Tuesday, November 6, 2007 - 5:00 PM
284g

Using Flow Fields To Stretch And Adhere DNA Molecules To Surfaces

Ronald G. Larson, Weixian Shi, and Ji Hoon Kim. Department of Chemical Engineering, University of Michigan, 2300 Hayward St., Ann Arbor, MI 48109

Single-molecule studies are increasingly used to investigate the dynamics and statistics of biochemical and biophysical interactions between DNA and proteins that that are difficult to discern in bulk experiments, which average over an ensemble of molecules. To do so, it is important to stretch and immobilize DNA molecules. Using fluorescence microscopy, we compare the degree of adsorption and stretching of DNA onto surfaces achieved by published stretching methods that use fluid flow: molecular combing, droplet drying, spin-stretching, and air-blowing. Molecular combing uses a receding meniscus to stretch out the DNA on a hydrophobic surface, while droplet drying uses the radial flow created by the nonuniform evaporation along the droplet surface to deposit DNA molecules onto an aminopropyltriethoxy-treated glass surface. In spin-stretching, we find that the effect of radial hydrodynamic flow created by the centrifugal force of the rotating disk is minimal and the DNA is stretched out on a hydrophobic substrate by the moving meniscus. In air-blowing, a jet of gas pushes liquid across a substrate, depositing stretched DNA molecules along the way. In our study, DNA molecules either combed or spin-stretched onto hydrophobic surfaces stretch to a greater degree, but fewer are deposited, at pH 8.0 than at lower pH, apparently because at pH 8.0 DNA adhesion occurs primarily only at the DNA extremities and so avoids trapped regions of incompletely stretched DNA, with the side effect that more molecules avoid adhesion altogether. We find by high-speed video microscopy that there is complex droplet deformation and motion during air-blowing, which complicates the deposition and stretching process, leading to radial deposition patterns. Our results are a first step towards understanding and optimizing the various proposed methods of DNA stretching and anchoring onto surfaces, which is important in studying their interactions with proteins.