Phosphate Base Research Articles

Increased optical pathlength through aqueous media for the infrared microanalysis of live cells

The study of live cells using Fourier transform infrared spectroscopy (FTIR) and FTIR microspectroscopy (FT-IRMS) intrinsically yields more information about cell metabolism than comparable experiments using dried or chemically fixed samples. There are, however, a number of barriers to obtaining high-quality vibrational spectra of live cells, including correction for the significant contributions of water bands to the spectra, and the physical stresses placed upon cells by compression in short pathlength sample holders. In this study, we present a water correction method that is able to result in good-quality cell spectra from water layers of 10 and 12 μm and demonstrate that sufficient biological detail is retained to separate spectra of live cells based upon their exposure to different novel anti-cancer agents. The IR brilliance of a synchrotron radiation (SR) source overcomes the problem of the strong water absorption and provides cell spectra with good signal-to-noise ratio for further analysis. Supervised multivariate analysis (MVA) and investigation of average spectra have shown significant separation between control cells and cells treated with the DNA cross-linker PL63 on the basis of phosphate and DNA-related signatures. Meanwhile, the same control cells can be significantly distinguished from cells treated with the protein kinase inhibitor YA1 based on changes in the amide II region. Each of these separations can be linked directly to the known biochemical mode of action of each agent.Graphical abstract

Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations

RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base-phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin-ricin loop, which may predetermine the S-turn topology and complex BPh patterns from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions.

Classification and energetics of the base-phosphate interactions in RNA

Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and superimposing base-phosphate (BPh) interactions from a reduced-redundancy subset of 3D structures from the PDB, we identified recurrent phosphate-binding sites on the RNA bases. Quantum chemical calculations were carried out on model systems representing each BPh interaction. The calculations show that the centers of each cluster obtained from the structure superpositions correspond to energy minima on the potential energy hypersurface. The calculations also show that the most stable phosphate-binding sites occur on the Watson–Crick edge of guanine and the Hoogsteen edge of cytosine. We modified the ‘Find RNA 3D' (FR3D) software suite to automatically find and classify BPh interactions. Comparison of the 3D structures of the 16S and 23S rRNAs of Escherichia coli and Thermus thermophilus revealed that most BPh interactions are phylogenetically conserved and they occur primarily in hairpin, internal or junction loops or as part of tertiary interactions. Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments.

Technological peculiarities of ceramic material production on the basis of phosphate bonding

The complex and energy-consuming technological processes involved in the production of construction ceramics and fireproof materials promote a search for new ways of their production. The technological peculiarities of producing non-baked ceramic materials are described, as shown in silicon nitride compositions with phosphate binders (PB), and also by the use of aluminosilicate raw material, alumina and zirconia, silicon carbide, and other powder components. The kinetics of hardening and structure forming in the silicon nitride-PB system at different heating temperatures for the binder P 2 O 5 and changing strength of the samples has been researched. The physicochemical processes operating during heating in the above mentioned system have been studied. It has been shown that the structure-forming process in the silicon nitride-PB system (additives included) depends on the moulding process, the type and the quantity of PB, the dispersion of powders, and the degree of their chemical activity. Analogous criteria are characteristic for other systems. The article highlights the technological peculiarities of producing ceramic materials with the use of PB that determine the ways of moulding articles depending on the tasks connected with development and design of new materials. Certain properties and areas of use are given.

Biochemical Analysis of Vagotomized Stomach Wall in Rats

The authors carried out a biochemical analysis of vagotomized rat stomach wall 2–3 weeks after a bilateral vagotomy. The biochemical extraction was performed by the Schneider-Schmidt-Thannhauser method. The phosphate fractions were measured colorimetrically according to Briggs. The nucleic acids were measured on the basis of phosphate and sugar components according to Seibert and Brown. The following compounds were determined: acid-soluble organic and inorganic phosphates, phospholipidphosphate, ribonucleic acidic phosphate, deoxyribonucleic acidic phosphate, phosphoproteid inorganic phosphate, ribonucleic acid and deoxyribonucleic acid from the whole, the glandular and the membranaceous stomach. These were compared with the some constituents of the normal rat stomach. After vagotomy a decrease was observed in acid-soluble inorganic phosphate, in organic acid-soluble phosphate, in phosphoprotein inorganic phosphate of the glandular, membranaceous and the total stomach. The phospholipid phosphate did not d...