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Quantitative transcription regulation studies in vivo and in vitro often make use of reporter proteins. Here we show that using Broccoli aptamers, quantitative study of transcription in various regulatory scenarios is possible without a translational step. To explore the method we studied several regulatory scenarios that we analyzed using thermodynamic occupancy-based models, and found excellent agreement with previous studies. In the next step we show that non-coding DNA can have a dramatic effect on the level of transcription, similar to the influence of the lac repressor with a strong affinity to operator sites. Finally, we point out the limitations of the method in terms of delay times coupled to the folding of the aptamer. We conclude that the Broccoli aptamer is suitable for quantitative transcription measurements. [ABSTRACT FROM AUTHOR]

Deformability and mutual attraction have recently been combined for the self-assembly of nanoparticles by grafting flexible polymers onto the surface of mutually attractive particles. This results in isotropic clusters (10) [...], Particles with directional interactions are promising building blocks for new functional materials and may serve as models for biological structures (1-3). Mutually attractive nanoparticles that are deformable owing to flexible surface groups, for example, may spontaneously order themselves into strings, sheets and large vesicles (4-6). Furthermore, anisotropic colloids with attractive patches can self-assemble into open lattices and the colloidal equivalents of molecules and micelles (7-9). However, model systems that combine mutual attraction, anisotropy and deformability have not yet been realized. Here we synthesize colloidal particles that combine these three characteristics and obtain self-assembled microcapsules. We propose that mutual attraction and deformability induce directional interactions via colloidal bond hybridization. Our particles contain both mutually attractive and repulsive surface groups that are flexible. Analogously to the simplest chemical bond--in which two isotropic orbitals hybridize into the molecular orbital of [H.sub.2]--these flexible groups redistribute on binding. Via colloidal bond hybridization, isotropic spheres self-assemble into planar monolayers, whereas anisotropic snowman-shaped particles self-assemble into hollow monolayer microcapsules. A modest change in the building blocks thus results in much greater complexity of the self-assembled structures. In other words, these relatively simple building blocks self-assemble into markedly more complex structures than do similar particles that are isotropic or non-deformable.

Genetic feedback loops can be used by cells to regulate internal processes or to keep track of time. It is often thought that, for a genetic circuit to display self-sustained oscillations, a degree of cooperativity is needed in the binding and unbinding of actor species. This cooperativity is usually modeled using a Hill function, regardless of the actual promoter architecture. Furthermore, genetic circuits do not operate in isolation and often transcription factors are shared between different promoters. In this work we show how mathematical modelling of genetic feedback loops can be facilitated with a mechanistic fold-change function that takes into account the titration effect caused by competing binding sites for transcription factors. The model shows how the titration effect facilitates self-sustained oscillations in a minimal genetic feedback loop: a gene that produces its own repressor directly without cooperative transcription factor binding. The use of delay-differential equations leads to a stability contour that predicts whether a genetic feedback loop will show self-sustained oscillations, even when taking the bursty nature of transcription into account. Author summary: Cells keep track of time by genetic feedback loops—transcription factor proteins that repress their own production and whose availability oscillates regularly in time. For oscillations to occur, the amount of transcription factor that is produced should be extremely sensitive to the amount of transcription factor that is present in the cell. In some genetic circuits, sensitivity comes from the fact that multiple transcription factors need to bind to the gene simultaneously to successfully inhibit its production, but it is also possible to generate this sensitivity when multiple binding sites compete for the same pool of transcription factors. In this work we show how to mathematically model this competition effect, and predict under which circumstances stable oscillations occur. [ABSTRACT FROM AUTHOR]

Hydrophobic polyelectrolytes (HPEs) can solubilize bilayer membranes, form micelles, or can reversibly aggregate as a function of pH. The transitions are often remarkably sharp. We show that these cooperative transitions occur by a competition between two or more conformational states and can be explained within the framework of Monod--Wymann--Changeux (MWC) theory that was originally formulated for allosteric interactions. Here, we focus on the pH-dependent destabilization and permeation of bilayer membranes by HPEs. We formulate the general conditions that lead to sharp conformational transitions involving simple macromolecules mediated by concentration variations of molecular ligands. That opens up potential applications ranging from medicine to the development of switchable materials. [ABSTRACT FROM AUTHOR]

