Nucleic acid nanostructures: Bottom-up control of geometry on the nanoscale

Reports on Progress in Physics

Volumn 68, Issue 1, 2005, Pages 237-270

  Seeman, Nadrian C ^a   Lukeman, Philip S ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 12544252352     PISSN: 00344885     EISSN: None     Source Type: Journal    
DOI: 10.1088/0034-4885/68/1/R05     Document Type: Article

References (95)

1. Seeman N C 1982 Nucleic acid junctions and lattices J. Theor. Biol. 99 237-47
2. Cohen S N, Chang A C Y, Boyer H W and Helling R B 1973 Construction of biologically functional bacterial plasmids in vitro Proc. Natl Acad. Sci. USA 70 3240-44
3. Qiu H, Dewan J C and Seeman N C 1997 A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT J. Mol. Biol. 267 881-98
4. Seeman N C 2003 At the crossroads of chemistry, biology and materials: structural DNA nanotechnology Chem. Biol. 10 1151-9
5. Holliday R 1964 A mechanism for gene conversion in fungi Genet. Res. 5 282-304
6. Ma R-I, Kallenbach N R, Sheardy R D, Petrillo M L and Seeman N C 1986 Three arm nucleic acid junctions are flexible Nucleic Acids Res. 14 9745-53
7. Wang Y, Mueller J E, Kemper B and Seeman N C 1991 The assembly and characterization of 5-arm and 6-arm DNA junctions Biochem. 30 5667-74
8. Williams R 1972 The Geometrical Foundation of Natural Structure (New York: Dover) pp 164-99
9. Seeman N C 1985 Macromolecular design, nucleic acid junctions and crystal formation J. Biomol. Struct. Dyn. 3 11-34
10. Manoharan H D, Lutz C P and Eigler D M 2000 Quantum mirages formed by coheren projection of electronic structure Nature 403 512-15
11. Cuberes M T, Schlittler R R and Ginzewski J K 1996 Room-temperature repositioning of individual C-60 molecules at Cu steps: operation of a molecular counting device Appl. Phys. Lett. 69 3016-18
12. Adleman L M 1994 Molecular computation of solutions to combinatorial problems Science 266 1021-4
13. Carter C W Jr 1997 Response surface methods for optimizing and improving reproducibility of crystal growth Methods Enzymol. A 276 74-99
14. Robinson B H and Seeman N C 1987 The design of a biochip: a self-assembling molecular-scale memory device Prot. Eng. 1 295-300
15. Zhang X, Yan H, Shen Z and Seeman N C 2002 Paranemic cohesion of topologically-closed DNA molecules J. Am. Chem. Soc. 124 12940-1
16. Jaeger L, Westhof E and Leontis N B 2001 Tecto-RNA: modular assembly units for the construction of RNA nano-objects Nucleic Acids Res. 29 455-63
17. Elghanian R, Storhoff J J, Mucic R C, Letsinger R L and Mirkin C A 1997 Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles Science 277 1078-81
18. Alivisatos A P, Johnsson K P, Peng X G, Wilson T E, Loweth C J, Bruchez M P and Schultz P G 1996 Organization of 'nanocrystal molecules' using DNA Nature 382 609-11
19. Mucic R C, Storhoff J J, Mirkin C A and Letsinger R L 1998 DNA-directed synthesis of binary nanoparticle network materials J. Am. Chem. Soc. 120 12674-5
20. Shi J F and Bergsrom D E 1997 Assembly of novel DNA cycles with rigid tetrahedral linkers Angew. Chem. Int. Edn Engl. 36 111-13
21. Eckardt L H, Naumann K, Pankau W M, Rein M, Schweitzer M, Windhab N and von Kiedrowski G 2003 DNA nanotechnology: chemical copying of connectivity Nature 420 286-6
