Abstract
DNA hybridization has been used to power a number of DNA-based nanostructures constructed out of DNA. Here some considerations that go into DNA-based motor design are briefly reviewed. The emphasis will be on the operation of toeholds, single-stranded sections of DNA that facilitate the process of strand removal during certain points in the operation of a DNA-based motor. Reaction kinetics measurements for toehold mediated strand exchange are reported. These measurements have served as a guide for choosing toehold lengths.
Similar content being viewed by others
References
V. Balzani, A. Credi, F. M. Raymo, and J. F. Stoddart, “Artifical molecular machines,” Angew. Chem. Int. Ed., vol. 39,no. 19, pp. 3349-3391, 2000.
R.J. Britten and D.E. Kohne, “Repeated Sequences in DNA,” Science, vol. 161,no. 3841, pp. 529-540, 1968.
J. H. Chen and N. C. Seeman, “Synthesis from DNA of a molecule with the connectivity of a cube,” Nature, vol. 350,no. 6319, pp. 631-633, 1991.
X. N. Chen, B. Zehnbauer, A. Gnirke, and P.-Y. Kwok, “Fluorescence energy transfer detection as a homogeneous DNA diagnostic method,” Proc. Natl. Acad. Sci. USA, vol. 94,no. 20, pp. 10756-10761, 1991.
A. K. Eggleston and S. C. Kowalczykowski, “An overview of homologous pairing and DNA strand exchange proteins,” Biochemie, vol. 73,no. 2–3, pp. 163-176, 1991.
M. Eigen and P. Schuster, The Hypercycle, A Principle of Natural Self-Organization, Springer: Berlin, 1979.
E. H. Ekland, J. W. Szostak, and D. P. Bartel, “Structurally complex and highly-active RNA ligases derived from random RNA sequences,” Science, vol. 269,no. 5222, pp. 364-370, 1995.
B. Essevaz-Roulet, U. Bockelmann, and F. Heslot, “Mechanical separation of the complementary strands of DNA,” Proc. Natl. Acad. Sci., USA, vol. 94,no. 22, pp. 11935-11940, 1997.
C. Green and C. Tibbetts, “Reassociation rate limited displacement of DNA strands by branch migration,” Nucl. Acids Res., vol. 9,no. 8, pp. 1905-1918, 1981.
M. J. Heller and L. E. Morrison, in Rapid Detection and Identification of Infectious Agents, D. T. Kingsbury and S. Falkow (eds.), Academic Press, New York, 1985, pp. 245-256.
K. D. James and A. D. Ellington, “The search for missing links between self-replicating nucleic-acids and the RNA world,” Origins of Life and Evolution of the Biosphere, vol. 25,no. 6, pp. 515-530, 1995.
W. K. Johnston, P. J. Unrau, M. S. Lawrence, M. E. Glasner, and D. P. Bartel, “RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension,” Science, vol. 292,no. 5520, pp. 1319-1325, 2001.
N. Koumura, R. W. J. Zijlstra, R. A. van Delden, N. Harada, and B. L. Feringa, “Light-driven monodirectional molecular rotor,” Nature, vol. 401,no. 6749, pp. 152-155, 1999.
T. Li and K.C. Nicolaou, “Chemical self-replication of palindromic duplex DNA,” Nature, vol. 369,no. 6477, pp. 218-221, 1994.
J. J. Li and W. Tan, “A single DNA molecule nanomotor,” Nano Lett., vol. 2,no. 4, pp. 315-318, 2002.
J. Liphardt, B. Onoa, S. B. Smith, I. Tinoco, Jr., and C. Bustamante, “Reversible unfolding of single RNA molecules by mechanical force,” Science, vol. 292,no. 5517, pp. 733-737, 2001.
C. D. Mao, T. H. LaBean, J. H. Reif, and N. C. Seeman, “Logical computation using algorithmic self-assembly of DNA triple-crossover molecules,” Nature, vol. 407,no. 6803, pp. 493-496, 2000.
C. D. Mao, W. Q. Sun, and N. C. Seeman, “Assembly of Borromean rings from DNA,” Nature, vol. 386,no. 6621, pp. 137-138, 1997.
C. D. Mao, W. Q. Sun, Z. Y. Shen, and N. C. Seeman, “A nanomechanical device based on the B-Z transition of DNA,” Nature, vol. 397,no. 6715, pp. 144-146, 1999.
