DNA Dynamics under Periodic Force Effects

The sensitivity of DNA to electromagnetic radiation in different ranges differs depending on various factors. The aim of this study was to examine the molecular dynamics of DNA under the influence of external periodic influences with different frequencies. In the present paper, within the framework of a mechanical model without simplifications, we investigated the effect of various frequencies of external periodic action in the range from 1011 s−1 to 108 s−1 on the dynamics of a DNA molecule. It was shown that under the influence of an external periodic force, a DNA molecule can perform oscillatory movements with a specific frequency characteristic of this molecule, which differs from the frequency of the external influence ω. It was found that the frequency of such specific vibrations of a DNA molecule depends on the sequence of nucleotides. Using the developed mathematical model describing the rotational motion of the nitrogenous bases around the sugar–phosphate chain, it is possible to calculate the frequency and amplitude of the oscillations of an individual DNA area. Such calculations can find application in the field of molecular nanotechnology.

Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update

The precise mapping and quantification of the numerous RNA modifications that are present in tRNAs, rRNAs, ncRNAs/miRNAs, and mRNAs remain a major challenge and a top priority of the epitranscriptomics field. After the keystone discoveries of massive m6A methylation in mRNAs, dozens of deep sequencing-based methods and protocols were proposed for the analysis of various RNA modifications, allowing us to considerably extend the list of detectable modified residues. Many of the currently used methods rely on the particular reverse transcription signatures left by RNA modifications in cDNA; these signatures may be naturally present or induced by an appropriate enzymatic or chemical treatment. The newest approaches also include labeling at RNA abasic sites that result from the selective removal of RNA modification or the enhanced cleavage of the RNA ribose-phosphate chain (perhaps also protection from cleavage), followed by specific adapter ligation. Classical affinity/immunoprecipitation-based protocols use either antibodies against modified RNA bases or proteins/enzymes, recognizing RNA modifications. In this survey, we review the most recent achievements in this highly dynamic field, including promising attempts to map RNA modifications by the direct single-molecule sequencing of RNA by nanopores.

Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases

The activity of cellular nucleoside triphosphatases (NTPases) must be tightly controlled to prevent spontaneous ATP hydrolysis leading to cell death. While most P-loop NTPases require activation by arginine or lysine fingers, some of the apparently ancestral ones are, instead, activated by potassium ions, but not by sodium ions. We combined comparative structure analysis of P-loop NTPases of various classes with molecular dynamics (MD) simulations of Mg-ATP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures, the conserved P-loop motif keeps the triphosphate chains of enzyme-bound NTPs in an extended, catalytically prone conformation, similar to that attained by ATP in water in the presence of potassium or ammonium ions bound between alpha- and gamma-phosphate groups. The smaller sodium ions could not reach both alpha- and gamma-phosphates of a protein-bound extended phosphate chain and therefore are unable to activate most potassium-dependent P-loop NTPases.

Chemical–mechanical properties of tribofilms and their relationship to ionic liquid chemistry

Hardness as a function of indentation depth for tribofilms formed from ZDDP and N_DEHP ionic liquid. Superimposed on the data is the corresponding phosphate chain length information acquired from XANES.

Study of the Structures and Physical Properties of Calcium Borophosphate Glass Containing Transition Metal Oxides

This research objected to study the effects of CeO2, Sb2O3 and CoO on the structures and properties of calcium borophosphate glass (CBF) in ternary system 0.42CaO-0.06B2O3-0.52P2O5. The batches were melted at 1200 °C with 5 °C /min for 1 h in an electric furnace. The melts were regular bulk formed by pouring into a stainless mold and were immediately transferred to an annealing lehr at 550 °C for 2 h for testing the properties. The structures and physical properties were investigated. The results showed that all doped CBF glass were completely melted representing only one broad peak in XRD patterns. The structural observations revealed the major units are cross-linking B-O-P and B-O-B triangle and B-O-B tetrahedral units. The dense packing of structural or the shorter phosphate chain length and whether the branching group were achieved as the series CeO2>Sb2O3>CoO. The density, refractive index, glossy, Abbe number increased slightly with increasing of transition oxide concentrations as the series CeO2>Sb2O3>CoO. The microhardness also increased with increasing the concentration of transition oxides as the series CeO2<Sb2O3<CoO due to CoO act as glass-network formers stronger than Sb2O3 and CeO2

Composition Dependence of the Glass Network Structure in Li+-ion Conducting Glasses of (LiCl)x(LiPO3)1-x Studied by 31P MAS NMR

In order to obtain information about the structure of a typical Li+-ion conducting glass of (LiCl)x(LiPO3)1-x, 31P MAS NMR measurements were performed for the glass samples with different LiCl compositions x from 0 to 0.4. NMR spectra of the samples indicated the existence of two kinds of P atoms; one is that within the-P-O-P-O-P-chain of LiPO3, P(Q2), and the other is that at the ends of the chain, P(Q1). The ratio of the amount of P(Q1) to that of P(Q2) was observed to increase with the increment of x. The result shows that the addition of LiCl to the glass former of LiPO3 changes the glass network structure by cutting P-O bonds in one-dimensional phosphate chain, and the increment of the Li+-ion conductivity with the increase of x is concluded to be brought not only by the increase of the amount of LiCl dissolved into the interstices between the phosphate glass networks but also by the dispersion of the phosphate glass network structure.

The structure of the genomicBacillus subtilisdUTPase: novel features in the Phe-lid

dUTPases are a ubiquitous family of enzymes that are essential for all organisms and catalyse the breakdown of 2-deoxyuridine triphosphate (dUTP). InBacillus subtilisthere are two homotrimeric dUTPases: a genomic and a prophage form. Here, the structures of the genomic dUTPase and of its complex with the substrate analogue dUpNHpp and calcium are described, both at 1.85 Å resolution. The overall fold resembles that of previously solved trimeric dUTPases. The C-terminus, which contains one of the conserved sequence motifs, is disordered in both structures. The crystal of the complex contains six independent protomers which accommodate six dUpNHpp molecules, with three triphosphates in thetransconformation and the other three in the activegaucheconformation. The structure of the complex confirms the role of several key residues that are involved in ligand binding and the position of the catalytic water. Asp82, which has previously been proposed to act as a general base, points away from the active site. In the complex Ser64 reorients in order to hydrogen bond the phosphate chain of the substrate. A novel feature has been identified: the position in the sequence of the `Phe-lid', which packs against the uracil moiety, is adjacent to motif III, whereas in all other dUTPase structures the lid is in a conserved position in motif V of the flexible C-terminal arm. This requires a reconsideration of some aspects of the accepted mechanism.