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.

The UPAL process: a direct method of preparing cast aluminium alloy-graphite particle composites

A direct method of preparing cast aluminium alloy-graphite particle composites using uncoated graphite particles is reported. The method consists of introducing and dispersing uncoated but suitably pretreated graphite particles in aluminium alloy melts, and casting the resulting composite melts in suitable permanent moulds. The optical pretreatment required for the dispersion of the uncoated graphite particles in aluminium alloy melts consists of heating the graphite particles to 400° C in air for 1 h just prior to their dispersion in the melts. The effects of alloying elements such as Si, Cu and Mg on the dispersability of pretreated graphite in molten aluminium have also been reported. It was found that additions of about 0.5% Mg or 5% Si significantly improve the dispersability of graphite particles in aluminium alloy melts as indicated by the high recoveries of graphite in the castings of these composites. It was also possible to disperse upto 3% graphite in LM 13 alloy melts and retain the graphite particles in a well distributed fashion in the castings using the pre-heat-treated graphite particles. The observations in this study have been related to the information presently available on wetting between graphite and molten aluminium in the presence of different elements and our own thermogravimetric analysis studies on graphite particles. Physical and mechanical properties of LM 13-3% graphite composite made using pre-heat-treated graphite powder, were found to be adequate for many applications, including pistons which have been successfully used in internal combustion engines.

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+.

Ni(II)chelates of 4,9-dimethyl-5,8-dizadodeca-4,8-diene-2,11-dione-3,10-diphenyl hydrazone and related molecules

Syntheses and structural characterization of Ni(II) chelates of a new series of symmetric and unsymmetric tetradentate linear ligands are described. Preparative routes involve either the direct reaction between a metal complex and arene diazonium diazonium salts or a simple metal incorporation into the independently synthesized ligands. Recent X-ray structure determination of 4,9-dimethyl-5,8-diazadodeca-4,8-diene-2,11-dione-3,10-di(4′-methyl phenyl) hydrazonatonickel(II) complex reveals the geometry around the Ni(II) to be very close to square planar. The expected distortion because of the disposition of bulky aromatic groups on the neighbouring nitrogens is minimized by their projection in the opposite directions from the plane. PMP, IR and electronic spectral data for the complexes are quite in agreement with this structure.

Thermal decomposition of alkali metal perchlorates

The effect of past mechanical history on the subsequent thermal decomposition kinetics of sodium, potassium, rubidium and caesium perchlorates, has been investigated. At low temperatures the decomposition of all these salts is significantly sensitized by pre-compression. At high temperatures, however, prior compression results in a lowered decomposition rate in the case of potassium, rubidium and caesium perchlorates and in an increase in the thermal reactivity of sodium perchlorate. The high temperature behaviour is shown to be an indirect consequence of the low temperature behaviour. The difference in behaviour between sodium perchlorate and the other alkali metal perchlorates is explained on the basis of the stability of the respective chlorates, formed during the low temperature decomposition. This is substantiated by experiments which show that the addition of sodium chlorate to sodium perchlorate brings about a sensitization while potassium perchlorate admixed with potassium chlorate results in a desensitization at high temperatures.

