Biomolecule separation is a fundamental analytical and preparative technique in biology, medicine, chemistry, and industry. Fractionation of biological molecules, such as nucleic acids and proteins, plays a central role in genomic analysis. In the new challenge of systems biology, as well as in the application of biomarker detection and biosensing, this task becomes even more important because solving the puzzle of interactions between proteins is far more complicated than deciphering genomes, due to the lack of protein's equivalent of amplification, fractionation and sequencing techniques.

This project seeks to use microfabricated regular nanofluidic filters (nanofilters) as controllable sieving medium for size- or charge-based fractionation of various biologically relevant macromolecules, such as ds DNA, proteins, and polysaccharides. Using standard microfabrication techniques, we have precisely fabricated nanofilters with gap thickness down to the vicinity of 10 nm. In such molecular-scale confining structures, molecular transport properties are largely affected by the steric constraints of nanofluidic structures.

In this project, we construct different nanofilter based separation devices and explore the steric and electrostatic partitioning of biomolecules with the nanofilter for size- or charge-fractionation of various biologically relevant macromolecules. In the proposed separation systems, unlike other conventional random nanoporous sieving materials, the nanofilters can be made uniform and controllable, also chemical groups on the wall can be tailored. In addition to the application of biomolecule separation, the nanofilter based artificial sieving structures provide an ideal platform for the theoretical study of molecular dynamics and stochastic motion in confining spaces because of their precisely characterized environments.

Links:

• Patterned One-Dimensional Periodic Nanofilter Array for Biomolecule Separation. (Jianping Fu, Pan Mao, Jongyoon Han)

• Molecular Sieving in Periodic Free-Energy Landscapes Created by Patterned Nanofilter Arrays. (Jianping Fu, Juhwan Yoo, Jongyoon Han)

• Large-Scale Nanofluidic Filter Array for High-Throuput Biomolecule Separation. (Pan Mao, Jongyoon Han)

• Characterization of Effect of Structural Parameters of the Nanofilter Array on Biomolecule Separation. Dispersion of Fractionated Biomolecule Bands in the Nanofilter Array. (Hansen Bow, Jianping Fu, Craig Rothman, Jongyoon Han)

• Design and Fabrication of Anisotropic Two-Dimensional Nanofilter Array (Anisotropic Nanofilter Array: ANA) for Continuous-Flow Biomolecule Separation. (Jianping Fu, Jongyoon Han)

• Continuous-Flow Ogston Sieving-Based Separation of Short DNA and SDS-Protein Complexes and Entropic Trapping-Based Separation of Long DNA Through the ANA. (Jianping Fu, Jongyoon Han)
• Continuous-Flow Size- or Charge-Based Separation of Proteins under Native Conditions through the ANA. (Reto B. Schoch, Jianping Fu, Jongyoon Han)

Movie links:

• Suppressing air bubbles trapped in the one-dimensional nanofilter array. (Real time. Air bubbles trapped in the nanofilter deep regions were suppressed by EOF flow. Video by Jianping Fu.)
• Fast SDS-protein complex separation in one-dimensional periodic array of nanofilter. (10X speed. Three proteins separated within 30 sec, Eav = 100 V/cm. Video by Jianping Fu.)

• Continuous-flow separation of short DNA (the PCR marker, 50 - 1,000 bp) through two-dimensional periodic array of nanofilters (Anisotropic Nanofilter Array: ANA), based on the Ogston sieving mechanism. (This video was taken with exposure time of 1300 ms/image and image size of 1300 µm X 1620 µm. The time scale in this movie has been compressed by a factor of 20. At the beginning of the movie, only Ey = 25 V/cm was applied. The orthogonal field Ex = 35 V/cm was applied at 3 sec in the movie, and the separation was finished at about 12 sec in the movie. Video by Jianping Fu.)

• Continuous-flow separation of long DNA (the Lambda DNA-Hind III digest, 2,000 - 23,000 bp) through ANA, based on the entropic trapping mechanism. (This video was taken with exposure time of 600 ms/image and image size of 3270 µm X 4080 µm. The time scale in this movie has been compressed by a factor of 20. At the beginning of the movie, only Ey = 100 V/cm was applied. The orthogonal field Ex = 185 V/cm was applied at 1 sec in the movie, and the separation was finished at about 5 sec in the movie. Video by Jianping Fu.)

• Continuous-flow separation of SDS-protein complexes through ANA. (This video was taken with exposure time of 1000 ms/image and image size of 3270 µm X 4080 µm. The time scale in this movie has been compressed by a factor of 20. At the beginning of the movie, only the vertical field Ey = 50 V/cm was applied. The horizontal field Ex = 75 V/cm was applied at 1 sec in the movie, and the separation was finished at about 6 sec in the movie. Video by Jianping Fu.)

References

1. Schoch, R. B., Fu, J., Bow, H. & Han, J. MicroScale Bioseparation 2007 Symposium, Vancouver, Canada.
2. Fu, J.*, Schoch, R. B.*, Stevens, A. L., Tannenbaum, S. R. & Han, J. Nature Nanotech. 2, 121-128 (2007). (pdf)
3. Bow, H., Fu, J., Rothman, C. & Han, J. Anal. Chem., submitted (2006).
4. Fu, J. & Han, J. Proceedings of the MicroTAS 2006 Symposium, Tokyo, Japan, vol. 1, pp. 519-521. (pdf)
5. Fu, J., Yoo, J. & Han, J. Phys. Rev. Lett. 97, 018103.1-3 (2006). (pdf‡)
6. Fu, J., Mao, P. & Han, J. Appl. Phys. Lett. 87, 263902.1-3 (2005). (pdf†)
7. Fu, J. & Han, J. American Physical Society National March Meeting 2006, Baltimore, Maryland. (pdf)
8. Fu, J. & Han, J. Proceedings of the MicroTAS 2005 Symposium, Boston, MA, vol. 2, pp. 1531-1533. (pdf)
9. Fu, J. & Han, J. 2005 Gordon Research Conf. on the Physics and Chemistry of Microfluidics, Oxford, UK.
10. Fu, J. & Han, J. MicroScale Bioseparation 2005 Symposium, New Orleans, Louisiana.
11. Fu, J. & Han, J. Proceedings of the MicroTAS 2004 Symposium, Malmo, Sweden, vol. 1, pp. 285-287.

* These authors contributed equally to this work.

† Copyright by American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.

‡ Copyright by the American Physical Society.