Advertisement

Nanorobotics pp 355-382 | Cite as

DNA Nanorobotics

  • Harish ChandranEmail author
  • Nikhil Gopalkrishnan
  • John Reif
Chapter

Abstract

This chapter overviews the current state of the emerging discipline of DNA nanorobotics that make use of synthetic DNA to self-assemble operational molecular-scale devices. Recently there have been a series of quite astonishing experimental results—which have taken the technology from a state of intriguing possibilities into demonstrated capabilities of quickly increasing scale and complexity. We first state the challenges in molecular robotics and discuss why DNA as a nanoconstruction material is ideally suited to overcome these. We then review the design and demonstration of a wide range of molecular-scale devices; from DNA nanomachines that change conformation in response to their environment to DNA walkers that can be programmed to walk along predefined paths on nanostructures while carrying cargo or performing computations, to tweezers that can repeatedly switch states. We conclude by listing major challenges in the field along with some possible future directions.

Keywords

Phosphodiester Bond Strand Displacement Biped Walker Template Strand Linear Track 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Winfree E, Liu F, Wenzler L, Seeman N (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–544CrossRefGoogle Scholar
  2. 2.
    LaBean T, Yan H, Kopatsch J, Liu F, Winfree E, Reif J, Seeman N (2000) Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J Am Chem Soc 122(9):1848–1860CrossRefGoogle Scholar
  3. 3.
    Yan H, Park SH, Finkelstein G, Reif J, LaBean T (2003) DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301(5641):1882–1884CrossRefGoogle Scholar
  4. 4.
    Shih W, Quispe J, Joyce G (2004) A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427(6975):618–621CrossRefGoogle Scholar
  5. 5.
    He Y, Chen Y, Liu H, Ribbe A, Mao C (2005) Self-assembly of hexagonal DNA two-dimensional (2D) arrays. J Am Chem Soc 127(35):12202–12203CrossRefGoogle Scholar
  6. 6.
    Rothemund P (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302CrossRefGoogle Scholar
  7. 7.
    He Y, Ye T, Su M, Zhang C, Ribbe A, Jiang W, Mao C (2008) Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452(7184):198–201CrossRefGoogle Scholar
  8. 8.
    Douglas S, Dietz H, Liedl T, Hogberg B, Graf F, Shih W (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459(7245):414–418CrossRefGoogle Scholar
  9. 9.
    Dietz H, Douglas S, Shih W (2009) Folding DNA into twisted and curved nanoscale shapes. Science 325(5941):725–730CrossRefGoogle Scholar
  10. 10.
    Zheng J, Birktoft J, Chen Y, Wang T, Sha R, Constantinou P, Ginell S, Mao C, Seeman N (2009) From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461(7260):74–78CrossRefGoogle Scholar
  11. 11.
    Yildiz A, Tomishige M, Vale R, Selvin P (2004) Kinesin walks hand-over-hand. Science 303(5658):676–678CrossRefGoogle Scholar
  12. 12.
    Toyoshima YY, Kron S, McNally E, Niebling K, Toyoshima C, Spudich J (1987) Myosin subfragment-1 is sufficient to move actin filaments in vitro. Nature 328(6130):536–539CrossRefGoogle Scholar
  13. 13.
    Pohl F, Jovin T (1972) Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly(dG-dC). Angew Chem Int Ed 67(3):375–396Google Scholar
  14. 14.
    Mao C, Sun W, Shen Z, Seeman N (1999) A nanomechanical device based on the B–Z transition of DNA. Nature 397:144–146CrossRefGoogle Scholar
  15. 15.
    Duckett D, Murchie A, Diekmann S, Kitzing E, Kemper B, Lilley D (1988) The structure of the holliday junction, and its resolution. Cell 55(1):79–89CrossRefGoogle Scholar
  16. 16.
    Yang X, Vologodskii A, Liu B, Kemper B, Seeman N (1998) Torsional control of double-stranded DNA branch migration. Biopolymers 45(1):69–83CrossRefGoogle Scholar
  17. 17.
    Gehring K, Leroy J-L, Gueron M, Tetrameric A (1993) DNA structure with protonated cytosine-cytosine base pairs. Nature 363(6429):561–565CrossRefGoogle Scholar
  18. 18.
    Liu D, Balasubramanian S, Proton-Fuelled A (2003) DNA nanomachine. Angew Chem Int Ed 42(46):5734–5736CrossRefGoogle Scholar
  19. 19.
    Liu D, Bruckbauer A, Abell C, Balasubramanian S, Kang D-J, Klenerman D, Zhou D, Reversible A (2006) pH-driven DNA nanoswitch array. J Am Chem Soc 128(6):2067–2071CrossRefGoogle Scholar
  20. 20.
    Liu H, Xu Y, Li F, Yang Y, Wang W, Song Y, Liu D (2007) Light-driven conformational switch of i-motif DNA. Angew Chem Int Ed 46(14):2515–2517CrossRefGoogle Scholar
  21. 21.
    Liedl T, Simmel F (2005) Switching the conformation of a DNA molecule with a chemical oscillator. Nano Lett 5(10):1894–1898CrossRefGoogle Scholar
  22. 22.
