Molecular Constructions (Superstructures) with Adjustable Properties Based on Double-Stranded Nucleic Acids

We describe formation of a molecular construction that consists of double-stranded molecules of nucleic acids (or synthetic polynucleotides) located at a distance of 30–50 Å in the spatial structure of particles of their cholesteric liquid-crystalline dispersion and crosslinked by polymeric chelate bridges. The resulting superstructure, which possesses peculiar physicochemical properties, can be used as an integral biosensor whose properties depend on temperature, the presence of chemical or biologically active compounds of different nature, etc.     

A two-component ribonucleotidyl transferase from E. coli

Some properties of an enzyme designated as a two-component ribonucleotidyl transferase from E. coli are presented. The enzyme in the presence of magnesium ions catalyzes the synthesis of polyribonucleotide chains using all four nucleoside triphosphates as substrates. The enzyme consists of two components; component A in the presence of Mg²⁺ catalyzes the synthesis of homo- and heteropolymers using ATP, CTP and UTP but not GTP as substrates. Component B itself does not catalyze any synthesis at all, but its addition to component A affects this component in two ways: quantitatively—the activity of component A considerably increases, and qualitatively—both components together are capable of catalyzing the synthesis of polyribonucleotides consisting of all four ribonucleotides.     

Effect of O(2′)-methylation on the stability of polynucleotide helices

The effect of ribose(O2′)-methylation on the stability of (O2′)-methylated polyribonucleotide helices has been studied by conformational energy calculations. The preferred orientation of the methyl group is found to further stabilize the helical phosphodiester conformation (g^?,g^?) due to the enhanced short-range interactions arising between the methyl groups and the adjacent ribose moieties. The experimentally observed increase in melting temperature of (O2′)-alkylated polyribonucleotides is thus attributable to the enhanced stability of the helical backbone conformation.     

Heterofunctional Magnetic Metal‐Chelate‐Epoxy Supports for the Purification and Covalent Immobilization of Benzoylformate Decarboxylase From Pseudomonas Putida and Its Carboligation Reactivity

In this study, the combined use of the selectivity of metal chelate affinity chromatography with the capacity of epoxy supports to immobilize poly‐His‐tagged recombinant benzoylformate decarboxylase from Pseudomonas putida (BFD, E.C. 4.1.1.7) via covalent attachment is shown. This was achieved by designing tailor‐made magnetic chelate–epoxy supports. In order to selectively adsorb and then covalently immobilize the poly‐His‐tagged BFD, the epoxy groups (300 µmol epoxy groups/g support) and a very small density of Co²⁺‐chelate groups (38 µmol Co²⁺/g support) was introduced onto magnetic supports. That is, it was possible to accomplish, in a simple manner, the purification and covalent immobilization of a histidine‐tagged recombinant BFD. The magnetically responsive biocatalyst was tested to catalyze the carboligation reactions. The benzoin condensation reactions were performed with this simple and convenient heterogeneous biocatalyst and were comparable to that of a free‐enzyme‐catalyzed reaction. The enantiomeric excess (ee) of (R)‐benzoin was obtained at 99 ± 2% for the free enzyme and 96 ± 3% for the immobilized enzyme. To test the stability of the covalently immobilized enzyme, the immobilized enzyme was reused in five reaction cycles for the formation of chiral 2‐hydroxypropiophenone (2‐HPP) from benzaldehyde and acetaldehyde, and it retained 96% of its original activity after five reaction cycles. Chirality 27:635–642, 2015. © 2015 Wiley Periodicals, Inc.     

