[Comparative Analysis of Family A DNA-Polymerases as a Searching Tool for Enzymes with New Properties]

DNA polymerases catalyze DNA synthesis during DNA replication, repair, and recombination. A number of DNA polymerases, such as the Taq enzyme from Thermus aquaticus, are used in various applications of molecular biology and biotechnology, in particular as DNA amplification tools. However, the efficiency of these enzymes depends on factors such as DNA origin, primer composition, template length, GC-content, and the ability to form stable secondary structures. These limitations in the use of currently known DNA polymerases lead to the search for new enzymes with improved properties. This review summarizes the main structural and molecular-kinetic features of the functioning of DNA-polymerases belonging to structural family A, including Taq polymerase. A phylogenetic analysis of these enzymes was carried out, which made it possible to establish a highly conserved consensus sequence containing 62 amino acid residues distributed over the structure of the enzyme. A comparative analysis of these amino acid residues among poorly studied DNA-polymerases revealed 7 enzymes that potentially have the properties necessary for use in DNA amplification.

Description of Dissolved Organic Matter Transformational Networks at the Molecular Level

Dissolved Organic Matter (DOM) is an important component of the global carbon cycle. Unscrambling the structural footprint of DOM is key to understand its biogeochemical transformations at the mechanistic level. Although numerous studies have improved our knowledge of DOM chemical makeup, its three-dimensional picture remains largely unrevealed. In this work, we compare four solid phase extracted (SPE) DOM samples from three different freshwater ecosystems using high resolution mobility and ultrahigh-resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FT-ICR MS/MS). Structural families were identified based on neutral losses at the level of nominal mass using continuous accumulation of selected ions-collision induced dissociation (CASI-CID)FT-ICR MS/MS. Comparison of the structural families indicated dissimilarities in the structural footprint of this sample set. The structural family representation using Cytoscape software revealed characteristic clustering patterns among the DOM samples, thus confirming clear differences at the structural level (Only 10% is common across the four samples.). The analysis at the level of neutral loss-based functionalities suggests that hydration and carboxylation are ubiquitous transformational processes across the three ecosystems. In contrast, transformation mechanisms involving methoxy moieties may be constrained in estuarine systems due to extensive upstream lignin biodegradation. The inclusion of the isomeric content (mobility measurements at the level of chemical formula) in the structural family description suggests that additional transformation pathways and/or source variations are possible and account for the dissimilarities observed. While the structural character of more and diverse types of DOM samples needs to be assessed and added to this database, the results presented here demonstrate that Graph-DOM is a powerful tool capable of providing novel information on the DOM chemical footprint, based on structural interconnections of precursor molecules generated by fragmentation pathways and collisional cross sections.

Structural and Molecular Kinetic Features of Activities of DNA Polymerases

DNA polymerases catalyze DNA synthesis during the replication, repair, and recombination of DNA. Based on phylogenetic analysis and primary protein sequences, DNA polymerases have been categorized into seven families: A, B, C, D, X, Y, and RT. This review presents generalized data on the catalytic mechanism of action of DNA polymerases. The structural features of different DNA polymerase families are described in detail. The discussion highlights the kinetics and conformational dynamics of DNA polymerases from all known polymerase families during DNA synthesis.

Cs3LiZn2(WO4)4 and Rb3Li2Ga(MoO4)4: different filled derivatives of the cation-deficient Cs6Zn5(MoO4)8 structure

Two new compounds, namely cubic tricaesium lithium dizinc tetrakis(tetraoxotungstate), Cs₃LiZn₂(WO₄)₄, and tetragonal trirubidium dilithium gallium tetrakis(tetraoxomolybdate), Rb₃Li₂Ga(MoO₄)₄, belong to the structural family of Cs₆Zn₅(MoO₄)₈ (space group I-43d, Z = 4), with a partially incomplete (Zn_5/6□_1/6) position. In Cs₃LiZn₂(WO₄)₄, this position is fully statistically occupied by (Zn_2/3Li_1/3), and in Rb₃Li₂Ga(MoO₄)₄, the 2Li + Ga atoms are completely ordered in two distinct sites of the space group I-42d (Z = 4). In the same way, the crystallographically equivalent A⁺ cations (A = Cs, Rb) in Cs₆Zn₅(MoO₄)₈, Cs₃LiZn₂(WO₄)₄ and isostructural A₃LiZn₂(MoO₄)₄ and Cs₃LiCo₂(MoO₄)₄ are divided into two sites in Rb₃Li₂Ga(MoO₄)₄, as in other isostructural A₃Li₂R(MoO₄)₄ compounds (AR = TlAl, RbAl, CsAl, CsGa, CsFe). In the title structures, the WO₄ and (Zn,Li)O₄ or LiO₄, GaO₄ and MoO₄ tetrahedra share corners to form open three-dimensional frameworks with the caesium or rubidium ions occupying cuboctahedral cavities. The tetrahedral frameworks are related to that of mayenite 12CaO·7Al₂O₃ and isotypic compounds. Comparison of isostructural Cs₃MZn₂(MoO₄)₄ (M = Li, Na, Ag) and Cs₆Zn₅(MoO₄)₈ shows a decrease of the cubic lattice parameter and an increase in thermal stability with the filling of the vacancies by Li⁺ in the Zn position of the Cs₆Zn₅(MoO₄)₈ structure, while filling of the cation vacancies by larger Na⁺ or Ag⁺ ions plays a destabilizing role. The series A₃Li₂R(MoO₄)₄ shows second harmonic generation effects compatible with that of β'-Gd₂(MoO₄)₃ and may be considered as nonlinear optical materials with a modest nonlinearity.