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1.
2.
Translesion DNA polymerases are more efficient at bypass of many DNA adducts than replicative polymerases. Previous work with the translesion polymerase Sulfolobus solfataricus Dpo4 showed a decrease in catalytic efficiency during bypass of bulky N2-alkyl guanine (G) adducts with N2-isobutylG showing the largest effect, decreasing ∼ 120-fold relative to unmodified deoxyguanosine (Zhang, H., Eoff, R. L., Egli, M., Guengerich, F. P. Versatility of Y-family Sulfolobus solfataricus DNA polymerase Dpo4 in translation synthesis past bulky N2-alkylguanine adducts. J. Biol. Chem. 2009; 284: 3563-3576). The effect of adduct size on individual catalytic steps has not been easy to decipher because of the difficulty of distinguishing early noncovalent steps from phosphodiester bond formation. We developed a mutant with a single Trp (T239W) to monitor fluorescence changes associated with a conformational change that occurs after binding a correct 2′-deoxyribonucleoside triphosphate (Beckman, J. W., Wang, Q., Guengerich, F. P. Kinetic analysis of nucleotide insertion by a Y-family DNA polymerase reveals conformational change both prior to and following phosphodiester bond formation as detected by tryptophan fluorescence. J. Biol. Chem. 2008; 283: 36711-36723) and, in the present work, utilized this approach to monitor insertion opposite N2-alkylG-modified oligonucleotides. We estimated maximal rates for the forward conformational step, which coupled with measured rates of product formation yielded rate constants for the conformational step (both directions) during insertion opposite several N2-alkylG adducts. With the smaller N2-alkylG adducts, the conformational rate constants were not changed dramatically (<  3-fold), indicating that the more sensitive steps are phosphodiester bond formation and partitioning into inactive complexes. With the larger adducts (≥  (2-naphthyl)methyl), the absence of fluorescence changes suggests impaired ability to undergo an appropriate conformational change, consistent with previous structural work.  相似文献   

3.
Bulky carcinogen-DNA adducts commonly cause replicative polymerases to stall, leading to a switch to bypass polymerases. We have investigated nucleotide incorporation opposite the major adduct of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in the DinB family polymerase, Dpo4, using molecular modeling and molecular dynamics (MD) simulations. PhIP, the most prevalent heterocyclic aromatic amine formed by cooking of proteinaceous food, is mutagenic in mammalian cells and is implicated in mammary and colon tumors. Our results show that the dG-C8-PhIP adduct can be accommodated in the spacious major groove Dpo4 open pocket, with Dpo4 capable of incorporating dCTP, dTTP or dATP opposite the adduct reasonably well. However, the PhIP ring system on the minor groove side would seriously disturb the active site, regardless of the presence and identity of dNTP. Furthermore, the simulations indicate that dATP and dTTP are better incorporated in the damaged system than in their respective mismatched but unmodified controls, suggesting that the PhIP adduct enhances incorporation of these mismatches. Finally, bulky C8-dG adducts, situated in the major groove, are likely to impede translocation in this polymerase (Rechkoblit et al. (2006), PLoS Biol., 4, e11). However, N2-dG adducts, which can reside on the minor groove side, appear to cause less hindrance when in this position.  相似文献   

4.
DNA bypass polymerases are utilized to transit bulky DNA lesions during replication, but the process frequently causes mutations. The structural origins of mutagenic versus high fidelity replication in lesion bypass is therefore of fundamental interest. As model systems, we investigated the molecular basis of the experimentally observed essentially faithful bypass of the guanine 10S-(+)-trans-anti-benzo[a]pyrene-N2-dG adduct by the Y-family human DNA polymerase κ, and the observed blockage of pol κ produced by the adenine 10S-(+)-trans-anti-benzo[a]pyrene-N2-dA adduct. These lesions are derived from the most tumorigenic metabolite of the ubiquitous cancer-causing pollutant, benzo[a]pyrene. We compare our results for the dG adduct with our earlier studies for the pol κ archaeal homolog Dpo4, which processes the same lesion in an error-prone manner. Molecular modeling, molecular mechanics calculations and molecular dynamics simulations were utilized. Our results show that the pol κ N-clasp is a key structural feature that accounts for the dA adduct blockage and the near-error-free bypass of the dG lesion. Absence of the N-clasp in Dpo4 explains the error-prone processing of the same lesion by this enzyme. Thus, our studies elucidate structure-function relationships in the fidelity of lesion bypass.  相似文献   

