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2013 | OriginalPaper | Chapter

11. Design, Fabrication, and Applications of DNA Nanomachines

Authors : Chen Song, Zhen-Gang Wang, Baoquan Ding

Published in: DNA Nanotechnology

Publisher: Springer Berlin Heidelberg

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Abstract

In this chapter, we outline the shared principles of design and fabrication of DNA nanomachines that are established and newly developed. Various functional DNA nanomachines and their applications are also discussed.
The DNA structures that act as building blocks of DNA nanomachines are introduced briefly. The molecular recognition mechanisms and dynamical properties of these building blocks are described for the elucidation of the design principles of DNA nanomachines. According to the driving mechanisms, the DNA nanomachines are divided into two categories. One category is buffer-dependent DNA nanomachines, which are triggered by changes in the environment, such as metal ions, pH, and protons. The other category is DNA strands-fueled nanomachines, in which the moving forces are generated through the hybridization of carefully designed DNA strands. A variety of DNA-based nanomachines with different functions have been constructed, such as tweezers, rotors, and walkers. Generating highly sensitive and selective response to their fuels (or stimuli), DNA nanomachines can be functionalized for various applications. The buffer-dependent DNA nanomachines have been successfully used as sensors. The specificity of DNA nanomachines is utilized for template synthesis to organize chemicals into close proximity and to control the synthesis process precisely. The switchability of DNA nanomachines is employed for carrying small molecules, nucleic strands, proteins, or even metal nanoparticles. The motions of the DNA nanomachines can also be used to control the loading and release of the nanoscale objects, as well as to transport and assemble the cargos. The immobilized DNA machines on solid phase succeed in generating signal-triggered responsive surface. Finally, we highlight some challenges and prospective.

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Literature
1.
go back to reference Seeman NC (1982) Nucleic-acid junctions and lattices. J Theor Biol 99(2):237–247CrossRef Seeman NC (1982) Nucleic-acid junctions and lattices. J Theor Biol 99(2):237–247CrossRef
2.
go back to reference Seeman NC, Kallenbach NR (1994) DNA branched junctions. Annu Rev Bioph Biom 23:53–86CrossRef Seeman NC, Kallenbach NR (1994) DNA branched junctions. Annu Rev Bioph Biom 23:53–86CrossRef
3.
go back to reference Seeman NC (1998) Nucleic acid nanostructures and topology. Angew Chem Int Ed 37(23):3220–3238CrossRef Seeman NC (1998) Nucleic acid nanostructures and topology. Angew Chem Int Ed 37(23):3220–3238CrossRef
4.
go back to reference Seeman NC (2001) DNA nicks and nodes and nanotechnology. Nano Lett 1(1):22–26CrossRef Seeman NC (2001) DNA nicks and nodes and nanotechnology. Nano Lett 1(1):22–26CrossRef
5.
go back to reference Seeman NC (2003) At the crossroads of chemistry, biology, and materials: structural DNA nanotechnology. Chem Biol 10(12):1151–1159CrossRef Seeman NC (2003) At the crossroads of chemistry, biology, and materials: structural DNA nanotechnology. Chem Biol 10(12):1151–1159CrossRef
6.
go back to reference Gueron M, Leroy JL (2000) The i-motif in nucleic acids. Curr Opin Struct Biol 10(3):326–331CrossRef Gueron M, Leroy JL (2000) The i-motif in nucleic acids. Curr Opin Struct Biol 10(3):326–331CrossRef
7.
go back to reference Snoussi K, Nonin-Lecomte S, Leroy JL (2001) The RNA i-motif. J Mol Biol 309(1):139–153CrossRef Snoussi K, Nonin-Lecomte S, Leroy JL (2001) The RNA i-motif. J Mol Biol 309(1):139–153CrossRef
8.
go back to reference Phan AT, Kuryavyi V, Patel DJ (2006) DNA architecture: from G to Z. Curr Opin Struct Biol 16(3):288–298CrossRef Phan AT, Kuryavyi V, Patel DJ (2006) DNA architecture: from G to Z. Curr Opin Struct Biol 16(3):288–298CrossRef
9.
go back to reference Lilley DMJ (2000) Structures of helical junctions in nucleic acids. Q Rev Biophys 33(2):109–159CrossRef Lilley DMJ (2000) Structures of helical junctions in nucleic acids. Q Rev Biophys 33(2):109–159CrossRef
10.
go back to reference Seeman NC (2010) Structural DNA, nanotechnology: growing along with Nano Letters. Nano Lett 10(6):1971–1978CrossRef Seeman NC (2010) Structural DNA, nanotechnology: growing along with Nano Letters. Nano Lett 10(6):1971–1978CrossRef
11.
go back to reference Rothemund PWK (2006) Folding DNA, to create nanoscale shapes and patterns. Nature 440(7082):297–302CrossRef Rothemund PWK (2006) Folding DNA, to create nanoscale shapes and patterns. Nature 440(7082):297–302CrossRef
12.
