A thermodynamic approach to designing structure-free combinatorial DNA word sets

An algorithm is presented for the generation of sets of non-interacting DNA sequences, employing existing thermodynamic models for the prediction of duplex stabilities and secondary structures. A DNA ‘word’ structure is employed in which individual DNA ‘words’ of a given length (e.g. 12mer and 16mer) may be concatenated into longer sequences (e.g. four tandem words and six tandem words). This approach, where multiple word variants are used at each tandem word position, allows very large sets of non-interacting DNA strands to be assembled from combinations of the individual words. Word sets were generated and their figures of merit are compared to sets as described previously in the literature (e.g. 4, 8, 12, 15 and 16mer). The predicted hybridization behavior was experimentally verified on selected members of the sets using standard UV hyperchromism measurements of duplex melting temperatures (T(m)s). Additional experimental validation was obtained by using the sequences in formulating and solving a small example of a DNA computing problem

The STRANDS project: long-term autonomy in everyday environments

Thanks to the efforts of the robotics and autonomous systems community, the myriad applications and capacities of robots are ever increasing. There is increasing demand from end users for autonomous service robots that can operate in real environments for extended periods. In the Spatiotemporal Representations and Activities for Cognitive Control in Long-Term Scenarios (STRANDS) project (http://strandsproject.eu), we are tackling this demand head-on by integrating state-of-the-art artificial intelligence and robotics research into mobile service robots and deploying these systems for long-term installations in security and care environments. Our robots have been operational for a combined duration of 104 days over four deployments, autonomously performing end-user-defined tasks and traversing 116 km in the process. In this article, we describe the approach we used to enable long-term autonomous operation in everyday environments and how our robots are able to use their long run times to improve their own performance

DNAzyme Hybridization, Cleavage, Degradation and Sensing in Undiluted Human Blood Serum

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/10.1021/acs.analchem.5b00220.RNA-cleaving DNAzymes provide a unique platform for developing biosensors. However, a majority of the work has been performed in clean buffer solutions, while the activity of some important DNAzymes in biological sample matrices is still under debate. Two RNA-cleaving DNAzymes (17E and 10-23) are the most widely used. In this work, we carefully studied a few key aspects of the 17E DNAzyme in human blood serum, including hybridization, cleavage activity, and degradation kinetics. Since direct fluorescence monitoring is difficult due to the opacity of serum, denaturing and nondenaturing gel electrophoresis were combined for studying the interaction between serum proteins and DNAzymes. The 17E DNAzyme retains its activity in 90% human blood serum with a cleavage rate of 0.04 min–1, which is similar to that in the PBS buffer (0.06 min–1) with a similar ionic strength. The activity in serum can be accelerated to 0.3 min–1 with an additional 10 mM Ca2+. As compared to 17E, the 10-23 DNAzyme produces negligible cleavage in serum. Degradation of both the substrate and the DNAzyme strand is very slow in serum, especially at room temperature. Degradation occurs mainly at the fluorophore label (linked to DNA via an amide bond) instead of the DNA phosphodiester bonds. Serum proteins can bind more tightly to the 17E DNAzyme complex than to the single-stranded substrate or enzyme. The 17E DNAzyme hybridizes extremely fast in serum. With this understanding, the detection of DNA using the 17E DNAzyme is demonstrated in serum.University of Waterloo || Natural Sciences and Engineering Research Council || Foundation for Shenghua Scholar of Central South University|| National Natural Science Foundation of China || Grant No. 21301195 Fellowship from the China Scholarship Council || CSC, Grant No. 20140637011

Arginine Cofactors on the Polymerase Ribozyme

The RNA world hypothesis states that the early evolution of life went through a stage in which RNA served both as genome and as catalyst. The central catalyst in an RNA world organism would have been a ribozyme that catalyzed RNA polymerization to facilitate self-replication. An RNA polymerase ribozyme was developed previously in the lab but it is not efficient enough for self-replication. The factor that limits its polymerization efficiency is its weak sequence-independent binding of the primer/template substrate. Here we tested whether RNA polymerization could be improved by a cationic arginine cofactor, to improve the interaction with the substrate. In an RNA world, amino acid-nucleic acid conjugates could have facilitated the emergence of the translation apparatus and the transition to an RNP world. We chose the amino acid arginine for our study because this is the amino acid most adept to interact with RNA. An arginine cofactor was positioned at ten different sites on the ribozyme, using conjugates of arginine with short DNA or RNA oligonucleotides. However, polymerization efficiency was not increased in any of the ten positions. In five of the ten positions the arginine reduced or modulated polymerization efficiency, which gives insight into the substrate-binding site on the ribozyme. These results suggest that the existing polymerase ribozyme is not well suited to using an arginine cofactor

