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1.
A new potentially tetradentate (N4) Schiff base ligand (L), 1,9,12,20-tetraazatetracyclo[18.2.2.02,7.014,19]tetracosa-2(7),3,5,8,12,14(19),15,17-octaene containing a piperazine moiety is described. Macrocyclic Schiff base complexes, [NiL](ClO4)2 (1) and [CuL](ClO4)2 (2) have been obtained from equimolar amounts of ligand (L) with nickel(II) and copper(II) metal ions. While the equilibrium reaction in the presence of cobalt(II) and zinc(II) metal ions with ligand L in a 1:1 molar ratio yielded the open-chain Schiff base complexes, [CoL′](ClO4)2 (3) and [ZnL′](ClO4)2 (4) containing two terminal primary amino groups. The ligand L′ is 1,4-bis(2-(2-aminoethyliminomethyl)phenyl)piperazine. The crystal structures of (1) and (4) have been also determined by X-ray diffraction. It was shown that the Ni(II) is coordinated to the ligand L by two nitrogen atoms of piperazine group and two nitrogen atoms of the imine groups, in a slightly distorted square-planar geometry. Also single crystal X-ray analysis of (4) confirmed a distorted octahedral arrangement in the vicinity of Zn atom with N6 donor set. The spectroscopic characterization of all complexes is consistent with their crystal structures.  相似文献   

2.
3.
In this work a confocal Raman microspectrometer is used to investigate the influence of Na(+) and Mg(2+) ions on the DNA structural changes induced by low pH. Measurements are carried out on calf thymus DNA at neutral pH (7) and pH 3 in the presence of low and high concentrations of Na(+) and Mg(2+) ions, respectively. It is found that low concentrations of Na(+) ions do not protect DNA against binding of H(+). High concentrations of monovalent ions can prevent protonation of the DNA double helix. Our Raman spectra show that low concentrations of Mg(2+) ions partly protect DNA against protonation of cytosine (line at 1262 cm(-1)) but do not protect adenine and guanine N(7) against binding of H(+) (characteristic lines at 1304 and 1488 cm(-1), respectively). High concentrations of Mg(2+) can prevent protonation of cytosine and protonation of adenine (disruption of AT pairs). By analyzing the line at 1488 cm(-1), which obtains most of its intensity from a guanine vibration, high magnesium salt protect the N(7) of guanine against protonation. A high salt concentration can prevent protonation of guanine, cytosine, and adenine in DNA. Higher salt concentrations cause less DNA protonation than lower salt concentrations. Magnesium ions are found to be more effective in protecting DNA against binding of H(+) as compared with calcium ions presented in a previous study. Divalent metal cations (Mg(2+), Ca(2+)) are more effective in protecting DNA against protonation than monovalent ions (Na(+)).  相似文献   

4.
Oxovanadium(IV) complexes of hydroxysalen derivatives have been prepared and tested as DNA reactive agents. The nuclease activity has been investigated under oxidative or reducing conditions, on the basis of the various oxidation states of vanadium: VIII, VIV and VV. In the absence of an activating agent, none of the compounds tested was able to induce cleavage of DNA, whereas in the presence of mercaptopropionic acid (MPA) or Oxone the four complexes induced DNA modifications. Under both conditions, the para-hydroxy complex was found to be the most active compound. Reaction of these salen complexes with DNA occurs essentially at guanine residues and is more efficient in the presence of Oxone than under reducing conditions. The extent of Oxone-mediated DNA oxidation by the four vanadyl complexes was clearly superior to VOSO4 and was observed without piperidine treatment. EPR studies provided information on the reactive metal-oxo species involved under each conditions and a mechanism of reaction with DNA is discussed.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0529-0Abbreviations BPE buffer bis-phosphate EDTA buffer - DMPO 5,5-dimethylpyrroline N-oxide - DMS dimethyl sulfate - HFS hyperfine structure - Lin linear - MPA 3-mercaptopropionic acid - Nck nicked - salen (salicylidene)ethylenediamine - Sc supercoiled - TBE buffer tris-borate EDTA buffer - Tris tris(hydroxymethyl)aminomethane  相似文献   

