Background

Nanotechnology is the technology to manipulate molecules and atoms on the nanoscale level. Its goal is to construct 2D and 3D structures[1][2][3][4], non-static structures that can perform dynamic movement, or systems constructed of various functional molecules. However, in order to realize an autonomous designs on the nanoscale, there is a need to design and implement desired components. In recent years, DNA which is a biomolecule able to form specific double-strands according to Watson-Crick base-pairing, has gained considerable attention as material, and technology utilizing DNA to manufacture various structures is termed "structural DNA nanotechnology"[5][6].

DNA is usually understood as a carrier of genetic information. However, from a chemical aspect, DNA is none other than a polymer constructed from multiple units forming a long chain; each unit called a nucleotide, consisting of three components: nucleobase, pentose sugar, and phosphate group. There are 4 types of bases: A, T, C, G, and complementary bases A-T and C-G are known to form specific base pairings, termed Watson-Crick base pairing, due to hydrogen bonding [7]. Since DNA molecules can selectively form double-strands according to the Watson-Crick base pairing, DNA strands with complementary sequences hybridize to form a double helix. As such, when seen from a "molecular" perspective, DNA can be perceived as a material with unique properties, in which string-like molecules autonomously form a double helix by hybridization of base pairs.
Nowadays, arbitrary sequences of DNA can be chemically synthesized. This implies that DNA molecules can be designed to minimize or maximize complementary sequences. Based on this theory, DNA branched structures [8][9] and sticky ends were proposed. Using these elements, a vast array of DNA nanostructure designs have been developed, such as DNA Tiles, DNA Origami [10][11][12], and DNA hydrogel [13].
Such DNA nanostructures are employed as frameworks and substructures, and by integrating various molecules with additional functions, molecular systems with high functionality are expected to be realized. For example, as of now, applications such as nano-reaction fields [14][15], biosensors, and drug delivery systems [16] have been proposed.

Problem & Solution

Development in the structural DNA nanotechnology field enabled the design of various molecular devices. These DNA nanostructures are advantageous in that they can self-assemble into desired structures according to specific interaction among DNA molecules.
The objective of DNA technology is not confined to constructing nanostructures, but also giving them specific functions. Realizing nanostructures with these functions will lead to developing technology such as nanoscale robots, which are robots that will take a specific role in a living system. However, upon constructing these nanostructures each individual component tries to perform random motion, in conventional designs. Even if multiple DNA nanostructures were to be combined to create a macrostructure, it would be difficult to address the entire construct as a single structure and control its movement. It is fundamentally difficult to transform a nanoscale robot since the components of the robot is subject to Brownian motion. Furthermore, although designs using stacking, a method of bonding bases by hydrogen bond, has been devised to enable structures to take more than two states, they still carry the downside of transformation being uncontrollable.[17] Thus, in order to transform DNA nanostructures into arbitrary shapes and sizes, cooperative motion of components in a nanostructure is necessary to perform a robust movement that is able to overcome local errors of components.

Here we thought that if the design had properties of deployable space structures such that movements of components are interlocked with movements of other components, these nanostructures could be controlled as a 1 degree-freedom (1-DOF) object. As a representative example of deployable space structures, we adopt the concept of Miura Folding.

Miura folding is a method originally developed for space structures such as deployable solar panels for space satellites and is also applied for folding maps. In the Miura Folding, a single paper is folded simultaneously into two directions. Since all parallelograms are interlocked and the folds are interdependent, the entire paper can be opened and folded in one motion by simply pulling and pushing on the corners of opposite ends. Thus, the entire structure can transform continuously in a smooth manner by applying only a small amount of force to part of the structure. Miura Folding is a solution which enables contraction of structures to become just as easy as its expansion.

In addition, Miura Folding is a desirable design in its transitioning of energy states upon transformation. Since Miura Folding is designed to never take a complete planar structure, although the angles of the folds may become exceedingly shallow, extreme stable states do not exist. Thus, the entire structure can transform continuously in a smooth manner by applying only a small amount of force to a part of the structure.

From the above reasons, our team decided to adopt Miura Folding to enable transforming of DNA nanostructures by translocking motions of individual components.

Reference

Background

  1. Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297 (2006).
  2. Douglas, S. M, et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature, 459(7245), 414 (2009).
  3. Dietz, H., Douglas, S. M., & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science, 325(5941), 725-730 (2009).
  4. Lee, J. B., et al. A mechanical metamaterial made from a DNA hydrogel. Nature Nanotechnology, 7(12), 816 (2012).
  5. Seeman, N. C. Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65–87 (2010).
  6. Aldaye, F. A., Palmer, A. L. & Sleiman, H. F. Assembling materials with DNA as the guide. Science 321, 1795–1799 (2008).
  7. Crick, F. H. C., & Watson, J. D. The complementary structure of deoxyribonucleic acid. Proc. R. Soc. Lond. A, 223(1152), 80-96 (1954).
  8. Seeman, N. C. Nucleic acid junctions and lattices. Journal of theoretical biology, 99(2), 237-247 (1982).
  9. Winfree, E., Liu, F., Wenzler, L. A., & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature, 394(6693), 539 (1998).
  10. Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297 (2006).
  11. Douglas, S. M, et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature, 459(7245), 414 (2009).
  12. Dietz, H., Douglas, S. M., & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science, 325(5941), 725-730 (2009).
  13. Lee, J. B., et al. A mechanical metamaterial made from a DNA hydrogel. Nature Nanotechnology, 7(12), 816 (2012).
  14. Suzuki, Y., Endo, M., Yang, Y., & Sugiyama, H. Dynamic assembly/disassembly processes of photoresponsive DNA origami nanostructures directly visualized on a lipid membrane surface. Journal of the American Chemical Society, 136(5), 1714-1717 (2014).
  15. Suzuki, Y., et al. DNA origami based visualization system for studying site-specific recombination events. Journal of the American Chemical Society, 136(1), 211-218 (2014).
  16. Takenaka, T., et al. Photoresponsive DNA nanocapsule having an open/close system for capture and release of nanomaterials. Chemistry–A European Journal, 20(46), 14951-14954 (2014).
  17. Vologodskii, A.V., Amirikyan, B.R., Lyubchenko, Y.L., Frank-Kamenetskii, M.D. 1984 Allowance for heterogeneous stacking in the DNA helix-coil transition theory J. Biomol. Struct. Dyn. 2, 131-148 (1984).