DNA Stretching Cross-Stream

A new experiment shows that in specially engineered fluid flows typical of coating processes, single DNA molecules can sometimes enter into a kind of flow instability in which the DNA orients itself perpendicular to the plane of the flow. The experiment, conducted at Rice University by Matteo Pasquali and Rajat Duggal, was part of a broader study of how polymer molecules behave in moving fluids, a subject pertinent to many biological and technological research areas, such as inkjet printing, paper coating, the movement of air in lung alveoli, and DNA arrays.

Studying polymers in complex fluid flows is difficult because single polymers are hard to resolve (being typically only 10-100 nm in size) and because polymers can influence each other and the flow itself even at very low concentration (down to few parts per million). That's why DNA (above 10 microns in contour length) was chosen and why the DNA was kept "ultradilute," so that it would not influence the flow and that only one DNA molecule is visible at a time. In the Rice experiment, a dilute suspension of DNA in water thickened by sugar is taken up by a rotating drum which moves past a glass knife edge. In this way a thin slice of solution can be moved as if on a conveyor belt past a lens. The lens focuses a blue-green light on the DNA and picks up green-yellow light emitted by the previously fluorescently-stained DNA molecules.

The resulting 30-frame-per-second film clearly can image individual DNAs at a time with a spatial resolution of 250 nm (the thickness of the molecule cannot be resolved but its length can be). The researchers had expected that in the complex flow (a flow in which the velocity of the fluid varies across the width of the channel) the DNA would deploy itself with the flow rather than at right angles. Indeed, this happened at the lowest drum rotation speeds; the direction of stretching changed once the drum speed became high enough to induce ripples on the surface of the liquid moving past the glass knife. (Journal of Rheology, July/August 2004)