22. Marsh T C, Vesenka J and Henderson E 1995 A new DNA nanostructure, the G-wire, imaged by scanning probe microscopy Nucleic Acids Res. 23 696-700
23. Sondermann A, Holste C, Möller R and Fritzsche W 2002 Assembly of G-quartet based DNA superstructures (G-wires) DNA-Based Molecular Construction: International Workshop ed W Fritszche (Melville, NY American Institute of Physics) pp 93-8
24. Niemeyer C M 2002 The development of semisynthetic DNA-protein conjugates Trends Biotechnol. 20 395-401
25. Caruthers M H 1985 Gene synthesis machines: DNA chemistry and its uses Science 230 281-5
26. Chen J and Seeman N C 1991 The synthesis from DNA of a molecule with the connectivity of a cube Nature 350 631-3
27. Zhang Y and Seeman N C 1992 A solid-support methodology for the construction of geometrical objects from DNA J Am. Chem. Soc. 114 2656-63
28. Qi J, Li X, Yang X and Seeman N C 1996 The ligation of triangles built from bulged three-arm DNA branched junctions J. Am. Chem. Soc. 118 6121-30
29. Hagerman P J 1988 Flexibility of DNA Ann. Rev. Biophys. Biophys. Chem. 17 265-86
30. Sa-Ardyen P, Vologodskii A V and Seeman N C 2003 The flexibility of DNA double crossover molecules Biophys. J. 84 3829-37
31. Seeman N C, Rosenberg J M and Rich A 1976 Sequence specific recognition of double helical nucleic acids by proteins Proc. Natl Acad. Sci. USA 73 804-8
32. Freier S M and Altmann K-H 1977 The ups and downs of nucleic acid duplex stability: structure-stability relationships on chemically-modified DNA: RNA duplexes Nucleic Acids Res. 25 4429-43
33. Nielsen P E, Egholm M, Berg R H and Buchardt O 1991 Sequence selective recognition of DNA by strand displacement with a thymine-substituted polyamide Science 254 1497-500
34. Churchill M E A, Tullius T D, Kallenbach N R and Seeman N C 1988 A Holliday recombination intermediate is twofold symmetric Proc. Natl Acad. Sci. USA 85 4653-6
35. Lilley D M J and Clegg R M 1993 The structure of the four-way junction in DNA Ann. Rev. Biophys. Biomol. Struct. 22 299-328
36. Petrillo M L, Newton C J, Cunningham R P, Ma R-I, Kallenbach N R and Seeman N C 1988 The ligation and flexibility of 4-arm DNA junctions Biopolymers 27 1337-52
37. Seeman N C 2001 DNA nicks and nodes and nanotechnology Nano Lett. 1 22-6
38. Fu T-J and Seeman N C 1993 DNA double crossover structures Biochemistry 32 3211-20
39. Li X, Yang X, Qi J and Seeman N C 1996 Antiparallel DNA double crossover molecules as components for nanoconstruction J. Am. Chem. Soc. 118 6131-40
40. LaBean T, Yan H, Kopatsch J, Liu F, Winfree E, Reif J H and Seeman N C 2000 The construction, analysis, ligation and self-assembly of DNA triple crossover complexes J. Am. Chem. Soc. 122 1848-60
41. Shen Z, Yan H, Wang T and Seeman N C 2004 Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology J. Am. Chem. Soc. 126 1666-74
42. Winfree E, Liu F, Wenzler L A and Seeman N C 1998 Design and self-assembly of two-dimensional DNA crystals Nature 394 539-44
43. Mao C, Sun W, Shen Z and Seeman N C 1999 A DNA nanomechanical device based on the B-Z transition Nature 397 144-6
44. Yan H, Zhang X, Shen Z and Seeman N C 2002 A robust DNA mechanical device controlled by hybridization topology Nature 415 62-5
45. Seeman N C 1990 De novo design of sequences for nucleic acid structure engineering J. Biomol. Struct. Dyn. 8 573-81
