DNA-based machines

Topics in Current Chemistry

Volumn 354, Issue , 2014, Pages 279-338

  Wang, Fuan ^a   Willner, Bilha ^a   Willner, Itamar ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Aptamer; Automaton; Catenane; DNA; DNAzyme; Electrocatalysis; Enzyme cascade; Fluorescence; Fluorescence quenching; Fluorescence Resonance Energy Transfer; FRET; Gear; Light; Logic Gate; Machine; Modified surface; Nanobiotechnology; Nanoparticles; Nanotechnology; pH; Photoisomerization; Quantum dot; Robot; Rotaxane; Rotor; Spring; Strand displacement; Surface enhanced fluorescence; Tetrahedron; Transporter; Tweezers; Walker

Indexed keywords

APTAMER; DNA; LOCKED NUCLEIC ACID; METAL NANOPARTICLE; OLIGONUCLEOTIDE; ROTAXANE;

BIOMECHANICS; CHEMISTRY; DRUG DELIVERY SYSTEM; ELECTROCHEMICAL ANALYSIS; GENETIC PROCEDURES; LIGHT; MOTION; PH; PHOTOCHEMISTRY; THERMODYNAMICS;

APTAMERS, NUCLEOTIDE; BIOMECHANICAL PHENOMENA; BIOSENSING TECHNIQUES; DNA; DRUG DELIVERY SYSTEMS; ELECTROCHEMICAL TECHNIQUES; HYDROGEN-ION CONCENTRATION; LIGHT; METAL NANOPARTICLES; MOTION; OLIGONUCLEOTIDES; PHOTOCHEMICAL PROCESSES; ROTAXANES; THERMODYNAMICS;

EID: 84921780217     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128_2013_515     Document Type: Article

References (166)

1. Schnitzler T, Herrmann A (2012) DNA block copolymers: functional materials for nanoscience and biomedicine. Acc Chem Res 45:1419–1430
2. Modi S, Bhatia D, Simmel FC et al (2010) Structural DNA nanotechnology: from bases to bricks, from structure to function. J Phys Chem Lett 1:1994–2005
3. Gehring K, Leroy JL, Gue´ron M (1993) A tetrameric DNA structure with protonated cytosine–cytosine base pairs. Nature 363:561–565
4. Chen L, Cai L, Zhang X et al (1994) Crystal structure of a four-stranded intercalated DNA: d(C4). Biochemistry 33:13540–13546
5. Collie GW, Parkinson GN (2011) The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem Soc Rev 40:5867–5892
6. Davis JT, Spada GP (2007) Supramolecular architectures generated by self-assembly of guanosine derivatives. Chem Soc Rev 36:296–313
7. Miyake Y, Togashi H, Tashiro M et al (2006) MercuryII-mediated formation of thymine- HgII-thymine base pairs in DNA duplexes. J Am Chem Soc 128:2172–2173
8. Tanaka Y, Oda S, Yamaguchi H et al (2007) 15N-15N J-coupling across Hg(II): direct observation of Hg(II)-mediated T–T base pairs in a DNA duplex. J Am Chem Soc 129:244–245
9. Ono A, Cao S, Togashi H et al (2008) Specific interactions between silver(I) ions and cytosine–cytosine pairs in DNA duplexes. Chem Commun 44:4825–4827
10. Park KS, Jung C, Park HG (2010) “Illusionary” polymerase activity triggered by metal ions: use for molecular logic-gate operations. Angew Chem Int Ed 49:9757–9760
11. Brivanlou AH, Darnell JE (2002) Signal transduction and the control of gene expression. Science 295:813–818
12. Thomas MC, Chiang CM (2006) The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol 41:105–178
13. Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326:1501
14. Teif VB, Rippe K (2009) Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities. Nucleic Acids Res 37:5641–5655
15. Xu Y (2011) Chemistry in human telomere biology: structure, function and targeting of telomere DNA/RNA. Chem Soc Rev 40:2719–2740
16. Mason M, Schuller A, Skordalakes E (2011) Telomerase structure function. Curr Opin Struct Biol 21:92–100
