Diagnosing viruses by the rolling circle amplified synthesis of DNAzymes

Circular DNA is used as a template for the amplified detection of M13 phage ssDNA by a rolling circle amplification (RCA) process that synthesizes DNAzyme chains, thus enabling the colorimetric or chemiluminescent detection of the analyte.     

Cooperative Multicomponent Self‐Assembly of Nucleic Acid Structures for the Activation of DNAzyme Cascades: A Paradigm for DNA Sensors and Aptasensors

Self‐assembly line : In the presence of a DNA analyte or low‐molecular‐weight substrates, multicomponent nucleic acids self‐assemble into cooperatively stabilized functional nanostructures (see scheme) that activate DNAzyme cascades.

     

Detection of Explosives Using Field‐Effect Transistors

The gate surfaces of ion‐sensitive field‐effect transistor (ISFET) devices were functionalized with the π‐donor units, 6‐hydroxydopamine ( 1 ) or 4‐aminothiophenol ( 2 ). Concentration of trinitrotoluene, TNT, on the gate via π‐donor‐acceptor interactions yields charge‐transfer complexes that alter the gate potential. This enables the label‐free analysis of TNT with a detection limit corresponding to 1×10^?7 M.     

Coherent Activation of DNA Tweezers: A “SET–RESET” Logic System

Open sesame : Aptamer–substrate complexes activate the coherent operation of two tweezers that act as a “SET–RESET” logic system. Each tweezer cycles between a fluorescent open state and a closed quenched state (Q=quencher, F=fluorophore) when triggered by adenosine monophosphate (AMP) and adenosine deaminase (AD).

     

The rotor-router model on regular trees

The rotor-router model is a deterministic analogue of random walk. It can be used to define a deterministic growth model analogous to internal DLA. We show that the set of occupied sites for this model on an infinite regular tree is a perfect ball whenever it can be, provided the initial rotor configuration is acyclic (that is, no two neighboring vertices have rotors pointing to one another). This is proved by defining the rotor-router group of a graph, which we show is isomorphic to the sandpile group. We also address the question of recurrence and transience: We give two rotor configurations on the infinite ternary tree, one for which chips exactly alternate escaping to infinity with returning to the origin, and one for which every chip returns to the origin. Further, we characterize the possible “escape sequences” for the ternary tree, that is, binary words a₁…an for which there exists a rotor configuration so that the kth chip escapes to infinity if and only if ak=1.     

Analysis of the distribution of diffusion coefficients in cat brain at 9.4 T using the inverse Laplace transformation

In this work, the usefulness of the inverse Laplace transformation (ILT) in the characterization of diffusion processes in the brain has been investigated. The method has been implemented on both phantom and in vivo cat brain data acquired at high resolution at 9.4 T. The results were compared with monoexponential and biexponential analyses of the same data. It is shown that in the case of diffusion restricted by white matter axonal tracts, the resulting diffusograms are in good agreement with the biexponential model. In gray matter, however, the non-monoexponential decay does not lead to a bimodal distribution in the ILT, even though the data can be fitted to a biexponential. This finding suggests the possibility of a distribution of diffusion coefficients rather than a discrete biexponential behavior. It is shown that this distribution is sensitive, for example, to experimental parameters such as the diffusion time. Thus, the ILT offers the possibility of implementing a unique tool for the analysis of heterogeneous diffusion, that is, the analysis of the diffusion coefficient distribution, which has the yet unexplored potential of being a valuable parameter in the characterization of tissue structure.     

Turbulence in noninteger dimensions by fractal Fourier decimation

Fractal decimation reduces the effective dimensionality D of a flow by keeping only a (randomly chosen) set of Fourier modes whose number in a ball of radius k is proportional to k(D) for large k. At the critical dimension D(c)=4/3 there is an equilibrium Gibbs state with a k(-5/3) spectrum, as in V. L'vov et al., Phys. Rev. Lett. 89, 064501 (2002). Spectral simulations of fractally decimated two-dimensional turbulence show that the inverse cascade persists below D=2 with a rapidly rising Kolmogorov constant, likely to diverge as (D-4/3)(-2/3).     

Charge renormalization of cylinders and spheres: Ion size effects

The effect of the counterion size on the degree of counterion condensation onto a cylindrical macroion and a spherical one in the absence of salt is studied theoretically within a modified Poisson–Boltzmann approach. We find that excluded volume interactions reduce the degree of condensation. Using a simple variational free energy we show that this reduction can be attributed to an effective increase in the macroion size due to the contribution of the condensed counterions. We also find that for a charged cylinder, the reduction in charge renormalization vanishes at infinite dilution because of the extended nature of the condensed layer. In contrast, excluded volume interactions can reduce the degree of charge renormalization of a sphere even at high dilutions. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3598–3615, 2004     

Lighting-up the dynamics of telomerization and DNA replication by CdSe-ZnS quantum dots

CdSe-ZnS core-shell quantum dots (QDs) act as photochemical centers for lighting-up the dynamics of telomerization or DNA replication.