Spectroscopic Characterization of Mitochondrial G-Quadruplexes

Guanine quadruplexes (G4s) are highly polymorphic four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of the first G4 structures within mitochondrial DNA has led to a small revolution in the field. In particular, the G-rich conserved sequence block II (CSB II) can form different types of G4s that are thought to play a crucial role in replication. In this study, we decipher the most relevant G4 structures that can be formed within CSB II: RNA G4 at the RNA transcript, DNA G4 within the non-transcribed strand and DNA:RNA hybrid between the RNA transcript and the non-transcribed strand. We show that the more abundant, but unexplored, G6AG7 (37%) and G6AG8 (35%) sequences in CSB II yield more stable G4s than the less profuse G5AG7 sequence. Moreover, the existence of a guanine located 1 bp upstream promotes G4 formation. In all cases, parallel G4s are formed, but their topology changes from a less ordered to a highly ordered G4 when adding small amounts of potassium or sodium cations. Circular dichroism was used due to discriminate different conformations and topologies of nucleic acids and was complemented with gel electrophoresis and fluorescence spectroscopy studies.

Mixed-metal phosphates K1.64Na0.36TiFe(PO4)3 and K0.97Na1.03Ti1.26Fe0.74(PO4)3 with a langbeinite framework

Single crystals of the langbeinite-type phosphates K1.65Na0.35TiFe(PO4)3 and K0.97Na1.03Ti1.26Fe0.74(PO4)3 were grown by crystallization from high-temperature self-fluxes in the system Na2O–K2O–P2O5–TiO2–Fe2O3 using fixed molar ratios of (Na+K):P = 1.0, Ti:P = 0.20 and Na:K = 1.0 or 2.0 over the temperature range 1273–953 K. The three-dimensional framework of the two isotypic phosphates are built up from [(Ti/Fe)2(PO4)3] structure units containing two mixed [(Ti/Fe)O6] octahedra (site symmetry 3) connected via three bridging PO4 tetrahedra. The potassium and sodium cations share two different sites in the structure that are located in the cavities of the framework. One of these sites has nine and the other twelve surrounding O atoms.

A new guaninate hydrate K+·C5H4N5O−·H2O: crystal structure from 100 to 300 K in a comparison with 2Na+·C5H3N5O2−·7H2O

A new guanine salt hydrate, K+·C5H4N5O−·H2O, was obtained and characterized by single-crystal X-ray diffraction in the temperature range 100 K–300 K and compared with that of the previously documented sodium salt hydrate (2Na+·C5H3N5O2−·7H2O) [Gur & Shimon (2015). Acta Cryst. E71, 281–283; Gaydamaka et al. (2019). CrystEngComm, 21, 4484–4492]. Both sodium and potassium salt hydrates have channels. However, the structure of the channels, the cation coordination, the protonation (and, respectively, the charge) of the guanine anions, as well as the role of water molecules in the crystal structure are different for the two salt hydrates. In the crystal structures of the potassium salt, the guanine anions are linked via hydrogen bonds into quartets that form open cylindrical channels in a honeycomb framework. Water molecules `line the walls' of the channels, whereas the potassium cations fill the intra-channel space. This contrasts with the structure of the sodium salt hydrate in which guanine anions form channels with water molecules filling in the channel space together with sodium cations coordinating them. The 1D anionic assembly generated through numerous hydrogen bonds and cation interactions with guanine anions and water molecules is energetically the most distinctive part of the structure of the potassium salt hydrate. In the case of the guanine sodium salt, the structure contains purely inorganic polymeric fragments – sodium cations coordinated to a water molecule forming a 1D polymeric structure and guanine anions interconnecting these polymers via hydrogen bonds with water molecules. The structural differences account for the difference in the anisotropy of strain on temperature variation for the two salt hydrates: whereas in both structures the values of the bulk thermal expansion coefficients are similar in the two structures and the major expansion is observed along the channel axes, the degree of anisotropy for the K salt is more than four times higher than that for the Na salt.

