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Séminaire de Johan R. C. van der Maarel

A nanochannel platform for single-DNA studies

Johan R. C. van der Maarel

Department of Physics, National Unversity of Singapore, Singapore

The study of single DNA molecules confined in a nanochannel is of importance from both biotechnological and biophysical points of view. We produce nanochannels in cheap PDMS based biochips. The two-dimensional cross-sectional diameter of the channels is in the range of 50 to 300 nm. We measure the extensions of single bacteriophage T4-DNA with a contour length of 60 microns with fluorescence microscopy. I will address three important and related issues concerning DNA confined in a nanospace. The first issue is the control of the conformation of DNA by the neutral crowding agent dextran. As a surprising result, we found that the DNA molecules take a more extended rather than a more compacted conformation in the presence of low concentrations of dextran. At higher concentrations, the DNA molecules collapse into a condensed state. The second issue concerns the effects of the like-charge proteins bovine serum albumin and hemoglobin. Here, we found that the DNA molecules are compressed and eventually condense into a compact form with increasing concentration of protein. The threshold concentration for condensation depends on channel cross-sectional diameter as well as ionic strength of the supporting medium. The critical values for full compaction are typically very low, less than one tenth of a millimolar. In the bulk phase and in the same environmental conditions, no protein-facilitated condensation was observed. For the third issue, we will discuss the effects of the nucleoid associated proteins HU, HNS, and HFQ on the confomation and condensation of DNA confined in a nanochannel. Our results show that the effect of crowding is not only related to osmotic pressure, but that the interplay with the anisotropic confinement is of paramount importance in controlling the conformation of DNA in a confined state. Our work contributes to the understanding of membrane-free biomolecular assemblies, which are key features of life.