and cytosine. In this work, we studied the methylation and oxidation of pyrimidine in CH₃OH:pyrimidine, H₂O:CH₃OH:pyrimidine, CH₄:pyrimidine, and H₂O:CH₄:pyrimidine ices irradiated with UV photons under astrophysically relevant conditions. The nucleobase thymine was detected in the residues from some of the mixtures. Our results suggest that the abundance of abiotic thymine produced by ice photolysis and delivered to the early Earth may have been significantly lower than that of uracil. Insofar as the delivery of extraterrestrial molecules was important for early biological chemistry on early Earth, these results suggest that there was more uracil than thymine available for emergent life, a scenario consistent with the RNA world hypothesis.

  5. Substrate specificity of pyrimidine nucleoside phosphorylases of NP-II family probed by X-ray crystallography and molecular modeling

    NASA Astrophysics Data System (ADS)

    Balaev, V. V.; Lashkov, A. A.; Prokofev, I. I.; Gabdulkhakov, A. G.; Seregina, T. A.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

    2016-09-01

    Pyrimidine nucleoside phosphorylases, which are widely used in the biotechnological production of nucleosides, have different substrate specificity for pyrimidine nucleosides. An interesting feature of these enzymes is that the three-dimensional structure of thymidine-specific nucleoside phosphorylase is similar to the structure of nonspecific pyrimidine nucleoside phosphorylase. The three-dimensional structures of thymidine phosphorylase from Salmonella typhimurium and nonspecific pyrimidine nucleoside phosphorylase from Bacillus subtilis in complexes with a sulfate anion were determined for the first time by X-ray crystallography. An analysis of the structural differences between these enzymes demonstrated that Lys108, which is involved in the phosphate binding in pyrimidine nucleoside phosphorylase, corresponds to Met111 in thymidine phosphorylases. This difference results in a decrease in the charge on one of the hydroxyl oxygens of the phosphate anion in thymidine phosphorylase and facilitates the catalysis through SN2 nucleophilic substitution. Based on the results of X-ray crystallography, the virtual screening was performed for identifying a potent inhibitor (anticancer agent) of nonspecific pyrimidine nucleoside phosphorylase, which does not bind to thymidine phosphorylase. The molecular dynamics simulation revealed the stable binding of the discovered compound—2-pyrimidin-2-yl-1H-imidazole-4-carboxylic acid—to the active site of pyrimidine nucleoside phosphorylase.

  6. Adaptive Reprogramming of De Novo Pyrimidine Synthesis Is a Metabolic Vulnerability in Triple-Negative Breast Cancer.

    PubMed

    Brown, Kristin K; Spinelli, Jessica B; Asara, John M; Toker, Alex

    2017-04-01

    Chemotherapy resistance is a major barrier to the treatment of triple-negative breast cancer (TNBC), and strategies to circumvent resistance are required. Using in vitro and in vivo metabolic profiling of TNBC cells, we show that an increase in the abundance of pyrimidine nucleotides occurs in response to chemotherapy exposure. Mechanistically, elevation of pyrimidine nucleotides induced by chemotherapy is dependent on increased activity of the de novo pyrimidine synthesis pathway. Pharmacologic inhibition of de novo pyrimidine synthesis sensitizes TNBC cells to genotoxic chemotherapy agents by exacerbating DNA damage. Moreover, combined treatment with doxorubicin and leflunomide, a clinically approved inhibitor of the de novo pyrimidine synthesis pathway, induces regression of TNBC xenografts. Thus, the increase in pyrimidine nucleotide levels observed following chemotherapy exposure represents a metabolic vulnerability that can be exploited to enhance the efficacy of chemotherapy for the treatment of TNBC.Significance: The prognosis for patients with TNBC with residual disease after chemotherapy is poor. We find that chemotherapy agents induce adaptive reprogramming of de novo pyrimidine synthesis and show that this response can be exploited pharmacologically, using clinically approved inhibitors of de novo pyrimidine synthesis, to sensitize TNBC cells to chemotherapy. Cancer Discov; 7(4); 391-9. ©2017 AACR.See related article by Mathur et al., p. 380This article is highlighted in the In This Issue feature, p. 339.

  7. Entropy-Driven One-Step Formation of Phi29 pRNA 3WJ from Three RNA Fragments

    PubMed Central

    2015-01-01

    The emerging field of RNA nanotechnology necessitates creation of functional RNA nanoparticles but has been limited by particle instability. It has been shown that the three-way junction of bacteriophage phi29 motor pRNA has unusual stability and can self-assemble from three fragments with high efficiency. It is generally believed that RNA and DNA folding is energy landscape-dependent, and the folding of RNA is driven by enthalpy. Here we examine the thermodynamic characteristics of the 3WJ components as 2′-fluoro RNA, DNA, and RNA. It was seen that the three fragments existed either in 3WJ complex or as monomers, with the intermediate of dimers almost undetectable. It seems that the three fragments can lead to the formation of the 3WJ complex efficiently within a rapid time. A low dissociation constant (apparent KD) of 11.4 nM was determined for RNA, inclusion of 2′-F pyrimidines strengthened the KD to 4.5 nM, and substitution of DNA weakened it to 47.7 nM. The ΔG°37, were −36, −28, and −15 kcal/mol for 3WJ2′-F, 3WJRNA, and 3WJDNA, respectively. It is found that the formation of the three-component complex was governed by entropy, instead of enthalpy, as usually found in RNA complexes. PMID:24694349

  8. Elucidation of cladofulvin biosynthesis reveals a cytochrome P450 monooxygenase required for anthraquinone dimerization

    PubMed Central

    Griffiths, Scott; Mesarich, Carl H.; Saccomanno, Benedetta; Vaisberg, Abraham; De Wit, Pierre J. G. M.; Cox, Russell; Collemare, Jérôme

    2016-01-01

    Anthraquinones are a large family of secondary metabolites (SMs) that are extensively studied for their diverse biological activities. These activities are determined by functional group decorations and the formation of dimers from anthraquinone monomers. Despite their numerous medicinal qualities, very few anthraquinone biosynthetic pathways have been elucidated so far, including the enzymatic dimerization steps. In this study, we report the elucidation of the biosynthesis of cladofulvin, an asymmetrical homodimer of nataloe-emodin produced by the fungus Cladosporium fulvum. A gene cluster of 10 genes controls cladofulvin biosynthesis, which begins with the production of atrochrysone carboxylic acid by the polyketide synthase ClaG and the β-lactamase ClaF. This compound is decarboxylated by ClaH to yield emodin, which is then converted to chrysophanol hydroquinone by the reductase ClaC and the dehydratase ClaB. We show that the predicted cytochrome P450 ClaM catalyzes the dimerization of nataloe-emodin to cladofulvin. Remarkably, such dimerization dramatically increases nataloe-emodin cytotoxicity against mammalian cell lines. These findings shed light on the enzymatic mechanisms involved in anthraquinone dimerization. Future characterization of the ClaM enzyme should facilitate engineering the biosynthesis of novel, potent, dimeric anthraquinones and structurally related compound families. PMID:27274078

  9. Elucidation of cladofulvin biosynthesis reveals a cytochrome P450 monooxygenase required for anthraquinone dimerization.

    PubMed

    Griffiths, Scott; Mesarich, Carl H; Saccomanno, Benedetta; Vaisberg, Abraham; De Wit, Pierre J G M; Cox, Russell; Collemare, Jérôme

    2016-06-21

    Anthraquinones are a large family of secondary metabolites (SMs) that are extensively studied for their diverse biological activities. These activities are determined by functional group decorations and the formation of dimers from anthraquinone monomers. Despite their numerous medicinal qualities, very few anthraquinone biosynthetic pathways have been elucidated so far, including the enzymatic dimerization steps. In this study, we report the elucidation of the biosynthesis of cladofulvin, an asymmetrical homodimer of nataloe-emodin produced by the fungus Cladosporium fulvum A gene cluster of 10 genes controls cladofulvin biosynthesis, which begins with the production of atrochrysone carboxylic acid by the polyketide synthase ClaG and the β-lactamase ClaF. This compound is decarboxylated by ClaH to yield emodin, which is then converted to chrysophanol hydroquinone by the reductase ClaC and the dehydratase ClaB. We show that the predicted cytochrome P450 ClaM catalyzes the dimerization of nataloe-emodin to cladofulvin. Remarkably, such dimerization dramatically increases nataloe-emodin cytotoxicity against mammalian cell lines. These findings shed light on the enzymatic mechanisms involved in anthraquinone dimerization. Future characterization of the ClaM enzyme should facilitate engineering the biosynthesis of novel, potent, dimeric anthraquinones and structurally related compound families.

  10. Ras-GTP dimers activate the mitogen-activated protein kinase (MAPK) pathway

    DOE PAGES

    Nan, Xiaolin; Tamgüney, Tanja M.; Collisson, Eric A.; ...

    2015-06-16

    Rat sarcoma (Ras) GTPases regulate cell proliferation and survival through effector pathways including Raf-MAPK, and are the most frequently mutated genes in human cancer. Although it is well established that Ras activity requires binding to both GTP and the membrane, details of how Ras operates on the cell membrane to activate its effectors remain elusive. Efforts to target mutant Ras in human cancers to therapeutic benefit have also been largely unsuccessful. Here we show that Ras-GTP forms dimers to activate MAPK. We used quantitative photoactivated localization microscopy (PALM) to analyze the nanoscale spatial organization of PAmCherry1-tagged KRas 4B (hereafter referredmore » to KRas) on the cell membrane under various signaling conditions. We found that at endogenous expression levels KRas forms dimers, and KRasG12D, a mutant that constitutively binds GTP, activates MAPK. Overexpression of KRas leads to formation of higher order Ras nanoclusters. Conversely, at lower expression levels, KRasG12D is monomeric and activates MAPK only when artificially dimerized. Moreover, dimerization and signaling of KRas are both dependent on an intact CAAX (C, cysteine; A, aliphatic; X, any amino acid) motif that is also known to mediate membrane localization. These results reveal a new, dimerization-dependent signaling mechanism of Ras, and suggest Ras dimers as a potential therapeutic target in mutant Ras-driven tumors.« less

  11. Ras-GTP dimers activate the mitogen-activated protein kinase (MAPK) pathway

    SciTech Connect

    Nan, Xiaolin; Tamgüney, Tanja M.; Collisson, Eric A.; Lin, Li -Jung; Pitt, Cameron; Galeas, Jacqueline; Lewis, Sophia; Gray, Joe W.; McCormick, Frank; Chu, Steven

    2015-06-16

    Rat sarcoma (Ras) GTPases regulate cell proliferation and survival through effector pathways including Raf-MAPK, and are the most frequently mutated genes in human cancer. Although it is well established that Ras activity requires binding to both GTP and the membrane, details of how Ras operates on the cell membrane to activate its effectors remain elusive. Efforts to target mutant Ras in human cancers to therapeutic benefit have also been largely unsuccessful. Here we show that Ras-GTP forms dimers to activate MAPK. We used quantitative photoactivated localization microscopy (PALM) to analyze the nanoscale spatial organization of PAmCherry1-tagged KRas 4B (hereafter referred to KRas) on the cell membrane under various signaling conditions. We found that at endogenous expression levels KRas forms dimers, and KRasG12D, a mutant that constitutively binds GTP, activates MAPK. Overexpression of KRas leads to formation of higher order Ras nanoclusters. Conversely, at lower expression levels, KRasG12D is monomeric and activates MAPK only when artificially dimerized. Moreover, dimerization and signaling of KRas are both dependent on an intact CAAX (C, cysteine; A, aliphatic; X, any amino acid) motif that is also known to mediate membrane localization. These results reveal a new, dimerization-dependent signaling mechanism of Ras, and suggest Ras dimers as a potential therapeutic target in mutant Ras-driven tumors.

  12. Transport of pyrimidine nucleosides in cells of Escherichia coli K 12.

    PubMed

    Mygind, B; Munch-Petersen

    1975-11-15

    1. The transport of pyrimidine mucleosides into cells of Escherichis coli has been investigated in mutant strains which cannot metabolize these nucleosides. Such cells transport and concentrate purimidine mucleosides several hindredfold. 2. The transport is inhibited by energy poisons and by sulfhydryl reagents. 3. Pyrimidine mucleosides compete mutually for transport. Adenosine is also a strong competitor while guanosine and inosine are weak competitors. 4. The rate of pyrimidine mucleoside transport is shown to be under control of the cytR and deoR gene products, which are also known to regulate the synthesis of nucleoside-catabolizing enzymes. The transport system is repressed by growth on glucose, as is the synthesis of the enzymes.

  13. Thiolated pyrimidine nucleotides may interfere thiol groups concentrated at lipid rafts of HIV-1 infected cells.

    PubMed

    Kanizsai, Szilvia; Ongrádi, Joseph; Aradi, János; Nagy, Károly

    2014-12-01

    Upon HIV infection, cells become activated and cell surface thiols are present in increased number. Earlier we demonstrated in vitro anti-HIV effect of thiolated pyrimidine nucleotide UD29, which interferes thiol function. To further analyse the redox processes required for HIV-1 entry and infection, toxicity assays were performed using HIV-1 infected monolayer HeLaCD4-LTR/ β-gal cells and suspension H9 T cells treated with several thiolated nucleotide derivatives of UD29. Selective cytotoxicity of thiolated pyrimidines on HIV-1 infected cells were observed. Results indicate that thiolated pyrimidine derivates may interfere with -SH (thiol) groups concentrated in lipid rafts of cell membrane and interacts HIV-1 infected (activated) cells resulting in a selective cytotoxicity of HIV-1 infected cells, and reducing HIV-1 entry.

  14. Pfaffian Correlation Functions of Planar Dimer Covers

    NASA Astrophysics Data System (ADS)

    Aizenman, Michael; Valcázar, Manuel Laínz; Warzel, Simone

    2017-01-01

    The Pfaffian structure of the boundary monomer correlation functions in the dimer-covering planar graph models is rederived through a combinatorial/topological argument. These functions are then extended into a larger family of order-disorder correlation functions which are shown to exhibit Pfaffian structure throughout the bulk. Key tools involve combinatorial switching symmetries which are identified through the loop-gas representation of the double dimer model, and topological implications of planarity.

  15. The two-state dimer receptor model: a general model for receptor dimers.

    PubMed

    Franco, Rafael; Casadó, Vicent; Mallol, Josefa; Ferrada, Carla; Ferré, Sergi; Fuxe, Kjell; Cortés, Antoni; Ciruela, Francisco; Lluis, Carmen; Canela, Enric I

    2006-06-01

    Nonlinear Scatchard plots are often found for agonist binding to G-protein-coupled receptors. Because there is clear evidence of receptor dimerization, these nonlinear Scatchard plots can reflect cooperativity on agonist binding to the two binding sites in the dimer. According to this, the "two-state dimer receptor model" has been recently derived. In this article, the performance of the model has been analyzed in fitting data of agonist binding to A(1) adenosine receptors, which are an example of receptor displaying concave downward Scatchard plots. Analysis of agonist/antagonist competition data for dopamine D(1) receptors using the two-state dimer receptor model has also been performed. Although fitting to the two-state dimer receptor model was similar to the fitting to the "two-independent-site receptor model", the former is simpler, and a discrimination test selects the two-state dimer receptor model as the best. This model was also very robust in fitting data of estrogen binding to the estrogen receptor, for which Scatchard plots are concave upward. On the one hand, the model would predict the already demonstrated existence of estrogen receptor dimers. On the other hand, the model would predict that concave upward Scatchard plots reflect positive cooperativity, which can be neither predicted nor explained by assuming the existence of two different affinity states. In summary, the two-state dimer receptor model is good for fitting data of binding to dimeric receptors displaying either linear, concave upward, or concave downward Scatchard plots.

  16. Role of Rydberg states in the photostability of heterocyclic dimers: the case of pyrazole dimer.

    PubMed

    Zilberg, Shmuel; Haas, Yehuda

    2012-11-26

    A new route for the nonradiative decay of photoexcited, H-bonded, nitrogen-containing, heterocyclic dimers is offered and exemplified by a study of the pyrazole dimer. In some of these systems the N(3s) Rydberg state is the lowest excited singlet state. This state is formed by direct light absorption or by nonradiative transition from the allowed ππ* state. An isomer of this Rydberg state is formed by H atom transfer to the other component of the dimer. The newly formed H-bonded radical pair is composed of two radicals (a H-adduct of pyrazole, a heterocyclic analogue of the NH(4) radical) and the pyrazolium π-radical. It is calculated to have a shallow local minimum and is the lowest point on the PES of the H-pyrazole/pyrazolium radical pair. This species can cross back to the ground state of the original dimer through a relatively small energy gap and compete with the H-atom loss channel, known for the monomer. In both Rydberg dimers, an electron occupies a Rydberg orbital centered mostly on one of the two components of the dimer. This Rydberg Center Shift (RCS) mechanism, proposed earlier (Zilberg, S.; Kahan, A.; Haas, Y. Phys. Chem. Chem. Phys. 2012, 14, 8836), leads to deactivation of the electronically excited dimer while keeping it intact. It, thus, may explain the high photostability of the pyrazole dimer as well as other heterocyclic dimers.

  17. Substrate-Induced Dimerization of Engineered Monomeric Variants of Triosephosphate Isomerase from Trichomonas vaginalis.

