An Insight into the Proofreading Functions of Multisubunit DNA-Dependent RNA Polymerases and Their Catalytic Mechanism

Aim: To analyze the active sites of the proofreading (PR) functions in the multisubunit DNA-dependent RNA polymerases (MSU RNAPs) from prokaryotes, chloroplasts and eukaryotes, and propose a plausible unified catalytic mechanism for these enzymes. Study Design: Data collected on these enzymes from bioinformatics, biochemical, site-directed mutagenesis (SDM), X-ray crystallography and cryo-electron microscopy (cryo-EM) were used for the analyses. Methodology: The protein sequence data of MSU RNAPs from prokaryotes, prokaryotic-types (plant chloroplasts) and eukaryotes were obtained from PUBMED and SWISS-PROT databases. The advanced version of Clustal Omega was used for protein sequence analysis. Along with the conserved motifs identified by the bioinformatics analysis, the data already available from biochemical and SDM experiments, and X-ray crystallographic and cryo-EM data on these enzymes are also used to confirm the possible amino acids involved in the active site of the PR function in these MSU RNAPs Results: All the seven types of MSU RNAPs (I-VII) reported from prokaryotes to eukaryotes were analyzed by the multiple sequence alignment (MSA) software, Clustal Omega, to find out conservations among them. The MSA analysis showed many conserved amino acid motifs including small and large peptide regions from the MSU RNAPs of prokaryotes, eukaryotes and plant chloroplasts. Interestingly, the catalytic amino acid and template-binding pairs are highly conserved in all these polymerases, with a few exceptions. Most of them use a basic amino acid (R/K/H) for initiating catalysis and an -YG/FG- pair for template-binding. Some odd type of catalytic amino acids and template-binding pairs are observed in human pathogens, parasites and organisms which cannot ferment sugars. In all the MSU RNAPs, the proposed polymerase catalytic region also possessed three invariant Cs and an invariant H within it. The invariant Cs is shown to bind a zinc atom and proposed to involve in the PR function by excising any misincorporated nucleotide during the transcription process. In the plant-specific MSU RNAPs IV and V, which involve in transcriptional gene silencing in plants, the catalytic and template-binding pairs do not follow the regular distance conservations as observed with other five of the MSU RNAPs. Their polymerase/PR active site regions are similar to RNAP III rather than to RNAP II, as all three make only low molecular weight RNAs. Conclusions: All the known MSU RNAPs possess three invariant Cs and an invariant H embedded within the polymerase active site itself. The three invariant Cs are shown to bind a zinc atom and the invariant H could act as the proton acceptor from a metal-bound water molecule, for initiating excision of the mismatches by a Zn-mediated hydrolysis. Thus, the PR function in MSU RNAPs is integrated within the polymerase active site itself, which is in sharp contrast to the PR functions reported in DNA-dependent DNA polymerases and RNA-dependent RNA polymerases. Therefore, all the seven MSU RNAPs from prokaryotes and eukaryotes are proposed to follow a unified mechanism to excise the mismatches during transcription. The discovery of intrinsic self-correcting RNA transcription mechanism fulfils the missing link in molecular evolution.

Preparation and Characterisation of the Cyano-Bridged Transition Metal Complexes Using N,N-Diethyl Thiourea as a Ligand

ABSTRACT New cyano bridged transition metal complexes, [Cu(detu)4Ni(CN)4]-2H2O (1) and [Zn(H2O)(detu)Ni(CN)4]-2H2O (2) (detu = N, N' diethyl thiourea) have been synthesised in powder form. Their structures were illuminated by using spectroscopic, thermal and elemental analysis techniques. The nickel atom exhibits square planar geometry in these complexes by coordinating with the cyano group's nitrogen atoms. The copper atom of 1 is six coordinated with two bridging cyano groups and four detu ligands. In contrast, the zinc atom of 2 is six coordinated with four bridging cyano groups, one detu ligand and one aqua ligand. In addition, the structure of 2 is formed from polymeric layers of |Zn-Ni(CN)41 „ with the detu and aqua ligands bonded to the zinc atom. Thermal stabilities and decomposition products of 1 and 2 were examined in the static air atmosphere between 30 and 900 °C. Keywords: btetracyanonickelate(II) complex, N,N'-diethyl thiourea, cyano-bridged complex, vibration spectra, thermal analysis.