Catalyzed air oxidation for treatment of thiosalt effulents

Continuous slurry reactor runs of two to four weeks duration were carried out for catalyzed air oxidation of thiosalts under a variety of conditions using poly (4-vinylpyridine) - Cu (II) and quaternized poly (4-vinylpyridine) - Cu (II) catalysts. Results obtained indicate that these catalysts have high activity and relatively long-term catalyst stability for thiosalt waste streams of < 1000 ppm thiosalt level. Using 2% (w/w) slurries of the poly (4-vinylpyridine) Cu (II) catalyst, effective oxidation of 700 ppm S2O32− influent to an effluent of < 100 ppm total thio-salts can be carried out continuously for at least one month when operating at 20 to 30°C with solution flow rates of$˜1l/h and aeration of 1300 XXX/h using a two-stage reactor system comprised of 12 l reactors. At higher thiosalt influent levels (i.e. > 1600 ppm) increased reaction temperatures enable depletion to < 100 ppm thiosalt effluent levels for up to one week of continuous operation. The catalysts deactivate much more readily at these higher influent levels as a result of greater copper losses and appreciable adsorption of S2O32− and S4O62−. The behaviour of continuous slurry reactors employed in the experimental studies, by use of batch reaction data for the poly (4-vinylpyridine) Cu (II) catalyzed oxidation of thiosalts, can be modelled successfully. Quaternized poly (4-vinylpyridine) Cu (II) catalyst has good long-term stability and copper losses are very low. The poly (4-vinylpyridine) Cu (II) catalyst, however, is susceptible to appreciable oxidation of the polymer matrix on long-term usage. This oxidation of the polymer matrix results in a substantial loss in the activity of the regenerated catalyst.

Effect of pretreatment on the sublimation of ammonium perchlorate

The effects of pretreatments on the sublimation of pure ammonium perchlorate (AP) were studied by differential thermal analysis. The addition of inorganic salts (doping), or preheating, lead to desensitisation of the sublimation process, whereas it was sensitised by precompression. Sublimation increased with decrease in the particle size of the AP from 500 to 200 microns, but decreased with a further decrease in size from 200 to 100 microns. The results are interpreted in terms of gross imperfections and strain in the AP crystals.

A One-Step Method for the Growth of Ga2O3-Nanorod-Based White-Light-Emitting Phosphors

A one-step synthesis of Ga2O3 nanorods by heating molten gallium in ambient air at high temperatures is presented. The high-temperature synthesis creates oxygen vacancies and incorporates nitrogen from the environment. The oxygen vacancy in Ga2O3 is responsible for the emission in the blue-green region, while nitrogen in Ga2O3 is responsible for red emission.

The role of lithium and magnesium perchlorate ammines in ammonium perchlorate decomposition

The preparation and thermal decomposition of lithium and magnesium perchlorate ammines have been investigated. The catalytic effect of these ammines on AP decomposition has been studied. The catalytic effect of lithium and magnesium salts on AP decomposition has been attributed to the formation of the metal perchlorate ammine intermediate. In the case of a magnesium salt: AP mixture, the melting of the magnesium perchlorate monoammine intermediate seems to play an important role in catalysing the decomposition.

Interaction of surfactants with DNA. Role of hydrophobicity and surface charge on intercalation and DNA melting

A probe, 9-(anthrylmethyl)trimethylammonium chloride, 1, was prepared. 1 binds to calf-thymus DNA or Escherichia coli genomic DNA with high affinity, as evidenced from the absorption titration. Strong hypochromism, spectral broadening and red-shifts in the absorption spectra were observed. Half-reciprocal plot constructed from this experiment gave binding constant of 5±0.5×104 M−1 in base molarity. We employed this anthryl probe-DNA complex for studying the effects of addition of various surfactant to DNA. Surfactants of different charge types and chain lengths were used in this study and the effects of surfactant addition to such probe-DNA complex were compared with that of small organic cations or salts. Addition of either salts or cationic surfactants led to structural changes in DNA and under these conditions, the probe from the DNA-bound complex appeared to get released. However, the cationic surfactants could induce such release of the probe from the probe-DNA complex at a much lower concentration than that of the small organic cations or salts. In contrast the anionic surfactants failed to promote any destabilization of such probe-DNA complexes. The effects of additives on the probe-DNA complexes were also examined by using a different technique (fluorescence spectroscopy) using a different probe ethidium bromide. The association complexes formed between the cationic surfactants and the plasmid DNA pTZ19R, were further examined under agarose gel electrophoresis and could not be visualized by ethidium bromide staining presumably due to cationic surfactant-induced condensation of DNA. Most of the DNA from such association complexes can be recovered by extraction of surfactants with phenol-chloroform. Inclusion of surfactants and other additives into the DNA generally enhanced the DNA melting temperatures by a few °C and at high [surfactant], the corresponding melting profiles got broadened.

