Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization

Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a loop of length m, we study homopolymeric single-stranded nucleic acid chains under external force and varying temperature. In the thermodynamic limit of a long strand, the chain displays a phase transition between a low temperature / low force compact (folded) structure and a high temperature / high force molten (unfolded) structure. The influence of c on phase diagrams, critical exponents, melting, and force extension curves is derived analytically. For vanishing pulling force, only for the limited range of loop exponents 2 < c < 2.479 a melting transition is possible; for c <= 2 the chain is always in the folded phase and for 2.479 < c always in the unfolded phase. A force induced melting transition with singular behavior is possible for all loop exponents c < 2.479 and can be observed experimentally by single molecule force spectroscopy. These findings have implications for the hybridization or denaturation of double stranded nucleic acids. The Poland-Scheraga model for nucleic acid duplex melting does not allow base pairing between nucleotides on the same strand in denatured regions of the double strand. If the sequence allows these intra-strand base pairs, we show that for a realistic loop exponent c ~ 2.1 pronounced secondary structures appear inside the single strands. This leads to a lower melting temperature of the duplex than predicted by the Poland-Scheraga model. Further, these secondary structures renormalize the effective loop exponent c^, which characterizes the weight of a denatured region of the double strand, and thus affect universal aspects of the duplex melting transition.Comment: 19 pages, 14 figures, supplementary materia

Single polymer adsorption in shear: flattening versus hydrodynamic lift and corrugation effects

The adsorption of a single polymer to a flat surface in shear is investigated using Brownian hydrodynamics simulations and scaling arguments. Competing effects are disentangled: in the absence of hydrodynamic interactions, shear drag flattens the chain and thus enhances adsorption. Hydrodynamic lift on the other hand gives rise to long-ranged repulsion from the surface which preempts the surface-adsorbed state via a discontinuous desorption transition, in agreement with theoretical arguments. Chain flattening is dominated by hydrodynamic lift, so overall, shear flow weakens the adsorption of flexible polymers. Surface friction due to small-wavelength surface potential corrugations is argued to weaken the surface attraction as well.Comment: 6 pages, 4 figure

Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures

Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium therefore provides useful information on the overall shape of the molecule can provide insights into the interplay of its functional domains. Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between arbitrary nucleotides can be computed in polynomial time by means of dynamic programming. A naive implementation would yield recursions with a very high time complexity of O(n^11). Although we were able to reduce this to O(n^6) for many practical applications a further reduction seems difficult. We conclude, therefore, that sampling approaches, which are much easier to implement, are also theoretically favorable for most real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Mesoscopic models for DNA stretching under force: new results and comparison to experiments

Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. It has been proposed that the first transition, at forces of 60--80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). We derive analytical formula using a coupled discrete worm like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connexion with previous fitting parameter values for denaturation profiles. We find that: (i) ssDNA is fitted, using an analytical formula, over a nanoNewton range with only three free parameters, the contour length, the bending modulus and the monomer size; (ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; (iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; (iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; (v) this formula fits perfectly well poly(dG-dC) and $\lambda$-DNA force-extension curves with consistent parameter values; (vi) a coherent picture, where S to ssDNA transitions are much more sensitive to base-pair sequence than the B to S one, emerges.Comment: 14 pages, 9 figure

In-depth mesocrystal formation analysis of microwave-assisted synthesis of LiMnPO4nanostructures in organic solution

In the present work, we report on the preparation of LiMnPO4 (lithiophilite) nanorods and mesocrystals composed of self-assembled rod subunits employing microwave-assisted precipitation with processing times on the time scale of minutes. Starting from metal salt precursors and H3PO4 as phosphate source, single-phase LiMnPO4 powders with grain sizes of approx. 35 and 65 nm with varying morphologies were obtained by tailoring the synthesis conditions using rac-1-phenylethanol as solvent. The mesocrystal formation, microstructure and phase composition were determined by electron microscopy, nitrogen physisorption, X-ray diffraction (including Rietveld refinement), dynamic light scattering, X-ray absorption and X-ray photoelectron spectroscopy, and other techniques. In addition, we investigated the formed organic matter by gas chromatography coupled with mass spectrometry in order to gain a deeper understanding of the dissolution\u2013precipitation process. Also, we demonstrate that the obtained LiMnPO4 nanocrystals can be redispersed in polar solvents such as ethanol and dimethylformamide and are suitable as building blocks for the fabrication of nanofibers via electrospinning

Entwicklung von Mediennutzungsverhalten und Anforderungen an IP-basierte Medien der Zielgruppe 65 bis 80 Jahre