    PubMed

    Lara-Gonzalez, Samuel; Estrella, Priscilla; Portillo, Carmen; Cruces, María E; Jimenez-Sandoval, Pedro; Fattori, Juliana; Migliorini-Figueira, Ana C; Lopez-Hidalgo, Marisol; Diaz-Quezada, Corina; Lopez-Castillo, Margarita; Trasviña-Arenas, Carlos H; Sanchez-Sandoval, Eugenia; Gómez-Puyou, Armando; Ortega-Lopez, Jaime; Arroyo, Rossana; Benítez-Cardoza, Claudia G; Brieba, Luis G

    2015-01-01

    The dimeric nature of triosephosphate isomerases (TIMs) is maintained by an extensive surface area interface of more than 1600 Å2. TIMs from Trichomonas vaginalis (TvTIM) are held in their dimeric state by two mechanisms: a ball and socket interaction of residue 45 of one subunit that fits into the hydrophobic pocket of the complementary subunit and by swapping of loop 3 between subunits. TvTIMs differ from other TIMs in their unfolding energetics. In TvTIMs the energy necessary to unfold a monomer is greater than the energy necessary to dissociate the dimer. Herein we found that the character of residue I45 controls the dimer-monomer equilibrium in TvTIMs. Unfolding experiments employing monomeric and dimeric mutants led us to conclude that dimeric TvTIMs unfold following a four state model denaturation process whereas monomeric TvTIMs follow a three state model. In contrast to other monomeric TIMs, monomeric variants of TvTIM1 are stable and unexpectedly one of them (I45A) is only 29-fold less active than wild-type TvTIM1. The high enzymatic activity of monomeric TvTIMs contrast with the marginal catalytic activity of diverse monomeric TIMs variants. The stability of the monomeric variants of TvTIM1 and the use of cross-linking and analytical ultracentrifugation experiments permit us to understand the differences between the catalytic activities of TvTIMs and other marginally active monomeric TIMs. As TvTIMs do not unfold upon dimer dissociation, herein we found that the high enzymatic activity of monomeric TvTIM variants is explained by the formation of catalytic dimeric competent species assisted by substrate binding.

  18. Substrate-Induced Dimerization of Engineered Monomeric Variants of Triosephosphate Isomerase from Trichomonas vaginalis

    PubMed Central

    Lara-Gonzalez, Samuel; Estrella, Priscilla; Portillo, Carmen; Cruces, María E.; Jimenez-Sandoval, Pedro; Fattori, Juliana; Migliorini-Figueira, Ana C.; Lopez-Hidalgo, Marisol; Diaz-Quezada, Corina; Lopez-Castillo, Margarita; Trasviña-Arenas, Carlos H.; Sanchez-Sandoval, Eugenia; Gómez-Puyou, Armando; Ortega-Lopez, Jaime; Arroyo, Rossana; Benítez-Cardoza, Claudia G.; Brieba, Luis G.

    2015-01-01

    The dimeric nature of triosephosphate isomerases (TIMs) is maintained by an extensive surface area interface of more than 1600 Å2. TIMs from Trichomonas vaginalis (TvTIM) are held in their dimeric state by two mechanisms: a ball and socket interaction of residue 45 of one subunit that fits into the hydrophobic pocket of the complementary subunit and by swapping of loop 3 between subunits. TvTIMs differ from other TIMs in their unfolding energetics. In TvTIMs the energy necessary to unfold a monomer is greater than the energy necessary to dissociate the dimer. Herein we found that the character of residue I45 controls the dimer-monomer equilibrium in TvTIMs. Unfolding experiments employing monomeric and dimeric mutants led us to conclude that dimeric TvTIMs unfold following a four state model denaturation process whereas monomeric TvTIMs follow a three state model. In contrast to other monomeric TIMs, monomeric variants of TvTIM1 are stable and unexpectedly one of them (I45A) is only 29-fold less active than wild-type TvTIM1. The high enzymatic activity of monomeric TvTIMs contrast with the marginal catalytic activity of diverse monomeric TIMs variants. The stability of the monomeric variants of TvTIM1 and the use of cross-linking and analytical ultracentrifugation experiments permit us to understand the differences between the catalytic activities of TvTIMs and other marginally active monomeric TIMs. As TvTIMs do not unfold upon dimer dissociation, herein we found that the high enzymatic activity of monomeric TvTIM variants is explained by the formation of catalytic dimeric competent species assisted by substrate binding. PMID:26618356

  19. Functional Role of Dimerization of Human Peptidylarginine Deiminase 4 (PAD4)

    PubMed Central

    Liu, Yi-Liang; Chiang, Yu-Hsiu; Liu, Guang-Yaw; Hung, Hui-Chih

    2011-01-01

    Peptidylarginine deiminase 4 (PAD4) is a homodimeric enzyme that catalyzes Ca2+-dependent protein citrullination, which results in the conversion of arginine to citrulline. This paper demonstrates the functional role of dimerization in the regulation of PAD4 activity. To address this question, we created a series of dimer interface mutants of PAD4. The residues Arg8, Tyr237, Asp273, Glu281, Tyr435, Arg544 and Asp547, which are located at the dimer interface, were mutated to disturb the dimer organization of PAD4. Sedimentation velocity experiments were performed to investigate the changes in the quaternary structures and the dissociation constants (Kd) between wild-type and mutant PAD4 monomers and dimers. The kinetic data indicated that disrupting the dimer interface of the enzyme decreases its enzymatic activity and calcium-binding cooperativity. The Kd values of some PAD4 mutants were much higher than that of the wild-type (WT) protein (0.45 µM) and were concomitant with lower kcat values than that of WT (13.4 s−1). The Kd values of the monomeric PAD4 mutants ranged from 16.8 to 45.6 µM, and the kcat values of the monomeric mutants ranged from 3.3 to 7.3 s−1. The kcat values of these interface mutants decreased as the Kd values increased, which suggests that the dissociation of dimers to monomers considerably influences the activity of the enzyme. Although dissociation of the enzyme reduces the activity of the enzyme, monomeric PAD4 is still active but does not display cooperative calcium binding. The ionic interaction between Arg8 and Asp547 and the Tyr435-mediated hydrophobic interaction are determinants of PAD4 dimer formation. PMID:21731701

  20. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface.

    PubMed

    Buryak, Ilya; Vigasin, Andrey A

    2015-12-21

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  1. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface

    SciTech Connect

    Buryak, Ilya; Vigasin, Andrey A.

    2015-12-21

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  2. 21 CFR 176.120 - Alkyl ketene dimers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Alkyl ketene dimers. 176.120 Section 176.120 Food... Use Only as Components of Paper and Paperboard § 176.120 Alkyl ketene dimers. Alkyl ketene dimers may... section. (a) The alkyl ketene dimers are manufactured by the dehydrohalogenation of the acyl...

  3. 21 CFR 176.120 - Alkyl ketene dimers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Alkyl ketene dimers. 176.120 Section 176.120 Food... Use Only as Components of Paper and Paperboard § 176.120 Alkyl ketene dimers. Alkyl ketene dimers may... section. (a) The alkyl ketene dimers are manufactured by the dehydrohalogenation of the acyl...

  4. Erwinia amylovora pyrC mutant causes fire blight despite pyrimidine auxotrophy.

    PubMed

    Ramos, L S; Sinn, J P; Lehman, B L; Pfeufer, E E; Peter, K A; McNellis, T W

    2015-06-01

    Erwinia amylovora bacteria cause fire blight disease, which affects apple and pear production worldwide. The Erw. amylovora pyrC gene encodes a predicted dihydroorotase enzyme involved in pyrimidine biosynthesis. Here, we discovered that the Erw. amylovora pyrC244::Tn5 mutant was a uracil auxotroph. Unexpectedly, the Erw. amylovora pyrC244::Tn5 mutant grew as well as the wild-type in detached immature apple and pear fruits. Fire blight symptoms caused by the pyrC244::Tn5 mutant in immature apple and pear fruits were attenuated compared to those caused by the wild-type. The pyrC244::Tn5 mutant also caused severe fire blight symptoms in apple tree shoots. A plasmid-borne copy of the wild-type pyrC gene restored prototrophy and symptom induction in apple and pear fruit to the pyrC244::Tn5 mutant. These results suggest that Erw. amylovora can obtain sufficient pyrimidine from the host to support bacterial growth and fire blight disease development, although de novo pyrimidine synthesis by Erw. amylovora is required for full symptom development in fruits. Significance and impact of the study: This study provides information about the fire blight host-pathogen interaction. Although the Erwinia amylovora pyrC mutant was strictly auxotrophic for pyrimidine, it grew as well as the wild-type in immature pear and apple fruits and caused severe fire blight disease in apple trees. This suggests that Erw. amylovora can obtain sufficient pyrimidines from host tissue to support growth and fire blight disease development. This situation contrasts with findings in some human bacterial pathogens, which require de novo pyrimidine synthesis for growth in host blood, for example.

  5. Adsorption, Dissociation, and Dehydrogenation of Water Monomer and Water Dimer on the Smallest 3D Aluminum Particle. The O-H Dissociation Barrier Disappears for the Dimer.

    PubMed

    Moc, Jerzy

    2016-11-03

    We present a detailed mechanistic study on the interaction and reaction of water monomer and water dimer with the smallest 3D aluminum particle (Al6) by employing density functional and explicitly correlated coupled cluster CCSD(T)-F12 theories. Water adsorption, dissociation, and dehydrogenation are considered. For the monomer reaction, where core-valence correlation and an extrapolation to the complete basis set limit is allowed for, our coupled cluster calculations predict the O-H dissociation barrier of about 2 kcal/mol. For the dimer reaction, two distinct reaction paths are identified, initiated by forming separate dimer complexes wherein (H2O)2 adsorbs mainly via the oxygen atom of the donor H2O molecule. The key O-H dissociation transition states of the dimer reaction involve a concerted migration of two H atoms resulting in the dissociation of the donor molecule and formation of the OH-water complex adsorbed on the metal cluster's surface. The most remarkable feature of both dimer reaction energy profiles is the lack of the overall energy barrier for the (rate-determining) O-H dissociation. The hydrogen bond acceptor molecule is suggested to have an extra catalytic effect on the O-H dissociation barrier of the hydrogen bond donor molecule by removing this barrier. A similar effect on the dehydrogenation step is indicated.

  6. High-resolution characterization of CPD hotspot formation in human fibroblasts

    PubMed Central

    Zavala, Anamaria G.; Morris, Robert T.; Wyrick, John J.; Smerdon, Michael J.

    2014-01-01

    Repair of DNA lesions must occur within the chromatin landscape and is associated with alterations in histone modifications and nucleosome rearrangement. To directly associate these chromatin features with DNA damage and repair, it is necessary to be able to map DNA adducts. We have developed a cyclobutane pyrimidine dimer (CPD)-specific immunoprecipitation method and mapped ultraviolet damage hotspots across human chromosomes 1 and 6. CPD hotspots occur almost equally in genic and intergenic regions. However, these hotspots are significantly more prevalent adjacent to repeat elements, especially Alu repeats. Nucleosome mapping studies indicate that nucleosomes are consistently positioned at Alu elements where CPD hotspots form, but by 2 h post-irradiation, these same regions are significantly depleted of nucleosomes. These results indicate that nucleosomes associated with hotspots of CPD formation are readily rearranged, potentially making them accessible to DNA repair machinery. Our results represent the first chromosome scale map of ultraviolet-induced DNA lesions in the human genome, and reveal the sequence features and dynamic chromatin changes associated with CPD hotspots. PMID:24137003

  7. Synthesis of N-substituted Cyclic Hydrocarbons, such as Pyrimidine, in The Ionosphere of Titan

    NASA Astrophysics Data System (ADS)

    Bera, P. P.; Peverati, R.; Head-Gordon, M.; Lee, T. J.

    2014-12-01

    The instruments on board the CASSINI spacecraft observed large carbonaceous molecules in the upper atmosphere of Titan. How these large polyatomic molecules are synthesized in such exotic conditions is, thus far, unknown. Molecular ions, including positive and negative ions, are in relative abundance in the ionosphere of Titan. Hence, barrierless ion-molecule interactions may play a major role in guiding molecules towards each other and initiating reactions. We study these condensation pathways to determine whether they are a viable means of forming large pure hydrocarbon molecules, and nitrogen-containing carbonaceous chains, stacks, and even cyclic compounds. By employing accurate quantum chemical methods we have investigated the processes of growth, structures, nature of bonding, mechanisms, and spectroscopic properties of the ensuing ionic products after pairing small carbon, hydrogen, and nitrogen-containing molecules with major ions observed in the upper atmosphere of Titan, e.g. C2H5+ and HCNH+. We have also studied the ion-neutral association pathways involving pure-carbon molecules e.g. acetylene, ethylene and other hydrocarbons, and their dissociation fragments in a plasma discharge. We have investigated how nitrogen atoms are incorporated into the carbon ring during growth. Specifically, we explored the mechanisms by which the synthesis of pyrimidine will be feasible in the atmosphere of Titan in conjunction with ion-mobility experiments. We have used accurate ab initio coupled cluster theory, Møller-Plesset perturbation theory, density functional theory, and coupled cluster theory quantum chemical methods together with large correlation consistent basis sets in these investigations. We found that a series of hydrocarbons with a specific stoichiometric composition prefers cyclic molecule formation rather than chains. Some of the association products we investigated have large oscillator strengths for charge-transfer type electronic excitations in the

  8. Mechanism of HIV-1 RNA dimerization in the central region of the genome and significance for viral evolution.

    PubMed

    Piekna-Przybylska, Dorota; Sharma, Gaurav; Bambara, Robert A

    2013-08-16

    The genome of HIV-1 consists of two identical or nearly identical RNA molecules. The RNA genomes are held in the same, parallel orientation by interactions at the dimer initiation site (DIS). Previous studies showed that in addition to interactions at DIS, sequences located 100 nucleotides downstream from the 5' splice site can dimerize in vitro through an intermolecular G-quartet structure. Here we report that the highly conserved G-rich sequence in the middle portion of the HIV-1 genome near the central polypurine tract (cPPT) dimerizes spontaneously under high ionic strength in the absence of protein. The antisense RNA does not dimerize, strongly indicating that RNA dimerization does not exclusively involve A:U and G:C base pairing. The cation-dependent reverse transcriptase pausing profile, CD spectra profile, and cation-dependent association and thermal dissociation characteristics indicate G-quartet structures. Different forms of G-quartets are formed including monomers and, significantly, intermolecular dimers. Our results indicate that RNA genome dimerization and parallel alignment initiated through interactions at DIS may be greatly expanded and stabilized by formation of an intermolecular G-quartet at a distant site near the cPPT. It is likely that formation of G-quartet structure near the cPPT in vivo keeps the RNA genomes in proximity over a long range, promoting genetic recombination in numerous hot spots.

  9. Visualization and ligand-induced modulation of dopamine receptor dimerization at the single molecule level

    PubMed Central

    Tabor, Alina; Weisenburger, Siegfried; Banerjee, Ashutosh; Purkayastha, Nirupam; Kaindl, Jonas M.; Hübner, Harald; Wei, Luxi; Grömer, Teja W.; Kornhuber, Johannes; Tschammer, Nuska; Birdsall, Nigel J. M.; Mashanov, Gregory I.; Sandoghdar, Vahid; Gmeiner, Peter

    2016-01-01

    G protein–coupled receptors (GPCRs), including dopamine receptors, represent a group of important pharmacological targets. An increased formation of dopamine receptor D2 homodimers has been suggested to be associated with the pathophysiology of schizophrenia. Selective labeling and ligand-induced modulation of dimerization may therefore allow the investigation of the pathophysiological role of these dimers. Using TIRF microscopy at the single molecule level, transient formation of homodimers of dopamine receptors in the membrane of stably transfected CHO cells has been observed. The equilibrium between dimers and monomers was modulated by the binding of ligands; whereas antagonists showed a ratio that was identical to that of unliganded receptors, agonist-bound D2 receptor-ligand complexes resulted in an increase in dimerization. Addition of bivalent D2 receptor ligands also resulted in a large increase in D2 receptor dimers. A physical interaction between the protomers was confirmed using high resolution cryogenic localization microscopy, with ca. 9 nm between the centers of mass. PMID:27615810

  10. Monitoring ultraviolet-B-induced DNA damage in individual diatom cells by immunofluorescent thymine dimer detection

    SciTech Connect

    Buma, A.G.J.; Van Hannen, E.J.; Roza, L.

    1995-04-01

    We developed a method to investigate the effect of ultraviolet-B radiation (UVBR) on the formation of thymine dimers in microalgal DNA that can be used for both laboratory and in situ research. Antibody labeling of dimers was followed by a secondary antibody (fluorescein isothiocyanate) staining to allow visualization of DNA damage with flow cytometry or fluorescence microscopy. Thymine dimer-specific fluorescence in nuclear DNA of the marine diatom Cyclotella sp. was linearly related to the UVBR dose. Simultaneous measurements of cellular DNA content showed that the vulnerability of G2 cells to DNA damage did not differ significantly from the vulnerability of G1 cells. The formation and removal of thymine dimers in Cyclotella sp. cells was monitored for 3 consecutive days at two realistic UVBR irradiance levels. Thymine dimers were removed within 24 h when exposed to a saturating photosynthetically active radiation intensity following the UVBR treatment. This new method allows the study of UVBR-induced DNA damage on a cell-to-cell basis. It is also feasible for field studies because cells remain intact and can be recognized readily after antibody treatment. 40 refs., 7 figs.