Metal-Nucleotide Interactions: Crystal Structures of Alkali (Li+, Na+, K+) and Alkaline Earth (Ca2+, Mg2+) Metal Complexes of Adenosine 2'-Monophosphate

Crystal structures of lithium, sodium, potassium, calcium and magnesium salts of adenosine 2'-monophosphate (2'-AMP) have been obtained at atomic resolution by X-ray crystallographic methods. 2'-AMP.Li belongs to the monoclinic space group P21 with a = 7.472(3)Å, b = 26.853(6) Å, c = 9.184(1)Å, b = 113.36(1)Å and Z= 4. 2'-AMP.Na and 2'-AMP.K crystallize in the trigonal space groups P31 and P3121 with a = 8.762(1)Å, c = 34.630(5)Å, Z= 6 and a = 8.931(4), Åc = 34.852(9)Å and Z= 6 respectively while 2'-AMP.Ca and 2'-AMP.Mg belong to space groups P6522 and P21 with cell parameters a = 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 10.023(2), c = 16.506(2), beta = 91.1(0) and Z = 2 respectively. All the structures were solved by direct methods and refined by full matrix least-squares to final R factors of 0.033, 0.028, 0.075, 0.069 and 0.030 for 2'-AMP.Li, 2'-AMP.Na, 2'- AMP.K, 2'-AMP.Ca and 2'-AMP.Mg, respectively. The neutral adenine bases in all the structures are in syn conformation stabilized by the O5'-N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry (cCN = -156.4(2)°) in 2'-AMP.Mg. Ribose moieties adopt C2'-endo puckering in 2'-AMP.Li and 2'-AMP.Ca, C2'-endo-C3'-exo twist puckering in 2'-AMP.Na and 2'-AMP.K and a C3'-endo-C2'-exo twist puckering in 2'-AMP.Mg structure. The conformation about the exocyclic C4'-C5' bond is the commonly observed gauche-gauche (g+) in all the structures except the gauche- trans (g-) conformation observed in 2'-AMP.Mg structure. Lithium ions coordinate with water, ribose and phosphate oxygens at distances 1.88 to 1.99Å. Na+ ions and K+ ions interact with phosphate and ribose oxygens directly and with N7 indirectly through a water oxygen. A distinct feature of 2'-AMP.Na and 2'-AMP.K structures is the involvement of ribose O4' in metal coordination. The calcium ion situated on a two-fold axis coordinates directly with three oxygens OW1, OW2 and O2 and their symmetry mates at distances 2.18 to 2.42Å forming an octahedron. A classic example of an exception to the existence of the O5'-N3 intramolecular hydorgen bond is the 2'-AMP.Mg strucure. Magnesium ion forms an octahedral coordination with three water and three phosphate oxygens at distances ranging from 2.02 to 2.11Å. A noteworthy feature of its coordination is the indirect link with N3 through OW3 oxygen resulting in macrochelation between the base and the phosphate group. Greater affnity of metal clays towards 5' compared to 2' and 3' nucleotides (J. Lawless, E. Edelson, and L. Manring, Am. Chem. Soc. Northwest Region Meeting, Seattle. 1978) due to macrochelation infered from solution studies (S. S. Massoud, H. Sigel, Eur. J. Biochem. 179, 451-458 (1989)) and interligand hydrogen bonding induced by metals postulated from metal-nucleotide structures in solid state (V. Swaminathan and M. Sundaralingam, CRC. Crit. Rev. Biochem. 6, 245-336 (1979)) are borne out by our structures also. The stacking patterns of adenine bases of both 2'-AMP.Na and 2'-AMP.K structures resemble the 2'-AMP.NH4 structure reported in the previous article. 2'-AMP.Li, 2'-AMP.Ca and 2'-AMP.Mg structures display base-ribose O4' stacking. An overview of interaction of monovalent and divalent cations with 2' and 5'-nucleotides has been presented.