5.
Y-family DNA polymerases bypass DNA adducts in a process known as translesion synthesis (TLS). Y-family polymerases make contacts with the minor groove side of the DNA substrate at the nascent base pair. The Y-family polymerases also contact the DNA major groove via the unique little finger domain, but they generally lack contacts with the major groove at the nascent base pair. Escherichia coli DinB efficiently and accurately copies certain minor groove guanosine adducts. In contrast, we previously showed that the presence in the DNA template of the major groove-modified base 1,3-diaza-2-oxophenothiazine (tC) inhibits the activity of E. coli DinB. Even when the DNA primer is extended up to three nucleotides beyond the site of the tC analog, DinB activity is strongly inhibited. These findings prompted us to investigate discrimination against other major groove modifications by DinB and its orthologs. We chose a set of pyrimidines and purines with modifications in the major groove and determined the activity of DinB and several orthologs with these substrates. DinB, human pol kappa, and Sulfolobus solfataricus Dpo4 show differing specificities for the major groove adducts pyrrolo-dC, dP, N6-furfuryl-dA, and etheno-dA. In general, DinB was least efficient for bypass of all of these major groove adducts, whereas Dpo4 was most efficient. DinB activity was essentially completely inhibited by the presence of etheno-dA, while pol kappa activity was strongly inhibited. All three of these DNA polymerases were able to bypass N6-furfuryl-dA with modest efficiency, with DinB being the least efficient. We also determined that the R35A variant of DinB enhances bypass of N6-furfuryl-dA but not etheno-dA. In sum, we find that whereas DinB is specific for bypass of minor groove adducts, it is specifically inhibited by major groove DNA modifications.  相似文献   

6.
3-Nitrobenzanthrone (3-NBA), a nitropolyaromatic hydrocarbon (NitroPAH) pollutant in diesel exhaust, is a potent mutagen and carcinogen. After metabolic activation, the primary metabolites of 3-NBA react with DNA to form dG and dA adducts. One of the three major adducts identified is N-(2′-deoxyguanosin-8-yl)-3-aminobenzanthrone (dGC8-N-ABA). This bulky adduct likely stalls replicative DNA polymerases but can be traversed by lesion bypass polymerases in vivo. Here, we employed running start assays to show that a site-specifically placed dGC8-N-ABA is bypassed in vitro by Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase. However, the nucleotide incorporation rate of Dpo4 was significantly reduced opposite both the lesion and the template position immediately downstream from the lesion site, leading to two strong pause sites. To investigate the kinetic effect of dGC8-N-ABA on polymerization, we utilized pre-steady-state kinetic methods to determine the kinetic parameters for individual nucleotide incorporations upstream, opposite, and downstream from the dGC8-N-ABA lesion. Relative to the replication of the corresponding undamaged DNA template, both nucleotide incorporation efficiency and fidelity of Dpo4 were considerably decreased during dGC8-N-ABA lesion bypass and the subsequent extension step. The lower nucleotide incorporation efficiency caused by the lesion is a result of a significantly reduced dNTP incorporation rate constant and modestly weaker dNTP binding affinity. At both pause sites, nucleotide incorporation followed biphasic kinetics with a fast and a slow phase and their rates varied with nucleotide concentration. In contrast, only the fast phase was observed with undamaged DNA. A kinetic mechanism was proposed for the bypass of dGC8-N-ABA bypass catalyzed by Dpo4.  相似文献   

7.
Silver carboxylates [Ag(O2CR): R=Me, tBu, 2,4,6-Me3C6H2], fluorocarboxlyates [Ag(O2CRf): Rf=C3F7, C6F13, C7F15] and their phosphine adducts [Ag(O2CR)·nPR3′: R=Me, tBu, 2,4,6-Me3C6H2, R′=Me, Ph, n=2; R=Me, R′=Me, n=3; Ag(O2CRf).2PPh3, Rf=C3F7, C6F13, C7F15] have been synthesised, characterised spectroscopically and used as precursors in the aerosol-assisted chemical vapour deposition of silver films. All the phosphine adducts produced films, though in general PMe3 adducts, proved more successful than PPh3 analogues. The fluoro-carboxylates and their PPh3 adducts all generated silver films, though the growth rate for the adducts was lower. All these latter films showed carbon impurities while fluorine was also evident in most cases. The X-ray structure of AgO2CC3F7·2PPh3 is also reported.  相似文献   