  11. CtBP1/BARS Gly172-->Glu mutant structure: impairing NAD(H)-binding and dimerization.

    PubMed

    Nardini, Marco; Valente, Carmen; Ricagno, Stefano; Luini, Alberto; Corda, Daniela; Bolognesi, Martino

    2009-03-27

    C-terminal binding proteins (CtBPs) are multi-functional proteins involved in nuclear transcriptional co-repression, Golgi membrane fission, and synaptic ribbon formation. Binding of NAD(H) to CtBPs promotes dimerization. CtBP dimers act as a scaffold for multimeric protein complex formation, thus bridging transcriptional repressors and their targets in the nucleus. Based on size-exclusion chromatography experiments and on the crystal structure of the NAD(H)-free G172E CtBP mutant, we show here that absence of NAD(H) induces flexibility/backbone conformational changes at the dimerization interface and at the CtBP interdomain region. The results presented shed first light on the correlation between NAD(H)-binding and functional CtBP dimerization.

  12. CtBP1/BARS Gly172 {yields} Glu mutant structure: Impairing NAD(H)-binding and dimerization

    SciTech Connect

    Nardini, Marco; Valente, Carmen; Ricagno, Stefano; Luini, Alberto; Corda, Daniela; Bolognesi, Martino

    2009-03-27

    C-terminal binding proteins (CtBPs) are multi-functional proteins involved in nuclear transcriptional co-repression, Golgi membrane fission, and synaptic ribbon formation. Binding of NAD(H) to CtBPs promotes dimerization. CtBP dimers act as a scaffold for multimeric protein complex formation, thus bridging transcriptional repressors and their targets in the nucleus. Based on size-exclusion chromatography experiments and on the crystal structure of the NAD(H)-free G172E CtBP mutant, we show here that absence of NAD(H) induces flexibility/backbone conformational changes at the dimerization interface and at the CtBP interdomain region. The results presented shed first light on the correlation between NAD(H)-binding and functional CtBP dimerization.

  13. Solvent Effects on the Monomer/Hydrogen-Bonded Dimer Equilibrium in Carboxylic Acids: (+)-(S)-Ketopinic Acid as a Case Study.

    PubMed

    Rodríguez Ortega, Pilar Gema; Montejo Gámez, Manuel; Márquez López, Fernando; López González, Juan Jesús

    2016-06-21

    The hydrogen-bond-assisted self-association process of a chiral semirigid carboxylic acid, namely, (+)-(S)-ketopinic acid, has been studied. The multiconformational monomer/dimer equilibrium has been evaluated by means of a concentration-dependent FTIR study that enabled the experimental equilibrium constants of the dimer formation reaction (Kdim ) to be determined in two solvents of different polarity. In CDCl3 , dimeric forms predominate, even in diluted solutions (KdimCF =5.074), whereas in CD3 CN the self-association process is hindered and monomers are always the main species, irrespective of solute concentration (KdimAN =0.194). The reliability of the dimerization constants and the derived mono- and dimeric experimental fractions have been proven by means of accurate matching between the experimental vibrational circular dichroism spectra of the species and the theoretical spectra generated by considering the simultaneous weighted contributions of the concomitant monomers and dimers.

  14. Multiply charged monopoles in cubic dimer model

    NASA Astrophysics Data System (ADS)

    Ganesh Jaya, Sreejith; Powell, Stephen

    2015-03-01

    The classical cubic dimer model is a 3D statistical mechanical system whose degrees of freedom are dimers that occupy the edges between nearest neighbour vertices of a cubic lattice. Dimer occupancies are subject to the local constraint that every vertex is associated with exactly one dimer. In the presence of an aligning interaction, it is known that the system exhibits an unconventional continuous thermal phase transition from a symmetry broken columnar phase to a Coulomb-phase. The transition is in the NCCP1 universality class, which also describes the Neel-VBS transition in the JQ model and the S =1/2 Heisenberg model with suppression of hedgehog defects. Using Monte-Carlo simulations of a pair of defects in a background of fluctuating dimers, we calculate the scaling exponents for fugacities of monopole defects of charge Q = 2 and 3 at this critical point. Our estimates suggest that Q = 3 monopoles are relevant and could therefore drive the JQ model away from the NCCP1 critical point on a hexagonal lattice.

  15. A dimeric state for PRC2

    PubMed Central

    Davidovich, Chen; Goodrich, Karen J.; Gooding, Anne R.; Cech, Thomas R.

    2014-01-01

    Polycomb repressive complex-2 (PRC2) is a histone methyltransferase required for epigenetic silencing during development and cancer. Long non-coding RNAs (lncRNAs) can recruit PRC2 to chromatin. Previous studies identified PRC2 subunits in a complex with the apparent molecular weight of a dimer, which might be accounted for by the incorporation of additional protein subunits or RNA rather than PRC2 dimerization. Here we show that reconstituted human PRC2 is in fact a dimer, using multiple independent approaches including analytical size exclusion chromatography (SEC), SEC combined with multi-angle light scattering and co-immunoprecipitation of differentially tagged subunits. Even though it contains at least two RNA-binding subunits, each PRC2 dimer binds only one RNA molecule. Yet, multiple PRC2 dimers bind a single RNA molecule cooperatively. These observations suggest a model in which the first RNA binding event promotes the recruitment of multiple PRC2 complexes to chromatin, thereby nucleating repression. PMID:24992961

  16. The diamagnetic susceptibility of the tubulin dimer.

    PubMed

    Bras, Wim; Torbet, James; Diakun, Gregory P; Rikken, Geert L J A; Diaz, J Fernando

    2014-01-01

    An approximate value of the diamagnetic anisotropy of the tubulin dimer, Δχ dimer, has been determined assuming axial symmetry and that only the α -helices and β -sheets contribute to the anisotropy. Two approaches have been utilized: (a) using the value for the Δχ α for an α -helical peptide bond given by Pauling (1979) and (b) using the previously determined anisotropy of fibrinogen as a calibration standard. The Δχ dimer ≈ 4 × 10(-27) JT(-2) obtained from these measurements are similar to within 20%. Although Cotton-Mouton measurements alone cannot be used to estimate Δχ directly, the value we measured, CMdimer = (1.41 ± 0.03) × 10(-8) T(-2)cm(2)mg(-1), is consistent with the above estimate for Δχ dimer. The method utilized for the determination of the tubulin dimer diamagnetic susceptibility is applicable to other proteins and macromolecular assemblies as well.

  17. Linking in domain-swapped protein dimers

    PubMed Central

    Baiesi, Marco; Orlandini, Enzo; Trovato, Antonio; Seno, Flavio

    2016-01-01

    The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, makes such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter G′, termed Gaussian entanglement, is strongly correlated with the linking number. Based on 110 non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with |G′| > 1. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties. PMID:27659606

  18. Novel inhibitors of Mycobacterium tuberculosis growth based on modified pyrimidine nucleosides and their analogues

    NASA Astrophysics Data System (ADS)

    Shmalenyuk, E. R.; Kochetkov, S. N.; Alexandrova, L. A.

    2013-09-01

    The review summarizes data on the synthesis and antituberculosis activity of pyrimidine nucleoside derivatives and their analogues. Enzymes from M. tuberculosis as promising targets for prototypes of new-generation drugs are considered. Nucleosides as inhibitors of drug-resistant M. tuberculosis strains are characterized. The bibliography includes 101 references.

  19. Design and Synthesis of New Benzimidazole and Pyrimidine Derivatives as α-glucosidase Inhibitor.

    PubMed

    Mobinikhaledi, Akbar; Asghari, Behvar; Jabbarpour, Mahsa

    2015-01-01

    In an endeavor to find a novel series of antihyperglycemic agents, new benzimidazole and pyrimidine derivatives were successfully synthesized efficiently in high yield with high purity, starting from amino acids in the presence of phosphorus oxychloride (POCl3). The synthesized compounds were identified by (1)H-NMR, (13)C-NMR, FT-IR spectroscopic techniques and elemental analysis. All products were assayed for their inhibitory effects on yeast and rat intestinal α-glucosidases. The results revealed that compounds with aromatic amino acids moiety showed significant inhibition activity on the tested enzymes. Among the benzimidazole derivatives 4c and 4d exhibited the best activity against both of the tested enzymes. Also, among the pyrimidine derivatives 5c and 5d possessed significant inhibition action on the enzymes. The IC50 values for the most potent benzimidazole yeast and intestinal α-glucosidases inhibitor (4d) were found to be 9.1 and 36.7 µM, respectively. The IC50 values for the inhibition of yeast and intestinal α-glucosidases by the most active pyrimidine compound (5d) were calculated to be 8.3 and 21.8 µM, respectively. Overall, this study proved that benzimidazole and pyrimidine derivatives with aromatic amino acids moieties can represent novel promising α-glucosidase inhibitors.

  20. Design and Synthesis of New Benzimidazole and Pyrimidine Derivatives as α-glucosidase Inhibitor

    PubMed Central

    Mobinikhaledi, Akbar; Asghari, Behvar; Jabbarpour, Mahsa

    2015-01-01

    In an endeavor to find a novel series of antihyperglycemic agents, new benzimidazole and pyrimidine derivatives were successfully synthesized efficiently in high yield with high purity, starting from amino acids in the presence of phosphorus oxychloride (POCl3). The synthesized compounds were identified by 1H-NMR, 13C-NMR, FT-IR spectroscopic techniques and elemental analysis. All products were assayed for their inhibitory effects on yeast and rat intestinal α-glucosidases. The results revealed that compounds with aromatic amino acids moiety showed significant inhibition activity on the tested enzymes. Among the benzimidazole derivatives 4c and 4d exhibited the best activity against both of the tested enzymes. Also, among the pyrimidine derivatives 5c and 5d possessed significant inhibition action on the enzymes. The IC50 values for the most potent benzimidazole yeast and intestinal α-glucosidases inhibitor (4d) were found to be 9.1 and 36.7 µM, respectively. The IC50 values for the inhibition of yeast and intestinal α-glucosidases by the most active pyrimidine compound (5d) were calculated to be 8.3 and 21.8 µM, respectively. Overall, this study proved that benzimidazole and pyrimidine derivatives with aromatic amino acids moieties can represent novel promising α-glucosidase inhibitors. PMID:26330860

  1. Synthesis, characterization and in silico biological activity of some 2-(N,N-dimethyl guanidinyl)-4,6-diaryl pyrimidines

    PubMed Central

    Kumarachari, Rajasekhar Komarla; Peta, Sivakumar; Surur, Abdrrahman Shemsu; Mekonnen, Yenus Tadesse

    2016-01-01

    Introduction: As pyrimidine is a basic nucleus in DNA and RNA, it has been found to be associated with diverse biological activities. Pyrimidine derivatives were reported to possess anticonvulsant, antimicrobial, anti-inflammatory, antitumor, and antihistaminic. Recently, our team reported the anti-inflammatory and antimicrobial evaluation of some pyrimidines. Objective: To synthesize, predict and evaluate biological activity of some 2-(N,N-dimethyl guanidinyl)-4,6-diaryl pyrimidines. Experimental: seven new pyrimidines were synthesized by following the standard procedures using substituted aromatic aldehydes, methyl ketones and metformin. After the biological activity was predicted using PASS, Molinspiration and Osiris property explorer, their anthelmintic activity was evaluated using Pheretima posthuma. The structural assignment of the title compounds (P1-7) has been made on the basis of elemental analysis, infrared, 1H-nuclear magnetic resonance and Mass spectral studies. Results: All the synthesized compounds were found to obey Lipinski's rule. All the synthesized compounds scored good bioactivity values as GPCR ligands and kinase inhibitors. Among the test compounds, P5 was found to be more potent anthelmintic inducing paralysis in 36-48 minutes and death in 40-51 minutes. Conclusion and Recommendation: The synthesized compound (P5) possessing methoxy group at position-4 of the benzene ring located at position-4 of pyrimidine exhibited good anthelmintic activity. The study revealed the necessity of synthesizing many more compounds with other substituents at position-4 of the benzene ring located at position-4 of pyrimidine. PMID:27413345

  2. Slab photonic crystals with dimer colloid bases

    SciTech Connect

    Riley, Erin K.; Liddell Watson, Chekesha M.

    2014-06-14

    The photonic band gap properties for centered rectangular monolayers of asymmetric dimers are reported. Colloids in suspension have been organized into the phase under confinement. The theoretical model is inspired by the range of asymmetric dimers synthesized via seeded emulsion polymerization and explores, in particular, the band structures as a function of degree of lobe symmetry and degree of lobe fusion. These parameters are varied incrementally from spheres to lobe-tangent dimers over morphologies yielding physically realizable particles. The work addresses the relative scarcity of theoretical studies on photonic crystal slabs with vertical variation that is consistent with colloidal self-assembly. Odd, even and polarization independent gaps in the guided modes are determined for direct slab structures. A wide range of lobe symmetry and degree of lobe fusion combinations having Brillouin zones with moderate to high isotropy support gaps between odd mode band indices 3-4 and even mode band indices 1-2 and 2-3.

  3. Pyrimidine phosphorothioate oligonucleotides form triple-stranded helices and promote transcription inhibition.

    PubMed Central

    Xodo, L; Alunni-Fabbroni, M; Manzini, G; Quadrifoglio, F

    1994-01-01

    The ability of phosphorothioate (POS) oligonucleotides to recognise and bind to homopurine-homopyrimidine DNA double-stranded sites via triple helix formation has been investigated. It has been found that the homologous pyrimidine POS sequences Y11-Si (i = 0, 1,2,3,4,10), which have been obtained by an increasing sulphur substitution in the sugar-phosphate backbone of d(CTTCCTCCTCT) (Y11), and the target hairpin duplex d(GAAGGAGGAGA-T4-TCTCCTCCTTC) (h26) can form stable triple helices, as indicated by PAGE, CD and UV melting experiments. The thermal stability of the triple helices depends on the number of POS linkages in the third Y11 strand, varying from 48 degrees C (Y11, with only phosphate groups, PO2) to 31 degrees C (Y11-S10 containing exclusively thioate groups). On average, a Tm depression of about 2 degrees C per POS linkage introduced in Y11 was observed. CD data indicate that the sulphurization of the third strand results in minimal changes of triple-stranded structures. The energetics of the triplex-to-hairpin plus single-strand transition has been determined by van't Hoff analyses of the melting curves. In free energy terms, the POS triplexes h26.Y11-Si are less stable than the normal PO2 h26.Y11 triplex by values between 2.7 and 5.4 kcal/mol, depending on the number of POS linkages contained in the third strand. Phosphorothioate oligonucleotides being resistant towards several nucleases offer an interesting choice as gene blockers in antisense strategy. Thus, their ability to inhibit transcription via triple helix formation has been examined in vitro. We found that triplex-forming POS oligonucleotides of 20 bases in length (with a cytosine contents of 45%), containing either 10% or 26% thioate groups, strongly repress the transcription activity of the bacteriophage T7 RNA polymerase at pH 6.9, when used in excess compared to the target (mol oligo/mol template = 125). The here reported data are useful for designing phosphorothioate oligonucleotides

  4. The enzymology of cytosolic pyrimidine 5'-nucleotidases: functional analysis and physiopathological implications.

    PubMed

    Magni, Giulio; Amici, Adolfo; Orsomando, Giuseppe

    2013-01-01

    In mammals, cellular 5'-nucleotidase (5'-NT) activity (EC 3.1.3.5) encompasses a number of genetically and structurally distinct enzyme forms, either membrane-bound or soluble, mainly cytosolic, that are characterized by broad specificity towards nucleoside 5'-monophosphate substrates differing in base (purine/pyrimidine) and/or sugar (oxy/deoxy-ribose) moieties. In particular, among the cytosolic 5'-NTs active towards pyrimidine nucleotides are cN-III and cdN, ubiquitously distributed in mammalian tissues and treated as a single entity in the early days. cN-III was first linked to a genetic defect , hereditary pyrimidine nucleotidase deficiency, associated to a nonspherocyt ic hemolytic anemia disorder of still unclear mechanism but metabolically characterized by abnormally high levels of pyrimidine compounds and ribonucleoproteins in erythrocytes, as evidenced by occurrence of basophilic stippling on blood smearings. Since the first review on pyrimidine-specific nucleotidases (Amici, A.; Magni, G., Arch. Biochem. Biophys., 2002, 397(2), 184- 190), excellent overviews on the topic appeared in the literature. In the present contribution, the major findings on these two enzymatic proteins, cN-III and cdN, will be described with particular emphasis on the relationships between their structure and function, as well as on their roles in normal and pathological conditions. The catalytic mechanism of both specific hydrolytic and phosphotransferase activities, possessed by both enzymes, will be discussed also in the light of recent solution of both cN-III and cdN three-dimensional structures. This review also focuses on possible therapeutic approaches involving cellular 5'-NTs in detoxifying common antiviral and antineoplastic drugs.

