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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Winfree E, Liu F, Wenzler L, Seeman N (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–544
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):1848–1860
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):1882–1884
Shih W, Quispe J, Joyce G (2004) A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427(6975):618–621
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):12202–12203
Rothemund P (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302
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):198–201
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):414–418
Dietz H, Douglas S, Shih W (2009) Folding DNA into twisted and curved nanoscale shapes. Science 325(5941):725–730
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):74–78
Yildiz A, Tomishige M, Vale R, Selvin P (2004) Kinesin walks hand-over-hand. Science 303(5658):676–678
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):536–539
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):375–396
Mao C, Sun W, Shen Z, Seeman N (1999) A nanomechanical device based on the B–Z transition of DNA. Nature 397:144–146
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):79–89
Yang X, Vologodskii A, Liu B, Kemper B, Seeman N (1998) Torsional control of double-stranded DNA branch migration. Biopolymers 45(1):69–83
Gehring K, Leroy J-L, Gueron M, Tetrameric A (1993) DNA structure with protonated cytosine-cytosine base pairs. Nature 363(6429):561–565
Liu D, Balasubramanian S, Proton-Fuelled A (2003) DNA nanomachine. Angew Chem Int Ed 42(46):5734–5736
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):2067–2071
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):2515–2517
Liedl T, Simmel F (2005) Switching the conformation of a DNA molecule with a chemical oscillator. Nano Lett 5(10):1894–1898
Liedl T, Olapinski M, Simmel F, Surface-Bound A, Switch DNA (2006) Driven by a chemical oscillator. Angew Chem Int Ed 45(30):5007–5010
Cao Y, Jin R, Mirkin C (2002) Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297(5586):1536–1540
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 477–479
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):1094–1098
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):17054–17060
Chen Y, Lee S-H, Mao C (2004) A DNA nanomachine based on a duplex-triplex transition. Angew Chem Int Ed 43(40):5335–5338
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):575–577
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):325–330
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):5014–5019
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):303–315
Bath J, Green S, Turberfield A, Free-Running A, Motor DNA (2005) Powered by a nicking enzyme. Angew Chem Int Ed 44(28):4358–4361
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):4355–4358
Chen Y, Wang M, Mao C (2004) An autonomous DNA nanomotor powered by a DNA enzyme. Angew Chem Int Ed 43(27):3554–3557
Yurke B, Turberfield A, Mills A, Simmel F, Neumann J (2000) A DNA-fuelled molecular machine made of DNA. Nature 406(6796):605–608
Bishop J, Klavins E (2007) An improved autonomous DNA nanomotor. Nano Lett 7(9):2574–2577
Sahu S, LaBean T, Reif J (2008) A DNA nanotransport device powered by polymerase φ. Nano Lett 8(11):3870–3878
Sherman W, Seeman N (2004) A precisely controlled DNA biped walking device. Nano Lett 4:1203–1207
Shin J-S, Pierce N, Synthetic A (2004) DNA walker for molecular transport. J Am Chem Soc 126(35):10834–10835
Tian Y, Mao C (2004) Molecular gears: a pair of DNA circles continuously rolls against each other. J Am Chem Soc 126(37):11410–11411
Yin P, Choi H, Calvert C, Pierce N (2008) Programming biomolecular self-assembly pathways. Nature 451(7176):318–322
Green S, Bath J, Turberfield A (2008) Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. Phys Rev Lett 101(23):238101
Venkataraman S, Dirks R, Rothemund P, Winfree E, Pierce N (2007) An autonomous polymerization motor powered by DNA hybridization. Nat Nanotechnol 2:490–494
Reif J, Sahu S (2009) Autonomous programmable DNA nanorobotic devices using dnazymes. Theor Comput Sci 410:1428–1439
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):12693–12699
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):206–210
Gu H, Chao J, Xiao S-J, Seeman N, Proximity-based A (2010) Programmable DNA nanoscale assembly line. Nature 465(7295):202–205
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Chandran, H., Gopalkrishnan, N., Reif, J. (2013). DNA Nanorobotics. In: Mavroidis, C., Ferreira, A. (eds) Nanorobotics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-2119-1_18
Download citation
DOI: https://doi.org/10.1007/978-1-4614-2119-1_18
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-2118-4
Online ISBN: 978-1-4614-2119-1
eBook Packages: EngineeringEngineering (R0)