8.
The 1,N6-(2-Hydroxy-3-hydroxymethylpropan-1,3-diyl)-2′-deoxyadenosine (1,N6-γ-HMHP-dA) adducts are formed upon bifunctional alkylation of adenine nucleobases in DNA by 1,2,3,4-diepoxybutane, the putative ultimate carcinogenic metabolite of 1,3-butadiene. The presence of a substituted 1,N6-propano group on 1,N6-γ-HMHP-dA is expected to block the Watson-Crick base pairing of the adducted adenine with thymine, potentially contributing to mutagenesis. In this study, the enzymology of replication past site-specific 1,N6-γ-HMHP-dA lesions in the presence of human DNA polymerases (hpols) β, η, κ, and ι and archebacterial polymerase Dpo4 was investigated. Run-on gel analysis with all four dNTPs revealed that hpol η, κ, and Dpo4 were able to copy the modified template. In contrast, hpol ι inserted a single base opposite 1,N6-γ-HMHP-dA but was unable to extend beyond the damaged site, and a complete replication block was observed with hpol β. Single nucleotide incorporation experiments indicated that although hpol η, κ, and Dpo4 incorporated the correct nucleotide (dTMP) opposite the lesion, dGMP and dAMP were inserted with a comparable frequency. HPLC-ESI-MS/MS analysis of primer extension products confirmed the ability of bypass polymerases to insert dTMP, dAMP, or dGMP opposite 1,N6-γ-HMHP-dA and detected large amounts of −1 and −2 deletion products. Taken together, these results indicate that hpol η and κ enzymes bypass 1,N6-γ-HMHP-dA lesions in an error-prone fashion, potentially contributing to A→T and A→C transversions and frameshift mutations observed in cells following treatment with 1,2,3,4-diepoxybutane.  相似文献   

9.
Carbamoyl methyl pyrazole compound of palladium(II) chloride of the type [PdCl2L2] (where L =  C5H7N2CH2CON(C4H9)2, C5H7N2CH2CON(iC4H9)2, C3H3N2CH2CON(C4H9)2, or C3H3N2CH2CON(iC4H9)2) has been synthesized and characterized by IR and 1H NMR spectroscopy. The structure of the compound [PdCl2{C3H3N2CH2CONiBu2}2] has been determined by single crystal X-ray diffraction and shows that the ligands are bonded through the soft pyrazolyl nitrogen atom to the palladium(II) chloride in a trans disposition.  相似文献   

10.
Methylation of the exocyclic amino group of guanine is a relatively common modification in rRNA and tRNA. Single methylation (N2-methylguanosine, m2G) is the second most frequently encountered nucleoside analog in Escherichia coli rRNAs. The most prominent case of dual methylation (N2,N2-dimethylguanosine, m22G) is found in the majority of eukaryotic tRNAs at base pair m22G26:A44. The latter modification eliminates the ability of the N2 function to donate in hydrogen bonds and alters its pairing behavior, notably vis-à-vis C. Perhaps a less obvious consequence of the N2,N2-dimethyl modification is its role in controlling the pairing modes between G and A. We have determined the crystal structure of a 13-mer RNA duplex with central tandem m22G:A pairs. In the structure both pairs adopt an imino-hydrogen bonded, pseudo-Watson–Crick conformation. Thus, the sheared conformation frequently seen in tandem G:A pairs is avoided due to a potential steric clash between an N2-methyl group and the major groove edge of A. Additionally, for a series of G:A containing self-complementary RNAs we investigated how methylation affects competitive hairpin versus duplex formation based on UV melting profile analysis.  相似文献   

11.
《Inorganica chimica acta》1988,141(2):275-279
The crystal structure of Mo2O5[SC6H4NHCH2C5H4N]2(C3N7NO)3 is reported and seen to consist of a single oxo-bridged species with each Mo atom bonded to cis dioxo groups and the nitrogen atoms and thiolate group of the tridentate ligand. 95Mo NMR spectra of this and three related complexes are presented and attempts made to interpret them in terms of their crystal structures.  相似文献   

