Some effects of metal ions on DNA structure and genetic information transfer

The reaction of metal ions with nucleic acids can lead to a variety of dramatic effects on nucleic acid structure, e.g., crosslinking of the polymer strands, degradation to oligomers and monomers, stabilization or destabilization, and the mispairing of bases. These effects have important implications for genetic information transfer. Metal ions are involved in many aspects of this transfer; we are presently concerned with the effect of metal ions on the orientation of the active site of RNA polymerase. Many of the effects of metal ions on nucleic acid structure involve changes in the conformation of the macromolecules. We have found that conditions that have been used to convert B DNA to Z DNA lead to at least two other conformational changes, and phase diagrams delineate the realms of stability of each of the forms. We have carried out a number of studies that demonstrate that the conversion of B to Z DNA is very closely correlated with a substantial decrease in the ability of the DNA to act as a template for RNA synthesis. A portion of this paper has been taken from another paper on “Changes of Biological Significance Induced by Metal Ions in the Structure of Nucleic Acids,” published in Annali dell' lstituto Superiore di Sanita.     

Systems biology of evolution: the involvement of metal ions

This article outlines a novel way of looking at the relevance of metal ions in organisms to the whole of life as part of an ecosystem bringing together the environment and cellular life. It does so by examining the evolution of the environment due to the “waste”, mainly oxygen, from cell metabolism which back reacts with the cells themselves. The oxygen generates a progressive change in the metal ions in the environment. The resultant change is buffered by ferrous iron and sulfide and is therefore slow so that there is a gradual adaptation of life to utilisation of elements in a time sequence. In order to appreciate this, systems (biological) evolution, it is necessary to describe the very nature of a thermodynamic flow system of which life is an example.     

Effects of metal ions on activity of plasmin

The effects of some metal ions on amidolytic and fibrinogenolytic activities of highly purified human plasmin were investigated in vitro. In the presence of Zn²⁺, Cu²⁺, Cd²⁺, and Au⁺ in the incubation mixture at the concentrations of 1×10⁻⁵−1×10⁻³ M, the anidolytic plasmin activity was strongly inhibited, whereas Ca²⁺ and Mg²⁺ at the same concentrations were not effective. The analysis of the kinetic study has shown that Zn²⁺ or Cu²⁺ acts as mixed-type inhibitors of plasmin activity. The inhibition of amidolytic plasmin activity by Zn²⁺ and Cu²⁺ was reduced in the presence of EDTA, histidine, or albumin. Incubation of plasmin with Zn²⁺ or Cu²⁺ (at the concentration of 5×10⁻⁴ M) resulted in complete loss of its proteolytic action on fibrinogen, whereas Cd²⁺ and Au⁺ under the same conditions only partially inhibited this process.     

Biodistributions of radioactive bipositive metal ions in tumor-bearing animals

Distributions of the nuclides ⁶⁵ZnCl₂, ⁸⁵SrCl₂, ⁵⁸CoCl₂ and ¹⁰³PdCl₂ in tumor-bearing animals were determined, and, in addition, the distributions of these nuclides in tumor tissues were observed. Their subcellular distribution in tumor and liver was also examined. Generally speaking, retention values of these bipositive metal ions in tumor were smaller than those of tri-, quadri- and pentavalent metal ions. In the case of ⁸⁵SrCl₂, a large amount of this nuclide was taken up by the bone and remained there for a long time. In the case of ¹⁰³PdCl₂, ^l03Pd was avidly taken up by the kidney and liver. Very little of the ¹⁰³Pd taken up into the kidney and liver was excreted. ⁶⁵Zn and ¹⁰³Pd were concentrated in the viable tumor tissue and were not seen in necrotic tumor tissue. In the case of ⁵⁸Co, lysosome played an important role in liver accumulation and played a minor role in tumor accumulation. The distribution of ⁵⁸Co in tumor and liver was fairly similar to that of ⁶⁷Ga, ¹¹¹In, ¹⁶⁹Yb, ⁴⁶Sc, ⁵¹Cr, ⁹⁵Zr, ¹⁸¹Hf, ⁹⁵Nb and ¹⁸²Ta which were reported previously. Lysosome did not play an important role in the accumulation of ⁶⁵Zn, ⁸⁵Sr and ¹⁰³Pd into tumor and liver.     

