Beyond DNA origami: The unfolding prospects of nucleic acid nanotechnology

Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology

Volumn 4, Issue 2, 2012, Pages 139-152

  Michelotti, Nicole ^a   Johnson Buck, Alexander ^a   Manzo, Anthony J ^a   Walter, Nils G ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE ENERGY; ARBITRARY SHAPE; DNA STRANDS; FUTURE APPLICATIONS; MOLECULAR RECOGNITION PROPERTIES; NANO-DEVICES; NANOMETER-SCALE PRECISION; SITE-SPECIFIC; SYNTHETIC NUCLEIC ACID; THREE-DIMENSIONAL SCAFFOLDS;

BIOMOLECULES; FUNCTIONAL MATERIALS; MEDICAL NANOTECHNOLOGY; MOLECULAR RECOGNITION; NANOELECTRONICS; NANOPARTICLES; NANOSTRUCTURED MATERIALS;

DNA;

DNA; MOLECULAR SCAFFOLD; NUCLEIC ACID; SELF ASSEMBLED MONOLAYER;

ALTERNATIVE ENERGY; ARTICLE; DNA ORIGAMI; DNA STRAND; MOLECULAR ELECTRONICS; MOLECULAR RECOGNITION; NANODEVICE; NANOMEDICINE; NANOTECHNOLOGY; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN UNFOLDING;

DNA; INTERDISCIPLINARY STUDIES; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS;

EID: 84857119035     PISSN: 19395116     EISSN: 19390041     Source Type: Journal    
DOI: 10.1002/wnan.170     Document Type: Article

References (117)

