The diffusion constant of a labeled protein sliding along DNA.

Long ago inferred by biochemists, the linear diffusion of proteins along DNA has recently been observed at a single-molecule level using fluorescence microscopy. This imaging technique requires labeling the protein of interest with a fluorophore, usually an organic nanosized dye that is not supposed to impact the dynamics of the protein. Yet individual proteins can also be tracked using much larger labels, like quantum dots or beads. We investigate here the impact of such a large label on the protein diffusion along DNA. Solving a Fokker-Planck equation, we estimate the diffusion constant of a protein-label complex diffusing in a periodic potential that mimics the DNA-protein interaction, the link between the protein and the label being modeled as a Hookean spring. Our results indicate that the diffusion constant can generally be calculated by considering that the motion of the protein in the DNA potential is decoupled from the Brownian motion of the label. Our conclusions are in good agreement with the experimental results we obtained with the restriction enzyme EcoRV, assuming a rotation-coupled diffusion of the enzyme along DNA.

Dark-field digital holographic microscopy for 3D-tracking of gold nanoparticles.

We present a new technique that combines off-axis Digital Holography and Dark Field Microscopy to track 100nm gold particles diffusing in water. We show that a single hologram is sufficient to localize several particles in a thick sample with a localization accuracy independent of the particle position. From our measurements we reconstruct the trajectories of the particles and derive their 3D diffusion coefficient. Our results pave the way for quantitative studies of the motion of single nanoparticle in complex media.

Imaging gold nanoparticles in living cell 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 environments. 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 cell environments.

Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins.

Facilitated diffusion of DNA-binding proteins is known to speed up target site location by combining three dimensional excursions and linear diffusion along the DNA. Here we explicitly calculate the distribution of the relocation lengths of such 3D excursions, and we quantify the short-range correlated excursions, also called hops, and the long-range uncorrelated jumps. Our results substantiate recent single-molecule experiments that reported sliding and 3D excursions of the restriction enzyme EcoRV on elongated DNA molecules. We extend our analysis to the case of anomalous 3D diffusion, likely to occur in a crowded cellular medium.

Transverse fluctuations of single DNA molecules attached at both extremities to a surface.

We present a simple method to stretch DNA molecules close to a surface without any chemical modification of either the molecules or the surface. By adjusting the pH of the solution, only the extremities of DNA molecules are tethered to a glass coverslip made hydrophobic, while stretching is achieved using a hydrodynamic flow. These extended molecules provide a very favorable template for DNA-protein interaction studies by purely optical means. Pursuing these experiments requires first a full characterization of the thermally driven fluctuations of the tethered DNA molecules. For this purpose, these fluctuations were recorded by fluorescence microscopy and were analyzed in terms of normal modes. Our experimental results are well described by a model accounting for the nonlinear elastic behavior of the chain. Remarkably, the proximity of the molecules to a rigid surface does not alter the main features of their dynamics, and our results are in agreement with previous studies on extended DNA in viscous solutions.

Statistical aging and nonergodicity in the fluorescence of single nanocrystals.

The relation between single particle and ensemble measurements is addressed for semiconductor CdSe nanocrystals. We record their fluorescence at the single molecule level and analyze their emission intermittency, which is governed by unusual random processes known as Lévy statistics. We report the observation of statistical aging and ergodicity breaking, both related to the occurrence of Lévy statistics. Our results show that the behavior of ensemble quantities, such as the total fluorescence of an ensemble of nanocrystals, can differ from the time-averaged individual quantities, and must be interpreted with care.

Bunching and antibunching in the fluorescence of semiconductor nanocrystals.

The fluorescence of single-colloidal CdSe quantum dots is investigated at room temperature by means of the autocorrelation function over a time scale of almost 12 orders of magnitude. Over a short time scale, the autocorrelation function shows complete antibunching, indicating single-photon emission and atomiclike behavior. Over longer time scales (up to tens of seconds), we measure a bunching effect that is due to fluorescence intermittency and that cannot be described by fluctuations between two states with constant rates. The autocorrelation function also exhibits nonstationary behavior related to power-law distributions of On and Off times.

Strong evaporative cooling of a trapped cesium gas.

Using forced radio-frequency evaporation, we have cooled cesium atoms prepared in the sublevel F = -m(F) = 3 and confined in a magnetic trap. At the end of the evaporation ramp, the sample contains ~ 7000 atoms at 80 nK, corresponding to a phase space density 3 x 10(-2). A molecular dynamics approach, including the effect of gravity, gives a good account for the experimental data, assuming a scattering length larger than 300 Angstrom.