The faster the separation speed, the better the separation resolution - nanotechnology makes it possible

(Nanowerk News) Prof. Yoshinobu Baba, Associate Prof. Noritada Kaji, and Assistant Prof. Takao Yasui from the Graduate School of Engineering at Nagoya University invented a new separation technology overcoming the conventional separation concept.
All the current separation technologies use a method that involves separation based on differences and interactions between physical or chemical characteristics. In general, the faster the separation speed, the worse is the separation resolution: for the better resolution, the separation speed can be slower.
To solve this problem, in this study (Nano Letters, "Arrangement of a Nanostructure Array To Control Equilibrium and Nonequilibrium Transports of Macromolecules"), the researchers have developed a technology that enables nanopillars (diameter φ500 nm) to pass through in only a particular direction, and improve the separation resolution at faster separation speeds.
Approximately 10 years ago, researchers or professionals in the medical field concluded that the analysis speed of genomes in seconds was sufficient, and that analysis in milliseconds was not necessary.
As the decoding process was estimated at a cost of approximately 10 billion dollars per person during that time (ca. 2001), researchers focused on decreasing this cost. Because of their efforts, the decoding process can be performed only at 1,000 dollars at present.
Since then, a brand new target was set for high speed genome analysis, i.e., one-hour-decoding.
Prof. Baba and his research group from the Graduate School of Engineering challenged high speed genome analysis as targets in 2001, thereby anticipating future requirements. Their research results were ahead of their time, and only now this can be regarded as a trending topic in the world.
“The concept of nanopillars did not exist in the real world at that time, but was just an imagined picture by Prof. Baba.”
Associate Prof. Noritada Kaji, as a student in 2001, remembers that Prof. Baba’s innovative ideas impacted many researchers.
A nanopillar is a nano-device that aligns pillar structures of the same nano-size (Figure 1). Prof. Baba suggested that our world would change if DNA could flow through the nanopillars at high speed and separate different sizes of DNA by using semiconductor technology.
Schematic image of nanopillar device
Figure 1. Schematic image of nanopillar device (Figure: Kaji et al., Anal. Chem. (2004) 76: 15-22. © American Chemical Society)
At that time, Prof. Baba and Associate Prof. Kaji (as a student in a master’s program) worked at the Faculty of Pharmaceutical Sciences, Tokushima University. Because of their background, they needed a partner who could provide technical help; therefore, a professor at the University of Tokyo, Emeritus Fellow Yasuhiro Horiike at National Institute for Materials Science (NIMS) was involved in the research.
However, the nanopillar device was not that easy to assemble.
Several students made an attempt, and the first one that was submitted three years later, in 2004, to Associate Prof. Kaji (as a Ph.D. student at that time). Moreover, only two devices materialized, although one proved to be impracticable.
As a Ph.D. student at that time, Associate Prof. Kaji enthusiastically concentrated on the research with the only device in the world, cautiously washed after every experiment (Figure 2).
SEM image of nanopillar structure
Figure 2. SEM image of nanopillar structure. The scale bar shows 500 nm. (Figure: Kaji et al., Anal. Chem. (2004) 76: 15-22. © American Chemical Society)
Finally he succeeded in separating six differently sized DNA molecules in only 680 s, which demonstrated the world’s fastest separation technology at that time, as Prof. Baba expected (Analytical Chemistry, "Separation of Long DNA Molecules by Quartz Nanopillar Chips under a Direct Current Electric Field").
Further development
Associate Prof. Kaji visited Emeritus Fellow Horiike at NIMS with Assistant Prof. Takao Yasui (as a student at that time) many times. They learned how to make the nanopillar devices, staying for several weeks at a time. In making a device themselves, they also developed variations, and brushed up their technical ability.
With his original nanopillar devices, Assistant Prof. Yasui (as a student at his master’s course at that time) developed his research theme: the separation principle. He compared the variations of nanopillar device with the one, which Associate Prof. Kaji used.
Movie 1. Big and small DNAs passing through the zig-zag alignment of nanopillars (Movie: by courtesy of Prof. Baba)
Consequently, he revealed that, in the zig-zag alignment (as Associate Prof. Kaji’s device), small DNA is sequenced first because big DNA is tumbled by the pillars, whereas in the straight pattern, big DNA is sequenced first (Movie 1). Furthermore, in the straight pattern, the higher the separation speed, the better the separation resolution (Movie 2).
“Imagine—when you are quickly folding washed clothes, your work may be rough.”
Similar to the relationship between efficiency and effectiveness, separation technology, such as filtration and chromatography, usually shows that the higher the separation speed, the worse the separation resolution, while a slower separation speed improves the separation resolution.
Movie 2. Big and small DNAs passing through the straight alignment of nanopillars (Movie: Yasui, et al. Nano Lett. (2015) 15: 3445. Copyright (2015) American Chemical Society)
Therefore, their technology brought a new phenomenon into separation technology, overcoming the conventional principle of separation.
“However, for the result produced, it is necessary to prove it logically to be approved by the world.”
Assistant Prof. Yasui (as a Ph.D. student at that time) mentioned that when he visited Harvard University in 2008, he learned important tips as a researcher in the nano-technology field. Following the principle of being able to prove something logically, he was faced with the task of explaining the mystery of separation.
The breakthrough was the principle reported by Prof. K. D. Dorfman and his theoretical physicists’ group in 2007, which described a nano-filter by simulation. According to the report, small particles can pass even through corners, and therefore the separation requires a longer time than when using bigger ones (Physical Review Letters, "Nonequilibrium Transport of Rigid Macromolecules in Periodically Constricted Geometries").
In the case of the nanopillar device, the same principle was demonstrated both by means of calculation and in experiments. When DNA size is small (short), DNA rotates and snakes through the nanopillars. In contrast, big (long) DNA hardly rotates and passes through the nanopillars immediately (Figure 3).
Small DNA requires more time by rotating and snaking through the nanopillar
>Figure 3. Small DNA requires more time by rotating and snaking through the nanopillars. (Figure: Yasui, et al., Nano Lett. (2015) 15: 3445. © American Chemical Society) (click on image to enlarge)
“We could break the status quo of separation technology, and furthermore, explain the logic.”
Assistant Prof. Yasui remarked that we are now able to take separation technology a step further. Cooperating with other nano-devices, a greater speed of genome analysis will be possible in the near future.
Source: Nagoya University
Subscribe to a free copy of one of our daily
Nanowerk Newsletter Email Digests
with a compilation of all of the day's news.