  5. Effect of pressure on heterocyclic compounds: Pyrimidine and s-triazine

    SciTech Connect

    Li, Shourui; Li, Qian; Li, Wenbo; Cui, Wen; Liu, Ran; Liu, Bingbing; Zou, Bo; Xiong, Lun; Li, Xiaodong; Liu, Jing; Yang, Ke

    2014-09-21

    We have examined the high-pressure behaviors of six-membered heterocyclic compounds of pyrimidine and s-triazine up to 26 and 26.5 GPa, respectively. Pyrimidine crystallizes in Pna2{sub 1} symmetry (phase I) with the freezing pressure of 0.3 GPa, and transforms to another phase (phase II) at 1.1 GPa. Raman spectra of several compression-decompression cycles demonstrate there is a critical pressure of 15.5 GPa for pyrimidine. Pyrimidine returns back to its original liquid state as long as the highest pressure is below 15.1 GPa. Rupture of the aromatic ring is observed once pressure exceeds 15.5 GPa during a compression-decompression cycle, evidenced by the amorphous characteristics of the recovered sample. As for s-triazine, the phase transition from R-3c to C2/c is well reproduced at 0.6 GPa, in comparison with previous Raman data. Detailed Raman scattering experiments corroborate the critical pressure for s-triazine may locate at 14.5 GPa. That is, the compression is reversible below 14.3 GPa, whereas chemical reaction with ring opening is detected when the final pressure is above 14.5 GPa. During compression, the complete amorphization pressure for pyrimidine and s-triazine is identified as 22.4 and 15.2 GPa, respectively, based on disappearance of Raman lattice modes. Synchrotron X-ray diffraction patterns and Fourier transform infrared spectra of recovered samples indicate the products in two cases comprise of extended nitrogen-rich amorphous hydrogenated carbon (a-C:H:N)

  6. Effect of pressure on heterocyclic compounds: pyrimidine and s-triazine.

    PubMed

    Li, Shourui; Li, Qian; Xiong, Lun; Li, Xiaodong; Li, Wenbo; Cui, Wen; Liu, Ran; Liu, Jing; Yang, Ke; Liu, Bingbing; Zou, Bo

    2014-09-21

    We have examined the high-pressure behaviors of six-membered heterocyclic compounds of pyrimidine and s-triazine up to 26 and 26.5 GPa, respectively. Pyrimidine crystallizes in Pna2₁ symmetry (phase I) with the freezing pressure of 0.3 GPa, and transforms to another phase (phase II) at 1.1 GPa. Raman spectra of several compression-decompression cycles demonstrate there is a critical pressure of 15.5 GPa for pyrimidine. Pyrimidine returns back to its original liquid state as long as the highest pressure is below 15.1 GPa. Rupture of the aromatic ring is observed once pressure exceeds 15.5 GPa during a compression-decompression cycle, evidenced by the amorphous characteristics of the recovered sample. As for s-triazine, the phase transition from R-3c to C2/c is well reproduced at 0.6 GPa, in comparison with previous Raman data. Detailed Raman scattering experiments corroborate the critical pressure for s-triazine may locate at 14.5 GPa. That is, the compression is reversible below 14.3 GPa, whereas chemical reaction with ring opening is detected when the final pressure is above 14.5 GPa. During compression, the complete amorphization pressure for pyrimidine and s-triazine is identified as 22.4 and 15.2 GPa, respectively, based on disappearance of Raman lattice modes. Synchrotron X-ray diffraction patterns and Fourier transform infrared spectra of recovered samples indicate the products in two cases comprise of extended nitrogen-rich amorphous hydrogenated carbon (a-C:H:N).

  7. Structure and Function of Nucleoside Hydrolases from Physcomitrella patens and Maize Catalyzing the Hydrolysis of Purine, Pyrimidine, and Cytokinin Ribosides1[W

    PubMed Central

    Kopečná, Martina; Blaschke, Hanna; Kopečný, David; Vigouroux, Armelle; Končitíková, Radka; Novák, Ondřej; Kotland, Ondřej; Strnad, Miroslav; Moréra, Solange; von Schwartzenberg, Klaus

    2013-01-01

    We present a comprehensive characterization of the nucleoside N-ribohydrolase (NRH) family in two model plants, Physcomitrella patens (PpNRH) and maize (Zea mays; ZmNRH), using in vitro and in planta approaches. We identified two NRH subclasses in the plant kingdom; one preferentially targets the purine ribosides inosine and xanthosine, while the other is more active toward uridine and xanthosine. Both subclasses can hydrolyze plant hormones such as cytokinin ribosides. We also solved the crystal structures of two purine NRHs, PpNRH1 and ZmNRH3. Structural analyses, site-directed mutagenesis experiments, and phylogenetic studies were conducted to identify the residues responsible for the observed differences in substrate specificity between the NRH isoforms. The presence of a tyrosine at position 249 (PpNRH1 numbering) confers high hydrolase activity for purine ribosides, while an aspartate residue in this position confers high activity for uridine. Bud formation is delayed by knocking out single NRH genes in P. patens, and under conditions of nitrogen shortage, PpNRH1-deficient plants cannot salvage adenosine-bound nitrogen. All PpNRH knockout plants display elevated levels of certain purine and pyrimidine ribosides and cytokinins that reflect the substrate preferences of the knocked out enzymes. NRH enzymes thus have functions in cytokinin conversion and activation as well as in purine and pyrimidine metabolism. PMID:24170203

  8. Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

    SciTech Connect

    Kostko, Oleg; Bravaya, Ksenia; Krylov, Anna; Ahmed, Musahid

    2009-12-14

    We report a combined theoretical and experimental study of ionization of cytosine monomers and dimers. Gas-phase molecules are generated by thermal vaporization of cytosine followed by expansion of the vapor in a continuous supersonic jet seeded in Ar. The resulting species are investigated by single photon ionization with tunable vacuum-ultraviolet (VUV) synchrotron radiation and mass analyzed using reflectron mass spectrometry. Energy onsets for the measured photoionization efficiency (PIE) spectra are 8.60+-0.05 eV and 7.6+-0.1 eV for the monomer and the dimer, respectively, and provide an estimate for the adiabatic ionization energies (AIE). The first AIE and the ten lowest vertical ionization energies (VIEs) for selected isomers of cytosine dimer computed using equation-of-motion coupled-cluster (EOM-IP-CCSD) method are reported. The comparison of the computed VIEs with the derivative of the PIE spectra, suggests that multiple isomers of the cytosine dimer are present in the molecular beam. The calculations reveal that the large red shift (0.7 eV) of the first IE of the lowest-energy cytosine dimer is due to strong inter-fragment electrostatic interactions, i.e., the hole localized on one of the fragments is stabilized by the dipole moment of the other. A sharp rise in the CH+ signal at 9.20+-0.05 eV is ascribed to the formation of protonated cytosine by dissociation of the ionized dimers. The dominant role of this channel is supported by the computed energy thresholds for the CH+ appearance and the barrierless or nearly barrierless ionization-induced proton transfer observed for five isomers of the dimer.

  9. Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface

    PubMed Central

    Calgaro, Marcos R.; Neto, Mario de Oliveira; Figueira, Ana Carolina M.; Santos, Maria A.M.; Portugal, Rodrigo V.; Guzzi, Carolina A.; Saidemberg, Daniel M.; Bleicher, Lucas; Vernal, Javier; Fernandez, Pablo; Terenzi, Hernán; Palma, Mario Sergio; Polikarpov, Igor

    2007-01-01

    The orphan receptor nerve growth factor-induced B (NGFI-B) is a member of the nuclear receptor's subfamily 4A (Nr4a). NGFI-B was shown to be capable of binding both as a monomer to an extended half-site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo- and/or heterodimers. To unveil the structural organization of NGFI-B in solution, we determined the quaternary structure of the NGFI-B LBD by a combination of ab initio procedures from small-angle X-ray scattering (SAXS) data and hydrogen–deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI-B LBD dimer is V-shaped, with the opening angle significantly larger than that of classical dimer's exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI-B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C-terminal fraction of the helix 3. Remarkably, the NGFI-B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI-B and to antagonism of NGFI-B–dependent transcription exercised by GR in cells. PMID:17600153

  10. Integrable oscillator type and Schrödinger type dimers

    NASA Astrophysics Data System (ADS)

    Khare, Avinash; Saxena, Avadh

    2017-02-01

    A PT-symmetric dimer is a two-site nonlinear oscillator dimer or a two-site nonlinear Schrödinger dimer where one site loses and the other site gains energy at the same rate. We present a wide class of integrable oscillator type dimers whose Hamiltonian is of arbitrary even order. Further, we also present a wide class of integrable nonlinear Schrödinger type dimers where again the Hamiltonian is of arbitrary even order. Finally, we consider a recently discussed complex dimer model and point out a few integrable cases in that model.

  11. Graded-index optical dimer formed by optical force.

    PubMed

    Akbarzadeh, Alireza; Koschny, Thomas; Kafesaki, Maria; Economou, Eleftherios N; Soukoulis, Costas M

    2016-05-30

    We propose an optical dimer formed from two spherical lenses bound by the pressure that light exerts on matter. With the help of the method of force tracing, we find the required graded-index profiles of the lenses for the existence of the dimer. We study the dynamics of the opto-mechanical interaction of lenses under the illumination of collimated light beams and quantitatively validate the performance of proposed dimer. We also examine the stability of dimer due to the lateral misalignments and we show how restoring forces bring the dimer into lateral equilibrium. The dimer can be employed in various practical applications such as optical manipulation, sensing and imaging.

  12. Rubidium dimer destruction by a diode laser

    SciTech Connect

    Ban, T.; Aumiler, D.; Pichler, G.

    2005-02-01

    We observed rubidium dimer destruction by excitation of rubidium vapor with diode laser light tuned across the Rb D{sub 2} resonance line in a 2400 GHz tuning interval. The destruction was measured for rubidium atom concentrations in the (1-9)x10{sup 16} cm{sup -3} range, pump beam power up to 43 mW, and with a 5 Torr of the helium buffer gas. We discuss the physical mechanisms involved and specify the molecular pathways which may effectively lead to the observed dimer destruction.

  13. Crystal structures of two 6-(2-hy­droxy­benzo­yl)-5H-thia­zolo[3,2-a]pyrimidin-5-ones

    PubMed Central

    Gomes, Ligia R.; Low, John Nicolson; Cagide, Fernando; Borges, Fernanda

    2015-01-01

    The title compounds, 6-(2-hy­droxy­benz­yl)-5H-thia­zolo[3,2-a]pyrimidin-5-one, C13H8N2O3S, (1), and 6-(2-hy­droxy­benz­yl)-3-methyl-5H-thia­zolo[3,2-a]pyrimidin-5-one, C14H10N2O3S, (2), were synthesized when a chromone-3-carb­oxy­lic acid, activated with (benzotriazol-1-yl­oxy)tripyrrolidinyl­phospho­nium hexa­fluorido­phosphate (PyBOP), was reacted with a primary heteromamine. Instead of the expected amidation, the unusual title thia­zolo­pyrimidine-5-one derivatives were obtained serendipitously and a mechanism of formation is proposed. Both compounds present an intra­molecular O—H⋯O hydrogen bond, which generates an S(6) ring. The dihedral angles between the heterocyclic moiety and the 2-hydroxybenzoyl ring are 55.22 (5) and 46.83 (6)° for (1) and (2), respectively. In the crystals, the mol­ecules are linked by weak C—H⋯O hydrogen bonds and π–π stacking inter­actions. PMID:26279863

  14. Molecular Interplay between the Dimer Interface and the Substrate-Binding Site of Human Peptidylarginine Deiminase 4

    PubMed Central

    Lee, Chien-Yun; Lin, Chu-Cheng; Liu, Yi-Liang; Liu, Guang-Yaw; Liu, Jyung-Hurng; Hung, Hui-Chih

    2017-01-01

    Our previous studies suggest that the fully active form of Peptidylarginine deiminase 4 (PAD4) should be a dimer and not a monomer. This paper provides a plausible mechanism for the control of PAD4 catalysis by molecular interplay between its dimer-interface loop (I-loop) and its substrate-binding loop (S-loop). Mutagenesis studies revealed that two hydrophobic residues, W347 and V469, are critical for substrate binding at the active site; mutating these two residues led to a severe reduction in the catalytic activity. We also identified several hydrophobic amino acid residues (L6, L279 and V283) at the dimer interface. Ultracentrifugation analysis revealed that interruption of the hydrophobicity of this region decreases dimer formation and, consequently, enzyme activity. Molecular dynamic simulations and mutagenesis studies suggested that the dimer interface and the substrate-binding site of PAD4, which consist of the I-loop and the S-loop, respectively, are responsible for substrate binding and dimer stabilization. We identified five residues with crucial roles in PAD4 catalysis and dimerization: Y435 and R441 in the I-loop, D465 and V469 in the S-loop, and W548, which stabilizes the I-loop via van der Waals interactions with C434 and Y435. The molecular interplay between the S-loop and the I-loop is crucial for PAD4 catalysis. PMID:28209966

  15. Dimers in α-pinene secondary organic aerosol: effect of hydroxyl radical, ozone, relative humidity and aerosol acidity

    NASA Astrophysics Data System (ADS)

    Kristensen, K.; Cui, T.; Zhang, H.; Gold, A.; Glasius, M.; Surratt, J. D.

    2014-04-01

    The formation of secondary organic aerosol (SOA) from both ozonolysis and hydroxyl radical (OH)-initiated oxidation of α-pinene under conditions of high nitric oxide (NO) concentrations with varying relative humidity (RH) and aerosol acidity was investigated in the University of North Carolina dual outdoor smog chamber facility. SOA formation from ozonolysis of α-pinene was enhanced relative to that from OH-initiated oxidation in the presence of initially high-NO conditions. However, no effect of RH on SOA mass was evident. Ozone (O3)-initiated oxidation of α-pinene in the presence of ammonium sulfate (AS) seed coated with organic aerosol from OH-initiated oxidation of α-pinene showed reduced nucleation compared to ozonolysis in the presence of pure AS seed aerosol. The chemical composition of α-pinene SOA was investigated by ultra-performance liquid chromatography/electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry (UPLC/ESI-HR-Q-TOFMS), with a focus on the formation of carboxylic acids and high-molecular weight dimers. A total of eight carboxylic acids and four dimers were identified, constituting between 8 and 12% of the total α-pinene SOA mass. OH-initiated oxidation of α-pinene in the presence of nitrogen oxides (NOx) resulted in the formation of highly oxidized carboxylic acids, such as 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA) and diaterpenylic acid acetate (DTAA). The formation of dimers was observed only in SOA produced from the ozonolysis of α-pinene in the absence of NOx, with increased concentrations by a factor of two at higher RH (50-90%) relative to lower RH (30-50%). The increased formation of dimers correlates with an observed increase in new particle formation at higher RH due to nucleation. Increased aerosol acidity was found to have a negligible effect on the formation of the dimers. SOA mass yield did not influence the chemical composition of SOA formed from α-pinene ozonolysis with respect to

  16. A detailed MSn study for the molecular identification of a dimer formed from oxidation of pinene

    NASA Astrophysics Data System (ADS)

    Beck, Martin; Hoffmann, Thorsten

    2016-04-01

    Dimeric products formed in the oxidation of α- and β-pinene have been frequently observed in laboratory and field studies of biogenic SOA formation. While their existence is undoubted, their exact chemical structures remain unclear. This study uses a combined two step approach aiming on the molecular identification of the most important of the various dimers that have been observed in biogenic secondary organic aerosol formation, a dimer with the molecular weight 358 g mol-1. The first step is the application of a functional group derivatization technique (esterification) to quantify the number of carboxylic acid groups in the target molecule. Based on the detailed interpretation of the MSn spectra (up to n = 7) of the derivatized product further information about the exact structure of the compound of interest is compiled. To increase the intensity of precursor ions for the MSn-studies and especially to facilitate successive fragmentation of the target molecule, which yields structurally informative product spectra, cationization reagents (Li+, NH4+) are introduced. The results clearly point to the formation of a dimer containing three carboxylic acid groups and a structure containing a terpenylic acid building block and a pinic acid building block, strongly supporting a structure suggestion by Claeys and coworkers (Yasmeen et al., 2010).

  17. Molecular Design Principles Underlying beta-strand Swapping in the Adhesive Dimerization of Cadherins

    SciTech Connect

    J Vendome; S Posy; X Jin; F Bahna; G Ahlsen; L Shapiro; B Honig

    2011-12-31

    Cell adhesion by classical cadherins is mediated by dimerization of their EC1 domains through the 'swapping' of N-terminal {beta}-strands. We use molecular simulations, measurements of binding affinities and X-ray crystallography to provide a detailed picture of the structural and energetic factors that control the adhesive dimerization of cadherins. We show that strand swapping in EC1 is driven by conformational strain in cadherin monomers that arises from the anchoring of their short N-terminal strand at one end by the conserved Trp2 and at the other by ligation to Ca{sup 2+} ions. We also demonstrate that a conserved proline-proline motif functions to avoid the formation of an overly tight interface where affinity differences between different cadherins, crucial at the cellular level, are lost. We use these findings to design site-directed mutations that transform a monomeric EC2-EC3 domain cadherin construct into a strand-swapped dimer.

