DNA Stretching and Immobilization through the Air/Water Dewetting Process

It is essential to stretch the DNA from its equilibrium coiled state for DNA genetic analysis and diagnosis. So far there are several ways to realize the DNA stretching process at the molecular level. Since DNA is prepared in the water solution, using the flow field seems to be a natural and convenient way to stretch DNA. By using the flow field, the DNA can be stretched by the viscous force when the flow velocity gradient is generated or by the meniscus force of dewetting air/water interface. The dewetting process seems to be a better method because DNA is not only stretched but also immobilized onto the substrate and therefore the relaxation of DNA could be prevented. In our research work, computational simulations and experimental observations are carried out to study DNA stretching and immobilization in the air-water dewetting process. To simulate this physical phenomenon, the Brownian dynamics simulation with bead-spring DNA model is integrated with a continuum fluid mechanics solver based on the finite volume method. Two cases of dewetting DNA stretching are studied in this work. One is the traditional molecular combing problem where a solid substrate is pulled out from the DNA solution. The other is draining water solution from a straight channel. For simplicity, in both cases DNA is initialized with one end attached to the wall in our simulation. By simulation, the detailed physical process of DNA stretching onto the wall is understood. We further compare the simulation results to our experimental observations for validation.