金属离子对生物絮凝剂REA-11合成的影响

考察了Mg2 、Na 、K 、Ca2 对谷氨酸棒杆菌生长及生物絮凝剂合成的影响。结果表明,培养基中添加适当的Mg2 对菌体的生长和絮凝剂的产生有一定的促进作用。K 和Ca2 对絮凝剂的产生具有一定的抑制作用。Na 的添加对菌体的生长和絮凝剂的产生均无显著影响。     

Preliminary studies of the enhanced electrochemiluminescence of 2,3-diaminonaphthalene in the presence of specific metal ions

Electrochemiluminescence (ECL) of 200 ppm 2,3-diaminonaphthalene (2,3-DAN) was studied alone and in conjunction with 100 ppm of 34 different metal and non-metal ions and revealed three relatively intense ECL responses from interactions of 2,3-DAN with Au⁺, Fe⁺³ and V⁺⁵. ECL responses from Cr⁺⁶ or Ru⁺³ with 2,3-DAN were less intense, but noteworthy, as was the coloured fluorescent product of the non-metal ion Se⁺⁴ interaction with 2,3-DAN. Several intense 2,3-DAN–metal ion ECL reactions were studied in greater detail and revealed various titration curves with ionic detection limits in the low ppm range, using a fixed level (200 ppm) of 2,3-DAN. © 1998 John Wiley & Sons, Ltd.     

Potential carcinogenicity of some transition metal ions

Potential carcinogenicity of some transition metal ions was tested using a direct-current polarography method. The measurements were based on the reduction of tested compounds in an anhydrous solution using α-lipoic acid as the detection compound. The potential carcinogenicity was expressed in terms of the parameter tg α, which is known to directly correlate with the carcinogenicity of tested compounds. For the metal ions tested, tg α was found to decrease in the following sequence: Fe(III) > Pb(II) > V(IV) > Fe(II) > Mn(II) > Cu(II). Zero values of tg α were found for Cd(II) and Mn(III).     

Complexation of a four-strand tetraalcohol with labile metal ions probed by electrospray mass spectrometry

The saturated, stereodefined tetraalcohol 2,3,5,6-endo,endo,endo,endo-tetrakis(hydroxymethyl)bicyclo[2.2.1]heptane (tetol, L¹) and the simple alcohol butane-1,3-diol (L²) form complexes with alkali metal ions (lithium, sodium, potassium, rubidium and caesium), alkali earth cations (magnesium, calcium, strontium and barium) and Ga(III) and Ce(IV) in aqueous solution, characterised by electrospray ionisation mass spectrometry (ESMS). Metal ion exchange between the Li⁺ complex of L¹ and the other metal ions is rapid, with a range of M(L¹)_n ^m+ species detected, in addition to solvated species. With the alkal metal ions, M(L¹)⁺ and M(L¹)₂ ⁺ are dominant, although speciation varies with metal ion size. For the alkaline earth ions, a range of complex ions up to n=8 are observed, although n=1-3 dominate. A preference for M(L¹)₂ ²⁺ with Mg²⁺ versus M(L¹)₃ ²⁺ with Ca²⁺ may again relate to a larger ion size. For the higher-charged Ga(III) and Ce(IV), hydroxo species M(OH)(L¹)_n ^(m−1)+ are dominant reflecting bulk solution behaviour, which the ESMS studies appear to map generally.     

Oxygen uptake activity by Nitrobacter spp. in the presence of metal ions and sulfooxyanions

Abstract Several metal ions inhibited the oxygen uptake activity of Nitrobacter agilis , but their effects on the kinetic parameters of nitrite oxidation were mixed. Growth of Nitrobacter winogradskyi was inhibited by persulfate (>0.1 mM), tetrathionate (>0.5 mM), and trithionate (>5 mM). Oxygen uptake activity was, however, relatively insensitive to persulfate and tetrathionate ions.     