  18. Anomalous ballistic transport in disordered bilayer graphene: A Dirac semimetal induced by dimer vacancies

    NASA Astrophysics Data System (ADS)

    Van Tuan, Dinh; Roche, Stephan

    2016-01-01

    We report anomalous quantum transport features in bilayer graphene in the presence of a random distribution of structural vacancies. By using an efficient real-space Kubo-Greenwood transport methodology, the impact of a varying density of dimer versus nondimer vacancies is investigated in very large scale disordered models. While nondimer vacancies are shown to induce localization regimes, dimer vacancies result in an unexpected ballistic regime whose energy window surprisingly enlarges with increasing impurity density. Such counterintuitive phenomenon is explained by the formation of an effective linear dispersion in the bilayer band structure, which roots in the symmetry breaking effects driven by dimer vacancies, and provides a realization of Dirac semimetals in high dimension.

  19. Observation and photophysical characterization of silicon phthalocyanine J-aggregate dimers in aqueous solutions.

    PubMed

    Doane, Tennyson; Chomas, Andrew; Srinivasan, Shriya; Burda, Clemens

    2014-06-23

    The use of macrocyclic molecules for both imaging and photodynamic therapy (PDT) has proven to be a powerful method for assessing and treating diseases, respectively. However, many potential candidates for these applications rely on rigid organic structures which are hydrophobic and thus lead to possible aggregation in aqueous solutions such as blood. Here, we describe the discovery of noncovalent J-aggregate dimers of the asymmetrically, axially modified silicon phthalocyanine 4 (Pc 4) in aqueous solutions through steady-state and time-resolved spectroscopy. Remarkably, the monomer-dimer equilibrium is dictated by water content and pH, with free monomers resulting in favorable solvation conditions even after formation of the dimer complex. This work sheds light on previous observations of Pc 4 behavior in cells during PDT, and can further elucidate the structure-activity relationship of these important molecules.

  20. A Uranyl Peroxide Dimer in the Gas Phase.

    PubMed

    Dau, Phuong D; Dau, Phuong V; Rao, Linfeng; Kovács, Attila; Gibson, John K

    2017-04-03

    The gas-phase uranyl peroxide dimer, [(UO2)2(O2)(L)2](2+) where L = 2,2'-trifluoroethylazanediyl)bis(N,N'-dimethylacetamide), was synthesized by electrospray ionization of a solution of UO2(2+) and L. Collision-induced dissociation of this dimer resulted in endothermic O atom elimination to give [(UO2)2(O)(L)2](2+), which was found to spontaneously react with water via exothermic hydrolytic chemisorption to yield [(UO2)2(OH)2(L)2](2+). Density functional theory computations of the energies for the gas-phase reactions are in accord with observations. The structures of the observed uranyl dimer were computed, with that of the peroxide of particular interest, as a basis to evaluate the formation of condensed phase uranyl peroxides with bent structures. The computed dihedral angle in [(UO2)2(O2)(L)2](2+) is 145°, indicating a substantial deviation from the planar structure with a dihedral angle of 180°. Energies needed to induce bending in the most elementary gas-phase uranyl peroxide complex, [(UO2)2(O2)](2+), were computed. It was found that bending from the lowest-energy planar structure to dihedral angles up to 140° required energies of <10 kJ/mol. The gas-phase results demonstrate the inherent stability of the uranyl peroxide moiety and support the notion that the uranyl-peroxide-uranyl structural unit is intrinsically planar, with only minor energy perturbations needed to form the bent structures found in studtite and uranyl peroxide nanostructures.

  1. 7-cyclopentyl-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d] pyrimidin-4-ylamine inhibits the proliferation and migration of vascular smooth muscle cells by suppressing ERK and Akt pathways.

    PubMed

    Seo, Hyang-Hee; Kim, Sang Woo; Lee, Chang Youn; Lim, Kyu Hee; Lee, Jiyun; Lim, Soyeon; Lee, Seahyoung; Hwang, Ki-Chul

    2017-03-05

    Excessive vascular smooth muscle cell (VSMC) proliferation and migration after vascular injury significantly contributes to the development of occlusive vascular disease. Therefore, inhibiting the proliferation and migration of VSMCs is a validated therapeutic modality for occlusive vascular disease such as atherosclerosis and restenosis. In the present study, we screened chemical compounds for their anti-proliferative effects on VSMCs using multiple approaches, such as MTT assays, wound healing assays, and trans-well migration assays. Our data indicate that 7-cyclopentyl-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d] pyrimidin-4-ylamine, a lymphocyte-specific protein tyrosine kinase (Lck) inhibitor, significantly inhibited both VSMC proliferation and migration. 7-cyclopentyl-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-ylamine suppresses VSMC proliferation and migration via down-regulating the protein kinase B (Akt) and extracellular signal regulated kinase (ERK) pathways, and it significantly decreased the expression of proliferating cell nuclear antigen (PCNA) and cyclin D1 and, the phosphorylation of retinoblastoma protein (pRb). Additionally, 7-cyclopentyl-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d] pyrimidin-4-ylamine suppressed the migration of VSMCs from endothelium-removed aortic rings, as well as neointima formation following rat carotid balloon injury. The present study identified 7-cyclopentyl-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-ylamine as a potent VSMC proliferation and migration inhibitor and warrants further studies to elucidate its more detailed molecular mechanisms, such as its primary target, and to further validate its in vivo efficacy as a therapeutic agent for pathologic vascular conditions, such as restenosis and atherosclerosis.

  2. Self-assembly in a model colloidal mixture of dimers and spherical particles

    NASA Astrophysics Data System (ADS)

    Prestipino, Santi; Munaò, Gianmarco; Costa, Dino; Caccamo, Carlo

    2017-02-01

    We investigate the structure of a dilute mixture of amphiphilic dimers and spherical particles, a model relevant to the problem of encapsulating globular "guest" molecules in a dispersion. Dimers and spheres are taken to be hard particles, with an additional attraction between spheres and the smaller monomers in a dimer. Using the Monte Carlo simulation, we document the low-temperature formation of aggregates of guests (clusters) held together by dimers, whose typical size and shape depend on the guest concentration χ. For low χ (less than 10%), most guests are isolated and coated with a layer of dimers. As χ progressively increases, clusters grow in size becoming more and more elongated and polydisperse; after reaching a shallow maximum for χ ≈50 % , the size of clusters again reduces upon increasing χ further. In one case only (χ =50 % and moderately low temperature) the mixture relaxed to a fluid of lamellae, suggesting that in this case clusters are metastable with respect to crystal-vapor separation. On heating, clusters shrink until eventually the system becomes homogeneous on all scales. On the other hand, as the mixture is made denser and denser at low temperature, clusters get increasingly larger until a percolating network is formed.

  3. Photo-stability of peptide-bond aggregates: N-methylformamide dimers.

    PubMed

    Crespo-Otero, Rachel; Mardykov, Artur; Sanchez-Garcia, Elsa; Sander, Wolfram; Barbatti, Mario

    2014-09-21

    The formation of weakly-bound dimers of N-methylformamide (NMF) and the photochemistry of these dimers after irradiation at 248 nm were explored using matrix-isolation spectroscopy. Calculations were used to characterize the diverse isomers and assign their IR spectra; non-adiabatic dynamics was simulated to understand their photo-deactivation mechanism. The most stable dimers, and , were obtained by trans-trans aggregation (N-HO[double bond, length as m-dash]C interactions) and could be identified in the matrix. The main products formed after irradiation are the trans-cis dimers ( and ), also stabilized by N-HO[double bond, length as m-dash]C interactions. In contrast to the photochemistry of the monomers, no dissociative products were observed after 248 nm irradiation of the dimers. The absence of dissociative products can be explained by a proton-transfer mechanism in the excited state that is faster than the photo-dissociative mechanism. The fact that hydrogen bonding has such a significant effect on the photochemical stability of NMF has important implications to understand the stability of peptide-bonded systems to UV irradiation.

  4. Change in dimerization mode by removal of a single unsatisfied polar residue located at the interface.

    SciTech Connect

    Pokkuluri, P. R.; Cai, X.; Johnson, G.; Stevens, F. J; Schiffer, M.; Center for Mechanistic Biology and Biotechnology

    2000-09-01

    The importance of unsatisfied hydrogen bonding potential on protein-protein interaction was studied. Two alternate modes of dimerization (conventional and flipped form) of an immunoglobulin light chain variable domain (V{sub L}) were previously identified. In the flipped form, interface residue Gln89 would have an unsatisfied hydrogen bonding potential. Removal of this Gln should render the flipped dimer as the more favorable quaternary form. High resolution crystallographic studies of the Q89A and Q89L mutants show, as we predicted, that these proteins indeed form flipped dimers with very similar interfaces. A small cavity is present in the Q89A mutant that is reflected in the {approx}100 times lower association constant than found for the Q89L mutant. The association constant of Q89A and Q89L proteins (4 x 10{sup 6} M{sup -1} and > 10{sup 8} M{sup -1}) are 10- and 1,000-fold higher than that of the wild-type protein that forms conventional dimers clearly showing the energetic reasons for the flipped dimer formation.

  5. Monoubiquitination and activity of the paracaspase MALT1 requires glutamate 549 in the dimerization interface.

    PubMed

    Cabalzar, Katrin; Pelzer, Christiane; Wolf, Annette; Lenz, Georg; Iwaszkiewicz, Justyna; Zoete, Vincent; Hailfinger, Stephan; Thome, Margot

    2013-01-01

    The mucosa-associated lymphoid tissue protein-1 (MALT1, also known as paracaspase) is a protease whose activity is essential for the activation of lymphocytes and the growth of cells derived from human diffuse large B-cell lymphomas of the activated B-cell subtype (ABC DLBCL). Crystallographic approaches have shown that MALT1 can form dimers via its protease domain, but why dimerization is relevant for the biological activity of MALT1 remains largely unknown. Using a molecular modeling approach, we predicted Glu 549 (E549) to be localized within the MALT1 dimer interface and thus potentially relevant. Experimental mutation of this residue into alanine (E549A) led to a complete impairment of MALT1 proteolytic activity. This correlated with an impaired capacity of the mutant to form dimers of the protease domain in vitro, and a reduced capacity to promote NF-κB activation and transcription of the growth-promoting cytokine interleukin-2 in antigen receptor-stimulated lymphocytes. Moreover, this mutant could not rescue the growth of ABC DLBCL cell lines upon MALT1 silencing. Interestingly, the MALT1 mutant E549A was unable to undergo monoubiquitination, which we identified previously as a critical step in MALT1 activation. Collectively, these findings suggest a model in which E549 at the dimerization interface is required for the formation of the enzymatically active, monoubiquitinated form of MALT1.

  6. Dimerization kinetics and products of. alpha. -substituted o-quinodimethanes derived from benzene and furan

    SciTech Connect

    Leung, Man-kit.

    1992-07-20

    Effects of the {alpha}-substitutions on the termini of the reactive diene unit of o-quinodimethanes revealed a non-concerted mechanism for furan-based and benzene-based o-quinodimethane (o-QDM) dimerizations. In section one, the coexistence of the cisoid and transoid transition states in the diradical formation step is evidenced by the stereochemistry of the dimers. In view of the results of the furan-based o-QDM dimerizauons, it is believed that the regioselectivity in the diradical cyclization step is controlled mainly by the interaction between the active sites on the furan moieties in the diradical ring closure step, not by the intemal bond rotations of the carbon chain of the diradical intermediate. In section two, it was found that the trend of the regioselectivity. along the size of the {alpha}-substituents, of benzene-based o-QDM dimerizations is opposite to that of the Diels-Alder reactions. On the basis of the trends, it is suggested that the Diels-Alder reaction mechanism of benzene-based o-QDM's is concerted while the dimerization mechanism of benzene-based o-QDM's is stepwise. Because of their similar activation parameters, it is proposed that the parent o-xylylene and other o-xylylenes dimerize via a similar two step, diradical mechanism.

  7. Terminal Interface Conformations Modulate Dimer Stability Prior to Amino Terminal Autoprocessing of HIV-1 Protease

    SciTech Connect

    Agniswamy, Johnson; Sayer, Jane M.; Weber, Irene T.; Louis, John M.

    2012-04-17

    The HIV-1 protease (PR) mediates its own release (autoprocessing) from the polyprotein precursor, Gag-Pol, flanked by the transframe region (TFR) and reverse transcriptase at its N- and C-termini, respectively. Autoprocessing at the N-terminus of PR mediates stable dimer formation essential for catalytic activity, leading to the formation of infectious virus. An antiparallel {beta}-sheet interface formed by the four N- and C-terminal residues of each subunit is important for dimer stability. Here, we present the first high-resolution crystal structures of model protease precursor-clinical inhibitor (PI darunavir or saquinavir) complexes, revealing varying conformations of the N-terminal flanking (S{sup -4}FNF{sup -1}) and interface residues (P{sup 1}QIT{sup 4}). A 180{sup o} rotation of the T{sup 4}-L{sup 5} peptide bond is accompanied by a new Q{sup 2}-L{sup 5} hydrogen bond and complete disengagement of PQIT from the {beta}-sheet dimer interface, which may be a feature for intramolecular autoprocessing. This result is consistent with drastically lower thermal stability by 14-20 C of PI complexes of precursors and the mature PR lacking its PQIT residues (by 18.3 C). Similar to the TFR-PR precursor, this deletion also results in a darunavir dissociation constant (2 x 10{sup 4})-fold higher and a markedly increased dimer dissociation constant relative to the mature PR. The terminal {beta}-sheet perturbations of the dimeric structure likely account for the drastically poorer inhibition of autoprocessing of TFR-PR relative to the mature PR, even though significant differences in active site-PI interactions in these structures were not observed. The novel conformations of the dimer interface may be exploited to target selectively the protease precursor prior to its N-terminal cleavage.

  8. Disruption of Rhodopsin Dimerization with Synthetic Peptides Targeting an Interaction Interface.

    PubMed

    Jastrzebska, Beata; Chen, Yuanyuan; Orban, Tivadar; Jin, Hui; Hofmann, Lukas; Palczewski, Krzysztof

    2015-10-16

    Although homo- and heterodimerizations of G protein-coupled receptors (GPCRs) are well documented, GPCR monomers are able to assemble in different ways, thus causing variations in the interactive interface between receptor monomers among different GPCRs. Moreover, the functional consequences of this phenomenon, which remain to be clarified, could be specific for different GPCRs. Synthetic peptides derived from transmembrane (TM) domains can interact with a full-length GPCR, blocking dimer formation and affecting its function. Here we used peptides corresponding to TM helices of bovine rhodopsin (Rho) to investigate the Rho dimer interface and functional consequences of its disruption. Incubation of Rho with TM1, TM2, TM4, and TM5 peptides in rod outer segment (ROS) membranes shifted the resulting detergent-solubilized protein migration through a gel filtration column toward smaller molecular masses with a reduced propensity for dimer formation in a cross-linking reaction. Binding of these TM peptides to Rho was characterized by both mass spectrometry and a label-free assay from which dissociation constants were calculated. A BRET (bioluminescence resonance energy transfer) assay revealed that the physical interaction between Rho molecules expressed in membranes of living cells was blocked by the same four TM peptides identified in our in vitro experiments. Although disruption of the Rho dimer/oligomer had no effect on the rates of G protein activation, binding of Gt to the activated receptor stabilized the dimer. However, TM peptide-induced disruption of dimer/oligomer decreased receptor stability, suggesting that Rho supramolecular organization could be essential for ROS stabilization and receptor trafficking.

  9. A new lignan dimer from Mallotus philippensis.

    PubMed

    Mai, Nguyen Thi; Cuong, Nguyen Xuan; Thao, Nguyen Phuong; Nam, Nguyen Hoai; Khoi, Nguyen Huu; Minh, Chau Van; Heyden, Yvan Vander; Thuan, Ngo Thi; Tuyen, Nguyen Van; Quetin-Leclercq, Joëlle; Kiem, Phan Van

    2010-03-01

    A new lignan dimer, bilariciresinol (1), was isolated from the leaves of Mallotus philippensis, along with platanoside (2), isovitexin (3), dihydromyricetin (4), bergenin (5), 4-O-galloylbergenin (6), and pachysandiol A (7). Their structures were elucidated by spectroscopic experiments including 1D and 2D NMR and FTICR-MS.

  10. Amplitude enhancement by a gold dimer

    NASA Astrophysics Data System (ADS)

    Hong, Xin; Wang, Jingxin; Jin, Zheng

    2016-10-01

    The unique optical properties such as brightness, non-bleaching, good bio-compatibility make gold particles ideal label candidates for molecular probes. Due to the strongly enhanced field, aggregation of gold nanoparticles finds themselves plenty of applications in bio-imaging. But limited by its small cross-section associated with nanometer sized particle, it is a big challenge to employ it in a single molecular detection. The field enhancement results from the effect of plasmonic coupling between two closely attached gold nanoparticle under the right excitation condition. With the aim to apply the gold dimer probe to find the molecules in our recently established optical detection method, we compared of the amplitude enhancement by the dimer relative to a single particle. The amplitude distribution under a highly focused illumination objective was calculated, whose results suggest that at the optimized excitation condition, the local field can be enhanced 190 fold. In consequence, experimental detection was carried out. Gold dimers were linked together by the hybridization of two single chain DNAs. Dimer and single particle probes were mixed together in one detection. Overwhelming contrast between these two kinds of probes were clearly exhibited in the experimental detection image. This method can provide a way to a high specific detection in early diagnosis.