    Liedl T, Olapinski M, Simmel F, Surface-Bound A, Switch DNA (2006) Driven by a chemical oscillator. Angew Chem Int Ed 45(30):5007–5010CrossRefGoogle Scholar
  23. 23.
    Cao Y, Jin R, Mirkin C (2002) Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297(5586):1536–1540CrossRefGoogle Scholar
  24. 24.
    Sharma J, Chhabra R, Yan H, Liu Y (2007) pH-driven conformational switch of i-motif DNA for the reversible assembly of gold nanoparticles. Chem Commun 477–479Google Scholar
  25. 25.
    Ren X, He F, Xu Q-H (2010) Direct visualization of conformational switch of i-motif DNA with a cationic conjugated polymer. Chem Asian J 5(5):1094–1098CrossRefGoogle Scholar
  26. 26.
    Shu W, Liu D, Watari M, Riener C, Strunz T, Welland M, Balasubramanian S, McKendry R, Molecular DNA (2005) Motor driven micromechanical cantilever arrays. J Am Chem Soc 127(48):17054–17060CrossRefGoogle Scholar
  27. 27.
    Chen Y, Lee S-H, Mao C (2004) A DNA nanomachine based on a duplex-triplex transition. Angew Chem Int Ed 43(40):5335–5338CrossRefGoogle Scholar
  28. 28.
    Brucale M, Zuccheri G, Samori B (2005) The dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex. Org Biomol Chem 3(4):575–577CrossRefGoogle Scholar
  29. 29.
    Modi S, Swetha MG, Goswami D, Gupta G, Mayor S, Krishnan Y (2009) A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nat Nanotechnol 4(5):325–330CrossRefGoogle Scholar
  30. 30.
    Yin P, Yan H, Daniell X, Turberfield A, Reif J, Unidirectional A, Walker DNA (2004) Moving autonomously along a linear track. Angew Chem Int Ed 116(37):5014–5019CrossRefGoogle Scholar
  31. 31.
    Sekiguchi H, Komiya K, Kiga D, Yamamura M (2008) A design and feasibility study of reactions comprising DNA molecular machine that walks autonomously by using a restriction enzyme. Nat Comput 7(3):303–315MathSciNetCrossRefGoogle Scholar
  32. 32.
    Bath J, Green S, Turberfield A, Free-Running A, Motor DNA (2005) Powered by a nicking enzyme. Angew Chem Int Ed 44(28):4358–4361CrossRefGoogle Scholar
  33. 33.
    Tian Y, He Y, Chen Y, Yin P, Mao C (2005) A DNAzyme that walks processively and autonomously along a one-dimensional track. Angew Chem Int Ed 44(28):4355–4358CrossRefGoogle Scholar
  34. 34.
    Chen Y, Wang M, Mao C (2004) An autonomous DNA nanomotor powered by a DNA enzyme. Angew Chem Int Ed 43(27):3554–3557CrossRefGoogle Scholar
  35. 35.
    Yurke B, Turberfield A, Mills A, Simmel F, Neumann J (2000) A DNA-fuelled molecular machine made of DNA. Nature 406(6796):605–608CrossRefGoogle Scholar
  36. 36.
    Bishop J, Klavins E (2007) An improved autonomous DNA nanomotor. Nano Lett 7(9):2574–2577CrossRefGoogle Scholar
  37. 37.
    Sahu S, LaBean T, Reif J (2008) A DNA nanotransport device powered by polymerase φ. Nano Lett 8(11):3870–3878CrossRefGoogle Scholar
  38. 38.
    Sherman W, Seeman N (2004) A precisely controlled DNA biped walking device. Nano Lett 4:1203–1207CrossRefGoogle Scholar
  39. 39.
    Shin J-S, Pierce N, Synthetic A (2004) DNA walker for molecular transport. J Am Chem Soc 126(35):10834–10835CrossRefGoogle Scholar
  40. 40.
    Tian Y, Mao C (2004) Molecular gears: a pair of DNA circles continuously rolls against each other. J Am Chem Soc 126(37):11410–11411CrossRefGoogle Scholar
  41. 41.
    Yin P, Choi H, Calvert C, Pierce N (2008) Programming biomolecular self-assembly pathways. Nature 451(7176):318–322CrossRefGoogle Scholar
  42. 42.
    Green S, Bath J, Turberfield A (2008) Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. Phys Rev Lett 101(23):238101CrossRefGoogle Scholar
  43. 43.
    Venkataraman S, Dirks R, Rothemund P, Winfree E, Pierce N (2007) An autonomous polymerization motor powered by DNA hybridization. Nat Nanotechnol 2:490–494CrossRefGoogle Scholar
  44. 44.
    Reif J, Sahu S (2009) Autonomous programmable DNA nanorobotic devices using dnazymes. Theor Comput Sci 410:1428–1439MathSciNetzbMATHCrossRefGoogle Scholar
  45. 45.
    Pei R, Taylor S, Stefanovic D, Rudchenko S, Mitchell T, Stojanovic M (2006) Behavior of polycatalytic assemblies in a substrate-displaying matrix. J Am Chem Soc 128(39):12693–12699CrossRefGoogle Scholar
  46. 46.
    Lund K, Manzo A, Dabby N, Michelotti N, Johnson-Buck A, Nangreave J, Taylor S, Pei R, Stojanovic M, Walter N, Winfree E, Yan H (2010) Molecular robots guided by prescriptive landscapes. Nature 465(7295):206–210CrossRefGoogle Scholar
  47. 47.
    Gu H, Chao J, Xiao S-J, Seeman N, Proximity-based A (2010) Programmable DNA nanoscale assembly line. Nature 465(7295):202–205CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Harish Chandran
    • 1
    Email author
  • Nikhil Gopalkrishnan
    • 1
  • John Reif
    • 1
    • 2
  1. 1.Department of Computer ScienceDuke UniversityDurhamUSA
  2. 2.Computing and Information TechnologyKing Abdulaziz UniversityJeddahSaudi Arabia

Personalised recommendations