Blinking statistics of a molecular beacon triggered by end-denaturation of DNA

We use a master equation approach based on the Poland-Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA, that is clamped at one end. In particular, we quantify the blinking dynamics of a fluorophore-quencher pair mounted within the denaturation wedge. We also study the behavioural changes in the presence of proteins, that selectively bind to single-stranded DNA. We show that such a setup could be well-suited as an easy-to-implement nanodevice for sensing environmental conditions in small volumes.Comment: 14 pages, 5 figures, LaTeX, IOP style. Accepted to J Phys Cond Mat special issue on diffusio

All-dielectric magnetic metasurface for advanced light control in dual polarizations combined with high-Q resonances

Nanostructured magnetic materials provide an efficient tool for light manipulation on sub-nanosecond and sub-micron scales, and allow for the observation of the novel effects which are fundamentally impossible in smooth films. For many cases of practical importance, it is vital to observe the magneto-optical intensity modulation in a dual-polarization regime. However, the nanostructures reported on up to date usually utilize a transverse Kerr effect and thus provide light modulation only for p-polarized light. We present a concept of a transparent magnetic metasurface to solve this problem, and demonstrate a novel mechanism for magneto-optical modulation. A 2D array of bismuth-substituted iron-garnet nanopillars on an ultrathin iron-garnet slab forms a metasurface supporting quasi-waveguide mode excitation. In contrast to plasmonic structures, the all-dielectric magnetic metasurface is shown to exhibit much higher transparency and superior quality-factor resonances, followed by a multifold increase in light intensity modulation. The existence of a wide variety of excited mode types allows for advanced light control: transmittance of both p- and s-polarized illumination becomes sensitive to the medium magnetization, something that is fundamentally impossible in smooth magnetic films. The proposed metasurface is very promising for sensing, magnetometry and light modulation applications

Development of an On-animal Separation-based Sensor for Monitoring Drug Metabolism in Freely Roaming Sheep

The development of an on-animal separation-based sensor that can be employed for monitoring drug metabolism in a freely roaming sheep is described. The system consists of microdialysis sampling coupled directly to microchip electrophoresis with electrochemical detection (MD-ME-EC). Separations were accomplished using an all-glass chip with integrated platinum working and reference electrodes. Discrete samples from the microdialysis flow were introduced into the electrophoresis chip using a flow-gated injection approach. Electrochemical detection was accomplished in-channel using a two-electrode isolated potentiostat. Nitrite was separated by microchip electrophoresis using reverse polarity and a run buffer consisting of 50 mM phosphate at pH 7.4. The entire system was under telemetry control. The system was first tested with rats to monitor the production of nitrite following introduction of nitroglycerin into the subdermal tissue using a linear probe. The data acquired using the on-line MD-ME-EC system was compared to that obtained off-line analysis by liquid chromatography with electrochemical detection (LC-EC), using a second microdialysis probe implanted parallel to the first probe in the same animal. The MD-ME-EC device was then used on-animal to monitor the subdermal metabolism of nitroglycerin in sheep. The ultimate goal is to use this device to simultaneously monitor drug metabolism and behavior in a freely roaming animal

Weak selection and stability of localized distributions in Ostwald ripening

We support and generalize a weak selection rule predicted recently for the self-similar asymptotics of the distribution function (DF) in the zero-volume-fraction limit of Ostwald ripening (OR). An asymptotic perturbation theory is developed that, when combined with an exact invariance property of the system, yields the selection rule, predicts a power-law convergence towards the selected self-similar DF and agrees well with our numerical simulations for the interface- and diffusion-controlled OR.Comment: 4 pages, 2 figures, submitted to PR

Bubble dynamics in DNA

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case.Comment: 9 pages, 2 figure

Decay of isolated surface features driven by the Gibbs-Thomson effect in analytic model and simulation

A theory based on the thermodynamic Gibbs-Thomson relation is presented which provides the framework for understanding the time evolution of isolated nanoscale features (i.e., islands and pits) on surfaces. Two limiting cases are predicted, in which either diffusion or interface transfer is the limiting process. These cases correspond to similar regimes considered in previous works addressing the Ostwald ripening of ensembles of features. A third possible limiting case is noted for the special geometry of "stacked" islands. In these limiting cases, isolated features are predicted to decay in size with a power law scaling in time: A is proportional to (t0-t)^n, where A is the area of the feature, t0 is the time at which the feature disappears, and n=2/3 or 1. The constant of proportionality is related to parameters describing both the kinetic and equilibrium properties of the surface. A continuous time Monte Carlo simulation is used to test the application of this theory to generic surfaces with atomic scale features. A new method is described to obtain macroscopic kinetic parameters describing interfaces in such simulations. Simulation and analytic theory are compared directly, using measurements of the simulation to determine the constants of the analytic theory. Agreement between the two is very good over a range of surface parameters, suggesting that the analytic theory properly captures the necessary physics. It is anticipated that the simulation will be useful in modeling complex surface geometries often seen in experiments on physical surfaces, for which application of the analytic model is not straightforward.Comment: RevTeX (with .bbl file), 25 pages, 7 figures from 9 Postscript files embedded using epsf. Submitted to Phys. Rev. B A few minor changes made on 9/24/9

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds

MicroRNAs targeting oncogenes are down-regulated in pancreatic malignant transformation from benign tumors

BACKGROUND MicroRNA (miRNA) expression profiles have been described in pancreatic ductal adenocarcinoma (PDAC), but these have not been compared with pre-malignant pancreatic tumors. We wished to compare the miRNA expression signatures in pancreatic benign cystic tumors (BCT) of low and high malignant potential with PDAC, in order to identify miRNAs deregulated during PDAC development. The mechanistic consequences of miRNA dysregulation were further evaluated. METHODS Tissue samples were obtained at a tertiary pancreatic unit from individuals with BCT and PDAC. MiRNA profiling was performed using a custom microarray and results were validated using RT-qPCR prior to evaluation of miRNA targets. RESULTS Widespread miRNA down-regulation was observed in PDAC compared to low malignant potential BCT. We show that amongst those miRNAs down-regulated, miR-16, miR-126 and let-7d regulate known PDAC oncogenes (targeting BCL2, CRK and KRAS respectively). Notably, miR-126 also directly targets the KRAS transcript at a "seedless" binding site within its 3'UTR. In clinical specimens, miR-126 was strongly down-regulated in PDAC tissues, with an associated elevation in KRAS and CRK proteins. Furthermore, miR-21, a known oncogenic miRNA in pancreatic and other cancers, was not elevated in PDAC compared to serous microcystic adenoma (SMCA), but in both groups it was up-regulated compared to normal pancreas, implicating early up-regulation during malignant change. CONCLUSIONS Expression profiling revealed 21 miRNAs down-regulated in PDAC compared to SMCA, the most benign lesion that rarely progresses to invasive carcinoma. It appears that miR-21 up-regulation is an early event in the transformation from normal pancreatic tissue. MiRNA expression has the potential to distinguish PDAC from normal pancreas and BCT. Mechanistically the down-regulation of miR-16, miR-126 and let-7d promotes PDAC transformation by post-transcriptional up-regulation of crucial PDAC oncogenes. We show that miR-126 is able to directly target KRAS; re-expression has the potential as a therapeutic strategy against PDAC and other KRAS-driven cancers