Common patterns in type II restriction enzyme binding sites

Restriction enzymes are among the best studied examples of DNA binding proteins. In order to find general patterns in DNA recognition sites, which may reflect important properties of protein–DNA interaction, we analyse the binding sites of all known type II restriction endonucleases. We find a significantly enhanced GC content and discuss three explanations for this phenomenon. Moreover, we study patterns of nucleotide order in recognition sites. Our analysis reveals a striking accumulation of adjacent purines (R) or pyrimidines (Y). We discuss three possible reasons: RR/YY dinucleotides are characterized by (i) stronger H-bond donor and acceptor clusters, (ii) specific geometrical properties and (iii) a low stacking energy. These features make RR/YY steps particularly accessible for specific protein–DNA interactions. Finally, we show that the recognition sites of type II restriction enzymes are underrepresented in host genomes and in phage genomes

The Effect of Co Incorporation on the CO Oxidation Activity of LaFe1−xCoxO3 Perovskites

Perovskite oxides are versatile materials due to their wide variety of compositions of- fering promising catalytic properties, especially in oxidation reactions. In the presented study, LaFe1−xCoxO3 perovskites were synthesized by hydroxycarbonate precursor co-precipitation and thermal decomposition thereof. Precursor and calcined materials were studied by scanning electron microscopy (SEM), attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), thermogravimetric analysis (TG), and X-ray powder diffraction (XRD). The calcined catalysts were in addition studied by transmission electron microscopy (TEM) and N2 physisorption. The obtained perovskites were applied as catalysts in transient CO oxidation, and in operando studies of CO oxidation in diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). A pronounced increase in activity was already observed by incorporating 5% cobalt into the structure, which contin- ued, though not linearly, at higher loadings. This could be most likely due to the enhanced redox properties as inferred by H2-temperature programmed reduction (H2-TPR). Catalysts with higher Co contents showing higher activities suffered less from surface deactivation related to carbonate poisoning. Despite the similarity in the crystalline structures upon Co incorporation, we observed a different promotion or suppression of various carbonate-related bands, which could indicate different surface properties of the catalysts, subsequently resulting in the observed non-linear CO oxidation activity trend at higher Co contents

Dynamics of Reactive Oxygen Species on Cobalt-Containing Spinel Oxides in Cyclic CO Oxidation

Reactive oxygen species (ROS) are considered to be responsible for the high catalytic activity of transition metal oxides like Co3-xFexO4 in oxidation reactions, but the detailed influences of catalyst composition and morphology on the formation of these reactive oxygen species are not fully understood. In the presented study, Co3O4 spinels of different mesostructures, i.e., particle size, crystallinity, and specific surface area, are characterized by powder X-ray diffraction, scanning electron microscopy, and physisorption. The materials were tested in CO oxidation performed in consecutive runs and compared to a Co3-xFexO4 composition series with a similar mesostructure to study the effects of catalyst morphology and composition on ROS formation. In the first run, the CO conversion was observed to be dominated by the exposed surface area for the pure Co-spinels, while a negative effect of Fe content in the spinels was seen. In the following oxidation run, a U-shaped conversion curve was observed for materials with high surface area, which indicated the in situ formation of ROS on those materials that were responsible for the new activity at low temperature. This activation was not stable at the higher reaction temperature but was confirmed after temperature-programmed oxidation (TPO). However, no activation after the first run was observed for low-surface-area and highly crystalline materials, and the lowest surface-area material was not even activated after TPO. Among the catalyst series studied here, a correlation of small particle size and large surface area with the ability for ROS formation is presented, and the benefit of a nanoscaled catalyst is discussed. Despite the generally negative effect of Fe, the highest relative activation was observed at intermediate Fe contents suggesting that Fe may be involved in ROS formation

DiProDB: a database for dinucleotide properties

DiProDB (http://diprodb.fli-leibniz.de) is a database of conformational and thermodynamic dinucleotide properties. It includes datasets both for DNA and RNA, as well as for single and double strands. The data have been shown to be important for understanding different aspects of nucleic acid structure and function, and they can also be used for encoding nucleic acid sequences. The database is intended to facilitate further applications of dinucleotide properties. A number of property datasets is highly correlated. Therefore, the database comes with a correlation analysis facility. Authors having determined new sets of dinucleotide property values are invited to submit these data to DiProDB

The Smallest Known Genomes of Multicellular and Toxic Cyanobacteria: Comparison, Minimal Gene Sets for Linked Traits and the Evolutionary Implications

Cyanobacterial morphology is diverse, ranging from unicellular spheres or rods to multicellular structures such as colonies and filaments. Multicellular species represent an evolutionary strategy to differentiate and compartmentalize certain metabolic functions for reproduction and nitrogen (N2) fixation into specialized cell types (e.g. akinetes, heterocysts and diazocytes). Only a few filamentous, differentiated cyanobacterial species, with genome sizes over 5 Mb, have been sequenced. We sequenced the genomes of two strains of closely related filamentous cyanobacterial species to yield further insights into the molecular basis of the traits of N2 fixation, filament formation and cell differentiation. Cylindrospermopsis raciborskii CS-505 is a cylindrospermopsin-producing strain from Australia, whereas Raphidiopsis brookii D9 from Brazil synthesizes neurotoxins associated with paralytic shellfish poisoning (PSP). Despite their different morphology, toxin composition and disjunct geographical distribution, these strains form a monophyletic group. With genome sizes of approximately 3.9 (CS-505) and 3.2 (D9) Mb, these are the smallest genomes described for free-living filamentous cyanobacteria. We observed remarkable gene order conservation (synteny) between these genomes despite the difference in repetitive element content, which accounts for most of the genome size difference between them. We show here that the strains share a specific set of 2539 genes with >90% average nucleotide identity. The fact that the CS-505 and D9 genomes are small and streamlined compared to those of other filamentous cyanobacterial species and the lack of the ability for heterocyst formation in strain D9 allowed us to define a core set of genes responsible for each trait in filamentous species. We presume that in strain D9 the ability to form proper heterocysts was secondarily lost together with N2 fixation capacity. Further comparisons to all available cyanobacterial genomes covering almost the entire evolutionary branch revealed a common minimal gene set for each of these cyanobacterial traits

DiProGB: the dinucleotide properties genome browser

Motivation: DiProGB is an easy to use new genome browser that encodes the primary nucleotide sequence by thermodynamical and geometrical dinucleotide properties. The nucleotide sequence is thus converted into a sequence graph. This visualization, supported by different graph manipulation options, facilitates genome analyses, because the human brain can process visual information better than textual information. Also, DiProGB can identify genomic regions where certain physical properties are more conserved than the nucleotide sequence itself. Most of the DiProGB tools can be applied to both, the primary nucleotide sequence and the sequence graph. They include motif and repeat searches as well as statistical analyses. DiProGB adds a new dimension to the common genome analysis approaches by taking into account the physical properties of DNA and RNA