Sporicidal action of peracetic acid and protective effects of transition metal ions

Although peracetic acid (PAA) is used widely for cold sterilization and disinfection, its mechanisms of sporicidal action are poorly understood. PAA at high concentrations (5–10%) can cause major loss of optical absorbance and microscopically-visible damage to bacterial spores. Spores killed by lower levels of PAA (0.02–0.05%) showed no visible damage and remained refractile. Treatment of spores ofBacillus megaterium ATCC 19213 with PAA at concentrations close to the lethal level sensitized the cells to subsequent heat killing. In addition, PAA was found to act in concert with hypochlorite and iodine to kill spores. Antioxidant sulfhydryl compounds or ascorbate protected spores against PAA killing. Trolox, a water-soluble form of -tocopherol, was somewhat protective, while other antioxidants, including -tocopherol, urate, bilirubin, ampicillin and ethanol were not protective. Chelators, including dipicolinate, were not protective, but transition metal ions, especially the reduced forms (Co²⁺, Cu⁺ and Fe²⁺) were highly protective. The net conclusions are that organic radicals formed from PAA are sporicidal and that they may act as reducing agents for spores that are normally in a highly oxidized state, in addition to their well known actions as oxidizing agents in causing damage to vegetative cells.     

Divalent metal ions influence catalysis and active-site accessibility in the cAMP-dependent protein kinase.

Phosphorylation of the peptide LRRASLG by the catalytic subunit of cAMP-dependent protein kinase was measured in the presence of various divalent metals to establish the role of electrophiles in the kinetic mechanism. Under conditions of low or high metal concentrations, the apparent second-order rate constant, kcat/Kpeptide, and the maximal rate constant, kcat, followed the trend Mg2+ > Co2+ > Mn2+. Competitive inhibition studies indicate that the former effect is not due to destabilization of the substrate complex, E.ATP.S. The effects of solvent viscosity on the steady-state kinetic parameters were interpreted according to a simple mechanism involving substrate binding, phosphotransfer, and product release steps and two metal chelation sites in the nucleotide pocket. Decreases in kcat and kcat/Kpeptide result mostly from attenuations in the dissociation rate constant for ADP and the association rate constant for the substrate, respectively. Decreases in the phosphoryl transfer rate constant have only negligible to moderate effects on these parameters. The low observed values for the association rate constant of the substrate indicate that the metals control the concentration of the productive binary form, Ea.ATP, and indirectly the accessibility of the active site. By comparison, Mg2+ is the best divalent metal catalyst because it uniformly lowers the transition state energies for all steps in the kinetic mechanism, permitting maximum flux of substrate to product. The data suggest that cAMP-dependent protein kinase uses metal ions to serve multiple roles in facilitating phosphotransfer and accelerating substrate association and product dissociation.     

Role of metal ions in triazine dye affinity chromatography: The metal mediated interaction of triazine dyes with firefly luciferase

Low concentrations of metals of the first row transition series, Zn²⁺, Co²⁺, Mn²⁺, Ni²⁺, Cu²⁺ and Fe²⁺, and to a lesser extent the group IIa ions, particularly Mg²⁺, influenced the interaction of firefly luciferase [Photinus luciferin:oxygen 4-oxidoreductase (decarboxylating, ATP-hydrolysing), EC 1.13.12.7] with a number of triazine dyes. For example Cu²⁺ promoted the binding of luciferase to Cibacron Brilliant Blue (BR-II) and Cibacron Blue F3GA a dichloro and monochloro triazine dye, respectively. On the other hand Zn²⁺ prevented dye inactivation and even enhanced the enzyme activity. Specificity was observed in the interference of different metals interacting with different dye-protein. This is made use of in triazine dye affinity chromatography.     

Oligonucleotide formation catalyzed by divalent metal ions. The uniqueness of the ribosyl system