17. Johnson A, O’Donnell M (2005) DNA ligase: getting a grip to seal the deal. Curr Biol 15: R90–R92
18. Dwivedi N, Dube D, Pandey J et al (2008) NAD(+)-dependent DNA ligase: a novel target waiting for the right inhibitor. Med Res Rev 28:545–568
19. Patel SS, Pandey M, Nandakumar D (2011) Dynamic coupling between the motors of DNA replication: hexameric helicase, DNA polymerase, and primase. Curr Opin Chem Biol 15:595–605
20. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510
21. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822
22. Osborne SE, Ellington AD (1997) Nucleic acid selection and the challenge of combinatorial chemistry. Chem Rev 97:349–370
23. Osborne SE, Matsumura I, Ellington AD (1997) Aptamers as therapeutic and diagnostic reagents: problems and prospects. Curr Opin Chem Biol 1:5–9
24. Lee JF, Stovall GM, Ellington AD (2006) Aptamer therapeutics advance. Curr Opin Chem Biol 10:282–289
25. Breaker RR, Joyce GF (1994) A DNA enzyme that cleaves RNA. Chem Biol 1:223–229
26. Willner I, Shlyahovsky B, Zayats M et al (2008) DNAzymes for sensing, nanobiotechnology and logic gate applications. Chem Soc Rev 37:1153–1165
27. Joyce GF (2007) Forty years of in vitro evolution. Angew Chem Int Ed 46:6420–6436
28. Stojanovic MN, de Prada P, Landry DW (2001) Aptamer-based folding fluorescent sensor for cocaine. J Am Chem Soc 123:4928–4931
29. Yang G, Arakawa-Uramoto H, Wang X et al (1996) Anti-cocaine catalytic antibodies: a synthetic solution to improved diversity. J Am Chem Soc 118:5881–5890
30. Bock LC, Griffin LC, Latham JA et al (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355:564–566
31. Macaya RF, Waldron JA, Beutel BA et al (1995) Structural and functional characterization of potent antithrombotic oligonucleotides possessing both quadruplex and duplex motifs. Biochemistry 34:4478–4492
32. Cox JC, Ellington AD (2001) Automated selection of anti-protein aptamers. Bioorg Med Chem 9:2525–2531
33. Cox JC, Hayhurst A, Hesselberth J et al (2002) Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res 30:e108
34. Kirby R, Cho EJ, Gehrke B et al (2004) Aptamer-based sensor arrays for the detection and quantitation of proteins. Anal Chem 76:4066–4075
35. Pan T, Uhlenbeck OC (1992) In vitro selection of RNAs that undergo autolytic cleavage with Pb2+. Biochemistry 31:3887–3895
36. Pan T, Uhlenbeck OC (1992) A small metalloribozyme with a two-step mechanism. Nature 358:560–563
37. Li Y, Geyer CR, Sen D (1996) Recognition of anionic porphyrins by DNA aptamers. Biochemistry 35:6911–6922
38. Travascio P, Li Y, Sen D (1998) DNA-enhanced peroxidase activity of a DNA-aptamerhemin complex. Chem Biol 5:505–517
39. Travascio P, Bennet AJ, Wang DY et al (1999) A ribozyme and a catalytic DNA with peroxidase activity: active sites versus cofactor-binding sites. Chem Biol 6:779–787
40. Travascio P, Witting PK, Mauk AG et al (2001) The peroxidase activity of a hemin-DNA oligonucleotide complex: free radical damage to specific guanine bases of the DNA. J Am Chem Soc 123:1337–1348
41. Pavlov V, Xiao Y, Gill R et al (2004) Amplified chemiluminescence surface detection of DNA and telomerase activity using catalytic nucleic acid labels. Anal Chem 76:2152–2156