Divalent Metal Ions Tune the Self-Splicing Reaction of the Yeast Mitochondrial Group II Intron Sc.ai5γ

Group II introns are large ribozymes, consisting of six functionally distinct domains that assemble in the presence of Mg2+ to the active structure catalyzing a variety of reactions. The first step of intron splicing is well characterized by a Michaelis–Menten-type cleavage reaction using a two-piece group II intron: the substrate RNA, the 5′-exon covalently linked to domains 1, 2, and 3, is cleaved upon addition of domain 5 acting as a catalyst. Here we investigate the effect of Ca2+, Mn2+, Ni2+, Zn2+, Cd2+, Pb2+, and [Co(NH3)6]3+ on the first step of splicing of the Saccharomyces cerevisiae mitochondrial group II intron Sc.ai5γ. We find that this group II intron is very sensitive to the presence of divalent metal ions other than Mg2+. For example, the presence of only 5% Ca2+ relative to Mg2+ results in a decrease in the maximal turnover rate k cat by 50%. Ca2+ thereby has a twofold effect: this metal ion interferes initially with folding, but then also competes directly with Mg2+ in the folded state, the latter being indicative of at least one specific Ca2+ binding pocket interfering directly with catalysis. Similar results are obtained with Mn2+, Cd2+, and [Co(NH3)6]3+. Ni2+ is a much more powerful inhibitor and the presence of either Zn2+ or Pb2+ leads to rapid degradation of the RNA. These results show a surprising sensitivity of such a large multidomain RNA on trace amounts of cations other than Mg2+ and raises the question of biological relevance at least in the case of Ca2+

Measuring bulk density variations in a moving powder bed via terahertz in-line sensing

Monitoring the relative density of static or moving powder inside a process line is essential for manufacturing high-quality products. The aim of this study was to predict density variations in a moving powder bed using terahertz reflection technology. We systematically investigated three grades (varying true density and particle size) of two materials: lactose and silicified microcrystalline cellulose (SMCC). These six powders specifically differ in their compressibility, which can be applied to assess the sensitivity and applicability of our method. The powders were filled into a round container, and terahertz reflection measurements were acquired continuously during the container's rotation. The setup allowed to adjust the relative density by compacting the powders into specific powder bed heights. Each powder was compacted to various relative densities (compression pressures up to 100 kPa). We calculated the surface refractive index based on the in-line terahertz measurements acquired during rotation, which has a linear dependence on the relative density of the powder. This was confirmed by correlating the refractive index values with the theoretical relative densities based on the bulk and true densities of the powder. The coefficient of determination (R2) was larger than 0.962 (Lactohale 100) for all six powders, with the highest coefficients for Lactohale 220 (R2 = 0.996) and SMCC 50 LD (R2 = 0.995). The results suggest that the proposed method can resolve relative densities averaged across the powder bed that are as small as 0.3% (Lactohale 100). The high acquisition rate of the terahertz system (15 Hz) made it possible to determine the powder density in 230 positions uniformly distributed throughout the container, facilitating the investigation of the relative density uniformity in the container as a function of the powder bed height. It was observed that SMCC powders undergo a smaller change in the relative density variations upon compaction than the lactose powders. Moreover, the relative density maps clearly indicate local density differences in the powder bed for all powders. The relative density variations that were introduced by packing of the container prevailed throughout the compaction process for all samples with the exception of Lactohale 220. The presented approach allows a precise resolution of the spatial distribution of relative density, which facilitates an in-depth analysis of powder behavior upon compaction

Investigation of the reactions of bis stannyl furan 2(#ETA#) one

SIGLEAvailable from British Library Document Supply Centre- DSC:DXN060689 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Efficient initial pool generation for weighted graph problems using parallel overlap assembly

Abstract. Most DNA computing algorithms for mathematical problems start with combinatorial generation of an initial pool. Several methods for initialpool generation have been proposed, including hybridization/ligation and mix/split methods. Here, we implement and compare parallel overlap assembly with the hybridization/ligation method. We applied these methods to the molecular algorithm to solve an instance of the graph problem with weighted edges. Our experimental results show that parallel overlap assembly is a better choice in terms of generation speed and material consumption than the hybridization/ligation method. Simulation of parallel overlap assembly was performed to investigate the potential and the limitation of the method.