12.
Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) has been shown to catalyze bypass of 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) in a highly efficient and relatively accurate manner. Crystal structures have revealed a potential role for Arg(332) in stabilizing the anti conformation of the 8-oxoG template base by means of a hydrogen bond or ion-dipole pair, which results in an increased enzymatic efficiency for dCTP insertion and makes formation of a Hoogsteen pair between 8-oxoG and dATP less favorable. Site-directed mutagenesis was used to replace Arg(332) with Ala, Glu, Leu, or His in order to probe the importance of Arg(332) in accurate and efficient bypass of 8-oxoG. The double mutant Ala(331)Ala(332) was also prepared to address the contribution of Arg(331). Transientstate kinetic results suggest that Glu(332) retains fidelity against bypass of 8-oxoG that is similar to wild type Dpo4, a result that was confirmed by tandem mass spectrometric analysis of full-length extension products. A crystal structure of the Dpo4 Glu(332) mutant and 8-oxoG:C pair revealed water-mediated hydrogen bonds between Glu(332) and the O-8 atom of 8-oxoG. The space normally occupied by Arg(332) side chain is empty in the crystal structures of the Ala(332) mutant. Two other crystal structures show that a Hoogsteen base pair is formed between 8-oxoG and A in the active site of both Glu(332) and Ala(332) mutants. These results support the view that a bond between Arg(332) and 8-oxoG plays a role in determining the fidelity and efficiency of Dpo4-catalyzed bypass of the lesion.  相似文献   

13.
《Inorganica chimica acta》1988,141(2):281-288
The crystal structures and 95Mo NMR spectra of two complexes formed between 2-α-hydroxybenzyl- benzimidazole (C6H5·CHOH·C7H5N2=HOBB), as its sodium salt, and MoO2Cl2 are reported. [MoO2- (OBB)2]·EtOH (OBB=deprotonated HOBB) crystallizes in space group P21/n, with a=12.8441(7), b=15.917(3), c=13.314(2) Å, β=97.163(8)° and Z =4. The structure was determined from 3096 observed reflections and refined to a final R value of 0.030. The complex is a six coordinate cis-dioxo species, the 95Mo spectrum of which shows a single sharp peak at 56 ppm in dimethylformamide (DMF). The second complex, [Mo2O5(OBB)2]·EtOH·H2O, crystallizes in space group Pbca, with a=22.482(4), b=16.442(3), c=18.407(3) Å and Z=8. The structure was determined from 2936 observed reflections and refined to a final R value of 0.061. The complex is a binuclear doubly bridged species in which one metal atom is six coordinate while the other is five coordinate. Its 95Mo NMR spectrum in DMF shows a sharp peak at 124 ppm and a second broader much weaker peak at 51 ppm.  相似文献   

14.
Primer extension studies have shown that the Y-family DNA polymerase IV (Dpo4) from Sulfolobus solfataricus P2 can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) [F. Boudsocq, S. Iwai, F. Hanaoka and R. Woodgate (2001) Nucleic Acids Res., 29, 4607–4616]. Our goal is to elucidate on a structural level how AAF-dG can be harbored in the Dpo4 active site opposite an incoming dCTP, using molecular modeling and molecular dynamics simulations, since AAF-dG prefers the syn glycosidic torsion. Both anti and syn conformations of the templating AAF-dG in a Dpo4 ternary complex were investigated. All four dNTPs were studied. We found that an anti glycosidic torsion with C1′-exo deoxyribose conformation allows AAF-dG to be Watson–Crick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting. The AAF is situated in the Dpo4 major groove open pocket with fluorenyl rings 3′- and acetyl 5′-directed along the modified strand, irrespective of dNTP. With AAF-dG syn, the fluorenyl rings are in the small minor groove pocket and the active site region is highly distorted. The anti-AAF-dG conformation with C1′-exo sugar pucker can explain the preferential incorporation of dC by Dpo4. Possible relevance of our new major groove structure for AAF-dG to other polymerases, lesion repair and solution conformations are discussed.  相似文献   

15.
A novel organic-inorganic hybrid pentaborate [Ni(C4H10N2)(C2H8N2)2][B5O6(OH)4]2 has been synthesized by hydrothermal reaction and characterized by FT-IR, Raman spectroscopy, elemental analyses and DTA-TGA. Its crystal structure was determined from single crystal X-ray diffraction. The structure consists of isolated polyborate anion [B5O6(OH)4] and nickel complex cation of [Ni(C4H10N2)(C2H8N2)2]2+, in which the two kinds of ligands come from the decomposition of triethylenetriamine material. The [B5O6(OH)4] units are connected to one another through hydrogen bonds, forming a three-dimensional framework with large channel along the a and c axes, in which the templating [Ni(C4H10N2)(C2H8N2)2]2+ cations are located. The assignments of the record FT-IR absorption frequencies and Raman shifts were given.  相似文献   