5.
The effect of crystal packing on the electronic structure of organic molecules was modeled by incorporation of the external electrostatic potential into the semiempirical Hamiltonian of the molecule. An empirical correction procedure was devised in order to compensate for systematic errors in the charge distribution typical of semiempirical methods. The model was applied to 79 crystal structures belonging to various syngonies and space groups. The effect of the crystal field is subject to wide variations depending on the crystal packing motif. The difference between the effect of the crystal field on the molecular electronic structure and the solvent effect modeled with COSMO is highlighted. The effect of intermolecular hydrogen bonds on the molecular electronic structure and electronic spectra was modeled with this approach, and it does not predominate over the effect of long-range electrostatic interactions. INDO/S calculations employing the crystal electrostatic potential give an insight into the origin of crystallochromy, in particular, they properly predict color difference for several groups of polymorphs. Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.Electronic Supplementary Material Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.  相似文献   

6.
Nuclear magnetic resonance spectroscopy has been used to characterize the versatile peroxidase from Pleurotus eryngii, both in the resting state and in the cyanide-inhibited form. The assignment of most of the hyperfine-shifted resonances has been achieved by two-dimensional NMR, allowing the comparison of the present system with other ligninolytic peroxidases. This information has enabled a detailed analysis of the interaction of the enzyme with one of its reducing substrates, Mn(II). Furthermore, comparison with the data collected on a mutant in the putative Mn(II) binding site, and an analysis of the enzyme kinetic properties, shed light on the factors affecting the function of this novel peroxidase.Electronic Supplementary Material Supplementary material is available for this article if you access the article at .Abbreviations ABTS 2,2-azinobis(3-ethylbenzothiazoline-6-sulfonate) - CcP cytochrome c peroxidase - CIP Coprinus cinereus peroxidase - HRP horseradish peroxidase - IPTG isopropyl--D-thiogalactopyranoside - LiP lignin peroxidase - MnP manganese peroxidase - RB5 Reactive Black 5 - VA veratryl alcohol (3,4-dimethoxybenzyl alcohol) - VP versatile peroxidase  相似文献   

7.
The structures of [Ni(5′-dGMP)(H2O)5] and [Co(5′-dGMP)(H2O)5] have been solved by single-crystal x-ray diffraction techniques. Their common geometry consists of a metal ion octahedrally coordinated to the N7 atom of guanine and five water ligands. The phosphate group of the nucleotide is hydrogenbonded to two of the coordinated water molecules.  相似文献   

8.
One-dimensional (1-D) helical coordination polymers, [MII(H2O)3(BPDC)]n · nH2O (M = Co (1), Fe (2)), have been prepared by the self-assembly of cobalt(II) and iron(II) ions, respectively, with 2,2′-bipyridyl-3,3′-dicarboxylic acid (H2BPDC) in an aqueous solution. X-ray crystal structures of compounds 1 and 2 show that each metal ion displays a distorted octahedral coordination geometry including three water oxygen atoms, one oxygen atom of the carboxylate of a BPDC2− belonging to the adjacent metal ion and two nitrogen atoms from the BPDC2− acting as a chelating ligand. In 1 and 2, one carboxylate oxygen atom of coordinated BPDC2− binds to the neighboring metal ion, which give rise to 1-D helical coordination polymers. The helical chains of 1 and 2 are linked by the hydrogen bonding interactions between the carboxylate oxygen atom of the BPDC2− ion belonging to a chain and the water molecule of the adjacent helical chain, which lead to 2-D networks extending along the ab plane. The supramolecules 1 and 2 show isomorphous structures regardless of the metal ions.  相似文献   

9.
Two new complexes, [Cu(mamba)2] and [Mn(mamba)2] (mamba, N-(2-methylpyridine)-2-aminomethyl benzoate) were synthesized and characterized by X-ray crystallography. Whereas the [Cu(mamba)2] complex crystallizes in a monoclinic P21/c space group, the [Mn(mamba)2] complex crystallizes in a triclinic space group. The nature of the metal ion greatly influences the lattices and the molecular structures of the compounds. In the crystal lattice of the copper complex are four cocrystallized methanol solvent, which are all involved in building six strong H-bonds with the complex. However, the lattice for the manganese complex contain only one cocrystallized methanol, along with one NaClO4, that is also involved in making one H-bond with the [Mn(mamba)2] unit. Nevertheless, the sodium ion is coordinated to the ClO4, the methanol and two [Mn(mamba)2] to form a stable extended chain metal complex. Electrochemical studies indicated that both complexes undergo quasi reversible one electron reduction in acetonitrile.  相似文献   

