Ring-like Formations In Drying DNA Drops Could Affect Hybridization Studies

Main Category: Genetics
Article Date: 14 May 2006 - 0:00 PDT

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Coffee drinkers are familiar with the ring-shaped stains that result from spilled drops that have dried, in which the brown stain is not evenly distributed, but instead concentrated at the edge. Now, a team led by Gerard Wong, a professor of materials science and engineering, physics, and bioengineering at the University of Illinois at Urbana-Champaign has found the same "coffee-ring" formation in drying drops of DNA.

To gain insights into the physics behind the ring phenomenon, Wong's team experimentally studied the dynamics of drying DNA droplets on glass surfaces. They report their findings in a paper accepted for publication in the journal Physical Review Letters, and posted on its Web site.

"As the droplet evaporated, DNA chains were transported outward by water flow to the drop's perimeter," Wong said. "At the droplet edge, the DNA became increasingly concentrated and formed a liquid crystal with concentric chain orientations. (Liquid crystals are materials that flow like a liquid, but can align in a preferred direction like a crystalline solid.) During the final stages of drying, stresses propagated from the rim inward through the liquid crystal, creating cracks that formed a periodic zigzag pattern."

To examine the structure and behavior of the DNA liquid crystal, the researchers used a relatively new imaging technique developed at Kent State University. Called fluorescence confocal polarizing microscopy, the technique imaged the DNA in the drying droplet in three dimensions.

"The DNA alignment parallel to the droplet's edge was counterintuitive," Wong said. "We had expected the DNA to extend along the direction of flow, which was mainly in the radial direction. But, instead of resembling the spokes of a bicycle wheel, the transported DNA resembled the rim of a bicycle wheel."

Since nearly all the DNA is concentrated in a narrow ring with almost no DNA in the rest of the stain, these effects should be accounted for in the design of arrays in which DNA droplets are sequentially deposited onto a glass surface for hybridization studies, the researchers report.

"Without optimization of the wetting conditions, it is possible to miss all the DNA in the ring stain of a dried droplet, resulting in false negatives," Wong said. "We need to think of strategies to minimize this effect."

The co-authors of the paper are postdoctoral research associate Ivan Smalyukh, graduate students Olena Zribi and John Butler, and professor Oleg D. Lavrentovich, director of the Liquid Crystal Institute at Kent State.

The work was funded by the Institute for Complex and Adaptive Matter and the National Science Foundation.

James E. Kloeppel, Physical Sciences Editor
kloeppel@uiuc.edu
University of Illinois at Urbana-Champaign
http://www.uiuc.edu

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