42. Teller C, Willner I (2010) Organizing protein-DNA hybrids as nanostructures with programmed functionalities. Trends Biotechnol 28:619–628
43. Aldaye FA, Palmer AL, Sleiman HF (2008) Assembling materials with DNA as the guide. Science 321:1795–1799
44. Kolpashchikov DM (2010) Binary probes for nucleic acid analysis. Chem Rev 110:4709– 4723
45. Du Y, Li B, Wang E (2013) “Fitting” makes “sensing” simple: label-free detection strategies based on nucleic acid aptamers. Acc Chem Res 46:203–213
46. Drummond TG, Hill MG, Barton JK (2003) Electrochemical DNA sensors. Nat Biotechnol 21:1192–1199
47. Polsky R, Gill R, Kaganovsky L et al (2006) Nucleic acid-functionalized Pt nanoparticles: catalytic labels for the amplified electrochemical detection of biomolecules. Anal Chem 78:2268–2271
48. Wang F, Willner B, Willner I (2013) DNA nanotechnology with one-dimensional selfassembled nanostructures. Curr Opin Biotechnol 24:562–574
49. Wang ZG, Wilner OI, Willner I (2009) Self-assembly of aptamer-circular DNA nanostructures for controlled biocatalysis. Nano Lett 9:4098–4102
50. Wilner OI, Shimron S, Weizmann Y et al (2009) Self-assembly of enzymes on DNA scaffolds: en route to biocatalytic cascades and the synthesis of metallic nanowires. Nano Lett 9:2040–2043
51. Liu Y, Lin C, Li H et al (2005) Aptamer-directed self-assembly of protein arrays on a DNA nanostructure. Angew Chem Int Ed 44:4333–4338
52. He Y, Chen Y, Liu H et al (2005) Self-assembly of hexagonal DNA two-dimensional (2D) arrays. J Am Chem Soc 127:12202–12203
53. Park SH, Barish R, Li H et al (2005) Three-helix bundle DNA tiles self-assemble into 2D lattice or 1D templates for silver nanowires. Nano Lett 5:693–696
54. Winfree E, Liu F, Wenzler LA et al (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–544
55. Wei B, Dai M, Yin P (2012) Complex shapes self-assembled from single-stranded DNA tiles. Nature 485:623–626
56. Ke Y, Voigt NV, Gothelf KV et al (2012) Multilayer DNA origami packed on hexagonal and hybrid lattices. J Am Chem Soc 134:1770–1774
57. Majumder U, Rangnekar A, Gothelf KV et al (2011) Design and construction of doubledecker tile as a route to three-dimensional periodic assembly of DNA. J Am Chem Soc 133:3843–3845
58. Ke Y, Ong LL, Shih WM et al (2012) Three-dimensional structures self-assembled from DNA bricks. Science 338:1177–1183
59. Gothelf KV (2012) Materials science. LEGO-like DNA structures. Science 338:1159–1160
60. Wilner OI, Orbach R, Henning A et al (2011) Self-assembly of DNA nanotubes with controllable diameters. Nat Commun 2:540
61. Sharma J, Chhabra R, Liu Y et al (2006) DNA-templated self-assembly of two-dimensional and periodical gold nanoparticle arrays. Angew Chem Int Ed 45:730–735
62. Wilner OI, Willner I (2012) Functionalized DNA nanostructures. Chem Rev 112:2528–2556
63. Wilner OI, Weizmann Y, Gill R et al (2009) Enzyme cascades activated on topologically programmed DNA scaffolds. Nat Nanotechnol 4:249–254
64. Fu J, Liu M, Liu Y et al (2012) Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures. J Am Chem Soc 134:5516–5519
65. Dittmer WU, Reuter A, Simmel FC (2004) A DNA-based machine that can cyclically bind and release thrombin. Angew Chem Int Ed 43:3550–3553
66. Krishnan Y, Simmel FC (2011) Nucleic acid based molecular devices. Angew Chem Int Ed 50:3124–3156
67. Teller C, Willner I (2010) Functional nucleic acid nanostructures and DNA machines. Curr Opin Biotechnol 21:376–391