10.
The influence of the distance between the anchoring site of the tethered [Ru(TAP)2dip]2+ complex (TAP=1,4,5,8-tetraazaphenanthrene; dip=4,7-diphenyl-1,10-phenanthroline) on a probe sequence and the guanines of the complementary target strand was studied by (1) the luminescence quenching of the complex (by electron transfer) and (2) the oligodeoxyribonucleotide adduct (ODN adduct) formation which results in photo-crosslinking of the two strands. Moving the guanine moieties away from the complex induces an important decrease of the efficiency of both processes, but clearly affects the ODN adduct formation more specifically than the quenching process. From these results, we determined the positions of the guanine bases in the duplex ODN that are able to form a photo-adduct with the tethered complex. We also examined the possible competition between a long-range hole migration in the duplex ODN and the formation of a photo-adduct by using a sequence labeled with the complex at the 5-phosphate end. Such a hole migration appears to be inefficient as compared to the ODN adduct formation. Finally, we studied the influence of the photo-crosslinking on the function of two different DNA polymerases. A 17-mer Ru(II)-labeled ODN was hybridized to its complementary sequence located on the 5-side of a 40-mer matrix. After illumination, the elongation of a 13-mer DNA primer hybridized to the 3-extremity of the same matrix was stopped at a position corresponding to the formation of the ODN adduct.Electronic Supplementary Material Supplementary material is available in the online version of this article at  相似文献   

11.
M-DNA is a complex formed between duplex DNA and divalent metal ions (Zn2+, Cu2+ or Ni2+) at pHs above 8. Previous results showed that the fluorescence of an electron donor fluorophore was quenched when an acceptor flourophore was placed in the opposite end of an M-DNA duplex suggesting electron transfer through the duplex and indicating M-DNA may operate as a better conductor than B-DNA. To further investigate the properties of M-DNA, oligodeoxynucleotides were prepared with fluorescein (Fl) as an electron donor placed at different positions along the helix. An internal position of the chromophore was made possible by attaching it to the extra hydroxyl arm in the branched monomer 4′-C-hydroxymethylthymidine. Upon excitation of the donor fluorophore, it was demonstrated that electrons could be injected into the side of an M-DNA helix thereby extending the range of nanoelectronic structures that can be prepared from DNA. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.  相似文献   

12.
The structure and conformation of nucleic acids are influenced by metal ions, polyamines, and the microenvironment. In poly(purine) · poly(pyrimidine) sequences, triplex DNA formation is facilitated by metal ions, polyamines and other ligands. We studied the effects of mono- and di-valent metal ions, and ammonium salts on the stability of triple- and double-stranded structures formed from poly(dA) and poly(dT) by measuring their respective melting temperatures. In the presence of metal ions, the absorbance versus temperature profile showed two transitions: Tm1 for triplex to duplex and single stranded DNA, and Tm2 for duplex DNA melting to single stranded DNA. Monovalent cations (Li+, Na+, K+, Rb+, Cs+ and 4NH+NH4+) promoted triplex DNA at concentrations ≥150 mM. Tm1 varied from 49.8 °C in the presence of 150 mM Li+ to 30.6 °C in the presence of 150 mM K+. 4NH+NH4+ was very effective in stabilizing triplex DNA and its efficacy decreased with increasing substitution of the hydrogen atoms with methyl, ethyl, propyl and butyl groups. As in the case of monovalent cations, a concentration-dependent increase in Tm1 was observed with divalent ions and triplex DNA stabilization decreased in the order: Mg2+ > Ca2+ > Sr2+ > Ba2+. All positively charged cations increased the melting temperature of duplex DNA. Values of Δn (number of ions released) on triplex DNA melting were 0.46 ± 0.06 and 0.18 ± 0.02, respectively, for mono- and di-valent cations, as calculated from 1/Tm1 versus ln[M+,2+] plots. The corresponding values for duplex DNA were 0.25 ± 0.02 and 0.12 ± 0.02, respectively, for mono- and di-valent cations. Circular dichroism spectroscopic studies showed distinct conformational changes in triplex DNA stabilized by alkali metal and ammonium ions. Our results might be useful in developing triplex forming oligonucleotide based gene silencing techniques.  相似文献   