1. Seeman NC. DNA in a material world. Nature 2003, 421:427-431.
2. Voet D, Voet JG. Biochemistry. 4th ed. New York: John Wiley and Sons; 2011.
3. Paabo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. Genetic analyses from ancient DNA. Annu Rev Genet 2004, 38:645-679.
4. Mattick JS, Taft RJ, Faulkner GJ. A global view of genomic information-moving beyond the gene and the master regulator. Trends Genet 2010, 26: 21-28.
5. Marek MS, Johnson-Buck A, Walter NG. The shape-shifting quasispecies of RNA: one sequence, many functional folds. Phys Chem Chem Phys 2011, 13:11524-11537.
6. Frank J, Gonzalez RL Jr. Structure and dynamics of a processive Brownian motor: the translating ribosome. Annu Rev Biochem 2010, 79: 381-412.
7. Will CL, Luhrmann R. Spliceosome structure and function. Cold Spring Harb Perspect Biol 2011, 3:a003707.
8. Newman AJ, Nagai K. Structural studies of the spliceosome: blind men and an elephant. Curr Opin Struct Biol 2010, 20:82-89.
9. Mattick JS. The genetic signatures of noncoding RNAs. PLoS Genet 2009, 5:e1000459.
10. Seeman NC. Nanomaterials based on DNA. Annu Rev Biochem 2010, 79:65-87.
11. Rothemund PW. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440:297-302.
12. Seeman NC. An overview of structural DNA nanotechnology. Mol Biotechnol 2007, 37:246-257.
13. Aldaye FA, Palmer AL, Sleiman HF. Assembling materials with DNA as the guide. Science 2008, 321:1795-1799.
14. Nangreave J, Han D, Liu Y, Yan H. DNA origami: a history and current perspective. Curr Opin Chem Biol 2010, 14:608-615.
15. Shih WM, Lin C. Knitting complex weaves with DNA origami. Curr Opin Struct Biol 2010, 20:276-282.
16. Torring T, Voigt NV, Nangreave J, Yan H, Gothelf KV. DNA origami: a quantum leap for self-assembly of complex structures. Chem Soc Rev. In press.
17. Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 1953, 171:737-738.
18. Williams NH, Takasaki B, Wall M, Chin J. Structure and nuclease activity of simple dinuclear metal complexes: quantitative dissection of the role of metal ions. Acc Chem Res 1999, 32:485-493.
19. Wang S, Kool ET. Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2'-hydroxyl effects. Biochemistry 1995, 34:4125-4132.
20. Lipps HJ, Rhodes D. G-quadruplex structures: in vivo evidence and function. Trends Cell Biol 2009, 19:414-422.
21. Grindley ND, Whiteson KL, Rice PA. Mechanisms of site-specific recombination. Annu Rev Biochem 2006, 75:567-605.
22. Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 2008, 9:179-191.
23. Strahl BD, Allis CD. The language of covalent histone modifications. Nature 2000, 403:41-45.
24. Chen J, Darst SA, Thirumalai D. Promoter melting triggered by bacterial RNA polymerase occurs in three steps. Proc Natl Acad Sci U S A 2010, 107:12523-12528.
25. Crick F. Central dogma of molecular biology. Nature 1970, 227:561-563.
26. Davidson BL, McCray PB Jr. Current prospects for RNA interference-based therapies. Nat Rev Genet 2011, 12:329-340.
27. Al-Hashimi HM, Walter NG. RNA dynamics: it is about time. Curr Opin Struct Biol 2008, 18:321-329.
28. Dambach MD, Winkler WC. Expanding roles for metabolite-sensing regulatory RNAs. Curr Opin Microbiol 2009, 12:161-169.
29. Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. The structural basis of ribosome activity in peptide bond synthesis. Science 2000, 289:920-930.
30. Ferre-D'Amare AR, Scott WG. Small self-cleaving ribozymes. Cold Spring Harb Perspect Biol 2010, 2:a003574.
31. Ehrlich M, Gama-Sosa MA, Carreira LH, Ljungdahl LG, Kuo KC, Gehrke CW. DNA methylation in thermophilic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine. Nucleic Acids Res 1985, 13:1399-1412.
32. Jones PA, Takai D. The role of DNA methylation in mammalian epigenetics. Science 2001, 293:1068-1070.
33. Campbell MA, Wengel J. Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals. Chem Soc Rev 2011.
