Photoreactive DNA as a Tool to Study Replication Protein A Functioning in DNA Replication and Repair

Replication protein A (RPA), eukaryotic single-stranded DNA-binding protein, is a key player in multiple processes of DNA metabolism including DNA replication, recombination and DNA repair. Human RPA composed of subunits of 70-, 32- and 14-kDa binds ssDNA with high affinity and interacts specifically with multiple proteins. The RPA heterotrimer binds ssDNA in several modes, with occlusion lengths of 8–10, 13–22 and 30 nucleotides corresponding to global, transitional and elongated conformations of protein. Varying the structure of photoreactive DNA, the intermediates of different stages of DNA replication or DNA repair were designed and applied to identify positioning of the RPA subunits on the specific DNA structures. Using this approach, RPA interactions with various types of DNA structures attributed to replication and DNA repair intermediates were examined. This review is dedicated to blessed memory of Prof. Alain Favre who contributed to the development of photoreactive nucleotide derivatives and their application for the study of protein–nucleic acids interactions.     

Anomalous High Temperature Structural Behavior of Potential Multifunctional Material SmCo0.5Cr0.5O3

Crystal structure parameters of the mixed cobaltite–chromite SmCo_0.5Cr_0.5O₃ in the temperature range of 298–1173 K were derived from in situ high-resolution X-ray synchrotron powder diffraction data. Similar to the parent SmCoO₃ compound, SmCo_0.5Cr_0.5O₃ reveals anomalous thermal expansion reflected in abnormal temperature dependence of the unit cell dimensions and the selected interatomic distances and angles. These anomalies are associated with temperature induced changes of spin state of Co³⁺ ions and coupled insulator-metal transition. Observed decreasing behavior of the bandwidth W points on the increasing population of the exited spin states of Co³⁺ ions in SmCo_0.5Cr_0.5O₃ with increasing temperature. First principle calculations revealed antiferromagnetic ground state of SmCo_0.5Cr_0.5O₃ as the most stable.     

One-potCuAAC synthesis of (1H-1,2,3-triazol-1-yl)methyl-1,3,4/1,2,4-oxadiazoles starting from available chloromethyl-1,3,4/1,2,4-oxadiazoles

The one-pot CuAAC synthesis of (1H-1,2,3-triazol-1-yl)methyl-1,3,4-oxadiazole and (1H-1,2,3-triazol-1-yl)methyl-1,2,4-oxadiazole derivatives via three-component reaction of consequent nucleophilic substitution of chlorine, with azide, and its further “click” reaction, with alkynes, in the presence of CuI was studied. The utility of newly synthesized 2-(azidomethyl)-1,3,4/1,2,4-oxadiazoles and chloromethyl-1,3,4/1,2,4-oxadiazole derivatives was explored, and their limitations were determined. Novel 5-([4-aryl-1H-1,2,3-triazol-1-yl]methyl)-3-(aryl)-1,2,4-oxadiazoles, 2-([4-aryl-1H-1,2,3-triazol-1-yl]methyl)-5-(aryl)-1,3,4-oxadiazoles were obtained in good yields.     

From 1D to 2D Cd(II) and Zn(II) Coordination Networks by Replacing Monocarboxylate with Dicarboxylates in Partnership with Azine Ligands: Synthesis,Crystal Structures,Inclusion, and Emission Properties

Eight mixed-ligand coordination networks, [Cd(2-aba)(NO₃)(4-bphz)_3/2]_n·n(dmf) (1), [Cd(2-aba)₂(4-bphz)]_n·0.75n(dmf) (2), [Cd(seb)(4-bphz)]_n·n(H₂O) (3), [Cd(seb)(4-bpmhz)]_n·n(H₂O) (4), [Cd(hpa)(3-bphz)]_n (5), [Zn(1,3-bdc)(3-bpmhz)]_n·n(MeOH) (6), [Cd(1,3-bdc)(3-bpmhz)]_n ·0.5n(H₂O)·0.5n(EtOH) (7), and [Cd(NO₃)₂(3-bphz)(bpe)]_n·n(3-bphz) (8) were obtained by interplay of cadmium nitrate tetrahydrate or zinc nitrate hexahydrate with 2-aminobenzenecarboxylic acid (H(2-aba)), three dicarboxylic acids, sebacic (decanedioic acid, H₂seb), homophthalic (2-(carboxymethyl)benzoic acid, H₂hpa), isophthalic (1,3-benzenedicarboxylic acid, H₂(1,3-bdc)) acids, bis(4-pyridyl)ethane (bpe) and with four azine ligands, 1,2-bis(pyridin-4-ylmethylene)hydrazine (4-bphz), 1,2-bis(1-(pyridin-4-yl)ethylidene) hydrazine (4-bpmhz), 1,2-bis(pyridin-3-ylmethylene)hydrazine (3-bphz), and 1,2-bis(1-(pyridin-3-yl) ethylidene)hydrazine (3-bpmhz). Compounds 1 and 2 are 1D coordination polymers, while compounds 3–8 are 2D coordination polymers. All compounds were characterized by spectroscopic and X-ray diffraction methods of analysis. The solvent uptakes and stabilities to the guest evacuation were studied and compared for 1D and 2D coordination networks. The de-solvated forms revealed a significant increase of emission in comparison with the as-synthesized crystals.     

