DNA-DNA kissing complexes as a new tool for the assembly of DNA nanostructures

Kissing-loop annealing of nucleic acids occurs in nature in several viruses and in prokaryotic replication, among other circumstances. Nucleobases of two nucleic acid strands (loops) interact with each other, although the two strands cannot wrap around each other completely because of the adjacent doublestranded regions (stems). In this study, we exploited DNA kissing-loop interaction for nanotechnological application. We functionalized the vertices of DNA tetrahedrons with DNA stem-loop sequences. The complementary loop sequence design allowed the hybridization of different tetrahedrons via kissingloop interaction, which might be further exploited for nanotechnology applications like cargo transport and logical elements. Importantly, we were able to manipulate the stability of those kissing-loop complexes based on the choice and concentration of cations, the temperature and the number of complementary loops per tetrahedron either at the same or at different vertices. Moreover, variations in loop sequences allowed the characterization of necessary sequences within the loop as well as additional stability control of the kissing complexes. Therefore, the properties of the presented nanostructures make them an important tool for DNA nanotechnology

A SRS2 homolog from Arabidopsis thaliana disrupts recombinogenic DNA intermediates and facilitates single strand annealing

Genetic and biochemical analyses of SRS2 homologs in fungi indicate a function in the processing of homologous recombination (HR) intermediates. To date, no SRS2 homologs have been described and analyzed in higher eukaryotes. Here, we report the first biochemical characterization of an SRS2 homolog from a multicellular eukaryote, the plant Arabidopsis thaliana. We studied the basic properties of AtSRS2 and were able to show that it is a functional 3′- to 5′-helicase. Furthermore, we characterized its biochemical function on recombinogenic intermediates and were able to show the unwinding of nicked Holliday junctions (HJs) and partial HJs (PX junctions). For the first time, we demonstrated strand annealing activity for an SRS2 homolog and characterized its strand pairing activity in detail. Our results indicate that AtSRS2 has properties that enable it to be involved in different steps during the processing of recombination intermediates. On the one hand, it could be involved in the unwinding of an elongating invading strand from a donor strand, while on the other hand, it could be involved in the annealing of the elongated strand at a later step

Fatty Acid Biosynthesis in Mitochondria of Grasses: Malonyl-Coenzyme A Is Generated by a MitochondrialLocalized Acetyl-Coenzyme A Carboxylase

We present biochemical evidence for the occurrence of a 250-kD multifunctional acetyl-coenzyme A carboxylase in barley (Hordeum vulgare) mitochondria. Organelles from 6-d-old barley seedlings were purified by differential centrifugation and Percoll density gradient centrifugation. Upon analysis by two-dimensional Blue-native (BN)/SDS-PAGE, an abundant 250-kD protein can be visualized, which runs at 500 kD on the native gel dimension. A similar 500-kD complex is present in etioplasts from barley. The mitochondrial 250-kD protein is biotinylated as indicated by specific reaction with an antibody directed against biotin. Peptide sequence analysis by electrospray ionization tandem mass spectrometry of the 250-kD proteins from both organellar fractions revealed amino acid sequences that are 100% identical to plastidic acetyl-coenzyme A carboxylase from wheat (Triticum aestivum). The 500-kD complex was also detected in wheat mitochondria, but is absent in mitochondrial fractions from Arabidopsis. Specific acetyl-coenzyme A carboxylation activity in barley mitochondria is higher than in etioplasts, suggesting an important role of mitochondria in fatty acid biosynthesis. Functional implications are discussed

Two Distinct MUS81-EME1 Complexes from Arabidopsis Process Holliday Junctions1[W]

The MUS81 endonuclease complex has been shown to play an important role in the repair of stalled or blocked replication forks and in the processing of meiotic recombination intermediates from yeast to humans. This endonuclease is composed of two subunits, MUS81 and EME1. Surprisingly, unlike other organisms, Arabidopsis (Arabidopsis thaliana) has two EME1 homologs encoded in its genome. AtEME1A and AtEME1B show 63% identity on the protein level. We were able to demonstrate that, after expression in Escherichia coli, each EME1 protein can assemble with the unique AtMUS81 to form a functional endonuclease. Both complexes, AtMUS81-AtEME1A and AtMUS81-AtEME1B, are not only able to cleave 3′-flap structures and nicked Holliday junctions (HJs) but also, with reduced efficiency, intact HJs. While the complexes have the same cleavage patterns with both nicked DNA substrates, slight differences in the processing of intact HJs can be detected. Our results are in line with an involvement of both MUS81-EME1 endonuclease complexes in DNA recombination and repair processes in Arabidopsis

Incorporation of 1-deoxy-d-xylulose into isoprene and phytol by higher plants and algae

AbstractIn further substantiating the novel mevalonate-independent pathway for isoprenoid biosynthesis, which generates isopentenyl diphosphate (IPP) via 1-deoxy-d-xylulose-5-phosphate, labeling experiments with 1-[2H1]deoxy-d-xylulose were performed with various higher plants and algae: efficient incorporation was observed into isoprene emitted by Populus, Chelidonium, and Salix, into the phytol moiety of chlorophylls in a red alga (Cyanidium), in two green algae (Scenedesmus, Chlamydomonas), and a higher plant (Lemna). By contrast, 13C-mevalonate applied was incorporated into isoprene and phytol to a much lower extent or not at all. This demonstrates that this `1-deoxy-d-xylulose-5-phosphate pathway' for biosynthesis of plastidic isoprenoids is widely distributed in photosynthetic organisms