The diffusion constant of a labeled protein sliding along DNA

International audienc

Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2′-deoxyadenosine mimic

The phototriggered cleavage of chemical bonds has found numerous applications in biology, particularly in the field of gene sequencing through photoinduced DNA strand scission. However, only a small number of modified nucleosides that are able to cleave DNA at selected positions have been reported in the literature. Herein, we show that a new photoactivable deoxyadenosine analogue, 3-nitro-3-deaza-2′-deoxyadenosine (d(3-NiA)), was able to induce DNA backbone breakage upon irradiation (λ > 320 nm). The d(3-NiA) nucleoside was chemically incorporated at desired positions into 40-mer oligonucleotides as a phosphoramidite monomer and subsequent hybridization studies confirmed that the resulting modified duplexes display a behaviour that is close to that of the related natural sequence. Enzymatic action of the Klenow fragment exonuclease free revealed the preferential incorporation of dAMP opposite the 3-NiA base. On the other hand, incorporation of the analogous 3-NiA triphosphate to a primer revealed high enzyme efficiency and selectivity for insertion opposite thymine. Furthermore, only the enzymatically synthesized base pair 3-NiA:T was a substrate for further extension by the enzyme. All the hybridization and enzymatic data indicate that this new photoactivable 3-NiA triphosphate can be considered as a photochemically cleavable dATP analogue

Three-body decay of a rubidium Bose-Einstein condensate

We have measured the three-body decay of a Bose-Einstein condensate of rubidium ($^{87}$Rb) atoms prepared in the doubly polarized ground state $F=m_F=2$. Our data are taken for a peak atomic density in the condensate varying between $2\times 10^{14}$ cm$^{-3}$ at initial time and $7\times 10^{13}$ cm$^{-3}$, 16 seconds later. Taking into account the influence of the uncondensed atoms onto the decay of the condensate, we deduce a rate constant for condensed atoms $L=1.8 (\pm 0.5) \times 10^{-29}$ cm$^{6}$s$^{-1}$. For these densities we did not find a significant contribution of two-body processes such as spin dipole relaxation.Comment: 14 pages, 4 figure

Impact of carbonates on the mineralisation of surface soil organic carbon in response to shift in tillage practice

The inorganic soil C pool is a major source of CO2 emission into the atmosphere along with the soil respiratory CO2 fluxes but is comparatively less studied than the organic C mineralisation processes. This study aims to understand how soil available carbonates influence the soil C dynamics under different tillage, mulching and temperature regimes. A 90-day incubation experiment was conducted by adding calcite nodules to soils (10% w/w) collected from an agricultural field maintained with or without 5 t ha−1 mulching under no-till (NT) or conventional tillage (CT) systems. Environmental Scanning Electron Microscope (ESEM) examination indicated greater morphological changes in the calcite nodules incubated with CT than NT soils. Soil samples incubated with calcite and mulching recorded 6.3% greater CO2 evolution than the un-mulched condition. Under the CT system, the overall CO2 emission rate was higher in the control treatment (43%), followed by a combined treatment of 5 t ha−1 mulch + CaCO3 (10% w/w) (29.2%), 5 t ha−1 mulch only treatment (27.9%), and 10% CaCO3 (w/w) (16.5%) treatment, with a rise in incubation temperature from 22 °C to 37 °C. Kinetic model calculations for CO2 emission indicated a greater half-life of easily mineralisable C pools in the NT system at 22 °C. Microbial biomass carbon (MBC) results further verified that the high temperature and disturbed soil conditions limit the availability of soil MBC under the CT systems, indicating a higher decomposition rate. Eventually, these results indicated that agricultural management practices, including tillage shift, explicitly influence the different functional components of soil organic matter (SOM)

Quantifying Hopping and Jumping in Facilitated Diffusion of DNA-Binding Proteins

International audienc

Ion beam etching redeposition for 3D multimaterial nanostructure manufacturing

A novel fabrication method based on the local sputtering of photoresist sidewalls during ion beam etching is presented. This method allows for the manufacture of three-dimensional multimaterial nanostructures at the wafer scale in only four process steps. Features of various shapes and profiles can be fabricated at sub-100-nm dimensions with unprecedented freedom in material choice. Complex nanostructures such as nanochannels, multimaterial nanowalls, and suspended networks were successfully fabricated using only standard microprocessing tools. This provides an alternative to traditional nanofabrication techniques, as well as new opportunities for biosensing, nanofluidics, nanophotonics, and nanoelectronics

Imaging Gold Nanoparticles in Living Cells Environments using Heterodyne Digital Holographic Microscopy

This paper describes an imaging microscopic technique based on heterodyne digital holography where subwavelength-sized gold colloids can be imaged in cell environment. Surface cellular receptors of 3T3 mouse fibroblasts are labeled with 40 nm gold nanoparticles, and the biological specimen is imaged in a total internal reflection configuration with holographic microscopy. Due to a higher scattering efficiency of the gold nanoparticles versus that of cellular structures, accurate localization of a gold marker is obtained within a 3D mapping of the entire sample's scattered field, with a lateral precision of 5 nm and 100 nm in the x,y and in the z directions respectively, demonstrating the ability of holographic microscopy to locate nanoparticles in living cells environments

Substrate-based atom waveguide using guided two-color evanescent light fields

We propose a dipole-force linear waveguide which confines neutral atoms up to lambda/2 above a microfabricated single-mode dielectric optical guide. The optical guide carries far blue-detuned light in the horizontally-polarized TE mode and far red-detuned light in the vertically-polarized TM mode, with both modes close to optical cut-off. A trapping minimum in the transverse plane is formed above the optical guide due to the differing evanescent decay lengths of the two modes. This design allows manufacture of mechanically stable atom-optical elements on a substrate. We calculate the full vector bound modes for an arbitrary guide shape using two-dimensional non-uniform finite elements in the frequency-domain, allowing us to optimize atom waveguide properties. We find that a rectangular optical guide of 0.8um by 0.2um carrying 6mW of total laser power (detuning +-15nm about the D2 line) gives a trap depth of 200uK for cesium atoms (m_F = 0), transverse oscillation frequencies of f_x = 40kHz and f_y = 160kHz, collection area ~ 1um^2 and coherence time of 9ms. We discuss the effects of non-zero m_F, surface interactions, heating rate, the substrate refractive index, and the limits on waveguide bending radius.Comment: 12 pages, 4 figures, revtex, submitted to Phys. Rev. A Replaced: final version accepted by PRA v.61 Feb 2000. (2 paragraphs added

Creating a low-dimensional quantum gas using dark states in an inelastic evanescent-wave mirror

We discuss an experimental scheme to create a low-dimensional gas of ultracold atoms, based on inelastic bouncing on an evanescent-wave mirror. Close to the turning point of the mirror, the atoms are transferred into an optical dipole trap. This scheme can compress the phase-space density and can ultimately yield an optically-driven atom laser. An important issue is the suppression of photon scattering due to ``cross-talk'' between the mirror potential and the trapping potential. We propose that for alkali atoms the photon scattering rate can be suppressed by several orders of magnitude if the atoms are decoupled from the evanescent-wave light. We discuss how such dark states can be achieved by making use of circularly-polarized evanescent waves.Comment: 8 pages, 4 figure