Association and dissociation of particles are elementary steps in many natural and technological relevant processes. For many such processes, the presence of multiple binding sites is essential. For instance, protein complexes and regular structures such as virus shells are formed from elementary building blocks with multiple binding sites. Here we address a fundamental question concerning the role of multivalency of binding sites in the association kinetics of such complexes. Using single replica transition interface sampling simulations, we investigate the influence of the multivalency on the binding kinetics and the association mechanism of patchy particles that form polyhedral clusters. When the individual bond strength is fixed, the kinetics naturally is very dependent on the multivalency, with dissociation rate constants exponentially decreasing with the number of bonds. In contrast, we find that when the total bond energy per particle is kept constant, association and dissociation rate constants turn out rather independent of multivalency, although of course still very dependent on the total energy. The association and dissociation mechanisms, however, depend on the presence and nature of the intermediate states. For instance, pathways that visit intermediate states are less prevalent for particles with five binding sites compared to the case of particles with only three bonds. The presence of intermediate states can lead to kinetic trapping and malformed aggregates. We discuss implications for natural forming complexes such as virus shells and for the design of artificial colloidal patchy particles. [ABSTRACT FROM AUTHOR]

A simple toy model is analyzed within the framework of multichemical equilibrium to explain the spontaneous formation of clusters of certain metal oxides (termed 'polyoxometalates' in the literature) in acidified aqueous solutions. It is shown that cluster formation in metal oxides closely resembles micelle formation in surfactant systems.

The studies show evidence for single molecular [Mo.sub.132]-type cluster and the formation of an open-basket-type [Mo.sub.116] defect structure.

The destabilization of emulsions is important for many applications but remains incompletely understood. We perform squeeze flow measurements on oil-in-water emulsions, finding that the spontaneous destabilization of emulsions is generally very slow under normal conditions, with a characteristic time scale given by the drainage of the continuous phase and the coalescence of the dispersed phase. We show that if the emulsion is compressed between two plates, the destabilization can be sped up significantly; on the one hand, the drainage is faster due to the application of the squeezing force. On the other hand, creep processes lead to rearrangements that also contribute to the destabilization. [ABSTRACT FROM AUTHOR]

We report the (spontaneous) formation of colloidal strings, Bernal spiral-like, and tubular clusters comprising spherical, isotropically functionalized colloidal particles in an aqueous environment. The formation of colloidal strings and Bernal spiral-like clusters is guided by an interplay between short-ranged hydrophobic attraction and relatively longer-ranged electrostatic repulsion acting between the colloids. When a dispersion of these colloids is densified via centrifugation, well-defined tubular aggregates were observed. [ABSTRACT FROM AUTHOR]

We report a computational study on the spontaneous self-assembly of spherical particles into two-dimensional crystals. The experimental observation of such structures stabilized by spherical objects appeared paradoxical so far. We implement patchy interactions with the patches point-symmetrically (icosahedral and cubic) arranged on the surface of the particle. In these conditions, preference for self-assembly into sheet-like structures is observed. We explain our findings in terms of the inherent symmetry of the patches and the competition between binding energy and vibrational entropy. The simulation results explain why hollow spherical shells observed in some Keplerate-type polyoxometalates (POM) appear. Our results also provide an explanation for the experimentally observed layer-by-layer growth of apoferritin - a quasi-spherical protein. [ABSTRACT FROM AUTHOR]

The Stokes-Einstein (SE) relation is a form of the fluctuation-dissipation theorem (FDT), and relates the diffusion coefficient of colloidal particles to the viscosity via the thermal energy k[sub B]T. We study the diffusion coefficient and viscosity of concentrated hard-sphere colloidal model systems in the frequency domain. We show that for these metastable fluid systems strong deviations from the SE relation occur, contrary to predictions of mode coupling theory. Using the FDT, these deviations can be quantified by an effective temperature, T[sub eff]. The deviation T[sub eff]/T-1 exhibits power-law behavior over several decades in frequency. [ABSTRACT FROM AUTHOR]

A facile and flexible synthesis is described for colloidal molecules with well-controlled shape and tunable patchiness. The cross-linked polystyrene spheres with a liquid protrusion have assembled into colloidal molecules by coalescence of the liquid protrusions.

A simple one-pot directed synthetic pathway for an oxomolybdate urea composite in which elementary molybdenum oxide building blocks are linked together with the aid of urea is reported. The method could be applied to design large rod-like crystals of an inorganic-organic hybrid extended structure of {Mo[O.sub.3](N[H.sub.2]-CO-N[H.sub.2])} consisting of right- and left-handed helical units.

The thermodynamically stable clusters containing up to 10 or more silver iodide pair were observed in aqueous electrolyte solutions using ultracentrifugation and cryoelectron microscopy. These clusters are in equilibrium with an excess phase of solid AgI.