go back to reference Qian LL, Wang Y, Zhang Z, Zhao J, Pan D, Zhang Y et al (2006) Analogic China map constructed by DNA. Chin Sci Bull 51(24):2973–2976CrossRef Qian LL, Wang Y, Zhang Z, Zhao J, Pan D, Zhang Y et al (2006) Analogic China map constructed by DNA. Chin Sci Bull 51(24):2973–2976CrossRef
13.
go back to reference Ding BQ, Wu H, Xu W, Zhao ZA, Liu Y, Yu HB et al (2010) Interconnecting gold islands with DNA origami nanotubes. Nano Lett 10(12):5065–5069CrossRef Ding BQ, Wu H, Xu W, Zhao ZA, Liu Y, Yu HB et al (2010) Interconnecting gold islands with DNA origami nanotubes. Nano Lett 10(12):5065–5069CrossRef
14.
go back to reference Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R, Mamdouh W et al (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459(7243):73–76CrossRef Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R, Mamdouh W et al (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459(7243):73–76CrossRef
15.
go back to reference Han DR, Pal S, Liu Y, Yan H (2010) Folding and cutting DNA into reconfigurable topological nanostructures. Nat Nanotechnol 5(10):712–717CrossRef Han DR, Pal S, Liu Y, Yan H (2010) Folding and cutting DNA into reconfigurable topological nanostructures. Nat Nanotechnol 5(10):712–717CrossRef
16.
go back to reference Han DR, Pal S, Nangreave J, Deng ZT, Liu Y, Yan H (2011) DNA origami with complex curvatures in three-dimensional space. Science 332(6027):342–346CrossRef Han DR, Pal S, Nangreave J, Deng ZT, Liu Y, Yan H (2011) DNA origami with complex curvatures in three-dimensional space. Science 332(6027):342–346CrossRef
17.
go back to reference Teller C, Willner I (2010) Functional nucleic acid nanostructures and DNA machines. Curr Opin Biotechnol 21(4):376–391CrossRef Teller C, Willner I (2010) Functional nucleic acid nanostructures and DNA machines. Curr Opin Biotechnol 21(4):376–391CrossRef
18.
go back to reference Perkins TT, Smith DE, Larson RG, Chu S (1995) Stretching of a single tethered polymer in a uniform-flow. Science 268(5207):83–87CrossRef Perkins TT, Smith DE, Larson RG, Chu S (1995) Stretching of a single tethered polymer in a uniform-flow. Science 268(5207):83–87CrossRef
19.
go back to reference Rivetti C, Walker C, Bustamante C (1998) Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J Mol Biol 280(1):41–59CrossRef Rivetti C, Walker C, Bustamante C (1998) Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J Mol Biol 280(1):41–59CrossRef
20.
go back to reference Wilson DS, Szostak JW (1999) In vitro selection of functional nucleic acids. Annu Rev Biochem 68:611–647CrossRef Wilson DS, Szostak JW (1999) In vitro selection of functional nucleic acids. Annu Rev Biochem 68:611–647CrossRef
21.
go back to reference Mayer G (2009) The chemical biology of aptamers. Angew Chem Int Ed 48(15):2672–2689CrossRef Mayer G (2009) The chemical biology of aptamers. Angew Chem Int Ed 48(15):2672–2689CrossRef
22.
go back to reference Lilley DMJ (2005) Structure, folding and mechanisms of ribozymes. Curr Opin Struct Biol 15(3):313–323CrossRef Lilley DMJ (2005) Structure, folding and mechanisms of ribozymes. Curr Opin Struct Biol 15(3):313–323CrossRef
23.
go back to reference Silverman SK (2008) Catalytic DNA, (deoxyribozymes) for synthetic applications: current abilities and future prospects. Chem Commun 30:3467–3485CrossRef Silverman SK (2008) Catalytic DNA, (deoxyribozymes) for synthetic applications: current abilities and future prospects. Chem Commun 30:3467–3485CrossRef
24.
go back to reference Jaschke A, Seelig B (2000) Evolution of DNA and RNA as catalysts for chemical reactions. Curr Opin Chem Biol 4(3):257–262CrossRef Jaschke A, Seelig B (2000) Evolution of DNA and RNA as catalysts for chemical reactions. Curr Opin Chem Biol 4(3):257–262CrossRef
25.
go back to reference Yang XP, Vologodskii AV, Liu B, Kemper B, Seeman NC (1998) Torsional control of double-stranded DNA branch migration. Biopolymers 45(1):69–83CrossRef Yang XP, Vologodskii AV, Liu B, Kemper B, Seeman NC (1998) Torsional control of double-stranded DNA branch migration. Biopolymers 45(1):69–83CrossRef
26.
go back to reference Mao CD, Sun WQ, Shen ZY, Seeman NC (1999) A nanomechanical device based on the B-Z transition of DNA. Nature 397(6715):144–146CrossRef Mao CD, Sun WQ, Shen ZY, Seeman NC (1999) A nanomechanical device based on the B-Z transition of DNA. Nature 397(6715):144–146CrossRef
27.
go back to reference Niemeyer CM, Adler M, Lenhert S, Gao S, Fuchs H, Chi LF (2001) Nucleic acid supercoiling as a means for ionic switching of DNA-nanoparticle networks. Chembiochem 2(4):260–264CrossRef Niemeyer CM, Adler M, Lenhert S, Gao S, Fuchs H, Chi LF (2001) Nucleic acid supercoiling as a means for ionic switching of DNA-nanoparticle networks. Chembiochem 2(4):260–264CrossRef
28.
