Schematic showing the motion of a DNA molecule descending a nanofluidic staircase by entropophoresis (top). The illustration is overlaid on a micrograph of the actual staircase. Lightwave interference gives each step a different color. Corresponding fluorescence micrographs (bottom) show how the DNA molecule contracts as the depth increases from about 4 nm (about 20 times bigger than a water molecule) at the left to about 342 nm at the deepest step on the right. The images of the DNA molecule are blurred and pixilated, making it appear larger than it is. These imaging errors are estimated and corrected in the final analysis of the size of the molecule. Credit: Strychalski, Stavis/NIST
Slinky, the coiled metal spring that “walks” down stairs with just a
push, momentum and gravity? Researchers at the National Institute of
Standards and Technology (NIST) have developed their own version of this
classic—albeit 10 million times smaller—as a novel technology for
manipulating and measuring DNA molecules and other nanoscale materials.
the first of two recent papers, Samuel Stavis, Elizabeth Strychalski
and colleagues demonstrated that a nanoscale fluidic channel shaped like
a staircase with many steps (developed previously at NIST and Cornell
University) can be used to control the otherwise random drift of a DNA
molecule through a fluid. Squeezed into the shallowest step at the top
of the staircase, a strand of DNA diffuses randomly across that step.
The DNA molecule seeks to increase its entropy—the universal tendency
towards disorder in a system—by relieving its confinement, and
therefore, “walks” down onto the next deeper step when it reaches the
motion of the molecule down the staircase, which the researchers termed
“entropophoresis” (entropy-driven transport), ends when it becomes
trapped on the deepest step at the bottom. Because this motion resembles
that of a Slinky, the researchers nicknamed their system the
“nanoslinky.” The researchers found that DNA molecules of different
sizes and shapes descended the staircase at different rates—which
suggests the structure could be used to separate, concentrate and
organize mixtures of nanoscale objects.
says that this novel technology provides advantages over traditional
nanofluidic methods for manipulating and measuring DNA.
over the behavior of a DNA molecule is built into the staircase
structure. After placing the molecule on the top step [by driving the
DNA strand up the staircase with an electric field], no external forces
are needed to make it move,” Stavis says. “The staircase is a passive
nanofluidic technology that automates complex manipulations and
measurements of DNA.”
NIST advance in nanofluidic technology dovetails nicely with a NIST
innovation in measurement science—specifically, determining the size of a
DNA molecule in nanofluidic “slitlike confinement” imposed by the
narrow gap between the floor of each step and the ceiling of the
channel. In the “nanoslinky” system, Strychalski explains, the coiled
and folded DNA strand contracts progressively as it moves down the
steps. “Because there are many steps, we can make more detailed
measurements than previous studies,” she says.
Getting the most from those measurements was the goal of the research reported in the NIST team’s second paper.
“The challenge was to make our measurements of DNA size more quantitative,” Strychalski says.
measurements of DNA dimensions in nanofluidic systems, Strychalski
says, have been limited by imaging errors from the optical microscopes
used to measure the dimensions of DNA molecules labeled with a
first problem is the diffraction limit, or the optical resolution, of
the fluorescence microscope,” she says. “The second problem is the pixel
resolution of the camera. Because a DNA molecule is not much larger
than the wavelength of light and the effective pixel size, images of
fluorescent DNA molecules are blurred and pixilated, and this increases
the apparent size of the molecule.”
improve their measurements of DNA molecules during their descent, the
NIST researchers used models to approximate the effects of diffraction
and pixilation. Applying these “numerical simulations” to the images of
DNA molecules confined by the staircase made the final measurements of
DNA size the most quantitative to date. These measurements also showed
that more work is needed to fully understand this complicated system.
to Stavis and Strychalski, the staircase is a simple prototype of a new
class of engineered nanofluidic structures with complex
three-dimensional surfaces. With further refinements, the technology may
someday be mass produced for measuring and manipulating not just DNA
molecules, but other types of biopolymers and nanoscale materials for
health care and nanomanufacturing.
Slinky is a registered trademark of POOF-Slinky, Inc.