34. Braasch DA, Corey DR. Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem Biol 2001, 8:1-7.
35. Rana TM. Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol 2007, 8:23-36.
36. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, Berg RH, Kim SK, Norden B, Nielsen PE. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 1993, 365:566-568.
37. Williams KA, Veenhuizen PT, de la Torre BG, Eritja R, Dekker C. Nanotechnology: carbon nanotubes with DNA recognition. Nature 2002, 420:761.
38. Lukeman PS, Mittal AC, Seeman NC. Two dimensional PNA/DNA arrays: estimating the helicity of unusual nucleic acid polymers. Chem Commun 2004, 1694-1695.
39. Chen F, Yang Z, Yan M, Alvarado JB, Wang G, Benner SA. Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity. Nucleic Acids Res 2011, 39:3949-3961.
40. Petrillo ML, Newton CJ, Cunningham RP, Ma RI, Kallenbach NR, Seeman NC. The ligation and flexibility of 4-arm DNA junctions. Biopolymers 1988, 27:1337-1352.
41. Holliday R. Mechanism for gene conversion in fungi. Genet Res 1964, 5:282-304.
42. Fu TJ, Seeman NC. DNA double-crossover molecules. Biochemistry 1993, 32:3211-3220.
43. LaBean TH, Yan H, Kopatsch J, Liu FR, Winfree E, Reif JH, Seeman NC. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J Am Chem Soc 2000, 122:1848-1860.
44. Shih WM, Quispe JD, Joyce GF. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 2004, 427:618-621.
45. Han D, Pal S, Nangreave J, Deng Z, Liu Y, Yan H. DNA origami with complex curvatures in three-dimensional space. Science 2011, 332:342-346.
46. Woo S, Rothemund PW. Programmable molecular recognition based on the geometry of DNA nanostructures. Nat Chem 2011, 3:620-627.
47. Lund K, Manzo AJ, Dabby N, Michelotti N, Johnson-Buck A, Nangreave J, Taylor S, Pei R, Stojanovic MN, Walter NG, et al. Molecular robots guided by prescriptive landscapes. Nature 2010, 465:206-210.
48. Gu HZ, Chao J, Xiao SJ, Seeman NC. A proximity-based programmable DNA nanoscale assembly line. Nature 2010, 465:202-286.
49. He Y, Liu DR. Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker. Nat Nanotechnol 2010, 5:778-782.
50. Maune HT, Han SP, Barish RD, Bockrath M, Goddard WA, Rothemund PWK, Winfree E. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nat Nanotechnol 2010, 5:61-66.
51. Eskelinen AP, Kuzyk A, Kaltiaisenaho TK, Timmermans MY, Nasibulin AG, Kauppinen EI, Torma P. Assembly of single-walled carbon nanotubes on DNA-origami templates through streptavidin-biotin interaction. Small 2011, 7:746-750.
52. Michelotti N, de Silva C, Johnson-Buck AE, Manzo AJ, Walter NG. A bird's eye view tracking slow nanometer-scale movements of single molecular nano-assemblies. Methods Enzymol 2010, 475:121-148.
53. von Delius M, Leigh DA. Walking molecules. Chem Soc Rev 2011, 40:3656-3676.
54. Qian L, Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 2011, 332:1196-1201.
55. Boeneman K, Prasuhn DE, Blanco-Canosa JB, Dawson PE, Melinger JS, Ancona M, Stewart MH, Susumu K, Huston A, Medintz IL. Self-assembled quantum dot-sensitized multivalent DNA photonic wires. J Am Chem Soc 2010, 132:18177-18190.
56. Hung AM, Micheel CM, Bozano LD, Osterbur LW, Wallraff GM, Cha JN. Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nat Nanotechnol 2010, 5:121-126.
57. Lin CX, Ke YG, Liu Y, Mertig M, Gu J, Yan H. Functional DNA nanotube arrays: bottom-up meets top-down. Angew Chem Int Ed Engl 2007, 46:6089-6092.
58. Niemeyer CM, Koehler J, Wuerdemann C. DNA-directed assembly of bienzymic complexes from in vivo biotinylated NAD(P)H: FMN oxidoreductase and luciferase. Chembiochem 2002, 3:242-245.
59. Ruiz-Carretero A, Janssen PGA, Stevens AL, Surin M, Herz LM, Schenning APHJ. Directing energy transfer in discrete one-dimensional oligonucleotide-templated assemblies. Chem Commun 2011, 47:884-886.