go back to reference Buranachai C, McKinney SA, Ha T (2006) Single molecule nanometronome. Nano Lett 6(3):496–500CrossRef Buranachai C, McKinney SA, Ha T (2006) Single molecule nanometronome. Nano Lett 6(3):496–500CrossRef
29.
go back to reference Fahlman RP, Hsing M, Sporer-Tuhten CS, Sen D (2003) Duplex pinching: a structural switch suitable for contractile DNA nanoconstructions. Nano Lett 3(8):1073–1078CrossRef Fahlman RP, Hsing M, Sporer-Tuhten CS, Sen D (2003) Duplex pinching: a structural switch suitable for contractile DNA nanoconstructions. Nano Lett 3(8):1073–1078CrossRef
30.
go back to reference Miyoshi D, Karimata H, Wang ZM, Koumoto K, Sugimoto N (2007) Artificial G-wire switch with 2,2′-bipyridine units responsive to divalent metal ions. J Am Chem Soc 129(18):5919–5925CrossRef Miyoshi D, Karimata H, Wang ZM, Koumoto K, Sugimoto N (2007) Artificial G-wire switch with 2,2′-bipyridine units responsive to divalent metal ions. J Am Chem Soc 129(18):5919–5925CrossRef
31.
go back to reference Liu DS, Balasubramanian S (2003) A proton-fuelled DNA nanomachine. Angew Chem Int Ed 42(46):5734–5736CrossRef Liu DS, Balasubramanian S (2003) A proton-fuelled DNA nanomachine. Angew Chem Int Ed 42(46):5734–5736CrossRef
32.
go back to reference Liu HJ, Xu Y, Li FY, Yang Y, Wang WX, Song YL et al (2007) Light-driven conformational switch of i-motif DNA. Angew Chem Int Ed 46(14):2515–2517CrossRef Liu HJ, Xu Y, Li FY, Yang Y, Wang WX, Song YL et al (2007) Light-driven conformational switch of i-motif DNA. Angew Chem Int Ed 46(14):2515–2517CrossRef
33.
go back to reference Liedl T, Simmel FC (2005) Switching the conformation of a DNA molecule with a chemical oscillator. Nano Lett 5(10):1894–1898CrossRef Liedl T, Simmel FC (2005) Switching the conformation of a DNA molecule with a chemical oscillator. Nano Lett 5(10):1894–1898CrossRef
34.
go back to reference Wang WX, Liu HJ, Liu DS, Xu YR, Yang Y, Zhou DJ (2007) Use of the interparticle i-motif for the controlled assembly of gold nanoparticles. Langmuir 23(24):11956–11959CrossRef Wang WX, Liu HJ, Liu DS, Xu YR, Yang Y, Zhou DJ (2007) Use of the interparticle i-motif for the controlled assembly of gold nanoparticles. Langmuir 23(24):11956–11959CrossRef
35.
go back to reference 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 5:477–479CrossRef 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 5:477–479CrossRef
36.
go back to reference Chen C, Song GT, Ren JS, Qu XG (2008) A simple and sensitive colorimetric pH meter based on DNA conformational switch and gold nanoparticle aggregation. Chem Commun 46:6149–6151CrossRef Chen C, Song GT, Ren JS, Qu XG (2008) A simple and sensitive colorimetric pH meter based on DNA conformational switch and gold nanoparticle aggregation. Chem Commun 46:6149–6151CrossRef
37.
go back to reference Wang WX, Yang Y, Cheng EJ, Zhao MC, Meng HF, Liu DS et al (2009) A pH-driven, reconfigurable DNA nanotriangle. Chem Commun 7:824–826CrossRef Wang WX, Yang Y, Cheng EJ, Zhao MC, Meng HF, Liu DS et al (2009) A pH-driven, reconfigurable DNA nanotriangle. Chem Commun 7:824–826CrossRef
38.
go back to reference Modi S, Swetha MG, Goswami D, Gupta GD, Mayor S, Krishnan Y (2009) A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nat Nanotechnol 4(5):325–330CrossRef Modi S, Swetha MG, Goswami D, Gupta GD, Mayor S, Krishnan Y (2009) A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nat Nanotechnol 4(5):325–330CrossRef
39.
go back to reference Chen Y, Lee SH, Mao C (2004) A DNA nanomachine based on a duplex-triplex transition. Angew Chem Int Ed 43(40):5335–5338CrossRef Chen Y, Lee SH, Mao C (2004) A DNA nanomachine based on a duplex-triplex transition. Angew Chem Int Ed 43(40):5335–5338CrossRef
40.
go back to reference 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):575–577CrossRef 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):575–577CrossRef
41.
go back to reference Jung YH, Lee KB, Kim YG, Choi IS (2006) Proton-fueled, reversible assembly of gold nanoparticles by controlled triplex formation. Angew Chem Int Ed 45(36):5960–5963CrossRef Jung YH, Lee KB, Kim YG, Choi IS (2006) Proton-fueled, reversible assembly of gold nanoparticles by controlled triplex formation. Angew Chem Int Ed 45(36):5960–5963CrossRef
42.
