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.