13.
Hemocyanins are oligomeric metalloproteins containing binuclear copper centers that reversibly combine with oxygen molecules. The structural stability and functional properties of these proteins are modified by divalent cations. Equilibrium dialysis was used to study the reversible interaction of Callinectes sapidus and Limulus polyphemus hemocyanins with the divalent cations calcium, cadmium, zinc, copper, and mercury. The number of binding sites and association constants for each cation were obtained from an analysis of the binding data by a nonlinear least-squares minimization procedure. Spectral analysis showed Limulus hemocyanin to possess two mercury-reactive sulfhydryl groups per subunit (Kassoc = 2.02 X 10(45) M-1). Callinectes hemocyanin contains only one such group (Kassoc = 2.29 X 10(34) M-1). Cadmium and zinc are shown to substitute for calcium ions. Oxygen binding studies with Limulus hemocyanin showed that all five divalent metal ions increase its oxygen affinity. Calcium ions increase cooperativity of oxygen binding, while heavy-metal ions have an opposite effect. Binding of two mercuric ions per Limulus hemocyanin subunit irreversibly fixes the 48 subunit aggregate in a high-affinity noncooperative conformational state. These results offer a striking contrast to the functional consequences of heavy-metal ion interactions with Callinectes hemocyanin [Brouwer, M., Bonaventura, C., & Bonaventura, J. (1982) Biochemistry 21, 2529-2538]. The functional alterations associated with metal ion interactions are discussed within the context of an extension of the two-state model for allosteric transitions of Monod et al. [Monod, J., Wyman, J., & Changeux, J.P. (1965) J. Mol. Biol. 12, 88-118]. Incubation of Limulus oxy- or deoxyhemocyanin with mercuric chloride results in the conversion of 60% of the binuclear copper sites to stable half-apo sites. The remaining active sites are stable with respect to mercury-induced copper displacement when oxygen is bridging both coppers. In the absence of oxygen these sites will eventually lose both copper atoms. Under the same conditions 50% of the binuclear copper sites of Callinectes deoxyhemocyanin are converted to half-apo sites. In this case oxygen completely protects against copper displacement [Brouwer, M., Bonaventura, C., & Bonaventura, J. (1982) Biochemistry 21, 2529-2538]. The binuclear copper center of Busycon carica is not affected at all, demonstrating profound differences between the active sites of hemocyanins of a chelicerate arthropod (Limulus), a crustacean arthropod (Callinectes), and a gastropod mollusc (Busycon).  相似文献   

14.
Two extrinsic probes, pyrene-maleimide and eosin-maleimide, were used to label specific SH groups of the enzyme myo-inositol monophosphatase. The fluorescence of pyrene-monophosphatase is enhanced upon addition of the activating metal ions Co(II) and Mg(II). Co(II) ions bind with a dissociation constant of 4 M, whereas the apparent activation constant K a is 0.4 mM. Energy transfer measurements demonstrated that the pyrene chromophore, covalently linked to Cys-218, is within 9 Å of the metal ion Tb(III) coordinated to the metal-binding site. The phosphorescence emitted by eosin covalently linked to the protein is quenched by the addition of the activating cations Co(II) and Mg(II). Phosphorescence titrations conducted under anaerobic conditions were used to determine a dissociation constant of approximately 3 M for the binding of Co(II) ions. The results are consistent with the hypothesis that two activating ions per monomeric subunit participate in the catalytic mechanism. The affinity of the tightly bound ion is at least 100-fold greater than the affinity of the weakly bound ion.  相似文献   

15.
An aza-oxa-thia macrocycle, 5,14-dioxa-2,17-dithia[6](1,2)benzeno[6](2,6)pyridinophane, L1, the related smaller macrocycle 2,14-dithia-11-oxa-[3](1,2)benzeno[6](2,6)pyridinophane, L2, and the complexes with Pd(II) and Cu(II) of the macrocycle, L1, have been synthesized. The crystal structure of L2 and those of the two metal complexes have been determined. In the complexes, the metal ions adopt exclusively square planar geometry in which the pyridine nitrogen, two sulfurs and one chlorine atom are coordinated and there is no appreciable interaction with the oxygen donors. Thus, the `hard-soft acid-base' principle is illustrated by the behaviour of L1. The structures of both complexes are compared with the previously reported mixed aza-thia macrocycle, 2,5,14,17-tetrathia[6](1,2)benzeno[6](2,6)pyridinophane. The crystal structure of the smaller macrocycle, L2, is also discussed and due to the nature of its smaller cavity, attempts to make complexes with it have not been successful.  相似文献   

16.
A platinum(II) complex containing the diamine ()sparteine has been synthesized for the first time and fully characterized by 1H and 13C NMR spectroscopy and X-ray crystallography. ()Sparteine is an alkaloid containing four fused rings and four asymmetric centers of configurations 6R, 7S, 9S, and 11S at the four tertiary carbon atoms. In the cis conformation it can act as a chelating N-donor ligand toward a metal ion. The steric bulkiness of this ligand is such that the Pt-N bond lengths are greater than normal and the angle between the cis-chlorido ligands is well below the theoretical value of 90°. This sparteine complex of platinum appears to be an ideal substrate for investigating the stereochemistry of adducts with nucleotides and DNA. For instance the orientation of a coordinated nucleobase can be determined with precision by monitoring the strength of NOE cross peaks between the sparteine protons pointing toward the metal center and key protons of the coordinated nucleobase(s) (e.g. H8 protons of guanine or adenine).  相似文献   