go back to reference Yurke B, Turberfield AJ, Mills AP, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406(6796):605–608CrossRef Yurke B, Turberfield AJ, Mills AP, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406(6796):605–608CrossRef
43.
go back to reference Chen Y, Mao CD (2004) Putting a brake on an autonomous DNA nanomotor. J Am Chem Soc 126(28):8626–8627CrossRef Chen Y, Mao CD (2004) Putting a brake on an autonomous DNA nanomotor. J Am Chem Soc 126(28):8626–8627CrossRef
44.
go back to reference Chen Y, Wang MS, Mao CD (2004) An autonomous DNA nanomotor powered by a DNA enzyme. Angew Chem Int Ed 43(27):3554–3557CrossRef Chen Y, Wang MS, Mao CD (2004) An autonomous DNA nanomotor powered by a DNA enzyme. Angew Chem Int Ed 43(27):3554–3557CrossRef
45.
go back to reference Dittmer WU, Simmel FC (2004) Transcriptional control of DNA-based nanomachines. Nano Lett 4(4):689–691CrossRef Dittmer WU, Simmel FC (2004) Transcriptional control of DNA-based nanomachines. Nano Lett 4(4):689–691CrossRef
46.
go back to reference Liang XG, Nishioka H, Takenaka N, Asanuma H (2008) A DNA nanomachine powered by light irradiation. Chembiochem 9(5):702–705CrossRef Liang XG, Nishioka H, Takenaka N, Asanuma H (2008) A DNA nanomachine powered by light irradiation. Chembiochem 9(5):702–705CrossRef
47.
go back to reference Ogura Y, Nishimura T, Tanida J (2009) Self-contained photonically-controlled DNA tweezers. Appl Phys Express 2(2):025004–025006CrossRef Ogura Y, Nishimura T, Tanida J (2009) Self-contained photonically-controlled DNA tweezers. Appl Phys Express 2(2):025004–025006CrossRef
48.
go back to reference Elbaz J, Moshe M, Willner I (2009) Coherent activation of DNA tweezers: a “SET-RESET” logic system. Angew Chem Int Ed 48(21):3834–3837CrossRef Elbaz J, Moshe M, Willner I (2009) Coherent activation of DNA tweezers: a “SET-RESET” logic system. Angew Chem Int Ed 48(21):3834–3837CrossRef
49.
go back to reference Elbaz J, Wang ZG, Orbach R, Willner I (2009) pH-stimulated concurrent mechanical activation of two DNA “tweezers”. a “SET-RESET” logic gate system. Nano Lett 9(12):4510–4514CrossRef Elbaz J, Wang ZG, Orbach R, Willner I (2009) pH-stimulated concurrent mechanical activation of two DNA “tweezers”. a “SET-RESET” logic gate system. Nano Lett 9(12):4510–4514CrossRef
50.
go back to reference Wang ZG, Elbaz J, Remacle F, Levine RD, Willner I (2010) All-DNA finite-state automata with finite memory. Proc Natl Acad Sci U S A 107(51):21996–22001CrossRef Wang ZG, Elbaz J, Remacle F, Levine RD, Willner I (2010) All-DNA finite-state automata with finite memory. Proc Natl Acad Sci U S A 107(51):21996–22001CrossRef
51.
go back to reference Marini M, Piantanida L, Musetti R, Bek A, Dong MD, Besenbacher F et al (2011) A revertible, autonomous, self-assembled DNA-origami nanoactuator. Nano Lett 11(12):5449–5454CrossRef Marini M, Piantanida L, Musetti R, Bek A, Dong MD, Besenbacher F et al (2011) A revertible, autonomous, self-assembled DNA-origami nanoactuator. Nano Lett 11(12):5449–5454CrossRef
52.
go back to reference Yan H, Zhang XP, Shen ZY, Seeman NC (2002) A robust DNA mechanical device controlled by hybridization topology. Nature 415(6867):62–65CrossRef Yan H, Zhang XP, Shen ZY, Seeman NC (2002) A robust DNA mechanical device controlled by hybridization topology. Nature 415(6867):62–65CrossRef
53.
go back to reference Chakraborty B, Sha RJ, Seeman NC (2008) A DNA-based nanomechanical device with three robust states. Proc Natl Acad Sci U S A 105(45):17245–17249CrossRef Chakraborty B, Sha RJ, Seeman NC (2008) A DNA-based nanomechanical device with three robust states. Proc Natl Acad Sci U S A 105(45):17245–17249CrossRef
54.
go back to reference Liu C, Jonoska N, Seeman NC (2009) Reciprocal DNA nanomechanical devices controlled by the same set strands. Nano Lett 9(7):2641–2647CrossRef Liu C, Jonoska N, Seeman NC (2009) Reciprocal DNA nanomechanical devices controlled by the same set strands. Nano Lett 9(7):2641–2647CrossRef
55.
go back to reference Ding B, Seeman NC (2006) Operation of a DNA robot arm inserted into a 2D DNA crystalline substrate. Science 314(5805):1583–1585CrossRef Ding B, Seeman NC (2006) Operation of a DNA robot arm inserted into a 2D DNA crystalline substrate. Science 314(5805):1583–1585CrossRef
56.