Responses to iron deficiency in Arabidopsis thaliana: The Turbo iron reductase does not depend on the formation of root hairs and transfer cells

Arabidopsis thaliana (L.) Heynh. Columbia wild type and a root hair-less mutant RM57 were grown on iron-containing and iron-deficient nutrient solutions. In both genotypes, ferric chelate reductase (FCR) of intact roots was induced upon iron deficiency and followed a Michaelis-Menten kinetic with a K _m of 45 and 54 M Fe^III-EDTA and a V _max of 42 and 33 nmol Fe²⁺·(g FW)^–1·min^–1 for the wild type and the mutant, respectively. The pH optimum for the reaction was around pH 5.5. The approximately four fold stimulation of FCR activity was independent of formation of root hairs and/or transfer cells induced by iron deficiency. Iron-deficiency-induced chlorosis and the development of a rigid root habit disappeared when ferric chelate was applied to the leaves, while FCR activity remained unchanged. The time course of the responses to iron deficiency showed that morphological and physiological responses were controlled separately.Abbreviations FCR ferric chelate reductase - FW fresh weight Thanks are due to Klaas Sjollema (Department of Electronmicroscopy, University of Groningen, The Netherlands) for help with the electron microscopy sample preparation and especially to Dr. Uwe Santore (Heinrich-Heine-University for electron microscopy. This work was supported by the SCIENCE programm of the European community; P.R.M.) and a Personal Research Grant by the Ministerium für Wissenschaft und Forschung of Nordrhein-Westfalen (P.R.M.) and last, not least by the productive discussions in ECOTRANS B.V.     

Synthesis and characterization of new unsaturated macrobicyclic and bis(macrocyclic) copper(II) complexes containing N-CH2-N linkages

New copper(II) complexes [CuL²]²⁺ (L²=7,7,9-trimethyl-1,3,6,10,13-pentaazabicyclo[11,2,1^1.13]hexadec-9-ene) and [Cu₂(L³)(H₂O)₂]⁴⁺ have been prepared by the reaction of [CuL¹]²⁺ (L¹=5,5,7-trimethyl-1,4,8,11,14-pentaazatetradce-7-ene) and formaldehyde. The mononuclear complex [CuL²]²⁺ has a square-planar coordination geometry with a 5-6-5-6 chelate ring sequence and is relatively stable even in low pH at room temperature. The dinuclear complex [Cu₂(L³)(H₂O)₂]⁴⁺ consists of two unsaturated 15-membered pentaaza macrocyclic units (7,7,9-trimethyl-1,3,6,10,13-pentaazacyclopentadec-9-ene) that are linked together by a methylene group in a tilted face-to-face arrangement [Cu?Cu distance: 7.413(2) Å ]. Each macrocyclic unit of [Cu₂(L³)(H₂O)₂]⁴⁺ contains one four-membered chelate ring and has a severely distorted octahedral coordination polyhedron. The dinuclear complex is quite stable in aqueous solutions containing an excess of formaldehyde or in dry acetonitrile but is decomposed to [CuL¹]²⁺ and [CuL²]²⁺ in pure water.     

Structural diversity of neutral bis-(β-iminoaldehyde) complexes of nickel(II)

Series of Ni^II and Cu^II complexes with dianionic [N₂O₂] ligands were synthesized and characterised applying spectroscopic and X-ray diffraction techniques. The ligands were obtained by 1:2 condensation of ethylene- and propylenediamine with malonic aldehyde derivatives (R² = H, R¹ = H or OCH₃). Although the molecular formulae of the complexes are quite similar, the X-ray investigations have proved a significant structural diversity in the solid state. Among others, we found some simple nearly planar molecules stacked in the crystal lattice with electron density of six-membered rings delocalised over the chelate rings as well as some very complex polymeric or nickel acetate bridged trinuclear complexes. The coordination of the nickel ion by surrounding oxygen and nitrogen atoms is square-planar in the simplest case and octahedral in the most complex one. Small topological differences in similar molecules generate completely different crystal structures.From magnetic studies, a small, negative value of J obtained confirms the occurrence of weak antiferromagnetic interactions between the Ni^II ions in polymeric chain of the propylenediamine dialdehyde substituted derivative.     

