Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions

DNA/RNA chromatography presents a versatile platform for the analysis of nucleic acids. Although the mechanism of separation of double stranded (ds) DNA fragments is largely understood, the mechanism by which RNA is separated appears more complicated. To further understand the separation mechanisms of RNA using ion pair reverse phase liquid chromatography, we have analysed a number of dsRNA and single stranded (ss) RNA fragments. The high-resolution separation of dsRNA was observed, in a similar manner to dsDNA under non-denaturing conditions. Moreover, the high-resolution separation of ssRNA was observed at high temperatures (75 °C) in contrast to ssDNA. It is proposed that the presence of duplex regions/secondary structures within the RNA remain at such temperatures, resulting in high-resolution RNA separations. The retention time of the nucleic acids reflects the relative hydrophobicity, through contributions of the nucleic sequence and the degree of secondary structure present. In addition, the analysis of RNA using such approaches was extended to enable the discrimination of bacterial 16S rRNA fragments and as an aid to conformational analysis of RNA. RNA:RNA interactions of the human telomerase RNA component (hTR) were analysed in conjunction with the incorporation of Mg²⁺ during chromatography. This novel chromatographic procedure permits analysis of the temperature dependent formation of dimeric RNA species.     

Liquid–liquid extraction of neodymium (III) and europium (III) using synergic mixture of furosemide and tribenzylamine in benzyl alcohol

The extraction behavior of Nd(III) and Eu(III) with 0.05 mol dm⁻³ furosemide in benzyl alcohol as single acidic extractant and then with equimolar (0.05 mol dm⁻³) synergic mixture of furosemide as acidic extractant and tribenzylamine as neutral donor in benzyl alcohol has been studied from aqueous solutions of pH 1 to 6. The effect of various parameters and of various cations and anions on the extraction of these metal ions was investigated. The composition of the extracted adducts was determined by slope analysis method that came out to be [(M(FS)₂)⁺ (CH₃COO)⁻] and [M(FS)₃·3TBA] where M = Nd(III) and Eu(III).

     

The structures of europium(III)- and uranium(IV) derivatives of [P5w3oo110]15-: Evidence for “cryptohydration”

The crystal structures of (Nh₄)_11.5K_0.5[ Eu(OH₂)P₅W₃₀O₁₁₀] ·24 H₂O, K₅H₅ [Eu(OH₂)P₅W₃₀O₁₁₀] ·31 H₂O, and (NH₄)₁₁[U(OH₂)P₅Wn₃₀O₁₁₀ ·12 H₂O have been determined. In each case, the anion has the overall virtual C_5v symmetry previously observed for the sodium derivative, [NaP₅W_{30 110}]14- The encrypted Eu³⁺ and U⁴⁺cations lie on the C₅ axis, but are displaced further than the Na⁺ from the equatorial plane defined by the five phosphorus atoms. Only minor differences are observed between the structures of the two salts of the europium derivative, although solutions of these display³¹P NMR spectra with chemical shifts differing by 10 ppm, provisionally attributed to the effects of protonation of the anion, The most significant feature of the three new structures is the presence of a water molecule within the central cavity and coor-dinated to the Eu³⁺ or U⁴⁺ cation.The coordination spheres of the central cations can therefore be described as monocapped pentagonal antiprisms.     

Proof of the existence of the cluster free energy

LetZ _p be the partition function over internal configurational degrees of freedom of ap-particle cluster. The existence of the limit, asp, of (p)^–1 logZ _p is demonstrated for the square, triangle, hexagon, simple cubic, face-centered cubic, and body-centered cubic lattice gas models, and for continuous space models with potentials satisfying stability and tempering conditions. Pairwise, finite-range bonding is assumed throughout.Supported in part by the Robert A. Welch Foundation.     