go back to reference Gu HZ, Chao J, Xiao SJ, Seeman NC (2009) Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate. Nat Nanotechnol 4(4):245–248CrossRef Gu HZ, Chao J, Xiao SJ, Seeman NC (2009) Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate. Nat Nanotechnol 4(4):245–248CrossRef
57.
go back to reference Sherman WB, Seeman NC (2004) A precisely controlled DNA biped walking device. Nano Lett 4(7):1203–1207CrossRef Sherman WB, Seeman NC (2004) A precisely controlled DNA biped walking device. Nano Lett 4(7):1203–1207CrossRef
58.
go back to reference Shin JS, Pierce NA (2004) A synthetic DNA walker for molecular transport. J Am Chem Soc 126(35):10834–10835CrossRef Shin JS, Pierce NA (2004) A synthetic DNA walker for molecular transport. J Am Chem Soc 126(35):10834–10835CrossRef
59.
go back to reference Tian Y, Mao CD (2004) Molecular gears: a pair of DNA circles continuously rolls against each other. J Am Chem Soc 126(37):11410–11411CrossRef Tian Y, Mao CD (2004) Molecular gears: a pair of DNA circles continuously rolls against each other. J Am Chem Soc 126(37):11410–11411CrossRef
60.
go back to reference Yin P, Yan H, Daniell XG, Turberfield AJ, Reif JH (2004) A unidirectional DNA walker that moves autonomously along a track. Angew Chem Int Ed 43(37):4906–4911CrossRef Yin P, Yan H, Daniell XG, Turberfield AJ, Reif JH (2004) A unidirectional DNA walker that moves autonomously along a track. Angew Chem Int Ed 43(37):4906–4911CrossRef
61.
go back to reference Bath J, Green SJ, Turberfield AJ (2005) A free-running DNA motor powered by a nicking enzyme. Angew Chem Int Ed 44(28):4358–4361CrossRef Bath J, Green SJ, Turberfield AJ (2005) A free-running DNA motor powered by a nicking enzyme. Angew Chem Int Ed 44(28):4358–4361CrossRef
62.
go back to reference Tian Y, He Y, Chen Y, Yin P, Mao CD (2005) Molecular devices – a DNAzyme that walks processively and autonomously along a one-dimensional track. Angew Chem Int Ed 44(28):4355–4358CrossRef Tian Y, He Y, Chen Y, Yin P, Mao CD (2005) Molecular devices – a DNAzyme that walks processively and autonomously along a one-dimensional track. Angew Chem Int Ed 44(28):4355–4358CrossRef
63.
go back to reference Turberfield AJ, Mitchell JC, Yurke B, Mills AP, Blakey MI, Simmel FC (2003) DNA fuel for free-running nanomachines. Phys Rev Lett 90(11):118102–118105CrossRef Turberfield AJ, Mitchell JC, Yurke B, Mills AP, Blakey MI, Simmel FC (2003) DNA fuel for free-running nanomachines. Phys Rev Lett 90(11):118102–118105CrossRef
64.
go back to reference Krishnan Y, Simmel FC (2011) Nucleic acid based molecular devices. Angew Chem Int Ed 50:3124–3156CrossRef Krishnan Y, Simmel FC (2011) Nucleic acid based molecular devices. Angew Chem Int Ed 50:3124–3156CrossRef
65.
go back to reference Yin P, Choi HMT, Calvert CR, Pierce NA (2008) Programming biomolecular self-assembly pathways. Nature 451(7176):318–322CrossRef Yin P, Choi HMT, Calvert CR, Pierce NA (2008) Programming biomolecular self-assembly pathways. Nature 451(7176):318–322CrossRef
66.
go back to reference Omabegho T, Sha R, Seeman NC (2009) A bipedal DNA Brownian motor with coordinated legs. Science 324(5923):67–71CrossRef Omabegho T, Sha R, Seeman NC (2009) A bipedal DNA Brownian motor with coordinated legs. Science 324(5923):67–71CrossRef
67.
go back to reference Green SJ, Bath J, Turberfield AJ (2008) Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. Phys Rev Lett 101(23):238101–238104CrossRef Green SJ, Bath J, Turberfield AJ (2008) Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. Phys Rev Lett 101(23):238101–238104CrossRef
68.
go back to reference Pei R, Taylor SK, Stefanovic D, Rudchenko S, Mitchell TE, Stojanovic MN (2006) Behavior of polycatalytic assemblies in a substrate-displaying matrix. J Am Chem Soc 128(39):12693–12699CrossRef Pei R, Taylor SK, Stefanovic D, Rudchenko S, Mitchell TE, Stojanovic MN (2006) Behavior of polycatalytic assemblies in a substrate-displaying matrix. J Am Chem Soc 128(39):12693–12699CrossRef
69.
go back to reference Lund K, Manzo AJ, Dabby N, Michelotti N, Johnson-Buck A, Nangreave J et al (2010) Molecular robots guided by prescriptive landscapes. Nature 465(7295):206–210CrossRef Lund K, Manzo AJ, Dabby N, Michelotti N, Johnson-Buck A, Nangreave J et al (2010) Molecular robots guided by prescriptive landscapes. Nature 465(7295):206–210CrossRef
70.