Ferric and cupric reductase activities in the green alga Chlamydomonas reinhardtii: experiments using iron-limited chemostats

Cells of the green alga Chlamydomonas reinhardtii Dangeard were grown in Fe-limited chemostat culture over a range of growth rates (0.15–1.5 d⁻¹). Greater cell densities and culture chlorophyll levels were achieved using an excess of chelator [ethylenediamine di-(o-hydroxyphenylacetic acid)] relative to FeCl₃ (80:1), compared to growth using a 1:1 chelator:FeCl₃ ratio. The C. reinhardtii cells reduced extracellular ferric chelates, and ferric chelate reductase activity increased with increasing Fe-limited growth rates. However Fe-sufficient cells exhibited a low rate of ferric chelate reductase activity, similar to severely Fe-limited cells. Iron-limited cells were capable of reducing a wide variety of ferric chelates, representing a wide range of stability constants, at similar rates, suggesting that the stability constants of ferric complexes are not important determinants of ferric reducing activity. Cupric reductase activity also increased with increasing Fe-limited growth rates, and Cu(II) was preferentially reduced compared to Fe(III). These results suggest that both reductase activities may represent the same plasma-membrane enzyme. The rate of cupric reduction was a function of the free [Cu²⁺], not the total [Cu(II)], suggesting that free Cu²⁺ is the actual substrate for cupric reductase activity. Received: 8 July 1998 / Accepted: 5 August 1998     

Adjustable ‘cross-linking’ of neighboring DNA molecules in liquid-crystalline dispersions through (daunomycin-copper) polymeric chelate complexes

The interaction of daunomycin molecules with double-stranded DNA in the liquid-crystalline state was investigated. It was shown that at a certain extent of daunomycin binding a change of the mechanism of anthracycline orientation with reference to the DNA chain occurs. This is testified by the alteration of the sense of spatial packing of the DNA molecules in liquid-crystalline dispersions formed as a result of phase separation in poly(ethyleneglycol)-containing solutions, as well as by the onset of the reaction of daunomycin with divalent copper ions. Using this reaction, polymeric (daunomycin-copper) chelate cross-links between the DNA molecules fixed in the liquid-crystalline dispersions were formed. The length of such cross-links is adjusted by the distance between the DNA molecules, which, in turn, depends on the concentration of poly(ethyleneglycol) used for phase separation. The above molecular building mechanism may lead to new interesting applications.     

Purification and properties of a ribonuclease from corn leaf tissues

An acid endoribonuclease isolated from corn leaf tissues was purified 530 times. Gel electrophoresis indicated that the enzyme was homogeneous. The enzyme showed an optimum pH at 5.5 and an apparent molecular weight of 32 000. Corn RNase attacks natural RNAs and synthetic polyribonucleotides and the relative rate of degradation was poly U > yeast RNA > E. coli tRNA > poly A ⪢ poly C. Zn²⁺, Mg²⁺, Mn²⁺ and EDTA inhibited the enzyme activity. No stimulation by K⁺ was observed. Cu²⁺ and heparin had no effect on the activity. The results suggest that the investigated RNase differs from other known corn ribonucleases.     

Resolution of an ATP-metal chelate from metal-free ATP by reverse-phase high-performance liquid chromatography

The modulation of many enzymatic reactions involved in the metabolism of nucleotide phosphates such as ATP often require divalent metal ions. In the present study reverse-phase high-performance liquid chromatography (HPLC) was used to study the chelation of divalent metal ions, such as Mn²⁺, Mg²⁺, and Ca²⁺, by ATP. The results of our study using radiolabeled [⁴⁵Ca] showed that the metal-ATP chelate formed in solution was retained longer than the metal-free ATP due to the nonpolar groups on the column packing. Recovery of the two forms of ATP showed that the [⁴⁵Ca] coeluted exclusively with the ATP-metal chelate. Other experiments showed that the retention time of the chelated form of the ATP was unaffected by eluent flow rate, but was affected by eluant pH and methanol concentration. The amount of ATP in the chelated form was found to be dependent on the amount of the metal in solution and that under appropriate conditions, i.e., with 0.1 m CaCl₂ in the mobile phase, on the divalent cation as well. Thus, we found that in terms of effectiveness in chelate formation, the metal ions were Ca²⁺ > Mg²⁺ > Mn²⁺. Recovery of the chelate and its reanalysis by HPLC revealed that the complex had dissociated. The chelate could be reformed by restoring the metal concentration to its original value and dissociated again by the addition of EDTA. The resolution of the ATP in a metal chelated form from the ATP in an unchelated form is discussed in terms of the stability of these chelates and the role of the hydrophobic groups of the column packing used in the reverse-phase HPLC in enhancement of this stability.     