68. Bath J, Turberfield AJ (2007) DNA nanomachines. Nat Nanotechnol 2:275–284
69. Beissenhirtz MK, Willner I (2006) DNA-based machines. Org Biomol Chem 4:3392–3401
70. SantaLucia J, Hicks D (2004) The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct 33:415–440
71. Zhang DY, Turberfield AJ, Yurke B et al (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318:1121–1125
72. Soloveichik D, Seelig G, Winfree E et al (2010) DNA as a universal substrate for chemical kinetics. Proc Natl Acad Sci U S A 107:5393–5398
73. Yurke B, Mills AP (2003) Using DNA to power nanostructures. Genet Program Evolvable Mach 4:111–122
74. Li Q, Luan G, Guo Q et al (2002) A new class of homogeneous nucleic acid probes based on specific displacement hybridization. Nucleic Acids Res 30:e5
75. Zhang DY, Seelig G (2011) Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem 3:103–113
76. Zhang DY, Winfree E (2009) Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc 131:17303–17314
77. Yurke B, Turberfield AJ, Mills AP et al (2000) A DNA-fuelled molecular machine made of DNA. Nature 406:605–608
78. Elbaz J, Wang ZG, Orbach R et al (2009) pH-stimulated concurrent mechanical activation of two DNA “tweezers”. A “SET-RESET” logic gate system. Nano Lett 9:4510–4514
79. Shimron S, Magen N, Elbaz J et al (2011) pH-programmable DNAzyme nanostructures. Chem Commun 47:8787–8789
80. Wang ZG, Elbaz J, Remacle F et al (2010) All-DNA finite-state automata with finite memory. Proc Natl Acad Sci U S A 107:21996–22001
81. Elbaz J, Moshe M, Willner I (2009) Coherent activation of DNA tweezers: a “SET-RESET” logic system. Angew Chem Int Ed 48:3834–3837
82. Liang X, Nishioka H, Takenaka N et al (2008) A DNA nanomachine powered by light irradiation. ChemBioChem 9:702–705
83. Shin JS, Pierce NA (2004) A synthetic DNA walker for molecular transport. J Am Chem Soc 126:10834–10835
84. Sherman WB, Seeman NC (2004) A precisely controlled DNA biped walking device. Nano Lett 4:1203–1207
85. Wang ZG, Elbaz J, Willner I (2011) DNA machines: bipedal walker and stepper. Nano Lett 11:304–309
86. Omabegho T, Sha R, Seeman NC (2009) A bipedal DNA Brownian motor with coordinated legs. Science 324:67–71
87. You M, Chen Y, Zhang X et al (2012) An autonomous and controllable light-driven DNA walking device. Angew Chem Int Ed 51:2457–2460
88. You M, Huang F, Chen Z et al (2012) Building a nanostructure with reversible motions using photonic energy. ACS Nano 6:7935–7941
89. Tian Y, He Y, Chen Y et al (2005) A DNAzyme that walks processively and autonomously along a one-dimensional track. Angew Chem Int Ed 44:4355–4358
90. Bath J, Green SJ, Turberfield AJ (2005) A free-running DNA motor powered by a nicking enzyme. Angew Chem Int Ed 44:4358–4361
91. Yin P, Yan H, Daniell XG et al (2004) A unidirectional DNA walker that moves autonomously along a track. Angew Chem Int Ed 43:4906–4911
92. Liu X, Niazov-Elkan A, Wang F et al (2013) Switching photonic and electrochemical functions of a DNAzyme by DNA machines. Nano Lett 13:219–225
93. Elbaz J, Tel-Vered R, Freeman R et al (2009) Switchable motion of DNA on solid supports. Angew Chem Int Ed 48:133–137
94. Lund K, Manzo AJ, Dabby N et al (2010) Molecular robots guided by prescriptive landscapes. Nature 465:206–210