go back to reference Wickham SFJ, Endo M, Katsuda Y, Hidaka K, Bath J, Sugiyama H et al (2011) Direct observation of stepwise movement of a synthetic molecular transporter. Nat Nanotechnol 6(3):166–169CrossRef Wickham SFJ, Endo M, Katsuda Y, Hidaka K, Bath J, Sugiyama H et al (2011) Direct observation of stepwise movement of a synthetic molecular transporter. Nat Nanotechnol 6(3):166–169CrossRef
71.
go back to reference Muscat RA, Bath J, Turberfield AJ (2011) A programmable molecular robot. Nano Lett 11(3):982–987CrossRef Muscat RA, Bath J, Turberfield AJ (2011) A programmable molecular robot. Nano Lett 11(3):982–987CrossRef
72.
go back to reference Wang ZG, Elbaz J, Willner I (2012) A dynamically programmed DNA transporter. Angew Chem Int Ed 51(48):4322–4326CrossRef Wang ZG, Elbaz J, Willner I (2012) A dynamically programmed DNA transporter. Angew Chem Int Ed 51(48):4322–4326CrossRef
73.
go back to reference Weizmann Y, Beissenhirtz MK, Cheglakov Z, Nowarski R, Kotler M, Willner I (2006) A virus spotlighted by an autonomous DNA machine. Angew Chem Int Ed 45(44):7384–7388CrossRef Weizmann Y, Beissenhirtz MK, Cheglakov Z, Nowarski R, Kotler M, Willner I (2006) A virus spotlighted by an autonomous DNA machine. Angew Chem Int Ed 45(44):7384–7388CrossRef
74.
go back to reference Shlyahovsky B, Li D, Weizmann Y, Nowarski R, Kotler M, Willner I (2007) Spotlighting of cocaine by an autonomous aptamer-based machine. J Am Chem Soc 129(13):3814–3815CrossRef Shlyahovsky B, Li D, Weizmann Y, Nowarski R, Kotler M, Willner I (2007) Spotlighting of cocaine by an autonomous aptamer-based machine. J Am Chem Soc 129(13):3814–3815CrossRef
75.
go back to reference Li D, Wieckowska A, Willner I (2008) Optical analysis of Hg2+ ions by oligonucleotide-gold-nanoparticle hybrids and DNA-based machines. Angew Chem Int Ed 47(21):3927–3931CrossRef Li D, Wieckowska A, Willner I (2008) Optical analysis of Hg2+ ions by oligonucleotide-gold-nanoparticle hybrids and DNA-based machines. Angew Chem Int Ed 47(21):3927–3931CrossRef
76.
go back to reference Zhu CF, Wen YQ, Li D, Wang LH, Song SP, Fan CH et al (2009) Inhibition of the in vitro replication of DNA by an aptamer-protein complex in an autonomous DNA machine. Chem Eur J 15(44):11898–11903CrossRef Zhu CF, Wen YQ, Li D, Wang LH, Song SP, Fan CH et al (2009) Inhibition of the in vitro replication of DNA by an aptamer-protein complex in an autonomous DNA machine. Chem Eur J 15(44):11898–11903CrossRef
77.
go back to reference Kuzuya A, Sakai Y, Yamazaki T, Xu Y, Komiyama M (2011) Nanomechanical DNA origami ‘single-molecule beacons’ directly imaged by atomic force microscopy. Nature Commun 2:1–8CrossRef Kuzuya A, Sakai Y, Yamazaki T, Xu Y, Komiyama M (2011) Nanomechanical DNA origami ‘single-molecule beacons’ directly imaged by atomic force microscopy. Nature Commun 2:1–8CrossRef
78.
go back to reference Gartner ZJ, Liu DR (2001) The generality of DNA-templated synthesis as a basis for evolving non-natural small molecules. J Am Chem Soc 123(28):6961–6963CrossRef Gartner ZJ, Liu DR (2001) The generality of DNA-templated synthesis as a basis for evolving non-natural small molecules. J Am Chem Soc 123(28):6961–6963CrossRef
79.
go back to reference Li XY, Liu DR (2004) DNA-templated organic synthesis: nature’s strategy for controlling chemical reactivity applied to synthetic molecules. Angew Chem Int Ed 43(37):4848–4870CrossRef Li XY, Liu DR (2004) DNA-templated organic synthesis: nature’s strategy for controlling chemical reactivity applied to synthetic molecules. Angew Chem Int Ed 43(37):4848–4870CrossRef
80.
go back to reference McKee ML, Milnes PJ, Bath J, Stulz E, Turberfield AJ, O’Reilly RK (2010) Multistep DNA-templated reactions for the synthesis of functional sequence controlled oligomers. Angew Chem Int Ed 49(43):7948–7951CrossRef McKee ML, Milnes PJ, Bath J, Stulz E, Turberfield AJ, O’Reilly RK (2010) Multistep DNA-templated reactions for the synthesis of functional sequence controlled oligomers. Angew Chem Int Ed 49(43):7948–7951CrossRef
81.