Summary Polymerization of various nucleoside-5-phosphorimidazolides has been conducted in neutral aqueous solution using divalent metal ions as catalysts. Oligonucleotide formation took place from each of the ribonucleoside-5-phosphorimidazolides, ImpC, ImpU, ImpA, ImpG, and ImpI. The yields and distributions of the resulting oligonucleotides varied depending on the difference of the nucleic acid base and the metal ions used. The catalytic effect of divalent metal ions on the formation of oligocytidylates occurred in the following order: Pb²⁺>Zn²⁺>Co²⁺, Mn²⁺>Cd²⁺>Cu²⁺>Ni²⁺>Ca²⁺, Mg²⁺, none >Hg²⁺. The order changes slightly for other types of oligoribonucleotide formation. Oligoribonucleotides up to hexamers were obtained in 35–55% overall yield, when Pb²⁺ ion was used as a catalyst. Zn²⁺ ions yielded oligoribonucleotides up to tetramers in 10–20% overall yield. The resulting oligonucleotides contained mainly 2–5 internucleotide linkages.Little or no oligonucleotide was obtained from nucleoside-5-phosphorimidazolides modified in the sugars, Imp(3-dA), Imp(2-dA), Imp(Ara), Imp(Aris), and Imp(Nep). The results indicate that a ribosyl system is required for the metal ion-catalyzed synthesis of oligonucleotides. Abbreviations. EDTA, ethylenediaminetetraacetic acid; Versenol,N-hydroxyethylethylenediaminetriacetic acid; Tris, tris-(hydroxymethyl)aminomethane; pN (N is A, C, G, U, I, 3-dA, 2-dA, AraA, Aris, or Nep), nucleoside-5-phosphate; Np, nucleoside-2(3)-phosphate; I, inosine; 3-dA, 3-deoxyadenosine; 2-dA, 2-deoxyadenosine; AraA, arabinosyladenine; Aris, aristeromycin; Nep, neplanocin A; ImpN, nucleoside-5-phosphorimidazolide; NppN, P₁,P₂-dinucleoside-5,5-pyrophosphate; (pN)_n (n=2, 3, ...), oligomers of pN, numbers given between a nucleoside and a phosphate indicate the type of internucleotide linkage, e.g., pC₂ p₅C is 5-phosphorylcytidyl-(2–5)-cytidine; , cyclic dimers of pN; BAP, bacterial alkaline phosphatase; N.Pl, nuclease Pl; VPDase, venom phosphodiesterase; HPLC, high pressure liquid chromatography     

The effects of metal ions on the structure and stability of the DNA gyrase B protein

The effects of mono- and divalent metal ions on the DNA gyrase B subunit, on its 43 kDa and 47 kDa domains, and on two mutants in the Toprim domain (D498A and D500C) were investigated by means of circular dichroism and protein melting experiments. Both types of metal ion, with the notable exception of Mn2+, did not affect the conformational properties of the enzyme subunit at room temperature, but were able to produce selective and differential effects on protein stability. In particular, monovalent (K+) ions increased the stability of the gyrase B structure, whereas destabilising effects were most prominent using Mn2+ as the metal ion. Ca2+ and Mg2+ produced comparable changes in the gyrase B melting profile. Additionally, we found that monovalent (K+) ions were more effective in the 43 kDa N-terminal domain where ATP binding occurs, whereas divalent ions caused large modifications in the conformational stability of the 47 kDa C-terminal domain. Our results on gyrase B mutants indicate that D498 interacts with Mn2+, whereas it has little effect on the binding of the other ions tested. A D500C mutation, in contrast, effectively impairs Mg2+ affinity, suggesting effective contacts between this ion and D500 in the wild-type enzyme. Hence, the sites of metal ion complexation within the Toprim domain are modulated by the nature of the ion species. These results suggest a double role played by metal ions in the catalytic steps involving DNA gyrase B. One has to do with direct involvement of cations complexed to the Toprim domain in the DNA cutting-rejoining process, the other, until now overlooked, is connected to the dramatic changes in protein flexibility produced by ion binding, which reduces the energy required for the huge conformational changes essential for the catalytic cycle to occur.     

Complexation of metal ions by pseudotripeptides with different functionalized N-alkyl residues

Summary Seven pseudotripeptides with the common structure Bz-His-ψ[CO−N(CH₂)n-X]Gly-His-NH₂ were synthesized on the solid phase using the Fmoc-strategy, trityl protection for both His residues and Boc-or-OBu^t-protection for N-aminoalkyl-and N-carboxyalkyl residues, respectively. Functionalized N-alkyl glycyl peptides were formed on the solid phase by amination of a bromoacetyl dipeptide. All seven pseudotripeptides are able to form chelate complexes with the metal ions Zn²⁺, Ni²⁺, Cu²⁺ and Co²⁺. The existence of monomeric 1∶1 complexes for these pseudopeptides was calculated from the MW estimated by MALDI-MS and from the isotope distribution pattern estimated by ESI.     