Im Rahmen der vorliegenden Diplomarbeit wurde das Mediennutzungsverhalten von älteren Menschen untersucht. Ausgangspunkt der Arbeit sind die demographische Entwicklung sowie der Wandel zu einer Informations- und Wissensgesellschaft in Deutschland. Aufgrund der steigenden Lebenserwartung und einer sinkenden Geburtenrate stehen einer zunehmenden Zahl älterer eine sinkende Zahl jüngerer Menschen gegenüber. Die Durchdringung nahezu sämtlicher Lebensbereiche mit Informations- und Kommunikationstechnologien stellt dabei für die älteren Bevölkerungsschichten aufgrund steigender physischer und psychischer Beeinträchtigungen eine größere Herausforderung dar. Ziel der Arbeit war es, ein Grundmodell zu entwickeln, welches die Einflussfaktoren auf das Nutzungsverhalten von Senioren in Bezug auf IP-basierte Medien abbildet und eine Vorhersage des Mediennutzungsverhaltens ermöglicht. Als Grundlage des Modells dienten die Theorie des geplanten Verhaltens und der Uses-and-Gratifications-Ansatz. Um das Modell zu entwickeln, wurden neben der Analyse der Literatur Leitfadeninterviews durchgeführt. In die Betrachtung wurde neben der Zielgruppe mit 65 bis 80 Jahren eine Gruppe im Alter von 50 bis 64 Jahren einbezogen. Der Vergleich beider Gruppen zeigte deutlich, dass die 50 bis 65-jährigen Probanden IP-basierte Medien bereits stärker in den Alltag integrieren und auch zur eigenen Unterhaltung nutzen, während die Gruppe der 65 bis 80-jährigen vorangig klassische Medien wie Fernsehen, Radio sowie Zeitung nutzt und fast außschließlich Informationen sucht. Für die jüngere Gruppe waren zudem Produkteigenschaften wie Ubiquität, Mobilität und Zeitunabhängigkeit der Nutzung von größerer Bedeutung. Es stellte sich in der Untersuchung auch heraus, dass die Gruppe zwischen 65 bis 80 Jahren ein sehr heterogenes Mediennutzungsverhalten besitzt. Dieses leitet sich aus der individuell wahrgenommenen Verhaltenskontrolle, der Einstellung gegenüber der Nutzung des Mediums und den Nutzungsmotiven ab, die zu sehr unterschiedlichen Erwartungen und Bewertungen IP-basierter Medien führen können. Aus den Interviews ließen sich außerdem spezielle Anforderungen und Gestaltungsempfehlungen ableiten, welche den Einstieg in neuartige IP-basierte Medien und die Mediennutzung nicht nur für ältere Menschen erleichtern können

Quasi-homogenous photocatalysis of quantum-sized Fe-doped TiO2_{2} in optically transparent aqueous dispersions

In this study, the preparation of anatase TiO2 nanocrystals via a facile non-aqueous sol–gel route and their characterization are reported. The 3–4 nm particles are readily dispersable in aqueous media and show excellent photoreactivity in terms of rhodamine B degradation. The catalytic performance can be further increased considerably by doping with iron and UV-light irradiation as a pre-treatment. The effect of surface ligands (blocked adsorption sites, surface defects etc.) on the photoreactivity was thoroughly probed using thermogravimetric analysis combined with mass spectrometry. Photoelectrochemical characterization of thin-film electrodes made from the same TiO2 nanocrystals showed the opposite trend to the catalytic experiments, that is, a strong decrease in photocurrent and quantum efficiency upon doping due to introduction of shallow defect states

Plasticity of Executive Control through Task Switching Training in Adolescents

Research has shown that cognitive training can enhance performance in executive control tasks. The current study was designed to explore if executive control, specifically task switching, can be trained in adolescents, what particular aspects of executive control may underlie training and transfer effects, and if acute bouts of exercise directly prior to cognitive training enhance training effects. For that purpose, a task switching training was employed that has been shown to be effective in other age groups. A group of adolescents (10–14 years, n = 20) that received a three-session task switching training was compared to a group (n = 20) that received the same task switching training but who exercised on a stationary bike before each training session. Additionally, a no-contact and an exercise only control group were included (both ns = 20). Analyses indicated that both training groups significantly reduced their switching costs over the course of the training sessions for reaction times and error rates, respectively. Analyses indicated transfer to mixing costs in a task switching task that was similar to the one used in training. Far transfer was limited to a choice reaction time task and a tendency for faster reaction times in an updating task. Analyses revealed no additional effects of the exercise intervention. Findings thus indicate that executive control can be enhanced in adolescents through training and that updating may be of particular relevance for the effects of task switching training