Manipulating molecules with nanochannels

(Nanowerk Spotlight) Nanofluidic channels, confining and transporting tiny amounts of fluid, are the pipelines that make the cellular activities of organisms possible. For instance, nanoscale channels carry nutrients into cells and waste from cells. Researchers are trying to mimic Nature by constructing nanochannels in order to be able to manipulate single molecules in, predominantly biomedical, applications. Although nanochannels adjustable in size are prevalent in Nature, it is challenging to fabricate them artificially because of conflicting requirements for rigid structural integrity (to prevent collapse) on one hand and reconfigurability of nanometer-sized features on the other (to allow adjustability). Recent work at the University of Michigan addresses these issues and introduces methods to rapidly prototype structurally stable yet reconfigurable nanochannels. By fabricating tuneable elastomeric nanochannels for nanofluidic manipulation, the researchers were able to properly balance the need for flexibility and rigidity.
"Our method of fabricating nanochannels is very simple" Dr. Shuichi Takayama explains to Nanowerk. "We do it by stretching a piece of surface treated rubber. People may have similar experiences where they have stretched an old rubber band and seen cracks form. We just do this in a finer, more controlled manner to make nanochannels. It does not require any of the typical expensive equipment needed to create nanostructures, such as e-beams or cleanrooms. Our tuneable nanochannels are unique in being able to adjust its cross-sectional size."
Takayama is Associate Professor of Biomedical Engineering and Associate Professor of Macromolecular Science and Engineering at the University of Michigan. His current research on nanochannels is preceded by exploring the concept of using cracking of surfaces to do nanopatterning and fabrication several years ago ("Fabrication of reconfigurable protein matrices by cracking").
Flow of fluorescein molecules through an array of tunable elastomeric nanochannels
Flow of fluorescein molecules through an array of five tunable elastomeric nanochannels and their accumulation at an air-filled microscale compartment. Running horizontally at the top is an air-filled microchannel. The nanochannels are triangular and are 80 nanometers high from base to top corner and 600 nm wide at the base (Image: Dr. Takayama)
"It initially started by accident" says Takayama. "We would find cracks on oxidized PDMS surfaces. Many people including ourselves knew this but generally considered it a nuisance. But one day, we thought that maybe we can take advantage of this. And that is how we got started."
In their 2005 paper, Takayama and his collaborators speculated how "crack patterning" could open new avenues in studies of dynamic interactions between cell and extracellular matrix for cellular science and biotechnology, and in other applications, such as proteomics or bio-nanoelectronics, where nano- or microscale protein patterns are used.
In their latest paper in Nature Materials ("Tuneable elastomeric nanochannels for nanofluidic manipulation"), they describe the use of nanoscale fracturing of oxidized PDMS (polydimethylsiloxane – the most widely used silicon-based organic polymer found in things ranging from Silly Putty to breast implants) to conveniently fabricate nanofluidic systems with arrays of nanochannels that can actively manipulate nanofluidic transport through dynamic modulation of the channel cross-section.
The researchers fabricated a nanofluidic system which consists of a parallel array of nanochannels made in PDMS. The PDMS is mechanically stretched to generate an ordered array of nanoscale cracks, which are then replicated onto ultraviolet-curable epoxy. Subsequently, a substrate with recessed nanochannels is prepared by casting PDMS prepolymer against the epoxy master.
Nanochannels formed by cracking have a triangular cross section in which channel closure proceeds gradually from the corners. Fluid flows are driven mainly by an electric field applied between the inlet and outlet compartments. Takayama notes that the channel geometry and materials mechanics are optimized so that the cross-sectional size of the nanochannels can be reversibly modulated in response to compressive forces applied perpendicularly to the nanochannels.
"As the nanochannels only allow the passage of molecules or nanoparticles that are smaller than their cross-section, the magnitude of applied force can be varied to choose subpopulations in a polydisperse mixture that can pass through the nanochannels" he says.
Controlled constriction of the elastomeric nanochannels can also trap and release single nanoparticles and dynamically manipulate single DNA molecules. Single molecule genetics is one area Takayama and his group are particularly interested in and in their paper they describe one example of reversible stretching and relaxing single DNA molecules.
"Bending and stretching of DNA is involved in regulation of how genes get turned on and off, so this type of capability to manipulate single DNA molecules may be useful in understanding these very important biological processes" he says. "Also, stretching of DNA molecules is of practical importance in genetic analysis. So the technology may have diagnostic application in the future, too."
As the researchers explain, the nanochannels they describe are straightforward to fabricate and provide a remarkably versatile example of an active nanostructure that can change its architecture during operation to create, control and manipulate various types of nanofluidic transport.
"We believe that our approach can be extended to higher levels of functionality through the integration of parallel and serial operations, sophisticated optics and a wealth of polymer chemistry" Takayama concludes.
Michael Berger By – Michael is author of three books by the Royal Society of Chemistry:
Nano-Society: Pushing the Boundaries of Technology,
Nanotechnology: The Future is Tiny, and
Nanoengineering: The Skills and Tools Making Technology Invisible
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