Poly[octacarbonylheptakis(tetrahydrofuran)diironmanganesedisodium(2 Mn—Fe)]

The reaction of Na2Fe(CO)4 with an excess of MnCl2 in tetrahydrofuran (THF) produced {Fe2Mn(C4H8O)2Na2(C4H8O)5(CO)8] n or C36H56Fe2MnNa2O15. The compound is a xenophilic dianion with short iron–manganese bond lengths of 2.6274 (10) and 2.6294 (10) Å. The sodium cations of the dianion are coordinated to THF ligands and have isocarbonyl interactions forming a polymeric (two-dimensional) structure in the crystal. One of the THF molecules was modeled with the carbon atoms being statistically disordered.

Characterization and Sodium Cations Sorption Capacity of Chemically Modified Biochars Produced from Agricultural and Forestry Wastes

Excessive amounts of sodium cations (Na+) in water is an important limiting factor to reuse poor quality water in agriculture or industry, and recently, much attention has been paid to developing cost-effective and easily available water desalination technology that is not limited to natural resources. Biochar seems to be a promising solution for reducing high loads of inorganic contaminant from water and soil solution, and due to the high availability of biomass in agriculture and forestry, its production for these purposes may become beneficial. In the present research, wheat straw, sunflower husk, and pine-chip biochars produced at 250, 450 and 550 °C under simple torrefaction/pyrolysis conditions were chemically modified with ethanol or HCl to determine the effect of these activations on Na sorption capacity from aqueous solution. Biochar sorption property measurements, such as specific surface area, cation exchange capacity, content of base cations in exchangeable forms, and structural changes of biochar surface, were performed by FTIR and EPR spectrometry to study the effect of material chemical activation. The sorption capacity of biochars and activated carbons was investigated by performing batch sorption experiments, and adsorption isotherms were tested with Langmuir’s and Freundlich’s models. The results showed that biochar activation had significant effects on the sorption characteristics of Na+, increasing its capacity (even 10-folds) and inducing the mechanism of ion exchange between biochar and saline solution, especially when ethanol activation was applied. The findings of this study show that biochar produced through torrefaction with ethanol activation requires lower energy demand and carbon footprint and, therefore, is a promising method for studying material applications for environmental and industrial purposes.

Formation of modified whitlockite-related calcium phosphates under conditions of coprecipitation from aqueous solutions

The features of phase formation during wet coprecipitation from aqueous system Сa2+–NO3––Х (Х – NaH2PO4, Na2HPO4, Na3PO4) at the molar ratio Са2+/РО43–=1.6 and room temperature have been investigated. It was found formation of whitlockite-related calcium phosphates (trigonal system, space group R-3c). The results of elemental analysis indicated the chemical modification of calcium phosphates by sodium cations (samples contained 0.3–0.6 wt.% Na+). According to the resulta of thermogravimetry, the synthesized samples contained up to 6 wt.% of sorption water. Heating of samples to the temperature of 6000C is accompanied by water removal and an increase in particle size from 20–50 nm to 500 nm. It was shown that the use of sodium nitrate as a source of sodium cations in the formation of sodium-containing calcium phosphates allows obtaining compositions of whitlockite- and apatite-related phases. The mass ratio of phases can be adjusted by changing the content of sodium cations in the initial solution. The synthesized samples were characterized by X-ray powder diffraction, thermogravimetry, scanning electron microscopy and FTIR spectroscopy methods. Optimized conditions for preparation of whitlockite-related sodium-containing calcium phosphates as well as composites based on them with apatite-related phase can be further used in the development of materials with the required resorption rate for orthopedics.

Protonated Forms of Layered Perovskite-Like Titanate NaNdTiO4: Neutron and X-ray Diffraction Structural Analysis

Structures of partially and completely protonated Ruddlesden–Popper phases, H0.7Na0.3NdTiO4·0.3H2O and HNdTiO4, have been established by means of neutron and X-ray diffraction analysis and compared among themselves as well as with that of the initial titanate NaNdTiO4. It was shown that while interlayer sodium cations in the partially protonated form are coordinated by nine oxygen atoms, including one related to intercalated water, in the fully protonated compound the ninth oxygen proves to be an axial anion belonging to the opposite slab of titanium-oxygen octahedra. Moreover, the partially protonated titanate was found to significantly differ from the other two in the octahedron distortion pattern. It is characterized by a weakly pronounced elongation of the octahedra towards the Nd-containing interlayer space making Ti4+ cations practically equidistant from both axial oxygen atoms, which is accompanied by a low-frequency shift of the bands relating to the asymmetric stretching mode of axial Ti–O bonds observed in the Raman spectra.

