Direct Observation of Node-to-Node Communication in Zeolitic Imidazolate Frameworks

Zeolitic imidazolate frameworks (ZIFs) with open-shell transition metal nodes represent a promising class of highly ordered light harvesting antennas for photoenergy applications. However, their charge transport properties within the framework, the key criterion to achieve efficient photoenergy conversion, are not yet explored. Herein, we report the first direct evidence of a charge transport pathway through node-to-node communication in both ground state and excited state ZIFs using the combination of paramagnetic susceptibility measurements and time-resolved optical and X-ray absorption spectroscopy. These findings provide unprecedented new insights into the photoactivity and charge transport nature of ZIF frameworks, paving the way for their novel application as light harvesting arrays in diverse photoenergy conversion devices

Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes

The temperature induced melting transition of a self-complementary DNA strand covalently attached at the 5′ end to the surface of a gold interdigitated microelectrode (GIME) was monitored in a novel, label-free, manner. The structural state of the hairpin was assessed by measuring four different electronic properties of the GIME (capacitance, impedance, dissipation factor and phase angle) as a function of temperature from 25°C to 80°C. Consistent changes in all four electronic properties of the GIME were observed over this temperature range, and attributed to the transition of the attached single-stranded DNA (ssDNA) from an intramolecular, folded hairpin structure to a melted ssDNA. The melting curve of the self-complementary single strand was also measured in solution using differential scanning calorimetry (DSC) and UV absorbance spectroscopy. Temperature dependent electronic measurements on the surface and absorbance versus temperature values measured in solution experiments were analyzed assuming a two-state process. The model analysis provided estimates of the thermodynamic transition parameters of the hairpin on the surface. Two-state analyses of optical melting data and DSC measurements provided evaluations of the thermodynamic transition parameters of the hairpin in solution. Comparison of surface and solution measurements provided quantitative evaluation of the effect of the surface on the thermodynamics of the melting transition of the DNA hairpin

Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines

The placement of the extreme thermophile Aquifex aeolicus in the bacterial phylogenetic tree has evoked much controversy. We investigated whether adaptations for growth at high temperatures would alter a key functional component of the replication machinery, specifically DnaG primase. Although the structure of bacterial primases is conserved, the trinucleotide initiation specificity for A. aeolicus was hypothesized to differ from other microbes as an adaptation to a geothermal milieu. To determine the full range of A. aeolicus primase activity, two oligonucleotides were designed that comprised all potential trinucleotide initiation sequences. One of the screening templates supported primer synthesis and the lengths of the resulting primers were used to predict possible initiation trinucleotides. Use of trinucleotide-specific templates demonstrated that the preferred initiation trinucleotide sequence for A. aeolicus primase was 5′-d(CCC)-3′. Two other sequences, 5′-d(GCC)-3′ and d(CGC)-3′, were also capable of supporting initiation, but to a much lesser degree. None of these trinucleotides were known to be recognition sequences used by other microbial primases. These results suggest that the initiation specificity of A. aeolicus primase may represent an adaptation to a thermophilic environment

SNP assay to detect the ‘Hyuuga’ red-brown lesion resistance gene for Asian soybean rust

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., has the potential to become a serious threat to soybean, Glycine max L. Merr., production in the USA. A novel rust resistance gene, Rpp?(Hyuuga), from the Japanese soybean cultivar Hyuuga has been identified and mapped to soybean chromosome 6 (Gm06). Our objectives were to fine-map the Rpp?(Hyuuga) gene and develop a high-throughput single nucleotide polymorphism (SNP) assay to detect this ASR resistance gene. The integration of recombination events from two different soybean populations and the ASR reaction data indicates that the Rpp?(Hyuuga) locus is located in a region of approximately 371 kb between STS70887 and STS70923 on chromosome Gm06. A set of 32 ancestral genotypes which is predicted to contain 95% of the alleles present in current elite North American breeding populations and the sources of the previously reported ASR resistance genes (Rpp1, Rpp2, Rpp3, Rpp4, Rpp5, and rpp5) were genotyped with five SNP markers. We developed a SimpleProbe assay based on melting curve analysis for SNP06-44058 which is tighly linked to the Rpp?(Hyuuga) gene. This SNP assay can differentiate plants/lines that are homozygous/homogeneous or heterozygous/heterogeneous for the resistant and susceptible alleles at the Rpp?(Hyuuga) locus

Identifying Fishes through DNA Barcodes and Microarrays

Background: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of ‘‘DNA barcoding’’ and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the ‘‘position of label’’ effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (.90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products

Reactivities and Electronic Structures of mu-1,2-Peroxo and mu-1,2-Superoxo CoIIICoIII Complexes: Electrophilic Reactivity and O2 Release Induced by Oxidation