  11. Direct participation of DNA in the formation of singlet oxygen and base damage under UVA irradiation.

    PubMed

    Yagura, Teiti; Schuch, André Passaglia; Garcia, Camila Carrião Machado; Rocha, Clarissa Ribeiro Reily; Moreno, Natália Cestari; Angeli, José Pedro Friedmann; Mendes, Davi; Severino, Divinomar; Bianchini Sanchez, Angelica; Di Mascio, Paolo; de Medeiros, Marisa Helena Gennari; Menck, Carlos Frederico Martins

    2017-03-18

    UVA light is hardly absorbed by the DNA molecule, but recent works point to a direct mechanism of DNA lesion by these wavelengths. UVA light also excite endogenous chromophores, which causes DNA damage through ROS. In this study, DNA samples were irradiated with UVA light in different conditions to investigate possible mechanisms involved in the induction of DNA damage. The different types of DNA lesions formed after irradiation were determined through the use of endonucleases, which recognize and cleave sites containing oxidized bases and cyclobutane pyrimidine dimers (CPDs), as well as through antibody recognition. The formation of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxodG) was also studied in more detail using electrochemical detection. The results show that high NaCl concentration and concentrated DNA are capable of reducing the induction of CPDs. Moreover, concerning damage caused by oxidative stress, the presence of sodium azide and metal chelators reduce their induction, while deuterated water increases the amounts of oxidized bases, confirming the involvement of singlet oxygen in the generation of these lesions. Curiously, however, high concentrations of DNA also enhanced the formation of oxidized bases, in a reaction that paralleled the increase in the formation of singlet oxygen in the solution. This was interpreted as being due to an intrinsic photosensitization mechanism, depending directly on the DNA molecule to absorb UVA and generate singlet oxygen. Therefore, the DNA molecule itself may act as a chromophore for UVA light, locally producing a damaging agent, which may lead to even greater concerns about the deleterious impact of sunlight.

  12. N-alkylated and O-alkylated regioisomers of 5-(hydroxyalkyl)pyrimidines: Synthesis and structural study

    NASA Astrophysics Data System (ADS)

    Meščić, Andrijana; Glavač, Danijel; Osmanović, Amar; Završnik, Davorka; Cetina, Mario; Makuc, Damjan; Plavec, Janez; Ametamey, Simon M.; Raić-Malić, Silvana

    2013-05-01

    Synthesis of novel 5-(2-hydroxyethyl) and 5-(3-hydroxypropyl) acyclic pyrimidine nucleosides is described. Introduction of penciclovir-like side chain in C-5 substituted pyrimidines occurred both at N-1 and O-2 position of pyrimidine moiety that was corroborated by correlation of signals in 2D HMBC spectra. Therefore, alkylation of 5-(acetoxyethyl)-4-methoxypyrimidin-2-one (2a) and 5-(acetoxypropyl)-4-methoxypyrimidin-2-one (2b) afforded mixture of N- and O-acyclic pyrimidine nucleosides in the ratio of 49: 45 (4a: 5a) and 41: 21 (4b: 5b). Structures of 5-(acetoxyalkyl)-4-methoxypyrimidin-2-ones, as the first examples of 4-methoxypyrimidin-2-ones, were unambiguously confirmed by single crystal X-ray diffraction analysis.

  13. Dimerization of Carboxylic Acids: An Equation of State Approach.

    PubMed

    Tsivintzelis, Ioannis; Kontogeorgis, Georgios M; Panayiotou, Costas

    2017-03-09

    The association term of the nonrandom hydrogen bonding theory, which is an equation of state model, is extended to describe the dimerization of carboxylic acids in binary mixtures with inert solvents and in systems of two different acids. Subsequently, the model is applied to describe the excess enthalpies and the vapor-liquid equilibrium of relevant binary mixtures containing low molecular weight organic acids. The model sheds light on the interplay of intermolecular interactions through the calculation of the various contributions to the mixing enthalpies, namely from hydrogen bonding and non-hydrogen bonding (dipolar, induced polar or dispersive) interactions. According to model predictions, the acid molecules are so strongly associated that the addition of inert solvents to carboxylic acids with small carbon numbers at ambient temperature does not dramatically alter their degree of association. Consequently, the observed endothermic dissolution process is mainly attributed to the hindering of polar interactions. Furthermore, upon mixing of two carboxylic acids, the rearrangement of hydrogen bonds due to the formation of cross associating species results in an insignificant contribution to the heats of mixing due to the rather constant dimerization enthalpy that is revealed by the available experimental data for low molecular weight compounds.

  14. Localized light-induced protein dimerization in living cells using a photocaged dimerizer

    PubMed Central

    Ballister, Edward R.; Aonbangkhen, Chanat; Mayo, Alyssa M.; Lampson, Michael A.; Chenoweth, David M.

    2015-01-01

    Regulated protein localization is critical for many cellular processes. Several techniques have been developed for experimental control over protein localization, including chemically induced and light-induced dimerization, which both provide temporal control. Light-induced dimerization offers the distinct advantage of spatial precision within subcellular length scales. A number of elegant systems have been reported that utilize natural light-sensitive proteins to induce dimerization via direct protein–protein binding interactions, but the application of these systems at cellular locations beyond the plasma membrane has been limited. Here we present a new technique to rapidly and reversibly control protein localization in living cells with subcellular spatial resolution using a cell-permeable, photoactivatable chemical inducer of dimerization. We demonstrate light-induced recruitment of a cytosolic protein to individual centromeres, kinetochores, mitochondria and centrosomes in human cells, indicating that our system is widely applicable to many cellular locations. PMID:25400104

  15. Dimerization of visual pigments in vivo

    PubMed Central

    Zhang, Tao; Cao, Li-Hui; Kumar, Sandeep; Enemchukwu, Nduka O.; Zhang, Ning; Lambert, Alyssia; Zhao, Xuchen; Jones, Alex; Wang, Shixian; Dennis, Emily M.; Fnu, Amrita; Ham, Sam; Rainier, Jon; Yau, King-Wai; Fu, Yingbin

    2016-01-01

    It is a deeply engrained notion that the visual pigment rhodopsin signals light as a monomer, even though many G protein-coupled receptors are now known to exist and function as dimers. Nonetheless, recent studies (albeit all in vitro) have suggested that rhodopsin and its chromophore-free apoprotein, R-opsin, may indeed exist as a homodimer in rod disk membranes. Given the overwhelmingly strong historical context, the crucial remaining question, therefore, is whether pigment dimerization truly exists naturally and what function this dimerization may serve. We addressed this question in vivo with a unique mouse line (S-opsin+Lrat−/−) expressing, transgenically, short-wavelength–sensitive cone opsin (S-opsin) in rods and also lacking chromophore to exploit the fact that cone opsins, but not R-opsin, require chromophore for proper folding and trafficking to the photoreceptor’s outer segment. In R-opsin’s absence, S-opsin in these transgenic rods without chromophore was mislocalized; in R-opsin’s presence, however, S-opsin trafficked normally to the rod outer segment and produced functional S-pigment upon subsequent chromophore restoration. Introducing a competing R-opsin transmembrane helix H1 or helix H8 peptide, but not helix H4 or helix H5 peptide, into these transgenic rods caused mislocalization of R-opsin and S-opsin to the perinuclear endoplasmic reticulum. Importantly, a similar peptide-competition effect was observed even in WT rods. Our work provides convincing evidence for visual pigment dimerization in vivo under physiological conditions and for its role in pigment maturation and targeting. Our work raises new questions regarding a potential mechanistic role of dimerization in rhodopsin signaling. PMID:27462111

  16. Regulation of cell proliferation under extreme and moderate hypoxia: the role of pyrimidine (deoxy)nucleotides.

    PubMed Central

    Amellem, O.; Löffler, M.; Pettersen, E. O.

    1994-01-01

    In the present study we have used flow cytometric DNA measurements on synchronised human NHIK 3025 cells to measure cell cycle progression under various conditions of reduced oxygenation. Our data indicate that addition of 0.1 mM deoxycytidine or uridine has no effect on the oxygen-dependent arrest in late G1 or on the inhibition of cell proliferation through S-phase under extremely hypoxic conditions. Following reoxygenation of cells exposed to extremely hypoxic conditions in G2 initiation of DNA synthesis in the subsequent cell cycle is delayed by several hours. This G2-induced delay is completely abolished for approximately 60% of the cell population by addition of deoxycytidine to hypoxic G2 cells. This finding supports our previous proposal that important steps in the preparation for DNA synthesis occur during G2 of the previous cell cycle, and it indicates that this preparation is connected to the de novo synthesis of pyrimidine deoxynucleotide precursors. The results show that cells are able to enter S-phase in the presence of 100-1,300 p.p.m. (0.01-0.13%) oxygen (here denoted 'moderate hypoxia'), but they are not able to complete DNA synthesis under such conditions. However, the cell cycle inhibition induced under moderate hypoxia is partially reversed in the presence of exogenously added deoxycytidine and uridine, while no such reversal is seen in the presence of purine deoxynucleosides (deoxyadenosine and deoxyguanosine). Thus, both deoxycytidine and uridine could replace reoxygenation under these conditions. These results indicate that the reduction of CDP to dCTP by ribonucleotide reductase, an enzyme which requires oxygen as an essential factor for the formation of tyrosyl radicals for its catalytic activity, does not seem to be the limiting step responsible for the reduced dCTP pool observed under moderate hypoxia. We conclude that the oxygen-dependent catalytic activity of the M2 subunit of ribonucleotide reductase is still intact and functional in

  17. 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

  18. Cation templating and electronic structure effects in uranyl cage clusters probed by the isolation of peroxide-bridged uranyl dimers.

    PubMed

    Qiu, Jie; Vlaisavljevich, Bess; Jouffret, Laurent; Nguyen, Kevin; Szymanowski, Jennifer E S; Gagliardi, Laura; Burns, Peter C

    2015-05-04

    The self-assembly of uranyl peroxide polyhedra into a rich family of nanoscale cage clusters is thought to be favored by cation templating effects and the pliability of the intrinsically bent U-O2-U dihedral angle. Herein, the importance of ligand and cationic effects on the U-O2-U dihedral angle were explored by studying a family of peroxide-bridged dimers of uranyl polyhedra. Four chemically distinct peroxide-bridged uranyl dimers were isolated that contain combinations of pyridine-2,6-dicarboxylate, picolinate, acetate, and oxalate as coordinating ligands. These dimers were synthesized with a variety of counterions, resulting in the crystallographic characterization of 15 different uranyl dimer compounds containing 17 symmetrically distinct dimers. Eleven of the dimers have U-O2-U dihedral angles in the expected range from 134.0 to 156.3°; however, six have 180° U-O2-U dihedral angles, the first time this has been observed for peroxide-bridged uranyl dimers. The influence of crystal packing, countercation linkages, and π-π stacking impact the dihedral angle. Density functional theory calculations indicate that the ligand does not alter the electronic structure of these systems and that the U-O2-U bridge is highly pliable. Less than 3 kcal·mol(-1) is required to bend the U-O2-U bridge from its minimum energy configuration to a dihedral angle of 180°. These results suggest that the energetic advantage of bending the U-O2-U dihedral angle of a peroxide-bridged uranyl dimer is at most a modest factor in favor of cage cluster formation. The role of counterions in stabilizing the formation of rings of uranyl ions, and ultimately their assembly into clusters, is at least as important as the energetic advantage of a bent U-O2-U interaction.

  19. Anion-controlled dimer distance induced unique solid-state fluorescence of cyano substituted styrene pyridinium

    PubMed Central

    Zhang, Gaobin; Zhang, Xuanjun; Kong, Lin; Wang, Shichao; Tian, Yupeng; Tao, Xutang; Yang, Jiaxiang

    2016-01-01

    Molecular packing arrangements play a key role in dominating the photophysical properties of luminophores in aggregated state but fine control of the molecular packing is a great challenge. This article describes a unique cyano substituted styrene pyridinium with interesting solid-state fluorescence that can be finely tuned by simple change of counteranions. The dilute solutions of the organic salts (PyCl, PyNO3, PyOTs and PyPh4B) exhibit very weak fluorescence. The crystals of the organic salts (PyCl, PyNO3, and PyOTs) show much enhanced fluorescence compared with their dilute solutions. It is interesting that the emissions changed from bluish-green to deep-blue and fluorescence quantum yields increase from 2.5% to 13.1% with the increasing of steric hindrance of the anions from chloridion, nitrate, to p-toluenesulfonate. Crystal and DFT studies reveal that the enhanced fluorescence is ascribed to the formation of dimers and bigger anions induce larger molecular separation in dimers. Tetraphenylboron anion with very large steric hindrance impedes the formation of dimers and thus results in non-fluorescent salt (PyPh4B). Meanwhile, this unique dimeric packing endows the crystal of PyNO3 with anisotropic fluorescence. PMID:27869183

  20. The unique physical properties of the hydrogen bonded in dimers liquid crystals

    NASA Astrophysics Data System (ADS)

    Petrov, M.; Katranchev, B.; Rafailov, P. M.

    2017-01-01

    The dimerization of aromatic carboxylic acids, is the base of the structure formation of hydrogen bonded in dimers liquid crystals (HBDLCs), that exhibit non-conventional mesomorphism. The structural units of these LCs are amphiphilic-type molecules, which after suitable functionalization, induce supramolecular complexes, nanocomposites based on HBDLCs. The liquid crystalline character of the nanocomposites strongly dependent on intermolecular hydrogen bonds between symmetric, where the H-donors and H acceptors are contained in similar and non-symmetric HBDLCs, where the H-donors and H acceptors are contained in unlike molecules. The strength and non-covalent character of the hydrogen bonds provides both sufficient HBDLCs complex stability and bonding flexibility with a possibility to design and drive the supramolecular geometry. We investigated a series of nanocomposites produced by mixture of HBDLC (p-n-alkyloxybenzoic acid - nOBA), serving as matrices, with non-mesogenic (single walled carbon nanotubes - SWCNTs, hydroxypiridine – HOPY) and mesogenic (cholesteryl benzoate - ChB) nano-particles in various shapes and sizes. A set of new chiral ferroelectric phases were found in the nanocomposites, otherwise do not appearing in the pristine achiral HBDLCs materials. A molecular model of an unique low-temperature ferroelectric smectic phase C based on the molecular dimer ring symmetry reduction (bent dimer formation) towards to the lowest triclinic one is presented for both symmetric and nonsymmetric supramolecular liquid crystal complexes.

  1. Anion-controlled dimer distance induced unique solid-state fluorescence of cyano substituted styrene pyridinium

    NASA Astrophysics Data System (ADS)

    Zhang, Gaobin; Zhang, Xuanjun; Kong, Lin; Wang, Shichao; Tian, Yupeng; Tao, Xutang; Yang, Jiaxiang

    2016-11-01

    Molecular packing arrangements play a key role in dominating the photophysical properties of luminophores in aggregated state but fine control of the molecular packing is a great challenge. This article describes a unique cyano substituted styrene pyridinium with interesting solid-state fluorescence that can be finely tuned by simple change of counteranions. The dilute solutions of the organic salts (PyCl, PyNO3, PyOTs and PyPh4B) exhibit very weak fluorescence. The crystals of the organic salts (PyCl, PyNO3, and PyOTs) show much enhanced fluorescence compared with their dilute solutions. It is interesting that the emissions changed from bluish-green to deep-blue and fluorescence quantum yields increase from 2.5% to 13.1% with the increasing of steric hindrance of the anions from chloridion, nitrate, to p-toluenesulfonate. Crystal and DFT studies reveal that the enhanced fluorescence is ascribed to the formation of dimers and bigger anions induce larger molecular separation in dimers. Tetraphenylboron anion with very large steric hindrance impedes the formation of dimers and thus results in non-fluorescent salt (PyPh4B). Meanwhile, this unique dimeric packing endows the crystal of PyNO3 with anisotropic fluorescence.

  2. 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.

  3. N-site de-methylation in pyrimidine bases as studied by low energy electrons and ab initio calculations.

    PubMed

    Almeida, D; Kinzel, D; Ferreira da Silva, F; Puschnigg, B; Gschliesser, D; Scheier, P; Denifl, S; García, G; González, L; Limão-Vieira, P

    2013-07-21

    Electron transfer and dissociative electron attachment to 3-methyluracil (3meU) and 1-methylthymine (1meT) yielding anion formation have been investigated in atom-molecule collision and electron attachment experiments, respectively. The former has been studied in the collision energy range 14-100 eV whereas the latter in the 0-15 eV incident electron energy range. In the present studies, emphasis is given to the reaction channel resulting in the loss of the methyl group from the N-sites with the extra charge located on the pyrimidine ring. This particular reaction channel has neither been approached in the context of dissociative electron attachment nor in atom-molecule collisions yet. Quantum chemical calculations have been performed in order to provide some insight into the dissociation mechanism involved along the N-CH3 bond reaction coordinate. The calculations provide support to the threshold value derived from the electron transfer measurements, allowing for a better understanding of the role of the potassium cation as a stabilising agent in the collision complex. The present comparative study gives insight into the dynamics of the decaying transient anion and more precisely into the competition between dissociation and auto-detachment.