46. Seeman N C and Kallenbach N R 1983 Design of immobile nucleic acid junctions Biophys. J. 44 201-9
47. Wu H M and Crothers D M 1984 The locus of sequence-directed and protein-induced DNA bending Nature 308 509-13
48. Gellert M, Lipsett M N and Davies D R 1962 Helix formation by guanylic acid Proc. Natl Acad. Sci. USA 48 2013-18
49. Eichman B F, Vargason J M, Mooers B H M and Ho P S 2000 The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions Proc. Natl Acad. Sci. USA 97 3971-6
50. Kallenbach N R, Ma R-I and Seeman N C 1983 An immobile nucleic acid junction constructed from oligonucleotides Nature 306 829-31
51. Rodbard D and Chrambach A 1971 Estimation of molecular radius, free mobility, and valence using polyacrylamide gel electrophoresis Anal. Biochem. 40 95-134
52. Chen J and Seeman N C 1991 The electrophoretic properties of a DNA cube and its sub-structure catenanes Electrophoresis 12 607-11
53. Yan H and Seeman N C 2001 Edge-sharing motifs in DNA nanotechnology J. Supramol. Chem. 1 229-37
54. Seeman N C 1985 The interactive manipulation and design of macromolecular architecture utilizing nucleic acid junctions J. Mol. Graphics 3 34-9
55. Liu D, Wang M, Deng Z, Walulu R and Mao C 2004 Tensegrity: construction of rigid DNA triangles with flexible four-arm DNA junctions J. Am. Chem. Soc. 126 2324-5
56. Mao C, Sun W and Seeman N C 1999 Designed two-dimensional DNA Holliday junction arrays visualized by atomic force microscopy J. Am. Chem. Soc. 121 5437-43
57. Zhang Y and Seeman N C 1994 The construction of a DNA truncated octahedron J. Am. Chem. Soc. 116 1661-9
58. Seeman N C, Chen J, Du S M, Mueller J E, Zhang Y, Fu T-J, Wang H, Wang Y and Zhang S 1993 Synthetic DNA knots and catenanes New J. Chem. 17 739-55
59. Sa-Ardyen P, Jonoska N and Seeman N C 2004 The construction of graphs whose edges are DNA helix axes J. Am. Chem. Soc. 126 6648-57
60. White J H, Millett K C and Cozzarelli N R 1987 Description of the topological entanglement of DNA catenanes and knots J. Mol. Biol. 197 585-603
61. Seeman N C 1992 The design of single-stranded nucleic acid knots Mol. Eng. 2 297-307
62. Rich A, Nordheim A and Wang A H-J 1984 The chemistry and biology of left-handed Z-DNA Ann. Rev. Biochem. 53 791-846
63. Du S M, Stollar B D and Seeman N C 1995 A synthetic DNA molecule in three knotted topologies J. Am. Chem. Soc. 117 1194-200
64. Du S M, Wang H, Tse-Dinh Y C and Seeman N C 1995 Topological transformations of synthetic DNA knots Biochemistry 34 673-82
65. Wang H, Di Gate R J and Seeman N C 1996 An RNA topoisomerase Proc. Natl Acad. Sci. USA 93 9477-82
66. Mao C, Sun W and Seeman N C 1997 Assembly of Borromean rings from DNA Nature 386 138-297
67. Sha R, Liu F, Millar D P and Seeman N C 2000 Atomic force microscopy of parallel DNA branched junction arrays Chem. Biol. 7 743-51
68. Yan H, Park S H, Finkelstein G, Reif J H and LaBean T H 2003 DNA-templated self-assembly of protein arrays and highly conductive nanowires Science 301 1882-4
69. Ding B, Sha R and Seeman N C 2004 J. Am. Chem. Soc. 126 10230-1
70. Brun Y, Gopalkrishnan M, Reishus D, Shaw B, Chelyapov N and Adleman L 2004 Building blocks for DNA self-assembly Preliminary Proc. Conf. on Foundations of Nanoscience (Snowbird, UT, 21-23 April 2004) ed J H Reif, pp 2-15
71. Yang X, Vologodskii A, Liu B, Kemper B and Seeman N C 19981 Torsional control of double stranded DNA branch migration Biopolymers 45 69-83