Complexation of metal ions by pseudotripeptides with different functionalized N-alkyl residues

Seven pseudotripeptides with the common structure Bz-His-[CO-N(CH₂)n-X]Gly-His-NH₂ were synthesized on the solid phase using the Fmoc-strategy, trityl protection for both His residues and Boc- or -OBu^t-protection for N-aminoalkyl- and N-carboxyalkyl residues, respectively. Functionalized N-alkyl glycyl peptides were formed on the solid phase by amination of a bromoacetyl dipeptide. All seven pseudotripeptides are able to form chelate complexes with the metal ions Zn²⁺, Ni²⁺, Cu²⁺ and Co²⁺. The existence of monomeric 1:1 complexes for these pseudopeptides was calculated from the MW estimated by MALDI-MS and from the isotope distribution pattern estimated by ESI.     

Inhibition of purified bovine liver glutathione reductase with some metal ions

Glutathione reductase (GR; E.C. 1.6.4.2) is a flavoprotein that catalyzes the NADPH-dependent reduction of oxidized glutathione (GSSG). In this study we tested the effects of Al³⁺, Ba²⁺, Ca²⁺, Li⁺, Mn²⁺, Mo⁶⁺, Cd²⁺, Ni²⁺, and Zn²⁺ on purified bovine liver GR. In a range of 10?μM–10?mM concentrations, Al³⁺, Ba²⁺, Li⁺, Mn²⁺, and Mo⁶⁺, and Ca²⁺ at 5?μM–1.25?mM, had no effect on bovine liver GR. Cadmium (Cd²⁺), nickel (Ni²⁺), and zinc (Zn²⁺) showed inhibitory effects on this enzyme. The obtained IC₅₀ values of Cd²⁺, Ni²⁺, and Zn²⁺ were 0.08, 0.8, and 1?mM, respectively. Cd²⁺ inhibition was non-competitive with respect to both GSSG (Ki_GSSG 0.221?±?0.02?mM) and NADPH (Ki_NADPH 0.113?±?0.008?mM). Ni²⁺ inhibition was non-competitive with respect to GSSG (Ki_GSSG 0.313?±?0.01?mM) and uncompetitive with respect to NADPH (Ki_NADPH 0.932?±?0.03?mM). The effect of Zn²⁺ on GR activity was consistent with a non-competitive inhibition pattern when the varied substrates were GSSG (Ki_GSSG 0.320?±?0.018?mM) and NADPH (Ki_NADPH 0.761?±?0.04?mM), respectively.     

Coordinated cations in dipicolinato complexes of divalent metal ions

Several salts of alkali, alkaline earth metal and organic ammonium cations of a complex anion [ML₂]²⁻ {Where L = dipicolinato dianion, M = copper(II), nickel(II) and zinc(II)} are prepared. The coordination effect of [ML₂]²⁻ with the cations such as sodium, potassium, calcium, magnesium, and organic cations namely diammonium cation of 1,5-pentanediamine, diammonium cation of 1,8-octyldiamine, mono ammonium cation of 4-aminobenzylamine are studied by determining their X-ray crystal structures. Depending on the nature of cations, four different types of structures are obtained. When calcium is the cation a polymeric structure with calcium ions bridging the [ML₂]²⁻ is observed. The salts having sodium and potassium cations form polymeric chain like structures by oxo and aqua bridges. In the case of magnesium, the hydrated form of magnesium cations coordinates to [ML₂]²⁻. The organic ammonium salts of [ML₂]²⁻ have the structural features of conventional ionic complexes. These salts easily exchange cations. The organic ammonium salts of [ML₂]²⁻ decomposes to give the corresponding metal oxides at relatively low temperature range 300-450 °C.     

Properties of microsolvated ions: from the microenvironment of chromophore and alkali metal ions in proteins to negative ions in water clusters

Here we discuss the fascinating chemistry and physics of microsolvated ions that bridge the transition from bare ions in gas phase to ions in solution. Such ions occur in many situations in biochemistry and are crucial for several functions; metal ions, for example, must remove their water shell to pass through ion pumps in membranes. Furthermore, only a few water molecules are buried in the hydrophobic pockets of proteins where they are bound to charged amino acid residues or ionic chromophores. Another aspect is the reactivity of microsolvated ions and the importance in atmospheric, organic and inorganic chemistry. We close by a discussion of the stability of molecular dianions, and how hydration affects the electronic binding energy. There is a vast literature on microsolvated ions, and in this review we are far from being comprehensive, rather we mainly bring examples of our own work.