Hydrazinium thiocyanate as a reagent for determination of copper

Hydrazinium thiocyanate, N2H5SCN, has been used for the determination of copper in copper salts. The reagent reduces the copper ions to the cuprous state and precipitates cuprous thiocyanate Cu2(SCN)2, quantitatively.

Ion exchange of sodium chloride and sodium bicarbonate solutions using strong acid cation resins in relation to coal seam water treatment

Coal seam gas production has resulted in the production of large volumes of associated water which contains dissolved salts dominated by sodium chloride and sodium bicarbonate. Ion exchange using synthetic resins has been proposed as a method for desalination of coal seam water to make it suitable for various beneficial reuse options. This study investigated the behaviour of solutions of sodium chloride and sodium bicarbonate with respect to exchange with Lanxess S108H strong acid cation (SAC) resin. Equilibrium isotherms were created for solutions of NaCl and NaHCO3 and an actual sample of coal seam water from the Surat Basin in southern Queensland. The exchange of sodium ions arising from sodium bicarbonate was found to be considerably more favourable than exchange of sodium ions from sodium chloride solutions. This latter behaviour was attributed to the secondary decomposition of bicarbonate species under acidic conditions which resulted in the evolution of carbon dioxide and formation of water. The isotherm profiles could not be satisfactorily fitted by a single isotherm model such as the Langmuir expression. Instead, two Langmuir equations had to be simultaneously applied in order to fit the sections of the isotherm attributable to sodium ion exchange from sodium bicarbonate and sodium chloride. The shape of the isotherm profile was dependent upon the ratio of sodium chloride to sodium bicarbonate in solution and there was a high degree of correlation between simulated and actual coal seam water solutions.

Dependence of pH and surfactant effect in the synthesis of magnetite(Fe3O4) nanoparticles and its properties

Nanoparticles of Fe3O4 were synthesized by co-precipitation in an aqueous solution containing ferrous and ferric salts (1:2) at varying pH with ammonia as a base. It was found that the value of pH influences the reaction mechanism for the formation of Fe3O4. Furthermore, the addition of mercaptoethanol significantly reduced the crystalline size of Fe3O4 nanoparticles from 15.03 to 8.02 nm. X-ray diffraction (XRD) spectra revealed that the synthesized nanoparticles were epsilon-Fe2O3 or Fe3O4 phase. To further prove the composition of the product, as-prepared Fe3O4 were examined by X-rayphotoelectron spectroscopy (XPS). Magnetic properties of the obtained particles were determined by vibrating sample magnetometer (VSM). Further analysis of the X-ray studies shows that while maintaining a pH value of 6 and 9 in a solution containing iron salts II and III ions produces epsilon-Fe2O3. Whereas a pH value of 11 produces magnetite (Fe3O4) phase. All of these results show that the pH has a major role in the observed phase formation of (Fe3O4) nanoparticles.

Hydrogel membrane electrolyte for electrochemical capacitors

Polymer electrolytes are known to possess excellent physicochemical properties that are very useful for electrochemical energy systems. The mobility in polymer electrolytes is understood to be mainly due to the segmental motion of polymer chains and the ion transport is generally restricted to the amorphous phase of the polymer. Gel polymer electrolytes (GPE) that are formed using plastizicers and polymers along with ionic salts are known to exhibit liquid-like ionic conductivity while maintaining the dimensional stability of a solid matrix. In the present study, the preparation and characterization of poly(vinyl alcohol)-based hydrogel membranes (PHMEs) as electrolyte for electrochemical capacitors have been reported. VaryingHClO4 dopant concentration leads to different characteristics of the capacitors. The EC comprising PHME doped with 2 M HClO4 and black pearl carbon (BPC) electrodes has been found to exhibit a maximum specific capacitance value of 97 F g(-1), a phase angle value of 78A degrees, and a maximum charge-discharge coulombic efficiency of 88%.