Impact of Na+ and Ca2+ Cations on the Adsorption of H2S on Binder-Free LTA Zeolites

Hydrogen sulfide is removed from natural gas via adsorption on zeolites. The process operates very effectively, but there is still potential for improvement. Therefore, in this article, the adsorption of hydrogen sulfide was investigated on eight LTA zeolites with different cation compositions. Starting with the zeolite NaA (4 A), which contains only Na+ cations, the Ca2+ cation content was gradually increased by ion exchange. Equilibrium isotherms from cumulative breakthrough curve experiments in a fixed-bed adsorber at 25°C and 85°C at 1.3 bar (abs.) were determined in the trace range up to a concentration of 2000 ppmmol. From a comparison of the isotherms of the different materials, a mechanistic proposal for the adsorption is developed, taking into account the specific positions of the cations in the zeolite lattice when the degree of exchange is increased. The shape of the isotherms indicates two energetically different types of adsorption sites. It is assumed that two mechanisms are superimposed: a chemisorptive mechanism with dissociation of hydrogen sulfide and covalent bonding of the proton and the hydrogen sulfide ion to the zeolite lattice and a physisorptive mechanism by electrostatic interaction with the cations in the lattice. As the degree of exchange increases, the proportion of chemisorption sites seems to decrease. Above an exchange degree of 50%, only evidence of physisorption can be found. It is shown that this finding points to the involvement of weakly bound sodium cations at cation position III in the chemisorption of hydrogen sulfide.

The role of local anaesthesia in intra-operative pain management in dental practice

Intra-operative pain management with the means of local anaesthesia is an important of dental practice. Local anaesthetics are drugs the most commonly used drugs in dentistry, being, at the same time, the safest and most effective pain preventing and pain relieving agents known to medicine.The mechanism of action of local anaesthetics involves interruption of the conduction of nerve impulses. These agents show high affinity for the voltage-dependent sodium channels (Nav), they block them, thus preventing the influx of sodium cations through the membranes of the neuron. The potential threshold is not reached and the potential itself is not present. The potency of local anaesthetic drugs depends primarily on the concentration of the solutions used, while possible side effects depend on the dose. In this paper the characteristics of local anaesthetics used in dental practice were presented as well as characteristics of vasoconstrictors added to anaesthetic solutions. The historical outline, the mechanism of action of local anaesthetics and the currently used both basic and additional methods of anaesthesia are discussed. Possible strategies for improving the effectiveness of anaesthesia by the means of physical and chemical methods were explained. General and local adverse reactions of dental anaesthetics were also discussed, along with ways to prevent and treat them.

Na2La4(NH2)14·NH3, a lanthanum-rich intermediate in the ammonothermal synthesis of LaN and the effect of ammonia loss on the crystal structure

Single crystals of Na2La4(NH2)14·NH3 were obtained from supercritical ammonia under ammonobasic conditions at a temperature of 573 K and 120 MPa pressure. It represents a lanthanum-rich intermediate in the ammonothermal synthesis of LaN. Upon aging, the title compound loses the crystal ammonia, resulting in pale crystals of Na2La4(NH2)14, the original space group P212121 being retained in a very similar unit cell. However, the crystal structure reacts to subtle changes in the composition as well as to the modified coordination of particularly the sodium cations interconnecting lanthanum amide layers within a third dimension. Results of Raman spectroscopic studies are reported. The observations of thermal analysis measurements indicating the formation of lanthanum nitride, in combination with the observed retrograde solubility in liquid ammonia, contribute to the knowledge of the ammonothermal crystal growth of lanthanum nitride.