go back to reference He Y, Liu DR (2011) A sequential strand-displacement strategy enables efficient six-step DNA-templated synthesis. J Am Chem Soc 133(26):9972–9975CrossRef He Y, Liu DR (2011) A sequential strand-displacement strategy enables efficient six-step DNA-templated synthesis. J Am Chem Soc 133(26):9972–9975CrossRef
82.
go back to reference He Y, Liu DR (2010) Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker. Nat Nanotechnol 5(11):778–782CrossRef He Y, Liu DR (2010) Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker. Nat Nanotechnol 5(11):778–782CrossRef
83.
go back to reference Chhabra R, Sharma J, Liu Y, Yan H (2006) Addressable molecular tweezers for DNA-templated coupling reactions. Nano Lett 6(5):978–983CrossRef Chhabra R, Sharma J, Liu Y, Yan H (2006) Addressable molecular tweezers for DNA-templated coupling reactions. Nano Lett 6(5):978–983CrossRef
84.
go back to reference Dittmer WU, Reuter A, Simmel FC (2004) A DNA-based machine that can cyclically bind and release thrombin. Angew Chem Int Ed 43(27):3550–3553CrossRef Dittmer WU, Reuter A, Simmel FC (2004) A DNA-based machine that can cyclically bind and release thrombin. Angew Chem Int Ed 43(27):3550–3553CrossRef
85.
go back to reference Xu Y, Hirao Y, Nishimura Y, Sugiyama H (2007) I-motif and quadruplex-based device that can control a protein release or bind and release small molecule to influence biological processes. Bioorgan Med Chem 15(3):1275–1279CrossRef Xu Y, Hirao Y, Nishimura Y, Sugiyama H (2007) I-motif and quadruplex-based device that can control a protein release or bind and release small molecule to influence biological processes. Bioorgan Med Chem 15(3):1275–1279CrossRef
86.
go back to reference Mao YD, Liu DS, Wang ST, Luo SN, Wang WX, Yang YL et al (2007) Alternating-electric-field-enhanced reversible switching of DNA nanocontainers with pH. Nucleic Acids Res 35(5):e33CrossRef Mao YD, Liu DS, Wang ST, Luo SN, Wang WX, Yang YL et al (2007) Alternating-electric-field-enhanced reversible switching of DNA nanocontainers with pH. Nucleic Acids Res 35(5):e33CrossRef
87.
go back to reference Cheng EJ, Xing YZ, Chen P, Yang Y, Sun YW, Zhou DJ et al (2009) A pH-triggered, fast-responding DNA hydrogel. Angew Chem Int Ed 48(41):7660–7663CrossRef Cheng EJ, Xing YZ, Chen P, Yang Y, Sun YW, Zhou DJ et al (2009) A pH-triggered, fast-responding DNA hydrogel. Angew Chem Int Ed 48(41):7660–7663CrossRef
88.
go back to reference Goodman RP, Heilemann M, Doose S, Erben CM, Kapanidis AN, Turberfield AJ (2008) Reconfigurable, braced, three-dimensional DNA nanostructures. Nat Nanotechnol 3(2):93–96CrossRef Goodman RP, Heilemann M, Doose S, Erben CM, Kapanidis AN, Turberfield AJ (2008) Reconfigurable, braced, three-dimensional DNA nanostructures. Nat Nanotechnol 3(2):93–96CrossRef
89.
go back to reference Walsh AS, Yin HF, Erben CM, Wood MJA, Turberfield AJ (2011) DNA cage delivery to mammalian cells. ACS Nano 5(7):5427–5432CrossRef Walsh AS, Yin HF, Erben CM, Wood MJA, Turberfield AJ (2011) DNA cage delivery to mammalian cells. ACS Nano 5(7):5427–5432CrossRef
90.
go back to reference Douglas SM, Bachelet I, Church GM (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335(6070):831–834CrossRef Douglas SM, Bachelet I, Church GM (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335(6070):831–834CrossRef
91.
go back to reference Fu J, Yan H (2012) Controlled drug release by a nanorobot. Nat Biotechnol 30(5):407–408CrossRef Fu J, Yan H (2012) Controlled drug release by a nanorobot. Nat Biotechnol 30(5):407–408CrossRef
92.
go back to reference Sharma J, Chhabra R, Andersen CS, Gothelf KV, Yan H, Liu Y (2008) Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold. J Am Chem Soc 130(25):7820–7821CrossRef Sharma J, Chhabra R, Andersen CS, Gothelf KV, Yan H, Liu Y (2008) Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold. J Am Chem Soc 130(25):7820–7821CrossRef
93.
go back to reference Zhao Z, Jacovetty EL, Liu Y, Yan H (2011) Encapsulation of gold nanoparticles in a DNA origami cage. Angew Chem Int Ed 50(9):2041–2044CrossRef Zhao Z, Jacovetty EL, Liu Y, Yan H (2011) Encapsulation of gold nanoparticles in a DNA origami cage. Angew Chem Int Ed 50(9):2041–2044CrossRef
94.