95. Wickham SF, Endo M, Katsuda Y et al (2011) Direct observation of stepwise movement of a synthetic molecular transporter. Nat Nanotechnol 6:166–169
96. Wickham SF, Bath J, Katsuda Y et al (2012) A DNA-based molecular motor that can navigate a network of tracks. Nat Nanotechnol 7:169–173
97. McGonigal PR, Stoddart JF (2013) Interlocked molecules: a molecular production line. Nat Chem 5:260–262
98. Balzani V, Credi A, Silvi S et al (2006) Artificial nanomachines based on interlocked molecular species: recent advances. Chem Soc Rev 35:1135–1149
99. Griffiths KE, Stoddart JF (2008) Template-directed synthesis of donor/acceptor [2]catenanes and [2]rotaxanes. Pure Appl Chem 80:485–506
100. Ballardini R, Balzani V, Credi A et al (1997) Controlling catenations, properties and relative ring component movements in catenanes with aromatic fluorine substituents. J Am Chem Soc 119:12503–12513
101. Kidd TJ, Leigh DA, Wilson AJ (1999) Organic “magic rings”-the hydrogen bond-directed assembly of catenanes under thermodynamic control. J Am Chem Soc 121:1599–1600
102. Raiteri P, Bussi G, Cucinotta CS et al (2008) Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angew Chem Int Ed 47:3536–3539
103. Amabilino DB, Ashton PR, Balzani V et al (1996) Self-assembly of [n]rotaxanes bearing dendritic stoppers. J Am Chem Soc 118:12012–12020
104. Bodis P, Panman MR, Bakker BH et al (2009) Two-dimensional vibrational spectroscopy of rotaxane-based molecular machines. Acc Chem Res 42:1462–1469
105. Forgan RS, Sauvage JP, Stoddart JF (2011) Chemical topology: complex molecular knots, links, and entanglements. Chem Rev 111:5434–5464
106. Cantrill SJ, Chichak KS, Peters AJ et al (2005) Nanoscale borromean rings. Acc Chem Res 38:1–9
107. Chichak KS, Cantrill SJ, Pease AR et al (2004) Molecular borromean rings. Science 304:1308–1312
108. Silvi S, Venturi M, Credi A (2011) Light operated molecular machines. Chem Commun 47:2483–2489
109. Li H, Fahrenbach AC, Coskun A et al (2011) A light-stimulated molecular switch driven by radical-radical interactions in water. Angew Chem Int Ed 50:6782–6788
110. Balzani V, Credi A, Venturi M (2009) Light powered molecular machines. Chem Soc Rev 38:1542–1550
111. Ye T, Kumar AS, Saha S et al (2010) Changing stations in single bistable rotaxane molecules under electrochemical control. ACS Nano 4:3697–3701
112. Katz E, Lioubashevsky O, Willner I (2004) Electromechanics of a redox-active rotaxane in a monolayer assembly on an electrode. J Am Chem Soc 126:15520–15532
113. Katz E, Sheeney-Haj-Ichia L, Willner I (2004) Electrical contacting of glucose oxidase in a redox-active rotaxane configuration. Angew Chem Int Ed 43:3292–3300
114. Deng WQ, Flood AH, Stoddart JF et al (2005) An electrochemical color-switchable RGB dye: tristable [2]catenane. J Am Chem Soc 127:15994–15995
115. Balzani V, Credi A, Langford SJ et al (2000) Constructing molecular machinery: a chemically-switchable [2]catenane. J Am Chem Soc 122:3542–3543
116. Romuald C, Arda´ A, Clavel C et al (2012) Tightening or loosening a pH-sensitive doublelasso molecular machine readily synthesized from an ends-activated [c2]daisy chain. Chem Sci 3:1851–1857
117. Fang L, Hmadeh M, Wu J et al (2009) Acid-base actuation of [c2]daisy chains. J Am Chem Soc 131:7126–7134