60. Stein IH, Steinhauer C, Tinnefeld P. Single-molecule four-color FRET visualizes energy-transfer paths on DNA origami. J Am Chem Soc 2011, 133:4193-4195.
61. Singh A, Tolev M, Meng M, Klenin K, Plietzsch O, Schilling CI, Muller T, Nieger M, Brase S, Wenzel W, et al. Branched DNA that forms a solid at 95 degrees C. Angew Chem Int Ed Engl 2011, 50:3227-3231.
62. Kwak M, Herrmann A. Nucleic acid/organic polymer hybrid materials: synthesis, superstructures, and applications. Angew Chem Int Ed Engl 2010, 49:8574-8587.
63. Ohno H, Kobayashi T, Kabata R, Endo K, Iwasa T, Yoshimura SH, Takeyasu K, Inoue T, Saito H. Synthetic RNA-protein complex shaped like an equilateral triangle. Nat Nanotechnol 2011, 6:115-119.
64. Hung AM, Noh H, Cha JN. Recent advances in DNA-based directed assembly on surfaces. Nanoscale 2010, 2:2530-2537.
65. Kershner RJ, Bozano LD, Micheel CM, Hung AM, Fornof AR, Cha JN, Rettner CT, Bersani M, Frommer J, Rothemund PW, et al. Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nat Nanotechnol 2009, 4:557-561.
66. Stojanovic MN, Mitchell TE, Stefanovic D. Deoxyribozyme-based logic gates. J Am Chem Soc 2002, 124:3555-3561.
67. Stojanovic MN, Stefanovic D. A deoxyribozyme-based molecular automaton. Nat Biotechnol 2003, 21:1069-1074.
68. Pei R, Matamoros E, Liu M, Stefanovic D, Stojanovic MN. Training a molecular automaton to play a game. Nat Nanotechnol 2010, 5:773-777.
69. Qian L, Winfree E, Bruck J. Neural network computation with DNA strand displacement cascades. Nature 2011, 475:368-372.
70. Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA. Logic-based models for the analysis of cell signaling networks. Biochemistry 2010, 49:3216-3224.
71. Ozbay E. Plasmonics: merging photonics and electronics at nanoscale dimensions. Science 2006, 311:189-193.
72. Anker JN, Hall WP, Lyandres O, Shah NC, Zhao J, Van Duyne RP. Biosensing with plasmonic nanosensors. Nat Mater 2008, 7:442-453.
73. Tan SJ, Campolongo MJ, Luo D, Cheng W. Building plasmonic nanostructures with DNA. Nat Nanotechnol 2011, 6:268-276.
74. Ding B, Deng Z, Yan H, Cabrini S, Zuckermann RN, Bokor J. Gold nanoparticle self-similar chain structure organized by DNA origami. J Am Chem Soc 2010, 132:3248-3249.
75. Lo PK, Karam P, Aldaye FA, McLaughlin CK, Hamblin GD, Cosa G, Sleiman HF. Loading and selective release of cargo in DNA nanotubes with longitudinal variation. Nat Chem 2010, 2:319-328.
76. Rothemund PW, Ekani-Nkodo A, Papadakis N, Kumar A, Fygenson DK, Winfree E. Design and characterization of programmable DNA nanotubes. J Am Chem Soc 2004, 126:16344-16352.
77. Palchetti I, Mascini M. Nucleic acid biosensors for environmental pollution monitoring. Analyst 2008, 133:846-854.
78. Sekella PT, Rueda D, Walter NG. A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage. RNA 2002, 8:1242-1252.
79. Modi S, Swetha MG, Goswami D, Gupta GD, Mayor S, Krishnan Y. A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nat Nanotechnol 2009, 4:325-330.
80. Wang J. DNA biosensors based on peptide nucleic acid (PNA) recognition layers. A review. Biosens Bioelectron 1998, 13:757-762.
81. Martinez K, Estevez MC, Wu Y, Phillips JA, Medley CD, Tan W. Locked nucleic acid based beacons for surface interaction studies and biosensor development. Anal Chem 2009, 81:3448-3454.
82. Piunno PA, Krull UJ. Trends in the development of nucleic acid biosensors for medical diagnostics. Anal Bioanal Chem 2005, 381:1004-1011.
83. Ke Y, Lindsay S, Chang Y, Liu Y, Yan H. Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays. Science 2008, 319:180-183.
84. Liu HJ, Torring T, Dong MD, Rosen CB, Besenbacher F, Gothelf KV. DNA-templated covalent coupling of G4 PAMAM dendrimers. J Am Chem Soc 2010, 132:18054-18056.
85. Crawford JM, Townsend CA. New insights into the formation of fungal aromatic polyketides. Nat Rev Microbiol 2010, 8:879-889.