Robust, alkali-stable, triscarbonyl metal derivatives of hexametalate anions, [M6O19[M'(CO)3]n](8-n)- (M = Nb, Ta; M' =Mn, Re; n = 1, 2)

Ten 1:1 and 2:1 complexes of [Mn(CO)(3)](+) and [Re(CO)(3)](+) with [Nb(6)O(19)](8)(-) and [Ta(6)O(19)](8)(-) have been isolated as potassium salts in good yields and characterized by elemental analysis, (17)O NMR and infrared spectroscopy, and single-crystal X-ray structure determinations. Crystal data for 1 (t-Re(2)Ta(6)): empirical formula, K(4)Na(2)Re(2)C(6)Ta(6)O(35)H(20), monoclinic, space group, C2/m, a = 17.648(3) A, b = 10.056(1) A, c = 13.171(2) A, beta = 112.531(2) degrees, Z = 2. 2 (t-Re(2)Nb(6)): empirical formula, K(6)Re(2)C(6)Nb(6)O(38)H(26), monoclinic, space group, C2/m, a = 17.724(1) A, b = 10.0664(6) A, c = 13.1965(7) A, beta = 112.067(1) degrees, Z = 2. 3 (t-Mn(2)Nb(6)): empirical formula, K(6)Mn(2)C(6)Nb(6)O(37)H(24), monoclinic, space group, C2/m, a = 17.812(2) A, b = 10.098(1) A, c = 13.109(2) A, beta = 112.733(2) degrees, Z = 2. 4 (c-Mn(2)Nb(6)): empirical formula, K(6)Mn(2)C(6)Nb(6)O(50)H(50), triclinic, space group, P1, a = 10.2617(6) A, b = 13.4198(8) A, c = 21.411(1) A, alpha = 72.738(1) degrees, beta = 112.067(1) degrees, gamma = 83.501(1) degrees, Z = 2. 5 (c-Re(2)Nb(6)): empirical formula, K(6)Re(2)C(6)Nb(6)O(54)H(58), monoclinic, space group, P2(1)/c, a = 21.687(2) A, b = 10.3085(9) A, c = 26.780(2) A, beta = 108.787(1) degrees, Z = 4. The complexes contain M(CO)(3) groups attached to the surface bridging oxygen atoms of the hexametalate anions to yield structures of nominal C(3)(v)() (1:1), D(3)(d)() (trans 2:1), and C(2)(v)() (cis 2:1) symmetry. The syntheses are carried out in aqueous solution or by aqueous hydrothermal methods, and the complexes have remarkably high thermal, redox, and hydrolytic stabilities. The Re-containing compounds are stable to 400-450 degrees C, at which point CO loss occurs. The Mn compounds lose CO at temperatures above 200 degrees C. Cyclic voltammetry of all complexes in 0.1 M sodium acetate show no redox behavior, except an irreversible oxidation process at approximately 1.0 V vs. Ag/AgCl. In contrast to the parent hexametalate anions that are stable only in alkaline (pH >10) solution, the new complexes are stable, at least kinetically, between pH 4 and pEta approximately 12.     

Phenyltin-substituted 9-tungstogermanate and comparison with its tungstosilicate analogue

Reaction of (C 6H 5)SnCl 3 with Na 10[ A-alpha-GeW 9O 34] in water results in the monomeric, trisubstituted Keggin species [{(C 6H 5)Sn(OH)} 3( A-alpha-GeW 9O 34)] (4-) ( 1), constituting the first organotin derivative of a trilacunary Keggin tungstogermanate. Polyanion 1 could be obtained as two different cesium salts depending on the applied isolation strategy: Cs 3Na[{(C 6H 5)Sn(OH)} 3( A-alpha-GeW 9O 34)].9H 2O ( CsNa-1) and Cs 3[{(C 6H 5)Sn(OH)} 3( A-alpha-HGeW 9O 34)].8H 2O ( Cs-H1). The monomeric phenyltin-containing tungstosilicate [{(C 6H 5)Sn(OH)} 3( A-alpha-SiW 9O 34)] (4-) ( 2) and the dimeric, sandwich-type derivative [{(C 6H 5)Sn(OH)} 3( A-alpha-H 3SiW 9O 34) 2] (8-) ( 3) have also been isolated as the cesium salts Cs 3Na[{(C 6H 5)Sn(OH)} 3( A-alpha-SiW 9O 34)].9H 2O ( CsNa-2), Cs 4[{(C 6H 5)Sn(OH)} 3( A-alpha-SiW 9O 34)].13H 2O ( Cs-2), and Cs 8[{(C 6H 5)Sn(OH)} 3( A-alpha-H 3SiW 9O 34) 2].23H 2O ( Cs-3), respectively. We have investigated in detail the similarities and differences in the reactivity of (C 6H 5)Sn (3+) with [ A-alpha-GeW 9O 34] (10-) vs [ A-alpha-SiW 9O 34] (10-). All five compounds have been characterized in the solid state by means of elemental analysis, infrared spectroscopy, thermogravimetry, and single-crystal X-ray diffraction, representing the first structural analysis for polyanions 1- 3. A full solution characterization of 1 by multinuclear NMR spectroscopy ( (1)H, (13)C, (119)Sn, and (183)W) has also been performed. The monomeric polyanions 1 and 2 are closely associated in the solid state through (Sn)O-H...O t (O t: terminal oxygen atom) hydrogen bonds reinforced by weak C-H...O t contacts to form 2-dimensional ( CsNa-1 and CsNa-2) or 1-dimensional ( Cs-H1) arrangements, and also dimeric entities ( Cs-2) depending on the network of intermolecular interactions.     