118. Hudson B, Vinograd J (1967) Catenated circular DNA molecules in HeLa cell mitochondria. Nature 216:647–652
119. Liu Y, Kuzuya A, Sha R et al (2008) Coupling across a DNA helical turn yields a hybrid DNA/organic catenane doubly tailed with functional termini. J Am Chem Soc 130:10882– 10883
120. Han D, Pal S, Liu Y et al (2010) Folding and cutting DNA into reconfigurable topological nanostructures. Nat Nanotechnol 5:712–717
121. Schmidt TL, Heckel A (2011) Construction of a structurally defined double-stranded DNA catenane. Nano Lett 11:1739–1742
122. Ackermann D, Jester SS, Famulok M (2012) Design strategy for DNA rotaxanes with a mechanically reinforced PX100 axle. Angew Chem Int Ed 51:6771–6775
123. Ackermann D, Schmidt TL, Hannam JS et al (2010) A double-stranded DNA rotaxane. Nat Nanotechnol 5:436–442
124. Mao C, Sun W, Seeman NC (1997) Assembly of Borromean rings from DNA. Nature 386:137–138
125. Elbaz J, Wang Z-G, Wang F et al (2012) Programmed dynamic topologies in DNA catenanes. Angew Chem Int Ed 51:2349–2353
126. Lu CH, Cecconello A, Elbaz J et al (2013) A three-station DNA catenane rotary motor with controlled directionality. Nano Lett 13:2303–2308
127. Lohmann F, Ackermann D, Famulok M (2012) Reversible light switch for macrocycle mobility in a DNA rotaxane. J Am Chem Soc 134:11884–11887
128. Wang W, Yang Y, Cheng E et al (2009) A pH-driven, reconfigurable DNA nanotriangle. Chem Commun 45:824–826
129. Song G, Chen M, Chen C et al (2010) Design of proton-fueled tweezers for controlled, multifunction DNA-based molecular device. Biochimie 92:121–127
130. Goodman RP, Heilemann M, Doose S et al (2008) Reconfigurable, braced, three-dimensional DNA nanostructures. Nat Nanotechnol 3:93–96
131. Han D, Huang J, Zhu Z et al (2011) Molecular engineering of photoresponsive threedimensional DNA nanostructures. Chem Commun 47:4670–4672
132. Muscat RA, Bath J, Turberfield AJ (2011) A programmable molecular robot. Nano Lett 11:982–987
133. Tian Y, Mao C (2004) Molecular gears: a pair of DNA circles continuously rolls against each other. J Am Chem Soc 126:11410–11411
134. Wang C, Huang Z, Lin Y et al (2010) Artificial DNA nano-spring powered by protons. Adv Mater 22:2792–2798
135. Venkataraman S, Dirks RM, Rothemund PW et al (2007) An autonomous polymerization motor powered by DNA hybridization. Nat Nanotechnol 2:490–494
136. Pelossof G, Tel-Vered R, Liu X et al (2013) Switchable mechanical DNA “arms” operating on nucleic acid scaffolds associated with electrodes or semiconductor quantum dots. Nanoscale 5:8977–8981
137. Stojanovic´ MN, Stefanovic´ D (2003) Deoxyribozyme-based half-adder. J Am Chem Soc 125:6673–6676
138. Liu X, Aizen R, Freeman R et al (2012) Multiplexed aptasensors and amplified DNA sensors using functionalized graphene oxide: application for logic gate operations. ACS Nano 6:3553–3563
139. Shlyahovsky B, Li Y, Lioubashevski O et al (2009) Logic gates and antisense DNA devices operating on a translator nucleic acid scaffold. ACS Nano 3:1831–1843
140. Saghatelian A, Vo¨lcker NH, Guckian KM et al (2003) DNA-based photonic logic gates: AND, NAND, and INHIBIT. J Am Chem Soc 125:346–347
141. Okamoto A, Tanaka K, Saito I (2004) DNA logic gates. J Am Chem Soc 126:9458–9463
142. Elbaz J, Wang F, Remacle F et al (2012) pH-programmable DNA logic arrays powered by modular DNAzyme libraries. Nano Lett 12:6049–6054
