Mélanie Favre

Scaling exponents and probability distributions of DNA end-to-end distance

The scaling of the average gyration radius of polymers as a function of their length can be experimentally determined from ensemble measurements, such as light scattering, and agrees with analytical estimates. Ensemble techniques, yet, do not give access to the full probability distributions. Single molecule techniques, instead, can deliver information on both average quantities and distribution functions. Here we exploit the high resolution of atomic force microscopy over long DNA molecules adsorbed on a surface to measure the average end-to-end distance as a function of the DNA length, and its full distribution function. We find that all the scaling exponents are close to the predicted 3D values (upsilon=0.589+/-0.006 and delta=2.58+/-0.77). These results suggest that the adsorption process is akin to a geometric projection from 3D to 2D, known to preserve the scaling properties of fractal objects of dimension df<2.

Parallel AFM imaging and force spectroscopy using two‐dimensional probe arrays for applications in cell biology

Atomic force microscopy (AFM) investigations of living cells provide new information in both biology and medicine. However, slow cell dynamics and the need for statistically significant sample sizes mean that data collection can be an extremely lengthy process. We address this problem by parallelizing AFM experiments using a two‐dimensional cantilever array, instead of a single cantilever. We have developed an instrument able to operate a two‐dimensional cantilever array, to perform topographical and mechanical investigations in both air and liquid. Deflection readout for all cantilevers of the probe array is performed in parallel and online by interferometry. Probe arrays were microfabricated in silicon nitride. Proof‐of‐concept has been demonstrated by analyzing the topography of hard surfaces and fixed cells in parallel, and by performing parallel force spectroscopy on living cells. These results open new research opportunities in cell biology by measuring the adhesion and elastic properties of a large number of cells. Both properties are essential parameters for research in metastatic cancer development. Copyright

Interactive measurement and characterization of DNA molecules by analysis of AFM images

In the past few years, computer‐based analysis of atomic‐force microscopic images has acquired increasing importance for studying biomolecules such as DNA. On the one hand, fully automated methods do not allow analysis of complex shapes; on the other hand, manual methods are usually time consuming and inaccurate. The semiautomated approach presented in this report overcomes the drawbacks of both methods.

Force spectroscopy of barnase-barstar single molecule interaction

Results of the single molecule force spectroscopy study of specific interactions between ribonuclease barnase and its inhibitor barstar are presented. Experimental data obtained for the force loading rate ranging 2–70 nN/s are well approximated by a single straight line, from which the dissociation barrier of the width of 0.12 nm and height of 0.75–0.85×10−19 J can be inferred. The measured value of specific interaction does not depend on the NaCl concentration. This apparently contradicts the well‐known dependence of the binding energy of this pair on the salt concentration, but such a “contradiction” is explained by the insensitivity of the force spectroscopy data to the relatively long‐range electrostatic interaction. The latter essentially contributes to the value of barnase–barstar binding energy revealed by biochemical measurements, and it is exactly this electrostatic interaction which is influenced by the salt concentration. Copyright

Single-molecule avidin-biotin association reaction studied by force-clamp spectroscopy.

Using single-molecule force-clamp spectroscopy, where the distance between the AFM tip and the sample surface is fixed and a few parallel avidin-biotin complexes are kept stretched by a certain force, we were able to observe the formation of single avidin-biotin bonds. Perspectives to use such an approach to study association reactions at single-molecule level in the conditions resembling those characteristic for some processes in vivo (e.g. virus-cell membrane attachment) are briefly discussed.

Modeling, filtering and optimization for AFM arrays

In this paper, we present new tools and results developed for Arrays of Microsystems and especially for Atomic Force Microscope (AFM) array design. For modeling, we developed a two-scale model of cantilever arrays in elastodynamics. A robust optimization toolbox is interfaced to aid for design before the microfabrication process. A model based algorithm of static state estimation using measurement of mechanical displacements by interferometry is stated. Quantization of interferometry data processing is analyzed for FPGA implementation. A robust H ∞ filtering problem of the coupled cantilevers is solved for time-invariant system with random noise effects. Our solution allows semi-decentralized computing based on functional calculus that can be implemented by networks of distributed electronic circuits as shown in a previous paper.