The design of single-stranded nucleic acid knots

A general strategy is described for the synthesis of single-stranded nucleic acid knots. Control of nucleic acid sequence is used to direct the formation of secondary structures that produce the target topology. The key feature of the strategy is the equation of a half-turn of double helical DNA or RNA with a node in a knot. By forming nodes from complementary DNA sequences, it appears possible to direct the assembly of any simple knot. Stabilization of individual nodes may be achieved by constructing them from long regions containing both B-DNA and Z-DNA. Control over the braiding of DNA that acts as a link between node-forming domains can be realized by condensing the nodes into well-defined DNA structures, such as extended domains of linear duplex, branched junctions, antijunctions or mesojunctions. Further topological control may be derived from the pairing of linker regions to complementary single-stranded molecules, thereby preventing them from braiding in an undesirable fashion.     

Two estimates of the metabolic costs of antibody production in migratory shorebirds: low costs, internal reallocation, or both?

We measured the costs of mounting a humoral immune response using two novel antigens (tetanus and diphtheria) in two shorebird species (Scolopacidae): Red Knot (Calidris canutus, measured in autumn) and Ruff (Philomachus pugnax, measured in spring). Metabolic rate was measured during the preinjection phase, at the building phase of the primary immune response, and at peak secondary immune response by determining the oxygen consumption of the postabsorptive birds at rest. Confirming earlier studies, Red Knots and Ruffs responded with lower antibody titers to the diphtheria than to the tetanus antigen. Although Red Knots and Ruffs produced the same amounts of antibodies, Red Knots showed a significant 13% increase in basal metabolic rate (BMR) during the secondary antibody response, whereas Ruffs showed a 15%, but only marginally significant, reduction in BMR. The results from this study suggest that the energetic costs of an immune response may be small, but the "negative cost" in Ruffs hints at the possibility of resource reallocation and the concomitant difficulty of measuring such costs during "basal" metabolic rate measurements.     

Knotting of linear DNA in nano-slits and nano-channels: a numerical study

The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic devices and by the introduction of algorithms capable of detecting knots in open chains, we investigate numerically the entanglement of linear, open DNA chains confined inside nano-slits. The results regard the abundance, type, and length of occurring knots and are compared with recent findings for DNA inside nano-channels. In both cases, the width of the confining region, D, spans the 30 nm–1 μm range and the confined DNA chains are 1–4 μm long. It is found that the knotting probability is maximum for slit widths in the 70–100 nm range. However, over the considered DNA contour lengths, the maximum incidence of knots remains below 20%, while for channel confinement it tops 50%. Further differences of the entanglement are seen for the average contour length of the knotted region, which drops significantly below D ~100 nm for channel-confinement, while it stays approximately constant for slit-like confinement. These properties ought to reverberate in different kinetic properties of linear DNA depending on confinement and could be detectable experimentally or exploitable in nano-technological applications.     

Phenolic extractives in Salix caprea wood and knots

Salix caprea stemwood and knots were found to contain the phenolic extractives vanillic acid, 3-p-coumaryl alcohol, coniferyl alcohol, sinapylaldehyde, dihydrokaempferol, catechin, naringenin, gallocatechin, dihydromyrcetin and taxifolin. The knots contained larger quantities of flavonoids than did stemwood of the same tree.