  4. Targeting DNA with "light-up" pyrimidine triple-helical forming oligonucleotides conjugated to stabilizing fluorophores (LU-TFOs).

    PubMed

    Renard, Brice-Loïc; Lartia, Rémy; Asseline, Ulysse

    2008-12-07

    The synthesis of triple-helix-forming oligonucleotides (TFOs) linked to a series of cyanine monomethines has been performed. Eight cyanines including one thiocyanine, four thiazole orange analogues, and three quinocyanines were attached to the 5'-end of 10-mer pyrimidine TFOs. The binding properties of these modified TFOs with their double-stranded DNA target were studied by absorption and steady-state fluorescence spectroscopy. The stability of the triplex structures depended on the cyanine structure and the linker size used to connect both entities. The most efficient cyanines able to stabilize the triplex structures, when attached at the 5'-end of the TFO, have been incorporated at both ends and provided triplex structures with increased stability. Fluorescence studies have shown that for the TFOs involving one cyanine, an important intensity increase (up to 37-fold) in the fluorescent signal was observed upon their hybridization with the double-stranded target, proving hybridization. The conjugates involving thiazole orange attached by the benzothiazole ring provided the most balanced properties in terms of triplex stabilization, fluorescence intensity and fluorescence enhancement upon hybridization with the double-stranded target. In order to test the influence of different parameters such as the TFO sequence and length, thiazole orange was used to label 17-mer TFOs. Hybridizations of these TFOs with different duplexes, designed to study the influence of mismatches at both internal and terminal positions on the triplex structures, confirmed the possibility of triplex formation without loss of specificity together with a strong fluorescence enhancement (up to 13-fold).

  5. Thermochemical properties and contribution groups for ketene dimers and related structures from theoretical calculations.

    PubMed

    Morales, Giovanni; Martínez, Ramiro

    2009-07-30

    This research's main goals were to analyze ketene dimers' relative stability and expand group additivity value (GAV) methodology for estimating the thermochemical properties of high-weight ketene polymers (up to tetramers). The CBS-Q multilevel procedure and statistical thermodynamics were used for calculating the thermochemical properties of 20 cyclic structures, such as diketenes, cyclobutane-1,3-diones, cyclobut-2-enones and pyran-4-ones, as well as 57 acyclic base compounds organized into five groups. According to theoretical heat of formation predictions, diketene was found to be thermodynamically favored over cyclobutane-1,3-dione and its enol-tautomeric form (3-hydroxycyclobut-2-enone). This result did not agree with old combustion experiments. 3-Hydroxycyclobut-2-enone was found to be the least stable dimer and its reported experimental detection in solution may have been due to solvent effects. Substituted diketenes had lower stability than substituted cyclobutane-1,3-diones with an increased number of methyl substituents, suggesting that cyclobutane-1,3-dione type dimers are the major products because of thermodynamic control of alkylketene dimerization. Missing GAVs for the ketene dimers and related structures were calculated through linear regression on the 57 acyclic base compounds. Corrections for non next neighbor interactions (such as gauche, eclipses, and internal hydrogen bond) were needed for obtaining a highly accurate and precise regression model. To the best of our knowledge, the hydrogen bond correction for GAV methodology is the first reported in the literature; this correction was correlated to MP2/6-31Gdagger and HF/6-31Gdagger derived geometries to facilitate its application. GAVs assessed by the linear regression model were able to reproduce acyclic compounds' theoretical thermochemical properties and experimental heat of formation for acetylacetone. Ring formation and substituent position corrections were calculated by consecutively

  6. Synthesis, and Fluorescence Properties of Coumarin and Benzocoumarin Derivatives Conjugated Pyrimidine Scaffolds for Biological Imaging Applications.

    PubMed

    Al-Masoudi, Najim A; Al-Salihi, Niran J; Marich, Yossra A; Markus, Timo

    2015-11-01

    Series of coumarin and 5,6-benzomcomarin substituted pyrimidine derivatives 11-15 and 22-25 were synthesized, aiming to develop new imaging fluorescent agents. Analogously, treatment of 4-chloropyrimidine analog 16 with coumarin 3-carbohyrazide 5 under MWI condition followed by boiling with NH4OAc in HOAc furnished coumarin-1,2,4-triazolo-pyrimidine analog 18. The fluorescence property was investigated spectrophotometrically in MeOH with Rhodamine 6G as standard dye. All the compounds showed emission in the region between 331 and 495 nm. The quantum yield of all the compounds were found to be weak, except methyl benzocoumarin 3-carboxylate 22 which showed (ΦF = 0.98) in comparison to Rhodamine 6G as standard (ΦF = 0.95).

  7. Direct Isolation of Purines and Pyrimidines from Nucleic Acids Using Sublimation

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Schubert, Michael; Bada, Jeffrey L.

    2003-01-01

    A sublimation technique was developed to isolate purines and pyrimidines directly from lambda-deoxyribonucleic acid (lambda-DNA) and Escherichia coli cells. The sublimation of adenine, cytosine, guanine, and thymine from lambda-DNA was tested under reduced pressure (approx. 0.5 Torr) at temperatures of >150 C. With the exception of guanine, approximately 60 -75% of each base was sublimed directly from the lambda-DNA and recovered on a coldfinger of the sublimation apparatus after heating to 450 C. Several nucleobases including adenine, cytosine, thymine, and uracil were also recovered from E. coli bacteria after heating the cells to the same temperature, although some thermal decomposition of the bases also occurred. These results demonstrate the feasibility of using sublimation to isolate purines and pyrimidines from native E. coli DNA and RNA without any chemical treatment of the cells.

  8. Biochemical, Mutational and In Silico Structural Evidence for a Functional Dimeric Form of the Ornithine Decarboxylase from Entamoeba histolytica

    PubMed Central

    Preeti; Tapas, Satya; Kumar, Pravindra; Madhubala, Rentala; Tomar, Shailly

    2012-01-01

    Background Entamoeba histolytica is responsible for causing amoebiasis. Polyamine biosynthesis pathway enzymes are potential drug targets in parasitic protozoan diseases. The first and rate-limiting step of this pathway is catalyzed by ornithine decarboxylase (ODC). ODC enzyme functions as an obligate dimer. However, partially purified ODC from E. histolytica (EhODC) is reported to exist in a pentameric state. Methodology and Results In present study, the oligomeric state of EhODC was re-investigated. The enzyme was over-expressed in Escherichia coli and purified. Pure protein was used for determination of secondary structure content using circular dichroism spectroscopy. The percentages of α-helix, β-sheets and random coils in EhODC were estimated to be 39%, 25% and 36% respectively. Size-exclusion chromatography and mass spectrophotometry analysis revealed that EhODC enzyme exists in dimeric form. Further, computational model of EhODC dimer was generated. The homodimer contains two separate active sites at the dimer interface with Lys57 and Cys334 residues of opposite monomers contributing to each active site. Molecular dynamic simulations were performed and the dimeric structure was found to be very stable with RMSD value ∼0.327 nm. To gain insight into the functional role, the interface residues critical for dimerization and active site formation were identified and mutated. Mutation of Lys57Ala or Cys334Ala completely abolished enzyme activity. Interestingly, partial restoration of the enzyme activity was observed when inactive Lys57Ala and Cys334Ala mutants were mixed confirming that the dimer is the active form. Furthermore, Gly361Tyr and Lys157Ala mutations at the dimer interface were found to abolish the enzyme activity and destabilize the dimer. Conclusion To our knowledge, this is the first report which demonstrates that EhODC is functional in the dimeric form. These findings and availability of 3D structure model of EhODC dimer opens up

  9. Magnetic anisotropy of heteronuclear dimers in the gas phase and supported on graphene: relativistic density-functional calculations.

    PubMed

    Błoński, Piotr; Hafner, Jürgen

    2014-04-09

    the relativistic electronic structure of free and supported dimers and it is demonstrated that the existence of a partially occupied quasi-degenerate state at the Fermi level favors the formation of a large magnetic anisotropy.

  10. Quenching of highly vibrationally excited pyrimidine by collisions with CO2.

    PubMed

    Johnson, Jeremy A; Duffin, Andrew M; Hom, Brian J; Jackson, Karl E; Sevy, Eric T

    2008-02-07

    Relaxation of highly vibrationally excited pyrimidine (C(4)N(2)H(4)) by collisions with carbon dioxide has been investigated using diode laser transient absorption spectroscopy. Vibrationally hot pyrimidine (E(')=40 635 cm(-1)) was prepared by 248-nm excimer laser excitation, followed by rapid radiationless relaxation to the ground electronic state. The nascent rotational population distribution (J=58-80) of the 00(0)0 ground state of CO(2) resulting from collisions with hot pyrimidine was probed at short times following the excimer laser pulse. Doppler spectroscopy was used to measure the CO(2) recoil velocity distribution for J=58-80 of the 00(0)0 state. Rate constants and probabilities for collisions populating these CO(2) rotational states were determined. The measured energy transfer probabilities, indexed by final bath state, were resorted as a function of DeltaE to create the energy transfer distribution function, P(E,E(')), from E(')-E approximately 1300-7000 cm(-1). P(E,E(')) is fitted to a single exponential and a biexponential function to determine the average energy transferred in a single collision between pyrimidine and CO(2) and parameters that can be compared to previously studied systems using this technique, pyrazineCO(2), C(6)F(6)CO(2), and methylpyrazineCO(2). P(E,E(')) parameters for these four systems are also compared to various molecular properties of the donor molecules. Finally, P(E,E(')) is analyzed in the context of two models, one which suggests that the shape of P(E,E(')) is primarily determined by the low-frequency out-of-plane donor vibrational modes and one which suggests that the shape of P(E,E(')) can be determined by how the donor molecule final density of states changes with DeltaE.

  11. Dichloridobis[2-methyl-sulfanyl-4-(pyridin-2-yl)pyrimidine-κN,N]cobalt(II).

    PubMed

    Yang, Wen-Na

    2011-09-01

    The asymmetric unit of the title compound, [CoCl(2)(C(10)H(9)N(3)S)(2)], contains one half-mol-ecule with the Co(II) atom situtated on a twofold rotational axis. The Co(II) atom, in an octa-hedral enviroment, is coordinated by four N atoms from two 2-methyl-sulfanyl-4-(pyridin-2-yl)pyrimidine ligands and two Cl atoms.

  12. Computational Study of Monosubstituted Azo(tetrazolepentazolium)-Based Ionic Dimers.

    PubMed

    Pimienta, Ian S O

    2015-06-04

    The structures of monosubstituted azo(tetrazolepentazolium) cations (N11CHR(+)), oxygen-rich anions such as N(NO2)2(-), NO3(-), and ClO4(-), and the corresponding ion pairs are investigated using ab initio quantum chemistry calculations. The substituents (R) used are H, F, CH3, CN, NH2, OH, OCH3, N3, NF2, and C2H3. The stability of the protonated cation is explored by examining the decomposition pathway of the protonated cation (N11CH2(+)) to yield molecular N2 fragments. The heats of formation of these cations, which are based on isodesmic (bond type conserving) reactions, are dependent on the nature of the substituents. Ionic dimer structures are obtained, but side reactions including proton transfer, binding, and hydrogen bonding are observed in the gas phase. Implicit solvation studies are performed to determine the solution properties of the ion pairs.

  13. Dispersion Energy Enforced Dimerization of a Cyclic Disilylated Plumbylene

    PubMed Central

    2012-01-01

    By reaction of 1,4-dipotassio-1,1,4,4-tetrakis(trimethylsilyl)tetramethyltetrasilane with PbBr2 in the presence of triethylphosphine a base adduct of a cyclic disilylated plumbylene could be obtained. Phosphine abstraction with B(C6F5)3 led to formation of a base-free plumbylene dimer, which features an unexpected single donor–acceptor PbPb bond. The results of density functional computations at the M06-2X and B3LYP level of theory indicate that the dominating interactions which hold the plumbylene subunits together and which define its actual molecular structure are attracting van der Waals forces between the two large and polarizable plumbylene subunits. PMID:22455750

  14. A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization

    NASA Astrophysics Data System (ADS)

    Xu, Jianfeng; Tsanakopoulou, Maria; Magnani, Christopher J.; Szabla, Rafał; Šponer, Judit E.; Šponer, Jiří; Góra, Robert W.; Sutherland, John D.

    2016-11-01

    Previous research has identified ribose aminooxazoline as a potential intermediate in the prebiotic synthesis of the pyrimidine nucleotides with remarkable properties. It crystallizes spontaneously from reaction mixtures, with an enhanced enantiomeric excess if initially enantioenriched, which suggests that reservoirs of this compound might have accumulated on the early Earth in an optically pure form. Ribose aminooxazoline can be converted efficiently into α-ribocytidine by way of 2,2‧-anhydroribocytidine, although anomerization to β-ribocytidine by ultraviolet irradiation is extremely inefficient. Our previous work demonstrated the synthesis of pyrimidine β-ribonucleotides, but at the cost of ignoring ribose aminooxazoline, using arabinose aminooxazoline instead. Here we describe a long-sought route through ribose aminooxazoline to the pyrimidine β-ribonucleosides and their phosphate derivatives that involves an extraordinarily efficient photoanomerization of α-2-thioribocytidine. In addition to the canonical nucleosides, our synthesis accesses β-2-thioribouridine, a modified nucleoside found in transfer RNA that enables both faster and more-accurate nucleic acid template-copying chemistry.

  15. Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

    PubMed

    Phan, Andy; Mailey, Katherine; Sakai, Jessica; Gu, Xiaobo; Schroeder, Susan J

    2017-02-17

    Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased towards small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with more than 6 nucleotides that occur frequently in viral RNA. This paper presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Protonated cytosine and uracil base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with more than 6 nucleotides are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2x2 have been measured (Mathews 2004). These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites.

  16. A human NDP-kinase B specifically binds single-stranded poly-pyrimidine sequences.

    PubMed Central

    Hildebrandt, M; Lacombe, M L; Mesnildrey, S; Véron, M

    1995-01-01

    Recently, a DNA binding protein 'PUF' was purified that binds to a poly-pyrimidine rich element in the human c-myc promoter. Cloning of the corresponding gene surprisingly identified this putative transcription factor as isoform B of the enzyme nucleoside diphosphate kinase (NDPK-B) [Postel et al. (1993) Science, 261, 478-480], the product of the potential metastasis suppressor gene nm23-H2. Using different recombinant NDP kinases, we demonstrate by electrophoretic mobility shift analysis (EMSA) that the NDP kinase DNA binding properties are predominantly observed with human isoform B. Unlike typical DNA binding proteins that are involved in transcriptional regulation, binding occurs to single-stranded DNA rather than to a double-stranded oligonucleotide. As a consequence, complexes of single-stranded DNA and NDPK-B are generated from double-stranded oligonucleotide hybrids in an ATP independent manner. In addition to the c-myc element, NDPK-B is binding in vitro to a variety of poly-pyrimidine rich sequences including dC or dT homo-oligomers, (CT)n dinucleotide repeats, the initiator region of the Adenovirus major late promoter and even poly-pyrimidine rich RNAs. The possible consequences of these findings in understanding the multiple roles of NDP kinase are discussed. Images PMID:7479028

  17. Absolute cross sections for electronic excitation of pyrimidine by electron impact

    SciTech Connect

    Regeta, Khrystyna; Allan, Michael; Mašín, Zdeněk; Gorfinkiel, Jimena D.

    2016-01-14

    We measured differential cross sections for electron-impact electronic excitation of pyrimidine, both as a function of electron energy up to 18 eV, and of scattering angle up to 180°. The emphasis of the present work is on recording detailed excitation functions revealing resonances in the excitation process. The differential cross sections were summed to obtain integral cross sections. These are compared to results of R-matrix calculations, which successfully reproduce both the magnitude of the cross section and the major resonant features. Comparison of the experiment to the calculated contributions of different symmetries to the integral cross section permitted assignment of several features to specific core-excited resonances. Comparison of the resonant structure of pyrimidine with that of benzene revealed pronounced similarities and thus a dominant role of π–π{sup ∗} excited states and resonances. Electron energy loss spectra were measured as a preparation for the cross section measurements and vibrational structure was observed for some of the triplet states. A detailed analysis of the electronic excited states of pyrimidine is also presented.

  18. Isolation of Purines and Pyrimidines from the Murchison Meteorite Using Sublimation

    NASA Technical Reports Server (NTRS)

    Glavin, D. P.; Bada, J. L.

    2004-01-01

    The origin of life on Earth, and possibly on other planets such as Mars, would have required the presence of liquid water and a continuous supply of prebiotic organic compounds. The exogenous delivery of organic matter by asteroids, comets, and carbonaceous meteorites could have contributed to the early Earth s prebiotic inventory by seeding the planet with biologically important organic compounds. A wide variety of prebiotic organic compounds have previously been detected in the Murchison CM type carbonaceous chondrite including amino acids, purines and pyrimidines. These compounds dominate terrestrial biochemistry and are integral components of proteins, DNA and RNA. Several purines including adenine, guanine, hypoxanthine, and xanthine, as well as the pyrimidine uracil, have previously been detected in water or formic acid extracts of Murchison using ion-exclusion chromatography and ultraviolet spectroscopy. However, even after purification of these extracts, the accurate identification and quantification of nucleobases is difficult due to interfering UV absorbing compounds. In order to reduce these effects, we have developed an extraction technique using sublimation to isolate purines and pyrimidines from other non-volatile organic compounds in Murchison acid extracts.