72. Li J J and Tan W 2002 A single DNA molecule nanomotor Nano Lett. 2 315-18
73. Alberti P and Mergny J-L 2002 DNA duplex-quadruplex exchange as the basis for a nanomolecular machine Proc. Natl Acad. Sci. USA 100 1569-73
74. Fahlman R P, Hsing M, Sporer-Tuhten C S and Sen D 2003 Duplex pinching: a structural switch suitable for contractile DNA nanoconstructions Nano Lett. 3 1073-8
75. Liu D and Balasubramanian S 2003 A proton-fuelled DNA nanomachine Angew. Chem. Int. Edn Engl. 42 5734-6
76. Yurke B, Turberfield A J, Mills A P Jr, Simmel F C and Newmann J L 2000 A DNA-fuelled molecular machine made of DNA Nature 406 605-8
77. Sherman W B and Seeman N C 2004 A precisely controlled DNA bipedal walking device Nano Lett. 4 1203-7
78. Dittmer W U and Simmel F C 2004 Transcriptional control of DNA-based nanomachines Nano Lett. 4 689-91
79. Feng L, Park S H, Reif J H and Yan H 2003 A two-state DNA lattice switched by DNA nanoactuator Angew. Chem. Int. Edn Engl. 42 4342-6
80. Shen W, Bruist M F, Goodman S D and Seeman N C 2004 A protein-driven DNA device that measures the excess binding energy of proteins that distort DNA Angew. Chem. Int. Edn Engl. 43 4750-2
81. Chen Y, Wang M and Mao C 2004 An automous DNA nanomotor powered by a DNA enzyme Angew. Chem. 116 3638-41
82. Seeman N C 1991 The construction of 3-D stick figures from branched DNA DNA Cell Biol. 10 475-86
83. Yurke B and Zhang D 2004 A clocked DNA-based replicator DNA-10, Preliminary Proc. 10th International Meeting on DNA-Based Computation (Italy, Milan, 7-10 June 2004) ed C Ferretti et al, pp 224-35
84. Eckardt L H, Naumann K, Pankau W M, Rein M, Scheitzer M, Windhab N and von Kiedrowski G 2002 Chemical copying of connectivity Nature 420 286
85. Shih W M, Quispe J D and Joyce G F 2004 DNA that folds into a nanoscale octahedron Nature 427 618-21
86. Jonoska N, Karl S A and Saito M 1999 Three-dimensional DNA structure in computing Biosystems 52 143-53
87. Winfree E 1996 DNA Based Computers Proc. DIMACS Workshop on the Computational Power of DNA Annealing and Ligation (Princeton University, 4 April 1995) ed R J Lipton and E B Baum (Providence, RI: American Mathematical Society), pp 199-219
88. Grunbaum B and Shephard G C 1987 Tilings and Pattern (New York: Freeman) pp 583-608
89. Rothemund P W K, Papadakis N and Winfree E Algorithmic self-assembly of DNA Sierpinski triangles DNA Computing IX ed J H Reif and J Chen (Berlin: Springer) at press
90. Mao C, LaBean T, Reif J H and Seeman N C 2000 Logical computation using algorithmic self-assembly of DNA triple crossover molecules Nature 407 493-6
91. Xiao S, Liu F, Rosen A, Hainfeld J F, Seeman N C, Musier-Forsyth K M and Kiehl R A 2002 Self-assembly of nanoparticle arrays by DNA scaffolding J. Nanopart. Res. 4 313-17
92. Zhu L, Lukeman P S, Canary J W and Seeman N C 2003 Nylon/DNA: single-stranded DNA with covalently stitched nylon lining J. Am. Chem. Soc. 125 10178-9
93. Doherty E A, Batey R T, Masquida B and Doudna J A 2001 A universal mode of helix packing in RNA Nature Struct. Biol. 8 339-43
94. Paukstelis P, Nowakowski J, Birktoft J J and Seeman N C 2004 An oligonucleotide that self-assembles into a 3D crystalline lattice Chem. Biol. 11 1119-26
95. Wang X and Seeman N C 2005 in preparation