Enhancement of peptide bond formation by polyribonucleotides on clay surfaces in fluctuating environments

Summary The condensation of glycine to form oligoglycine during temperature and moisture fluctuations on clay surfaces was enhanced up to fourfold by polyribonucleotides. Polydeoxyribonucleotides gave no enhancement. Yields were greatly reduced in the absence of clay. A small preference was observed among the polyribonucleotide bases with enhancements in the order of Poly G > Poly A = Poly U > Poly C at high density of polynucleotide on the clay surface and Poly G > Poly U > Poly C > Poly A at low density. This and other experiments seem to indicate a codonic bias in the interaction of polynucleotides with amino acids reacting to form peptide bonds. A mechanism is proposed which involves (1) activation of glycine on the clay surface, (2) formation of esters between glycine and the 2-OH groups of the polyribonucleotide, and (3) formation of peptide bonds between adjacent amino acyl esters. If this mechanism is correct, it may provide the basis for a simple, direct-template translation process.Abbreviations Poly A Polyadenylic acid - Poly C Polycytidylic acid - Poly G Polyguanylic acid - Poly U Polyuridylic acid - Poly dA Polydeoxyadenylic acid     

Polyribonucleotide synthesis by subfractions of microsomes from rat liver

1. The microsome fraction of rat liver has been fractionated and the ability of the fractions to incorporate ribonucleotides into polyribonucleotides has been studied. Activity was found in the rough-surfaced vesicle (light) fraction and in the free-ribosome fraction and this latter activity has been examined. 2. The free-ribosome fraction contains ribosome monomers, dimers and trimers together with some higher oligomers and ferritin. In addition to catalysing the incorporation of ribonucleotides into acid-insoluble material it contains diesterase activity. It catalyses the incorporation of UMP from UTP, but not UDP, AMP from ATP and CMP from CTP into polyribonucleotide material, and for UTP the product appears to be a homopolymer not more than eight units long attached to the ends of primer polyribonucleotide strands. 3. The activity could not be removed from the free-ribosome fraction by washing or by isolation in the presence of ethylenediaminetetra-acetic acid. 4. Partially hydrolysed polyuridylic acid but not polyadenylic acid could serve as a primer for the incorporation of UMP, but some activity was always associated with an endogenous primer. 5. Analysis of RNA extracted from the free-ribosome fraction after incubation with [³H]UTP showed the presence of 28s, 18s, 5s and transfer RNA types, but no radioactivity was associated with any of these RNA fractions.     

On the specificity of the folin and lowry reagents for amine derivatives.

Reactivities of several amine derivatives with the Folin and Lowry reagents were examined. Tertiary amines reacted with the Folin reagent to produce a blue color, and secondary amines having a 2-hydroxyethyl group reacted with the Folin reagent only in the presence of Cu²⁺, i.e., with the Lowry reagent. On the other hand, primary and quarternary amines and amine N-oxides produced no color with either reagent. Reactivities of tertiary amines were greatly influenced by the nature of the N-substituted groups, and the color yield of those forming stable chelate complexes with metals was strongly inhibited by the presence of Cu²⁺, indicating that the formation of a stable complex with Cu²⁺ reduces the reactivity of tertiary amino nitrogen. The requirement of Cu²⁺ for the color development with secondary amines having a 2-hydroxyethyl group may be due to the formation of weak chelate complex with Cu²⁺.     