143. Elbaz J, Lioubashevski O, Wang F et al (2010) DNA computing circuits using libraries of DNAzyme subunits. Nat Nanotechnol 5:417–422
144. Qian L, Winfree E (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science 332:1196–1201
145. Qian L, Winfree E, Bruck J et al (2011) Neural network computation with DNA strand displacement cascades. Nature 475:368–372
146. Stojanovic MN, Semova S, Kolpashchikov D et al (2005) Deoxyribozyme-based ligase logic gates and their initial circuits. J Am Chem Soc 127:6914–6915
147. Pei H, Liang L, Yao G et al (2012) Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors. Angew Chem Int Ed 51:9020–9024
148. Wang ZG, Elbaz J, Willner I (2012) A dynamically programmed DNA transporter. Angew Chem Int Ed 51:4322–4326
149. Shimron S, Cecconello A, Lu CH et al (2013) Metal nanoparticle-functionalized DNA tweezers: from mechanically programmed nanostructures to switchable fluorescence properties. Nano Lett 13:3791–3795
150. Elbaz J, Cecconello A, Fan Z et al (2013) Powering the programmed nanostructure and function of gold nanoparticles with catenated DNA machines. Nat Commun 4:2000
151. Xin L, Zhou C, Yang Z et al (2013) Regulation of an enzyme cascade reaction by a DNA machine. Small 9:3088–3091
152. Liu M, Fu J, Hejesen C et al (2013) A DNA tweezer-actuated enzyme nanoreactor. Nat Commun 4:2127
153. Tanaka K, Clever GH, Takezawa Y et al (2006) Programmable self-assembly of metal ions inside artificial DNA duplexes. Nat Nanotechnol 1:190–194
154. Clever GH, Kaul C, Carell T (2007) DNA-metal base pairs. Angew Chem Int Ed 46:6226– 6236
155. Takezawa Y, Shionoya M (2012) Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson–Crick base pairs. Acc Chem Res 45:2066–2076
156. Kosman J, Juskowiak B (2011) Peroxidase-mimicking DNAzymes for biosensing applications: a review. Anal Chim Acta 707:7–17
157. Sen D, Poon LC (2011) RNA and DNA complexes with hemin [Fe(III) heme] are efficient peroxidases and peroxygenases: how do they do it and what does it mean? Crit Rev Biochem Mol Biol 46:478–492
158. Arthanari H, Basu S, Kawano TL et al (1998) Fluorescent dyes specific for quadruplex DNA. Nucleic Acids Res 26:3724–3728
159. Paramasivan S, Bolton PH (2008) Mix and measure fluorescence screening for selective quadruplex binders. Nucleic Acids Res 36:e106
160. Modi S, Swetha MG, Goswami D et al (2009) A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nat Nanotechnol 4:325–330
161. Modi S, Nizak C, Surana S et al (2013) Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nat Nanotechnol 8:459–467
162. Surana S, Bhat JM, Koushika SP et al (2011) An autonomous DNA nanomachine maps spatiotemporal pH changes in a multicellular living organism. Nat Commun 2:340
163. Douglas SM, Bachelet I, Church GM (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335:831–834
164. Zhang Z, Balogh D, Wang F et al (2012) Smart mesoporous SiO2 nanoparticles for the DNAzyme-induced multiplexed release of substrates. J Am Chem Soc 135:1934–1940
165. Zhang Z, Balogh D, Wang F et al (2013) Biocatalytic release of an anti-cancer drug from nucleic acids-capped mesoporous SiO2 using DNA or molecular biomarkers as triggering stimuli. ACS Nano 7:8455–8468
166. He Y, Liu DR (2010) Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker. Nat Nanotechnol 5:778–782