Hot Branching Dynamics in a Light‐Harvesting Iron Carbene Complex Revealed by Ultrafast X‐ray Emission Spectroscopy

Iron N‐heterocyclic carbene (NHC) complexes have received a great deal of attention recently because of their growing potential as light sensitizers or photocatalysts. We present a sub‐ps X‐ray spectroscopy study of an Fe^IINHC complex that identifies and quantifies the states involved in the deactivation cascade after light absorption. Excited molecules relax back to the ground state along two pathways: After population of a hot ³MLCT state, from the initially excited ¹MLCT state, 30 % of the molecules undergo ultrafast (150 fs) relaxation to the ³MC state, in competition with vibrational relaxation and cooling to the relaxed ³MLCT state. The relaxed ³MLCT state then decays much more slowly (7.6 ps) to the ³MC state. The ³MC state is rapidly (2.2 ps) deactivated to the ground state. The ⁵MC state is not involved in the deactivation pathway. The ultrafast partial deactivation of the ³MLCT state constitutes a loss channel from the point of view of photochemical efficiency and highlights the necessity to screen transition‐metal complexes for similar ultrafast decays to optimize photochemical performance.     

Multivalent ions and biomolecules: Attempting a comprehensive perspective

Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca²⁺, to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the “atomistic/molecular” local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.     

Biological properties of two enantiomorphic forms of N‐(2,6‐dimethylphenyl)‐4‐hydroxy‐2,2‐dioxo‐1H‐2λ6,1‐benzothiazine‐3‐carboxamide,a structural analogue of piroxicam

The title benzothiazine‐3‐carboxamide, C₁₇H₁₆N₂O₄S, crystallized in two enantiomorphic crystal forms with the space groups P3₂ and P3₁ despite the absence of a classic stereogenic atom. The molecular structures are mirror images of each other. Only one sulfonyl O atom takes part in intramolecular hydrogen bonding as a proton acceptor and this atom is different in the two enantiomorphic structures. As a result, the S atom becomes a pseudo‐stereogenic centre. This fact is worth taking into account due to the different biological activities of the enantiomorphic forms. One form possesses a high analgesic activity, while the other form revealed a high anti‐inflammatory activity.     

Molecular Characteristics and Antioxidant Activity of Spruce (Picea abies) Hemicelluloses Isolated by Catalytic Oxidative Delignification

Spruce (Picea abies) wood hemicelluloses have been obtained by the noncatalytic and catalytic oxidative delignification in the acetic acid-water-hydrogen peroxide medium in a processing time of 3–4 h and temperatures of 90–100 °C. In the catalytic process, the H₂SO₄, MnSO₄, TiO₂, and (NH₄)₆Mo₇O₂₄ catalysts have been used. A polysaccharide yield of up to 11.7 wt% has been found. The hemicellulose composition and structure have been studied by a complex of physicochemical methods, including gas and gel permeation chromatography, Fourier-transform infrared spectroscopy, and thermogravimetric analysis. The galactose:mannose:glucose:arabinose:xylose monomeric units in a ratio of 5:3:2:1:1 have been identified in the hemicelluloses by gas chromatography. Using gel permeation chromatography, the weight average molar mass M_w of hemicelluloses has been found to attain 47,654 g/mol in noncatalytic delignification and up to 42,793 g/mol in catalytic delignification. Based on the same technique, a method for determining the α and k parameters of the Mark–Kuhn–Houwink equation for hemicelluloses has been developed; it has been established that these parameters change between 0.33–1.01 and 1.57–472.17, respectively, depending on the catalyst concentration and process temperature and time. Moreover, the FTIR spectra of the hemicellulose samples contain all the bands characteristic of heteropolysaccharides, specifically, 1069 cm⁻¹ (C–O–C and C–O–H), 1738 cm⁻¹ (ester C=O), 1375 cm⁻¹ (–C–CH₃), 1243 cm⁻¹ (–C–O–), etc. It has been determined by the thermogravimetric analysis that the hemicelluloses isolated from spruce wood are resistant to heating to temperatures of up to ~100 °C and, upon further heating, start destructing at an increasing rate. The antioxidant activity of the hemicelluloses has been examined using the compounds simulating the 2,2-diphenyl-2-picrylhydrazyl free radicals.