Nucleic Acid Engineering - Engineering DNA as Both a Genetic and a Generic Material

DNA is a truly amazing material. Biologically, it is an information storage molecule carrying genetic codes for gene regulation and protein production. It is essentially what life is made of. Mechanically, DNA can be rigid or flexible, tunable by its composition and length. Physically, DNA is very small - only 2 nanometer in diameter; yet its length is customizable with a resolution about 0.34 nm.

Chemically, DNA is water soluble, stable (think of mummy), non-toxic (think of sushi), biocompatible and biodegradable. DNA can be obtained from a variety of sources including live cells and a machine (e.g., a DNA synthesizer). DNA can also be programmed. Most uniquely, thousands of different enzymes have been evolved that can be employed to manipulate DNA at the angstrom level accuracy.

Thus, DNA provides an ideal platform as an additional materials building block for both nanotechnology and nanobiotechnology. Since the pioneering work of Prof. Nadrian Seeman and others, DNA has been used in so many ways that it is no longer regarded as a sole biomolecule.

Nucleic Acid Engineering

Prof. Dan Luo's group at Cornell has been focused on engineering nucleic acids (DNA and RNA) as a true polymer for real world applications. Their work aims at creating novel, bulk-scale DNA materials in high yield and low cost and with simple design that fully utilizes both DNA's biological and non-biological properties.

Using branched DNA (X-shaped, Y-shaped, etc.), the Luo group has built tree-shaped DNA (dendrimers-like DNA, or DL-DNA), DNA nanobarcodes, DNA hydrogels, DNA liposomes, and DNA-organized nanoparticles. Recently, the Luo group has developed a DNA-based, anisotropic, branched, and crosslinkable monomer (termed "ABC monomer") as a universal nanoscale material building block.

Using these DNA ABC monomers, the Luo group invented "target-driven polymerization" process where DNA polymers can only be synthesized in the presence of a pathogen DNA. The polymerization process amplifies signal within polymer itself, enabling accurate and sensitive molecular sensing. The technology will have wide applications in diagnostics as well as in multi-drug delivery.

In addition, 1D nano-wires, 2D superlattices, 3D supracrystals, and free-standing monolayer sheets have been achieved through soft-lithography but with a nanometer feature size by using DNA as an organizer. Very recently (in 2009), the Luo group has created a DNA gel that can produce large amounts of proteins without any living cells (termed "protein producing gel" or "P-gel"). P-gel successfully converts the central dogma from inside a cell to a gel-based chemical reaction in a test tube. Cloning, transformation and cell culturing are no longer needed for protein production.

The Luo group envisions that P-gel will become a platform technology for producing as well as engineering proteins efficiently and effectively. Furthermore, the Luo group has created an "unforgettable" DNA gel. These examples illustrate the fact that DNA is both a genetic and a generic material and that through Nucleic Acid Engineering one can create new materials via DNA with novel properties and real-world applications. For more information, please refer to the recent (in last 5 years) publications from the Luo group.

References

1. N. Park, J.S. Kahn, E.J. Rice, M.R. Hartman, H. Funabashi, J. Xu, S.H. Um, D. Luo, High-yield cell-free protein production from P-gel, Nature Protocols, 4, 1759-1770 (2009)
2. J.B. Lee, Y.H. Roh, S. Um, H. Funabashi, W. Cheng, J.J. Cha, P. Kiatwuthinon, D.A. Muller, D. Luo, Multifunctional nano-architectures from DNA-based ABC monomers, Nature Nanotechnology, 4, 430-436 (2009)
3. W. Cheng, M. J. Campolongo, J. J. Cha, S. J. Tan, C. C. Umbach, D. A. Muller, D. Luo, Free-Standing Nanoparticle Superlattice Sheets Controlled by DNA (Article), Nature Materials, 8, 519-525 (2009)
4. N. Park, S. H. Um, H. Funabashi, J. Xu, D. Luo, A Cell-free Protein Producing Gel, (Article), Nature Materials, 8, 432-437 (2009)
5. W. Cheng, N. Park, M.T. Walter, M.R. Hartman, D. Luo, Nanopatterning Self-Assembled Nanoparticle Superlattices by Molding Microdroplets (Cover Article) Nature Nanotechnology, 3, 682-690 (2008)
6. S. Um, J. Lee, N. Park, S. Kwon, C. Umbach, D. Luo, Enzyme catalyzed assembly of DNA hydrogels, Nature Materials 5, 797-801 (2006)
7. S. Um, J. Lee, S. Kwon, D. Luo, DNA nanobarcodes, Nature Protocols 1, 995-1000 (2006)
8. Y. Li, Y. Cu and D. Luo, DNA fluorescence nanobarcodes for multiplexed pathogen detection, Nature Biotechnology 23, 885-889 (2005)
9. Y. Li, Y.D. Tseng, S.Y. Kown, L. d'Espaux, J.S. Bunch, P.L McEuen and D. Luo. Controlled assembly of dendrimer-like DNA. Nature Materials, 3, 38-42 (2004)