Deriving structural information from non-coding ribonucleic acids by mass spectrometry

The purpose of this study is to describe the development of application of mass spectrometry for the structural analyses of non-coding ribonucleic acids during past decade. Mass spectrometric methods are compared of traditional gel electrophoretic methods, the characteristics of performance of mass spectrometric, analyses are studied and the future trends of mass spectrometry of ribonucleic acids are discussed. Non-coding ribonucleic acids are short polymeric biomolecules which are not translated to proteins, but which may affect the gene expression in all organisms. Regulatory ribonucleic acids act through transient interactions with key molecules in signal transduction pathways. Interactions are mediated through specific secondary and tertiary structures. Posttranscriptional modifications in the structures of molecules may introduce new properties to the organism, such as adaptation to environmental changes or development of resistance to antibiotics. In the scope of this study, the structural studies include i) determination of the sequence of nucleobases in the polymer chain, ii) characterisation and localisation of posttranscriptional modifications in nucleobases and in the backbone structure, iii) identification of ribonucleic acid-binding molecules and iv) probing of higher order structures in the ribonucleic acid molecule. Bacteria, archaea, viruses and HeLa cancer cells have been used as target organisms. Synthesised ribonucleic acids consisting of structural regions of interest have been frequently used. Electrospray ionisation (ESI) and matrix-assisted laser desorption ionisation (MALDI) have been used for ionisation of ribonucleic analytes. Ammonium acetate and 2-propanol are common solvents for ESI. Trihydroxyacetophenone is the optimal MALDI matrix for ionisation of ribonucleic acids and peptides. Ammonium salts are used in ESI buffers and MALDI matrices as additives to remove cation adducts. Reverse phase high performance liquid chromatography has been used for desalting and fractionation of analytes either off-line of on-line, coupled with ESI source. Triethylamine and triethylammonium bicarbonate are used as ion pair reagents almost exclusively. Fourier transform ion cyclotron resonance analyser using ESI coupled with liquid chromatography is the platform of choice for all forms of structural analyses. Time-of-flight (TOF) analyser using MALDI may offer sensitive, easy-to-use and economical solution for simple sequencing of longer oligonucleotides and analyses of analyte mixtures without prior fractionation. Special analysis software is used for computer-aided interpretation of mass spectra. With mass spectrometry, sequences of 20-30 nucleotides of length may be determined unambiguously. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Sequencing in conjunction with other structural studies enables accurate localisation and characterisation of posttranscriptional modifications and identification of nucleobases and amino acids at the sites of interaction. High throughput screening methods for RNA-binding ligands have been developed. Probing of the higher order structures has provided supportive data for computer-generated three dimensional models of viral pseudoknots. In conclusion. mass spectrometric methods are well suited for structural analyses of small species of ribonucleic acids, such as short non-coding ribonucleic acids in the molecular size region of 20-30 nucleotides. Structural information not attainable with other methods of analyses, such as nuclear magnetic resonance and X-ray crystallography, may be obtained with the use of mass spectrometry. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Ligand screening may be used in the search of possible new therapeutic agents. Demanding assay design and challenging interpretation of data requires multidisclipinary knowledge. The implement of mass spectrometry to structural studies of ribonucleic acids is probably most efficiently conducted in specialist groups consisting of researchers from various fields of science.

Role of magnesium ion on the interaction between chromomycin A3 and deoxyribonucleic acid

Abstract is not available.

Mixed ligand complexes in vinyl polymerization. I. [N,N-ethylenebis (salicylideneiminato)](acetylacetonato)cobalt(III) as an initiator

Polymerization of methyl methacrylate in the presence of a mixed ligand complex, [N,N-ethylenebis(salicylideneiminato)](acetylacetonato)cobalt(III) in benzene was studied. The rate of polymerization was proportional to the square root of the concentration of the chelate and the monomer exponent was 1.67 and 1.69 at 60 and 70°C, respectively. The activation energy and the kinetic and transfer constants were evaluated. A free-radical mechanism has been proposed.

2-Thioacetamido thiazole as an ambidentate ligand. Complexes of Zn(II), Cd(II), Hg(II) and Cu(I)

Metal complexes of thiazoles have been studied in recent years[I-3] because of their biochemical importance[4,5]. However, data on metal complexes of thiazole derivatives containing another coordinating function are limited[2]. We have synthesized and examined the donor characteristics of a new ligand, 2-thioacetamide thiazole (TATZ)(I) towards chlorides and bromides of Zn(II), Cd(II), Hg(II) and Cu(I). The presence of four potential donor atoms and extensive charge delocalization should render TATZ a versatile ligand.

Synthesis of Azo Coupled Crown Ethers Containing Transition Metal and other Chromophoric Environments and Their Ion Complexation Properties

The crown ethers, 2,3-benzo-1,4,7,10,13-pentaoxa-cyclopentadeca-2-ene and 2,3, ll,12-dibenzo-l,4,7,10,13,16-hexaoxscyclooctadeca-2,11-diene are incorporated into H,N'-ethylenebis(acetylacetoneimino) nickel(II) and copper(II), phenol, and β-naphthol by diazo coupling reactions. The selective nature of the coupling reaction has-been demonstrated by the isolation of both asymmetric mono- and symmetric bis(glyoxalarylcrownhydrazoneimino) metal(II) complexes. An interesting binuclear complex containing two intramolecularly rearranged (glyoxal-hydrazonearylimino) metal(II) groups joined by 18-crown-6 result8 when bis(arenediazonium)-18-crown-6 is coupled with the metal(I1) Schiff bases. The substituted ethers form cationic salts with NaClO4, KCNS, NH4CNS, 14g(CNS)2 and Ca(CNS)2. All the synthesised ethers exhibit ion selectivity sequence as K+ > Na+ and Ca2+ > Mg2+.