16.
N2 fixation by bacteria in associative symbiosis with washed roots of 13 Poaceae and 8 other noncultivated plant species in Finland was demonstrated by the acetylene reduction method. The roots most active in C2H2 reduction were those of Agrostis stolonifera, Calamagrostis lanceolata, Elytrigia repens, and Phalaris arundinacea, which produced 538 to 1,510 nmol of C2H4·g−1 (dry weight)· h−1 when incubated at pO2 0.04 with sucrose (pH 6.5), and 70 to 269 nmol of C2H4· g−1 (dry weight)·h−1 without an added energy source and unbuffered. Azospirillum lipferum, Enterobacter agglomerans, Klebsiella pneumoniae, and a Pseudomonas sp. were the acetylene-reducing organisms isolated. The results demonstrate the presence of N2-fixing organisms in associative symbiosis with plant roots found in a northern climatic region in acidic soils ranging down to pH 4.0.  相似文献   

17.
Two new coordination complexes, Cu(datz)Cl2 and Cu(datz)2Cl2, where datz is 1,5-diaminotetrazole, have been obtained by the reaction of copper(II) chloride with datz. For one of them, Cu(datz)2Cl2, the crystal structure, magnetic susceptibility and thermal properties are reported. For the other compound only spectroscopic and thermal properties are presented. In Cu(datz)2Cl2 the Cu atoms were found to be octahedrally coordinated. Equatorial positions are occupied by two chloride anions and two tetrazole ligands via their N4 donor atoms. Surprisingly, the amino groups at the N1 atom of the tetrazole ring of nearby molecules are in axial positions. Each copper atom is linked with four others through the datz molecules to form 2D polymeric networks parallel to the yz plane. Magnetic properties of Cu(datz)2Cl2 and the data of quantum-chemical calculations of molecular electrostatic potential and energies of hydronation of nitrogen atoms for datz using MP2/6-31G* and B3LYP/6-31G* levels of theory are in agreement with the structural data obtained.  相似文献   

18.
The trifluoro- and tribromoborane adducts of some methyl substituted pyrazines were synthesized and characterized. The 2:1 molecular adducts (e.g., C4H4N2·2BX3) could be isolated with unsubstituted, 2-methyl, 2,3-dimethyl, and 2,6-dimethyl pyrazines. The 1:1 molecular adducts could be isolate only with 2,6-dimethylpyrazine. The adducts were characterized by elemental analyses and infrared spectroscopy. The adducts were studied using 11B-NMR and chemical shift assignments made. The chemical shift assignments and the different reactivities of the two nitrogen sites in 2,6-dimethylpyrazine are discussed.  相似文献   

19.
The interplay between cis-[PtCl2{CNC6H3(2,6-Me2)}2] and Ph2CNH results in the addition of benzophenone imine to one isonitrile ligand to yield the aminoimino-carbene cis-[PtCl2{CNC6H3(2,6-Me2)}{C(NCPh2)N(H)C6H3(2,6-Me2)}]. The formulation of the latter compound is based on the coherent 1H and 13C{1H} NMR and ESI-MS data. This adduct is not stable in solution even at room temperature leading to diamino-carbene cis-[PtCl2{CNC6H3(2,6-Me2)}{C(NH2)N(H)C6H3(2,6-Me2)}], which is, formally, the product of the addition of ammonia to one isonitrile ligand in cis-[PtCl2{CNC6H3(2,6-Me2)}2].  相似文献   

20.
The title compound, [C18H45N6O3Pt3]2(SO4)3·14H2O, belongs to space group C2/c, with a = 25.90(2) Å, b = 14.33(2) Å, c = 23.74(3) Å, β = 122.88(7)°, and Z = 4. The structure was refined on 2899 independent nonzero reflections to an R factor of 0.042. The crystal contains hydroxobridged cyclic [Pt3(OH)3(C6H14N2)3]3+ ions, in which the Pt3O3, ring has a chair conformation. The coordination around each Pt atom is square planar and the cyclohexyl ring lies roughly in the same plane. A large cavity between two trimeric ions related by a twofold axis is filled with one SO42- ion and five water molecules, which participate in an intricate network of hydrogen bonds among themselves and with the hydroxo and amino groups of the complex cation. These units are held together in the crystal by stacking interactions between Pt(OH)2(C6H14N2) “planes” belonging to adjacent molecules, as well as by hydrogen bonds involving the remaining SO42- ions and water molecules. The presence of the cyclohexane ring precludes λ-δ interconversion in the chelate ring and imparts rigidity to the Pt(trans-dach)2+ unit.  相似文献   

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