Biospecific nanoparticles for multiplex phosphorescence analysis (PHOSPHAN)

We have developed a technology for the production of polymeric nanoparticles containing the incorporated phosphorescent label (europium ions–naphthoyltrifluoroacetone complexes) and streptavidin that is covalently bound on the surface. The aggregation-stable biospecific nanoparticles (40–60 nm in diameter) include up to 2000 molecular tags/particle and retain biological activity and stable phosphorescence for at least 20 months. They can be used in phosphorescence analysis (PHOSPHANTM)-based biochip technology as an effective detector system to record phosphorescence from microzones (microarrays) printed on the well bottoms of standard polystyrene microplates. The creation of a dense monolayer on the surface of a microzone requires up to 10⁸ particles/microarray, or 10⁹ particles/mm² of area; this is in good agreement with theoretical estimates. The detection limit is as low as 300–400 phosphorescent nanoparticles per a microzone with an area of ~0.1 mm². It has been demonstrated in the model of thyroid stimulating hormone (TSH) detection in filter paper dried blood that the newly developed detector system is five times more sensitive than the conventional methods of multiplex PHOSPHAN (with Pt-coproporphyrin phosphorescent label) and lanthanide immune fluoroassay (with fluorescent Eu³⁺ chelate complexes registered in the enhancement solution). The sensitivity of phosphorescent nanoparticle-based detector system is as low as 6.8 × 10⁵ molecules/1.5 μL sample, which corresponds to a TSH concentration of 1.5 × 10^–14 M.     

Voltage-dependent cationic channel of Escherichia coli

Verapamil and dimethylcurine are Ca²⁺ entry blockers of essentially different chemical structures which presumably bind to the same arylalkylamine receptor of the L-type Ca channel. A systematic conformational analysis of methoxyverapamil (D-600) and dimethylcurine has been carried out using a molecular mechanics method. The lowest minimum-energy conformations of D-600 are predisposed to chelate Ca²⁺ by four oxygen atoms of the stacked methoxyphenyl moieties. Comparison of the lowest energy conformations of D-600-Ca²⁺ and dimethylcurine revealed a similar spatial disposition of cationic groups and methoxyphenyl moieties in the two compounds. A three-dimensional model of arylalkylamine receptor was suggested which incorporates two nucleophilic areas of the Ca channel. Dimethylcurine binds to these areas by its quaternary amine functions, whereas D-600 does so by amine function and via coordinated Ca²⁺. The results support the hypotheses on ternary complex formation between the ligands of Ca channel, their receptors, and Ca²⁺.     

Nucleic acid binding properties of Escherichia coli ribosomal protein S1. II. Co-operativity and specificity of binding site II.

The following properties characterize the interaction of nucleic acid binding site II of Escherichia coli ribosomal protein S1 with oligo- and polyribonucleotides; all have been determined with site I complexed with oligo- or polydeoxyribonucleotides. (1) The intrinsic binding constant (K) of site II to single-stranded polyribonucleotides is fairly independent of base composition, though cytidinecontaining polymers bind with approximately threefold higher intrinsic affinities than do the comparable adenine-containing species. (2) Poly(rC) is bound to site II co-operatively; the co-operativity parameter (ω) ? 31. Poly(rA) shows no binding co-operativity. The site size (n) for both polyribonucleotides binding at site II is about ten nucleotide residues. (3) The K value for site II is ? 4 × 10⁵m^?1 for poly(rA), and ? 1 × 10⁶m^?1 for poly(rC), in 0.12 m-Na⁺. Unlike site I, the binding affinity of site II increases somewhat with increasing salt concentration, suggesting that phosphate—basic protein residue contacts are not involved. (4) Varying Mg^{2 +} concentration has no effect on K, and changes in the concentration of either Mg²⁺ or Na⁺ do not affect the magnitude of site II co-operativity. (5) Reaction of the exocyclic amino groups of poly (rC) with formaldehyde drastically reduces the affinity of site II for this polynucleotide, while the affinity of poly (rC) for site I is not altered by this treatment. (6) No major sequence specificity of K for site II is found with either homogeneous polynucleotides or the 3′ terminal dodecanucleotide of 16 S ribosomal RNA; we conclude that selectivity of S1 binding via site II depends largely on the presence or absence of base compositiondependent binding co-operativity.The binding properties of site II probably account for the ability of S1 to inhibit translation at high S1 to ribosome ratios (“factor i” activity). Possible mechanisms for the role of S1 protein as a part of the phage Qβ replicase complex and in protein synthesis are discussed in relation to the binding properties of site I and site II.     