Depenbrock F, Limpke T, Bill E, et al. Reactivities and Electronic Structures of mu-1,2-Peroxo and mu-1,2-Superoxo CoIIICoIII Complexes: Electrophilic Reactivity and O2 Release Induced by Oxidation. Inorganic Chemistry . 2023;62(43):17913-17930.Peroxo complexes are key intermediates in water oxidation catalysis (WOC). Cobalt plays an important role in WOC, either as oxides CoOx or as {CoIII(mu-1,2-peroxo)CoIII} complexes, which are the oldest peroxo complexes known. The oxidation of {CoIII(mu-1,2-peroxo)CoIII} complexes had usually been described to form {CoIII(mu-1,2-superoxo)CoIII} complexes; however, recently the formation of {CoIV(mu-1,2-peroxo)CoIII} species were suggested. Using a bis(tetradentate) dinucleating ligand, we present here the synthesis and characterization of {CoIII(mu-1,2-peroxo)(mu-OH)CoIII} and {CoIII(mu-OH)2CoIII} complexes. Oxidation of {CoIII(mu-1,2-peroxo)(mu-OH)CoIII} at -40 °C in CH3CN provides the stable {CoIII(mu-1,2-superoxo)(mu-OH)CoIII} species and activates electrophilic reactivity. Moreover, {CoIII(mu-1,2-peroxo)(mu-OH)CoIII} catalyzes water oxidation, not molecularly but rather via CoOx films. While {CoIII(mu-1,2-peroxo)(mu-OH)CoIII} can be reversibly deprotonated with DBU at -40 °C in CH3CN, {CoIII(mu-1,2-superoxo)(mu-OH)CoIII} undergoes irreversible conversions upon reaction with bases to a new intermediate that is also the decay product of {CoIII(mu-1,2-superoxo)(mu-OH)CoIII} in aqueous solution at pH > 2. Based on a combination of experimental methods, the new intermediate is proposed to have a {CoII(mu-OH)CoIII} core formed by the release of O2 from {CoIII(mu-1,2-superoxo)(mu-OH)CoIII} confirmed by a 100% yield of O2 upon photocatalytic oxidation of {CoIII(mu-1,2-peroxo)(mu-OH)CoIII}. This release of O2 by oxidation of a peroxo intermediate corresponds to the last step in molecular WOC

Spectroscopic and Magnetic Studies of Co(II) Scorpionate Complexes: Is There a Halide Effect on Magnetic Anisotropy?

The observation of single-molecule magnetism in transition-metal complexes relies on the phenomenon of zero-field splitting (ZFS), which arises from the interplay of spin–orbit coupling (SOC) with ligand-field-induced symmetry lowering. Previous studies have demonstrated that the magnitude of ZFS in complexes with 3d metal ions is sometimes enhanced through coordination with heavy halide ligands (Br and I) that possess large free-atom SOC constants. In this study, we systematically probe this “heavy-atom effect” in high-spin cobalt(II)–halide complexes supported by substituted hydrotris(pyrazol-1-yl)borate ligands (TptBu,Me and TpPh,Me). Two series of complexes were prepared: [CoIIX(TptBu,Me)] (1-X; X = F, Cl, Br, and I) and [CoIIX(TpPh,Me)(HpzPh,Me)] (2-X; X = Cl, Br, and I), where HpzPh,Me is a monodentate pyrazole ligand. Examination with dc magnetometry, high-frequency and -field electron paramagnetic resonance, and far-infrared magnetic spectroscopy yielded axial (D) and rhombic (E) ZFS parameters for each complex. With the exception of 1-F, complexes in the four-coordinate 1-X series exhibit positive D-values between 10 and 13 cm–1, with no dependence on halide size. The five-coordinate 2-X series exhibit large and negative D-values between −60 and −90 cm–1. Interpretation of the magnetic parameters with the aid of ligand-field theory and ab initio calculations elucidated the roles of molecular geometry, ligand-field effects, and metal–ligand covalency in controlling the magnitude of ZFS in cobalt–halide complexes

Differential Adhesion of Microspheres Mediated by DNA Hybridization I: Experiment

We have developed a novel method to study collective behavior of multiple hybridized DNA chains by measuring the adhesion of DNA-coated micron-scale beads under hydrodynamic flow. Beads coated with single-stranded DNA probes are linked to surfaces coated with single target strands through DNA hybridization, and hydrodynamic shear forces are used to discriminate between strongly and weakly bound beads. The adhesiveness of microspheres depends on the strength of interaction between DNA chains on the bead and substrate surfaces, which is a function of the degree of DNA chain overlap, the fidelity of the match between hybridizing pairs, and other factors that affect the hybridization energy, such as the salt concentration in the hybridization buffer. The force for bead detachment is linearly proportional to the degree of chain overlap. There is a detectable drop in adhesion strength when there is a single base mismatch in one of the hybridizing chains. The effect of single nucleotide mismatch was tested with two different strand chemistries, with mutations placed at several different locations. All mutations were detectable, but there was no comprehensive rule relating the drop in adhesive strength to the location of the defect. Since adhesiveness can be coupled to the strength of overlap, the method holds promise to be a novel methodology for oligonucleotide detection