J. C. Mitchell and B. Yurke, “DNA Scissors,” in DNA Computing, N. Jonoska and N. C. Seeman (eds.), 7th International Workshop on DNA-Based Computers, DNA7 Tampa, FL, USA, June 10–13, 2001, Springer, 2002, pp. 263-268.
L. E. Morrison, T. C. Halder, and L. M. Stols, “Solution-phase detection of polynucleotides using interacting fluorescent labels and competitive hybridization,” Anal. Biochem., vol. 183,no. 2, pp. 231-244, 1989.
L. E. Morrison and L. M. Stols, “Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution,” Biochemistry, vol. 32,no. 12, pp. 3095-3104, 1993.
C.M. Niemeyer and M. Adler, “Nanomechanical Devices Based on DNA,” Angew. Chem. Int. Ed., vol. 41,no. 20, pp. 3779-3783, 2002.
N. Paul and G. F. Joyce, “A self-replicating ligase ribozyme,” Proc. Natl. Acad. Sci. USA, vol. 99,no. 20, pp. 12733-12740, 2002.
C. M. Radding, K. L. Beattie, W. K. Holloman, and R. C. Wiegand, “Uptake of homologous single-stranded fragments by superhelical DNA: IV branch migration,” J. Mol. Biol., vol. 116,no. 4, pp. 825-839, 1977.
M. Rief, H. Clausen-Schaumann, and H.E. Gaub, “Sequence-dependent mechanics of single DNA molecules,” Nat. Struct. Biol., vol. 6,no. 4, pp. 346-349, 1999.
J. SantaLucia, Jr., “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics,” Proc. Natl. Acad. Sci. USA, vol. 95,no. 4, pp. 1460-1465, 1998.
D. Sievers and G. von Kiedrowski, “Self replication of complementary nucleotide-based oligomers,” Nature, vol. 369,no. 6477, pp. 221-224, 1994.
F. C. Simmel and B. Yurke, “Using DNA to construct and power a nanoactuator,” Phys. Rev. E, vol. 63,no. 4, art. no. 041913, 2001.
F. C. Simmel and B. Yurke, “A DNA-based molecular device switchable between three distinct mechanical states,” Appl. Phys. Lett., vol. 80,no. 5, pp. 883-885, 2002.
S. B. Smith, Y. J. Cui, and C. Bustamante, “Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules,” Science, vol. 271,no. 5250, pp. 795-799, 1996.
B. Tinland, A. Pluen, J. Sturm, and G. Weill, “Persistence length of single-stranded DNA,” Macromolecules, vol. 30,no. 19, pp. 5763-5765, 1997.
A.J. Turberfield, B. Yurke, and A.P. Mills, Jr., “DNA hybridization catalysts and molecular tweezers,” in DNA Based Computers V, E. Winfree and D.K. Gifford (eds.), DLMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 54, 2000, pp. 171-182.
J.G. Wetmur and N. Davidson, “Kinetics of Renaturation of DNA,” J. Mol. Biol., vol. 31,no. 3, pp. 349-370, 1968.
E. Winfree, F. R. Lui, L. A. Wenzler, and N. C. Seeman, “Design and self-assembly of two-dimensional DNA crystals,” Nature, vol. 394,no. 6693, pp. 539-544, 1998.
H. Yan, X. P. Zhang, Z. Y. Shen, and N. C. Seeman, “A robust DNA mechanical device controlled by hybridization topology,” Nature, vol. 415,no. 6867, pp. 62-65, 2002.
B. Yurke, A. J. Turberfield, A. P. Mills, Jr., F. C. Simmel, and J. L. Neumann, “A DNA-fuelled molecular machine made of DNA,” Nature, vol. 406,no. 6796, pp. 605-608, 2000.
Y. W. Zhang and N. C. Seeman, “Construction of a DNA-truncated Octahedron,” J. Am. Chem. Soc., vol. 116,no. 5, pp. 1661-1669, 1994.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Yurke, B., Mills, A.P. Using DNA to Power Nanostructures. Genet Program Evolvable Mach 4, 111–122 (2003). https://doi.org/10.1023/A:1023928811651
Issue Date:
DOI: https://doi.org/10.1023/A:1023928811651