Reactive state selectivity in photodimerization through micellar counter-ion effects: photodimerization of acenaphthylenes

Photodimerization of acenaphthylene and 5,6-dichloroacenaphthylene solubilized in sodium dodecylsulphate (SDS), cetyltrimethylammonium chloride (CTAC), dodecyltrimethylammonium chloride (DTAC), cetyltrimethylammonium bromide (CTAB) and Triton X-100 micelles gives a mixture of cis and trans dimers. The magnitude of the cis:trans ratio is sensitive to the type of micelle used. In CTAB micelles the heavy atom effect of the bromide counter-ions leads to an increased triplet-derived trans dimer yield, whereas in micelles with light atom counter-ions (CTAC, DTAC and SDS) the singlet-derived cis dimer predominates.

2,6-Lutidine-N-oxide complexes of rare-earth bromides

2,6-Lutidine-N-oxide (LNO) complexes of rare-earth bromides of the composition $$MBr_3 .(LNO)_{4_{ - n} } .nH_2 O$$ wheren = l for M = La, Pr, Nd, Sm, Gd, Ho, Er; andn = 0 for M = Y have been prepared and characterised by analyses, conductance and infrared data. Infrared spectra of the complexes indicate that the coordination of ligand to the metal ion takes place through the oxygen of the ligand, and the water molecule in the complexes present is coordinated to the metal. A coordination number of seven has been suggested to all the rare-earth metal ions.

Nature of the thiamin-binding protein from chicken egg yolk

A simple, rapid and efficient procedure for the purification of thiamin-binding protein from chicken egg yolk was developed. The method involved removal, by exclusion, of lipoproteins from DEAE-cellulose and subsequent elution of water-soluble proteins held on the ion-exchanger with 1 M-NaCl, followed by treatment of the eluted protein fraction with an aqueous suspension of dextran/charcoal to generate apoprotein from the holoprotein. The resultant protein fraction was subjected to bioaffinity chromatography on thiamin pyrophosphate--AE (aminoethyl)-Sepharose. The protein eluted specifically with 10 microM-thiamin at pH 7.0, was homogeneous by the criteria of polyacrylamide-gel disc electrophoresis, had a mol.wt. of 38 000 +/- 2000 and was not a glycoprotein. The purified thiamin-binding protein specifically interacted with riboflavin-binding protein with no detectable deleterious affect on its (14C)thiamin-binding capacity. The protein bound [14C]thiamin with a molar ratio of 1.0, with dissociation constant (Kd) 0.41 microM. This protein-ligand interaction was inhibited by thiamin analogues and antagonists. The absorption spectrum of the protein in the presence of thiamin exhibited significant hypochromism at the 278 nm band, indicating the involvement of aromatic amino acid residues of the protein, during its binding to the ligand. The protein cross-reacted with the monospecific antiserum to egg-white thiamin-binding protein, showing thereby that thiamin-binding proteins present in chicken egg yolk and white are the products of the same structural gene.

Propagation of ion-acoustic waves in a multi-component plasma

The authors derive the Korteweg-de Vries equation in a multicomponent plasma that includes any number of positive and negative ions. The solitary wave solutions are also found explicitly for the case of isothermal and non-isothermal electrons.

Electron paramagnetic resonance study of vanadyl ion in K2Zn(SO4)2·6H2O and K2Mg(SO4)2·6H2O

EPR study of the vanadyl ion has been carried out in its paramagnetically dilute form in K2Zn(SO4)2·6H2O and K2Mg(SO4)2·6H2O at room temperature at X-band. The vanadyl ion enters the divalent metal site and preferentially orients itself in the direction of the water molecules forming the octahedron and forms the vanadyl sulfate pentahydrate complex. The g and A tensorscorresponding to the two populous V-O orientations have been analyzed to obtain the principal values and their direction cosines with respect to the crystallographics axes. It is found that the g and A tensor have the same principal frames of reference within the limits of eperimental error. A correlation between the metal-water distance and the populations of the different V-O orientations is observed.

Nonlinear saturation of ion-acoustic instability

It is proposed that the wave mediated indirect wave-particle interaction may be responsible for nonlinear saturation of current driven low frequency ion-acoustic turbulence. This process decreases the growth rate and increases the damping rate of the wave. Comparison has been made with some experiments.

Complexes of lanthanide iodides with 3-methylpyridine-1-oxide

Complexes of lanthanide iodides with 3-methylpyridine-1-oxide of the formula Ln(3-MePyO)8I3.xH2O where x = 0 for Ln = La and Tb, x = 1 for Ln = Pr, and x = 2 for Ln = Nd, Sm, Dy, Yb, and Y have been prepared and characterized by chemical analyses, conductance, infrared, proton nmr, and DTA data. Infrared and proton nmr data have been interpreted in terms of the coordination of the ligand to the metal ion through the oxygen of the N—O group. Proton nmr spectrum of the Yb(III) complex is indicative of a restricted rotation of the pyridine ring about the N—O bond.

Effect of ionic temperature on propagation of ion-acoustic solitary waves in a collisionless plasma of warm-ion fluid and non-isothermal electrons

Using a perturbation technique, we derive Modified Korteweg—de Vries (MKdV) equations for a mixture of warm-ion fluid (γ i = 3) and hot and non-isothermal electrons (γ e> 1), (i) when deviations from isothermality are finite, and (ii) when deviations from isothermality are small. We obtain stationary solutions for these equations, and compare them with the corresponding solutions for a mixture of warm-ion fluid (γ i = 3) and hot, isothermal electrons (γ i = 1).