DNA Staining in Agarose Gels with ZN2+-Cyclen-Pyrene

A pyrene-labeled Zn²⁺-cyclen complex for the staining of DNA in agarose gels is reported. The metal chelate coordinates reversibly to the DNA phosphate backbone, which induces the formation of pyrene excimers. The typical pyrene excimer emission is used for the detection of the DNA. Staining is limited to agarose gels and is less sensitive than ethidium bromide, but DNA amounts as low as 10 ng and short DNA strands (～300 b.p.) are detectable. Gel extraction as a standard technique in molecular biology was successfully performed after staining with Zn²⁺-cyclen-pyrene. Cytotoxicity tests on HeLa and V-79 cells reveal that the zinc-cyclen pyrene probe is significant less toxic compared to ethidium bromide.     

Novel extracellular ribonuclease from Bacillus intermedius--binase II: purification and some properties of the enzyme

The recombinant enzyme binase II was isolated from the culture liquid of Bacillus subtilis 3922 transformed with the pJF28 plasmid bearing the birB gene. The procedure of the enzyme purification included precipitation by polyethylene glycol with subsequent chromatography on DEAE-cellulose, heparin-Sepharose, and Toyopearl TSK-gel. The enzyme was purified 142-fold yielding a preparation with specific activity 1633 U/mg. The molecular weight of binase II is 30 kD. The enzyme is activated by Mg²⁺ and virtually completely inhibited by EDTA. The pH optimum for the reaction of RNA hydrolysis is 8.5. The properties of the enzyme are close to those of RNase Bsn from B. subtilis. The character of cleaving of synthetic single- and double-stranded polyribonucleotides by binase II suggests that the enzyme binds the substrate in the helix conformation, and its catalytic mechanism is close to that of RNase VI from cobra venom.     

Metal chelates in the storage and transport of neurotransmitters: interactions of Cu2+ with ATP and biogenic amines

Abstract— The thermodynamic stabilities of the coordinate binding of Cu²⁺ ion with adenosinetriphos-phate (ATP) and several biogenic amines have been determined in aqueous model systems in an attempt to examine the possible correlation between metal-amine binding and the in vivo affinities of the amines for granule-binding. In each of the ternary chelate systems consisting of Cu²⁺-ATP-amine (1:1:1), the Cu²⁺ ion is preferentially bound by ATP in the pH range 3–5 with a stability constant of Log K_ML= 517. In the pH range 5–8 each of the biogenic amines coordinates with Cu²⁺ -ATP chelate to form the respective ternary chelate. The nature and strength of binding of fourteen different amines with Cu²⁺-ATP have been evaluated on the basis of the stabilities of the ternary chelates. On the basis of the quantitative equilibrium data generated in this study, it appears that both pyrocatechol moiety and the ethanolamine side-chain of the catechol amines are involved in the coordination of copper. The metal-binding stabilities of the biogenic amines are then correlated with the molecular structure, donor basicities and the in vivo affinities of the amines for granule-binding in order to rationalize the possible involvement of metal chelates in the monoamine binding, storage and transport.