  19. Respiratory syncytial virus infection in macaques is not suppressed by intranasal sprays of pyrimidine biosynthesis inhibitors.

    PubMed

    Grandin, Clément; Hourani, Marianne-Lucas; Janin, Yves L; Dauzonne, Daniel; Munier-Lehmann, Hélène; Paturet, Adeline; Taborik, Fabrice; Vabret, Astrid; Contamin, Hugues; Tangy, Frédéric; Vidalain, Pierre-Olivier

    2016-01-01

    There is imperious need for efficient therapies against ubiquitous and life-threatening respiratory viruses, foremost among them being the human respiratory syncytial virus (hRSV). Several research groups who performed functional screens for broad-spectrum antivirals identified compounds targeting the de novo pyrimidine biosynthesis pathway. Despite their strong antiviral activity in vitro, whether such antimetabolites are effective in vivo remains highly controversial. Here, we evaluated two potent pyrimidine biosynthesis inhibitors developed in our laboratory, IPPA17-A04 and GAC50, in a model of mild hRSV-infection in cynomolgus macaques. In this model, hRSV replication is restricted to the epithelium of the upper respiratory tract, and is compatible with a topical treatment by intranasal sprays. The local administration of palivizumab, a neutralizing anti-hRSV antibody used in clinics, significantly reduced virus replication. In contrast, pyrimidine biosynthesis inhibitors did not show any inhibitory effect on hRSV growth when delivered topically as experimented in our model. Our results should help to better define the potential applications of this class of antimetabolites in the treatment of viral infections.

  20. Differential cross sections for electron-impact excitation of the electronic states of pyrimidine

    NASA Astrophysics Data System (ADS)

    Brunger, Michael; Jones, Darryl; Bellm, Susan

    2012-06-01

    Pyrimidine (C4N2H4) is an important molecule, as it forms the basis of larger biomolecules, such as the DNA bases thymine, cytosine and uracil. There is a pressing demand for low-energy electron scattering data from such biological analogs in order to model radiation induced damage [1]. We therefore present the first measurements for absolute differential cross section data for low-energy electron-impact excitation of the electronic states of pyrimidine. The present measurements were performed using a crossed-beam apparatus [2] for incident electron energies ranging between 15 to 50eV while covering a 10 to 90^o angular range. Here the absolute scale has been determined through a normalisation to the recently measured elastic scattering differential cross section data for pyrimidine [3]. [1] F. Ferreira da Silva, D. Almeida, G. Martins, A. R. Milosavljevic, B. P. Marinkovic, S. V. Hoffmann, N. J. Mason, Y. Nunes, G. Garcia and P. Limao-Vieira, Phys Chem Chem Phys 12, 6717 (2010). [2] M. J. Brunger and P. J. O. Teubner, Phys Rev A 41, 1413 (1990). [3] P. Palihawadana, J. Sullivan, M. Brunger, C. Winstead, V. McKoy, G. Garcia, F. Blanco and S. Buckman, Phys Rev A 84, 062702 (2011).

  1. Intermediate energy cross sections for electron-impact vibrational-excitation of pyrimidine

    SciTech Connect

    Jones, D. B.; Ellis-Gibbings, L.; García, G.; Nixon, K. L.; Lopes, M. C. A.; Brunger, M. J.

    2015-09-07

    We report differential cross sections (DCSs) and integral cross sections (ICSs) for electron-impact vibrational-excitation of pyrimidine, at incident electron energies in the range 15–50 eV. The scattered electron angular range for the DCS measurements was 15°–90°. The measurements at the DCS-level are the first to be reported for vibrational-excitation in pyrimidine via electron impact, while for the ICS we extend the results from the only previous condensed-phase study [P. L. Levesque, M. Michaud, and L. Sanche, J. Chem. Phys. 122, 094701 (2005)], for electron energies ⩽12 eV, to higher energies. Interestingly, the trend in the magnitude of the lower energy condensed-phase ICSs is much smaller when compared to the corresponding gas phase results. As there is no evidence for the existence of any shape-resonances, in the available pyrimidine total cross sections [Baek et al., Phys. Rev. A 88, 032702 (2013); Fuss et al., ibid. 88, 042702 (2013)], between 10 and 20 eV, this mismatch in absolute magnitude between the condensed-phase and gas-phase ICSs might be indicative for collective-behaviour effects in the condensed-phase results.

  2. Fluorescent property of 3-hydroxymethyl imidazo[1,2-a]pyridine and pyrimidine derivatives

    PubMed Central

    2012-01-01

    Background Imidazo[1,2-a]pyridines and pyrimidines are important organic fluorophores which have been investigated as biomarkers and photochemical sensors. The effect on the luminescent property by substituents in the heterocycle and phenyl rings, have been studied as well. In this investigation, series of 3-hydroxymethyl imidazo[1,2-a]pyridines and pyrimidines were synthesized and evaluated in relation to fluorescence emission, based upon the hypothesis that the hydroxymethyl group may act as an enhancer of fluorescence intensity. Results Compounds of both series emitted light in organic solvents dilutions as well as in acidic and alkaline media. Quantitative fluorescence spectroscopy determined that both fused heterocycles fluoresced more intensely than the parent unsubstituted imidazo[1,2-a]azine fluorophore. In particular, 3-hydroxymethyl imidazo[1,2-a]pyridines fluoresced more intensely than 3-hydroxymethyl imidazo[1,2-a]pyrimidines, the latter emitting blue light at longer wavelengths, whereas the former emitted purple light. Conclusion It was concluded that in most cases the hydroxymethyl moiety did act as an enhancer of the fluorescence intensity, however, a comparison made with the fluorescence emitted by 2-aryl imidazo[1,2-a]azines revealed that in some cases the hydroxymethyl substituent decreased the fluorescence intensity. PMID:22871219

  3. Improvement of pyrazolo[3,4-d]pyrimidines pharmacokinetic properties: nanosystem approaches for drug delivery

    PubMed Central

    Vignaroli, Giulia; Calandro, Pierpaolo; Zamperini, Claudio; Coniglio, Federica; Iovenitti, Giulia; Tavanti, Matteo; Colecchia, David; Dreassi, Elena; Valoti, Massimo; Schenone, Silvia; Chiariello, Mario; Botta, Maurizio

    2016-01-01

    Pyrazolo[3,4-d]pyrimidines are a class of compounds with a good activity against several cancer cell lines. Despite the promising anticancer activity, these molecules showed a poor aqueous solubility. This issue could threat the future development of pyrazolo[3,4-d]pyrimidines as clinical drug candidates. With the aim of improving their solubility profile and consequently their pharmacokinetic properties, we have chosen four compounds (1–4) on the base of their anti-neuroblastoma activity and we have developed albumin nanoparticles and liposomes for the selected candidates. Albumin nanoparticles and liposomes were prepared and characterized regarding size and ζ-potential distribution, polidispersity index, entrapment efficiency and activity against SH-SY5Y human neuroblastoma cell line. The most promising nanosystem, namely LP-2, was chosen to perform further studies: confocal microscopy, stability and drug release in physiological conditions, and biodistribution. Altogether, the obtained data strongly indicate that the encapsulation of pyrazolo[3,4-d]pyrimidines in liposomes represent an effective method to overcome the poor water solubility. PMID:26898318

  4. Purine and pyrimidine metabolism: Convergent evidence on chronic antidepressant treatment response in mice and humans

    PubMed Central

    Park, Dong Ik; Dournes, Carine; Sillaber, Inge; Uhr, Manfred; Asara, John M.; Gassen, Nils C.; Rein, Theo; Ising, Marcus; Webhofer, Christian; Filiou, Michaela D.; Müller, Marianne B.; Turck, Christoph W.

    2016-01-01

    Selective Serotonin Reuptake Inhibitors (SSRIs) are commonly used drugs for the treatment of psychiatric diseases including major depressive disorder (MDD). For unknown reasons a substantial number of patients do not show any improvement during or after SSRI treatment. We treated DBA/2J mice for 28 days with paroxetine and assessed their behavioral response with the forced swim test (FST). Paroxetine-treated long-time floating (PLF) and paroxetine-treated short-time floating (PSF) groups were stratified as proxies for drug non-responder and responder mice, respectively. Proteomics and metabolomics profiles of PLF and PSF groups were acquired for the hippocampus and plasma to identify molecular pathways and biosignatures that stratify paroxetine-treated mouse sub-groups. The critical role of purine and pyrimidine metabolisms for chronic paroxetine treatment response in the mouse was further corroborated by pathway protein expression differences in both mice and patients that underwent chronic antidepressant treatment. The integrated -omics data indicate purine and pyrimidine metabolism pathway activity differences between PLF and PSF mice. Furthermore, the pathway protein levels in peripheral specimens strongly correlated with the antidepressant treatment response in patients. Our results suggest that chronic SSRI treatment differentially affects purine and pyrimidine metabolisms, which may explain the heterogeneous antidepressant treatment response and represents a potential biosignature. PMID:27731396

  5. Steroidal pyrimidines: Synthesis, characterization, molecular docking studies with DNA and in vitro cytotoxicity

    NASA Astrophysics Data System (ADS)

    Shamsuzzaman; Dar, Ayaz Mahmood; Yaseen, Zahid; Alam, Khursheed; Hussain, Altaf; Gatoo, Manzoor Ahmad

    2013-08-01

    A series of new steroid pyrimidines (7-9) were synthesized by reacting steroidal thiosemicarbazones (4-6) with diethyl malonate. The new compounds were characterized by IR, 1H NMR, 13C NMR, MS and analytical data. The interaction studies of compounds (7-9) with DNA were carried out by employing gel electrophoresis, UV-vis and fluorescence spectroscopy. The acting force between the compounds (7-9) and DNA was mainly hydrophobic while the other interactions like van der Waals, hydrogen bonding cannot be ruled out. The gel electrophoresis pattern also demonstrated that the compound 7 alone or in presence of Cu (II) causes the nicking of supercoiled pBR322 and it seems to follow the mechanistic pathway involving generation of hydroxyl radicals that are responsible for initiating DNA strand scission. The docking study of compounds (7-9) suggested that the intercalation of compounds in between the nucleotide base pairs might be due to the presence of pyrimidine moiety in steroid molecule. MTT assay was carried out to check the toxicity of new compounds (7-9) against the different human cancer as well as non-cancer cell lines A545, MCF-7, HeLa, HL-60, SW480, HepG2, HT-29, A549, 184B5, MCF10A, NL-20, HPC and HPLF. Apoptotic degradation of DNA in presence of steroidal pyrimidines (7-9) was analyzed by agarose gel electrophoresis and visualized by ethidium bromide staining (comet assay).

  6. Vibrational spectroscopic studies and Natural Bond Orbital analysis of 4,6-dichloro-2-(methylthio)pyrimidine based on density functional theory.

    PubMed

    Balachandran, V; Lakshmi, A; Janaki, A

    2011-10-15

    The FT-IR and FT-Raman spectra of 4,6-dichloro-2-(methylthio)pyrimidine (DMP) have been recorded and analyzed. The optimized geometry, intramolecular hydrogen bonding, and harmonic vibrational wave numbers of DMP have been investigated with the help of B3LYP density functional theory (DFT) method supplemented with 6-31G** basis set. The infrared and Raman spectra were predicted theoretically from the calculated intensities. Natural Bond Orbital (NBO) analysis of DMP has been performed to indicate the presence of intramolecular C-H⋯Cl hydrogen bonding. The formation of Lewis and non-Lewis orbitals and second-order perturbation energies of DMP have also been reported.

  7. Targeting the cis-dimerization of LINGO-1 with low MW compounds affects its downstream signalling

    PubMed Central

    Cobret, L; De Tauzia, M L; Ferent, J; Traiffort, E; Hénaoui, I; Godin, F; Kellenberger, E; Rognan, D; Pantel, J; Bénédetti, H; Morisset-Lopez, S

    2015-01-01

    Background and Purpose The transmembrane protein LINGO-1 is a negative regulator in the nervous system mainly affecting axonal regeneration, neuronal survival, oligodendrocyte differentiation and myelination. However, the molecular mechanisms regulating its functions are poorly understood. In the present study, we investigated the formation and the role of LINGO-1 cis-dimers in the regulation of its biological activity. Experimental Approach LINGO-1 homodimers were identified in both HEK293 and SH-SY5Y cells using co-immunoprecipitation experiments and BRET saturation analysis. We performed a hypothesis-driven screen for identification of small-molecule protein–protein interaction modulators of LINGO-1 using a BRET-based assay, adapted for screening. The compound identified was further assessed for effects on LINGO-1 downstream signalling pathways using Western blotting analysis and AlphaScreen technology. Key Results LINGO-1 was present as homodimers in primary neuronal cultures. LINGO-1 interacted homotypically in cis-orientation and LINGO-1 cis-dimers were formed early during LINGO-1 biosynthesis. A BRET-based assay allowed us to identify phenoxybenzamine as the first conformational modulator of LINGO-1 dimers. In HEK-293 cells, phenoxybenzamine was a positive modulator of LINGO-1 function, increasing the LINGO-1-mediated inhibition of EGF receptor signalling and Erk phosphorylation. Conclusions and Implications Our data suggest that LINGO-1 forms constitutive cis-dimers at the plasma membrane and that low MW compounds affecting the conformational state of these dimers can regulate LINGO-1 downstream signalling pathways. We propose that targeting the LINGO-1 dimerization interface opens a new pharmacological approach to the modulation of its function and provides a new strategy for drug discovery. PMID:25257685

  8. Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei.

    PubMed

    Campos-Acevedo, Adam A; Sotelo-Mundo, Rogerio R; Pérez, Javier; Rudiño-Piñera, Enrique

    2017-04-01

    The quaternary structure of the redox protein thioredoxin (Trx) has been debated. For bacterial Trx, there is no question regarding its monomeric state. In humans and other eukaryotes, the presence of a cysteine residue at the crystallographic symmetry axis points to the relevance of dimer formation in solution and in vivo. Crystallographic data for shrimp thioredoxin (LvTrx) obtained under different redox conditions reveal a dimeric arrangement mediated by a disulfide bond through residue Cys73 and other hydrophobic interactions located in the crystallographic interface, as reported for human Trx. Through the analysis of five mutants located at the crystallographic interface, this study provides structural and biochemical evidence for the existence in solution of monomeric and dimeric populations of wild-type LvTrx and five mutants. Based on the results of biochemical assays, SAXS studies and the crystallographic structures of three of the studied mutants (Cys73Ser, Asp60Ser and Trp31Ala), it is clear that the Cys73 residue is essential for dimerization. However, its mutation to Ser produces an enzyme which has similar redox activity in vitro to the wild type. A putative regulatory function of dimerization is proposed based on structural analysis. Nonetheless, the biological role of LvTrx dimerization needs to be experimentally unveiled. Additionally, the findings of this work reopen the discussion regarding the existence of similar behaviour in human thioredoxin, which shares a Cys at position 73 with LvTrx, a structural feature that is also present in some Trxs from vertebrates and crustaceans.

  9. Calcium-dependent Dimerization of Human Soluble Calcium Activated Nucleotidase: Characterization of the Dimer Interface

    SciTech Connect

    Yang,M.; Horii, K.; Herr, A.; Kirley, T.

    2006-01-01

    Mammals express a protein homologous to soluble nucleotidases used by blood-sucking insects to inhibit host blood clotting. These vertebrate nucleotidases may play a role in protein glycosylation. The activity of this enzyme family is strictly dependent on calcium, which induces a conformational change in the secreted, soluble human nucleotidase. The crystal structure of this human enzyme was recently solved; however, the mechanism of calcium activation and the basis for the calcium-induced changes remain unclear. In this study, using analytical ultracentrifugation and chemical cross-linking, we show that calcium or strontium induce noncovalent dimerization of the soluble human enzyme. The location and nature of the dimer interface was elucidated using a combination of site-directed mutagenesis and chemical cross-linking, coupled with crystallographic analyses. Replacement of Ile{sup 170}, Ser{sup 172}, and Ser{sup 226} with cysteine residues resulted in calcium-dependent, sulfhydryl-specific intermolecular cross-linking, which was not observed after cysteine introduction at other surface locations. Analysis of a super-active mutant, E130Y, revealed that this mutant dimerized more readily than the wild-type enzyme. The crystal structure of the E130Y mutant revealed that the mutated residue is found in the dimer interface. In addition, expression of the full-length nucleotidase revealed that this membrane-bound form can also dimerize and that these dimers are stabilized by spontaneous oxidative cross-linking of Cys{sup 30}, located between the single transmembrane helix and the start of the soluble sequence. Thus, calcium-mediated dimerization may also represent a mechanism for regulation of the activity of this nucleotidase in the physiological setting of the endoplasmic reticulum or Golgi.

  10. Excitonic interaction in the fluorene dimer

    NASA Astrophysics Data System (ADS)

    Wessel, John; Beck, Steven; Highstrete, Clark

    1994-12-01

    The fluorene van der Waals dimer exhibits