A Zn(II) complex with a pyridyl- and carboxylate-containing ligand: synthesis and structural characterization

The hydrothermal reaction of Zn(II) nitrate hydrate with 5-(pyridin-4-yl)isophthalic acid (H2L) yields the complex [Zn2(L)2(H2O)2] · 2(H2O) (1), which has been characterized by single crystal X-ray diffraction, IR spectroscopic, elemental, and thermogravimetric analyses. Complex 1 exhibits a 3-nodal (3,6)-connected 2D net structure with (4.62)2(42.610.83)(63)4 topology. Its luminescence property was investigated, but the results show that the coordination to the zinc atom has no significant effect on the emission of the ligand.

The crystal structures and Hirshfeld surface analyses of a cadmium(II) and a zinc(II) mononuclear complex of the new tetrakis-substituted pyrazine ligand N,N′,N′′,N′′′-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)

The whole molecule of the cadmium(II) complex, diiodido{N,N′,N′′,N′′′-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)-κ3 N 2,N 1,N 6}cadmium(II), [CdI2(C36H40N6)], (I), of the ligand N,N′,N′′,N′′′-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline) (L), is generated by a twofold rotation symmetry; the twofold axis bisects the cadmium atom and the nitrogen atoms of the pyrazine ring. The ligand coordinates in a mono-tridentate manner and the cadmium atom has a fivefold CdN3I2 coordination environment with a distorted shape. In the zinc(II) complex, dichlorido{N,N′,N′′,N′′′-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)-κ3 N 2,N 1,N 6}zinc(II) dichloromethane 0.6-solvate, [ZnCl2(C36H40N6)]·0.6CH2Cl2, (II), ligand L also coordinates in a mono-tridentate manner and the zinc atom has a fivefold ZnN3Cl2 coordination environment with a distorted shape. It crystallized as a partial dichloromethane solvate. In the crystal of I, the complex molecules are linked by weak C—H...I contacts, forming ribbons propagating along [100]. In the crystal of II, the complex molecules are linked by a series of C—H...π interactions, forming layers lying parallel to the (1\overline{1}1) plane. In the crystals of both compounds there are metal–halide...π(pyrazine) contacts present. The Hirshfeld analyses confirm the importance of the C—H...halide contacts in the crystal packing of both compounds.

Destructive Effect of Zinc on TEX - A DFT Treatment

Various metal components like Al, B, Zr etc., as energetic particles are employed in thermobaric explosives. In composite systems compatibility of ingredients with each other is an important point to be considered. In the present study, effect of zinc on TEX, which is a caged explosive of nitramine type is investigated within the constraints of density functional theory at the levels of B3LYP/6-31+G(d), ωB97X-D/6-31G(d) and ωB97X-D/6-31+G(d). Various quantum chemical properties have been calculated for the TEX+Zn composite and compared with TEX. The zinc atom interacts with TEX molecule via destructive reduction of the explosive. The B3LYP/6-31+G(d) level of calculation predicts cleavage of one of the etheric bond of the cage as well as N-NO2 bond. Whereas, ωB97X-D/6-31G(d) and ωB97X-D/6-31+G(d) level of treatments show cleavage of only one of the N-NO2 bonds. In all the cases the zinc atom acquires some positive charge development.

Interaction of CL-20 and Zinc – A DFT Treatment

CL-20 or HNIW is a novel, caged-type explosive material having six nitramine groups. In the present study, interaction of CL-20 with zinc atom has been investigated within the constraints of density functional theory at the level of B3LYP/6-31+G(d,p). Zinc, in chemistry is known as a good reducing metal for many functional groups, presently not only reduces one of the nitro groups but also causes cleavage of one of the nitramine bond (from the base ring) and the C-N bond of the cage. The zinc atom acquires some positive charge after all.