86. Andrianantoandro E, Basu S, Karig DK, Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2006, 2:2006.0028.
87. Lee SK, Chou H, Ham TS, Lee TS, Keasling JD. Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr Opin Biotechnol 2008, 19:556-563.
88. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010, 329:52-56.
89. Wilner OI, Shimron S, Weizmann Y, Wang ZG, Willner I. Self-assembly of enzymes on DNA scaffolds: en route to biocatalytic cascades and the synthesis of metallic nanowires. Nano Lett 2009, 9:2040-2043.
90. Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R, Mamdouh W, Golas MM, Sander B, Stark H, Oliveira CL, et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 2009, 459:73-76.
91. Endo M, Hidaka K, Kato T, Namba K, Sugiyama H. DNA prism structures constructed by folding of multiple rectangular arms. J Am Chem Soc 2009, 131:15570-15571.
92. Venkataraman S, Dirks RM, Ueda CT, Pierce NA. Selective cell death mediated by small conditional RNAs. Proc Natl Acad Sci U S A 2010, 107:16777-16782.
93. Surana S, Bhat JM, Koushika SP, Krishnan Y. An autonomous DNA nanomachine maps spatiotemporal pH changes in a multicellular living organism. Nat Commun 2011, 2:340.
94. Bhatia D, Surana S, Chakraborty S, Koushika SP, Krishnan Y. A synthetic icosahedral DNA-based host-cargo complex for functional in vivo imaging. Nat Commun 2011, 2:339.
95. Mei Q, Wei X, Su F, Liu Y, Youngbull C, Johnson R, Lindsay S, Yan H, Meldrum D. Stability of DNA origami nanoarrays in cell lysate. Nano Lett 2011, 11:1477-1482.
96. Lu W, Lieber CM. Nanoelectronics from the bottom up. Nat Mater 2007, 6:841-850.
97. Engheta N. Circuits with light at nanoscales: optical nanocircuits inspired by metamaterials. Science 2007, 317:1698-1702.
98. Tour JM, Kittrell C, Colvin VL. Green carbon as a bridge to renewable energy. Nat Mater 2010, 9:871-874.
99. Solomon S, Plattner GK, Knutti R, Friedlingstein P. Irreversible climate change due to carbon dioxide emissions. Proc Natl Acad Sci U S A 2009, 106:1704-1709.
100. Delebecque CJ, Lindner AB, Silver PA, Aldaye FA. Organization of intracellular reactions with rationally designed RNA assemblies. Science 2011, 333:470-474.
101. Moghimi SM, Hunter AC, Murray JC. Nanomedicine: current status and future prospects. FASEB J 2005, 19:311-330.
102. Brandenburg B, Lee LY, Lakadamyali M, Rust MJ, Zhuang X, Hogle JM. Imaging poliovirus entry in live cells. PLoS Biol 2007, 5:e183.
103. Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E. An autonomous molecular computer for logical control of gene expression. Nature 2004, 429:423-429.
104. Krishna H, Caruthers MH. Solid-phase synthesis, thermal denaturation studies, nuclease resistance, and cellular uptake of (oligodeoxyribonucleoside)methylborane phosphine-DNA chimeras. J Am Chem Soc 2011, 133:9844-9854.
105. Rueda D, Walter NG. Single molecule fluorescence control for nanotechnology. J Nanosci Nanotechnol 2005, 5:1990-2000.
106. Walter NG, Huang CY, Manzo AJ, Sobhy MA. Do-it-yourself guide: how to use the modern single-molecule toolkit. Nat Methods 2008, 5:475-489.
107. von Delius M, Leigh D. Walking molecules. Chem Soc Rev 2011, 40:3656-3676.
108. Faisal A, Alison P, Hanadi S. Assembling materials with DNA as the guide. Science 2008, 321:1795-1799
109. Hu Y, Fine DH, Tasciotti E, Bouamrani A, Ferrari M. Nanodevices in diagnostics. WIREs Nanomed Nanobiotechnol 2011, 3:11-32.
110. Nadrian S. DNA in a material world. Nature 2003, 421:427-431.
111. Nadrian S. Nanomaterials based on DNA. Annu Rev Biochem 2010, 79:65-87.
112. Rothemund PW. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440:297-302.
113. Yang D, Campolongo MJ, Nhi Tran TN, Ruiz RC, Kahn JS, Luo D. Novel DNA materials and their applications. WIREs Nanomed Nanobiotechnol 2010, 2:648-669.