17.
Divalent Mg2+ ions often serve as cofactors in enzyme or ribozyme-catalyzed phosphoryl transfer reactions. In this work, the interaction of Mg2+ ions and di-metal bridge complexes with phosphates, phosphoranes, and other biological ligands relevant to RNA catalysis are characterized with density functional methods. The effect of bulk solvent is treated with two continuum solvation methods (PCM and COSMO) for comparison. The relative binding affinity for different biological ligands to Mg2+ are quantified in different protonation states. The structure and stability of the single-metal and di-metal complexes are characterized, and the changes in phosphate and phosphorane geometry induced by metal ion binding are discussed. Di-metal bridge complexes are a ubiquitous motif and the key factors governing their electrostatic stabilization are outlined. The results presented here provide quantitative characterization of metal ion binding to ligands of importance to RNA catalysis, and lay the groundwork for design of new generation quantum models that can be applied to the full biological enzymatic systems.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0583-7An erratum to this article can be found at  相似文献   

18.
Y G Gao  M Sriram    A H Wang 《Nucleic acids research》1993,21(17):4093-4101
Metal ion coordination to nucleic acids is not only required for charge neutralization, it is also essential for the biological function of nucleic acids. The structural impact of different metal ion coordinations of DNA helices is an open question. We carried out X-ray diffraction analyses of the interactions of the two transition metal ions Co(II) and Cu(II) and an alkaline earth metal ion Ba(II), with DNA of different conformations. In crystals, Co(II) ion binds exclusively at the N7 position of guanine bases by direct coordination. The coordination geometry around Co(II) is octahedral, although some sites have an incomplete hydration shell. The averaged Co-N7 bond distance is 2.3 A. The averaged Co-N7-C8 angle is 121 degrees, significantly smaller than the value of 128 degrees if the Co-N7 vector were to bisect the C5-N7-C8 bond angle. Model building of Co(II) binding to guanine N7 in B-DNA indicates that the coordinated waters in the axial positions would have a van der Waals clash with the neighboring base on the 5' side. In contrast, the major groove of A-DNA does not have enough room to accommodate the entire hydration shell. This suggests that Co(II) binding to either B-DNA or A-DNA may induce significant conformational changes. The Z-DNA structure of Cu(II)-soaked CGCGTG crystal revealed that the Cu(II) ion is bis-coordinated to N7 position of G10 and #G12 (# denotes a symmetry-related position) bases with a trigonal bipyramid geometry, suggesting a possible N7-Cu-N7 crosslinking mechanism. A similar bis-coordination to two guanines has also been seen in the interaction of Cu(II) in m5CGUAm5CG Z-DNA crystal and of Ba(II) with two other Z-DNA crystals.  相似文献   

19.
Abstract

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 Å from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, O6 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.  相似文献   

20.
A potential tetradentate indolecarboxamide ligand, H4L3 is synthesized and investigated for its coordination abilities towards Ni(II) and Cu(II) ions. Two H4L3 ligands in their tetra-deprotonated form [L3]4−, were found to coordinate two metal centers resulting in the formation of [Ni2(L3)2]4− (5) and [Cu2(L3)2]4− (6) complexes. The crystal structure of 6 displays the formation of a dinuclear structure where two fully deprotonated ligands, [L3]4− hold two copper(II) ions together. Even more interesting is the fact that both deprotonated ligands, [L3]4− coordinate the copper ions in an identical and symmetrical fashion. The Na+ cations present in the complex 6 stitch together the dinuclear units resulting in the formation of a coordination chain polymer. Four sodium ions connect two dinuclear units via interacting with the Oamide groups. Further, Na+ cations were found to coordinate several DMF molecules; some of them are terminal and a few are bridging in nature. The solution state structure (determined by the NMR spectral analysis) of the diamagnetic complex 5 also supported the fact that two deprotonated ligands, coordinate two nickel ions in an identical and symmetrical fashion. Absorption spectral studies reveal that the solid-state square-planar geometry is retained in solution and both complexes do not show any tendency to coordinate potential axial ligands. The variable-temperature magnetic measurements and EPR spectra indicate spin-spin exchange between two copper centers in complex 6. The electrochemical results for both complexes show three irreversible oxidative responses that correspond to the oxidation of first and second metal ion followed by the ligand oxidation, respectively.  相似文献   

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