First diastereoselective synthesis of methyl caffeoyl- and feruloyl-muco-quinates

We report on a diastereoselective synthesis of six derivatives of caffeoyl- and feruloyl-muco-quinic acids. All the muco-quinic acid derivatives were obtained in excellent yield in five steps starting from quinic acid, caffeic acid and ferulic acid. Allyl ether protection of trans-hydroxy cinnamic acids was here introduced to chlorogenic acids synthesis. We show that muco-quinic acid derivatives, which are formally diastereoisomers of chlorogenic acids, can be readily distinguished by their tandem mass spectra.     

Transition metal containing decatungstosilicate dimer [M(H(2)O)(2)(gamma-SiW(10)O(35))(2)](10-) (M = Mn(2+), Co(2+), Ni(2+))

The new, monometal substituted silicotungstates [Mn(H(2)O)(2)(gamma-SiW(10)O(35))(2)](10-) (1), [Co(H(2)O)(2)(gamma-SiW(10)O(35))(2)](10-) (2) and [Ni(H(2)O)(2)(gamma-SiW(10)O(35))(2)](10-) (3) have been synthesized and isolated as the potassium salts K(10)[Mn(H(2)O)(2)(gamma-SiW(10)O(35))(2)] x 8.25 H(2)O (K-1), K(10)[Co(H(2)O0(2)(gamma-SiW(10)O(35))(2)] x 8.25 H(2)O (K-2) and K(10)[Ni(H(2)O)(2)(gamma-SiW(10)O(35))(2)] x 13.5 H(2)O (K-3), which have been characterized by IR spectroscopy, single crystal X-ray diffraction, elemental analysis and cyclic voltammetry. Polyanions 1-3 are composed of two (gamma-SiW(10)O(36)) units fused on one side via two W-O-W' bridges and on the other side by an octahedrally coordinated trans-MO(4)(OH(2))(2) transition metal fragment, resulting in a structure with C(2v) point group symmetry. Anions 1-3 were synthesized by reaction of the dilacunary precursor [gamma-SiW(10)O(36)](8-) with Mn(2+), Co(2+) and Ni(2+) ions, respectively, in 1 M KCl solution at pH 4.5. The electrochemical properties of 1-3 were studied by cyclic voltammetry and controlled potential coulometry in a pH 5 buffer medium. The waves associated with the W-centers are compared with each other and with those of the parent lacunary precursor [gamma-SiW(10)O(36)](8-) in the same medium. They appear to be dominated by the acid-base properties of the intermediate reduced species. A facile merging of the waves for 3 is observed while those for 1 and 2 remain split. Controlled potential coulometry of the single wave of 3 or the combined waves of 1 and 2 is accompanied by catalysis of the hydrogen evolution reaction. No redox activity was detected for the Ni(2+) center in 3, whereas the Co(2+) center in 2 shows a one-electron redox process. The two-electron, chemically reversible process of the Mn(2+) center in 1 is accompanied by a film deposition on the electrode surface.