go back to reference Pilo-Pais M, Goldberg S, Samano E, LaBean TH, Finkelstein G (2011) Connecting the nanodots: programmable nanofabrication of fused metal shapes on DNA templates. Nano Lett 11(8):3489–3492CrossRef Pilo-Pais M, Goldberg S, Samano E, LaBean TH, Finkelstein G (2011) Connecting the nanodots: programmable nanofabrication of fused metal shapes on DNA templates. Nano Lett 11(8):3489–3492CrossRef
95.
go back to reference Shen XB, Song C, Wang JY, Shi DW, Wang ZA, Liu N et al (2012) Rolling up gold nanoparticle-dressed DNA origami into three-dimensional plasmonic chiral nanostructures. J Am Chem Soc 134(1):146–149CrossRef Shen XB, Song C, Wang JY, Shi DW, Wang ZA, Liu N et al (2012) Rolling up gold nanoparticle-dressed DNA origami into three-dimensional plasmonic chiral nanostructures. J Am Chem Soc 134(1):146–149CrossRef
96.
go back to reference Gu HZ, Chao J, Xiao SJ, Seeman NC (2010) A proximity-based programmable DNA nanoscale assembly line. Nature 465(7295):202–205CrossRef Gu HZ, Chao J, Xiao SJ, Seeman NC (2010) A proximity-based programmable DNA nanoscale assembly line. Nature 465(7295):202–205CrossRef
97.
go back to reference Kufer SK, Puchner EM, Gumpp H, Liedl T, Gaub HE (2008) Single-molecule cut-and-paste surface assembly. Science 319(5863):594–596CrossRef Kufer SK, Puchner EM, Gumpp H, Liedl T, Gaub HE (2008) Single-molecule cut-and-paste surface assembly. Science 319(5863):594–596CrossRef
98.
go back to reference Liedl T, Olapinski M, Simmel FC (2006) A surface-bound DNA switch driven by a chemical oscillator. Angew Chem Int Ed 45(30):5007–5010CrossRef Liedl T, Olapinski M, Simmel FC (2006) A surface-bound DNA switch driven by a chemical oscillator. Angew Chem Int Ed 45(30):5007–5010CrossRef
99.
go back to reference Liu DS, Bruckbauer A, Abell C, Balasubramanian S, Kang DJ, Klenerman D et al (2006) A reversible pH-driven DNA nanoswitch array. J Am Chem Soc 128(6):2067–2071CrossRef Liu DS, Bruckbauer A, Abell C, Balasubramanian S, Kang DJ, Klenerman D et al (2006) A reversible pH-driven DNA nanoswitch array. J Am Chem Soc 128(6):2067–2071CrossRef
100.
go back to reference Shu WM, Liu DS, Watari M, Riener CK, Strunz T, Welland ME et al (2005) DNA molecular motor driven micromechanical cantilever arrays. J Am Chem Soc 127(48):17054–17060CrossRef Shu WM, Liu DS, Watari M, Riener CK, Strunz T, Welland ME et al (2005) DNA molecular motor driven micromechanical cantilever arrays. J Am Chem Soc 127(48):17054–17060CrossRef
101.
go back to reference Wang ST, Liu HJ, Liu DS, Ma XY, Fang XH, Jiang L (2007) Enthalpy-driven three-state switching of a superhydrophilic/superhydrophobic surface. Angew Chem Int Ed 46(21):3915–3917CrossRef Wang ST, Liu HJ, Liu DS, Ma XY, Fang XH, Jiang L (2007) Enthalpy-driven three-state switching of a superhydrophilic/superhydrophobic surface. Angew Chem Int Ed 46(21):3915–3917CrossRef
102.
go back to reference Xia F, Guo W, Mao YD, Hou X, Xue JM, Xia HW et al (2008) Gating of single synthetic nanopores by proton-driven DNA molecular motors. J Am Chem Soc 130(26):8345–8350CrossRef Xia F, Guo W, Mao YD, Hou X, Xue JM, Xia HW et al (2008) Gating of single synthetic nanopores by proton-driven DNA molecular motors. J Am Chem Soc 130(26):8345–8350CrossRef
103.
go back to reference Hou X, Guo W, Xia F, Nie FQ, Dong H, Tian Y et al (2009) A biomimetic potassium responsive nanochannel: G-quadruplex DNA conformational switching in a synthetic nanopore. J Am Chem Soc 131(22):7800–7805CrossRef Hou X, Guo W, Xia F, Nie FQ, Dong H, Tian Y et al (2009) A biomimetic potassium responsive nanochannel: G-quadruplex DNA conformational switching in a synthetic nanopore. J Am Chem Soc 131(22):7800–7805CrossRef
104.
go back to reference Elbaz J, Tel-Vered R, Freeman R, Yildiz HB, Willner I (2008) Switchable motion of DNA on solid supports. Angew Chem Int Ed 48(1):133–137CrossRef Elbaz J, Tel-Vered R, Freeman R, Yildiz HB, Willner I (2008) Switchable motion of DNA on solid supports. Angew Chem Int Ed 48(1):133–137CrossRef
Metadata
Title
Design, Fabrication, and Applications of DNA Nanomachines
Authors
Chen Song
Zhen-Gang Wang
Baoquan Ding
Copyright Year
2013
Publisher
Springer Berlin Heidelberg
DOI
https://doi.org/10.1007/978-3-642-36077-0_11

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