Three-dimensional DNA crystals with pH-responsive noncanonical junctions

Journal of the American Chemical Society

Volumn 134, Issue 30, 2012, Pages 12557-12564

  Muser, Stephanie E ^a   Paukstelis, Paul J ^a  

^a University of Maryland   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3D LATTICES; ADAPTIVE FEATURES; BASE PAIRS; BASE-PAIRING MOTIFS; BIOMATERIAL SCAFFOLDS; CONFORMATIONAL CHANGE; CRYSTAL DESIGN; CRYSTAL PACKINGS; DNA CRYSTALS; DNA MOTIF; DNA SEGMENTS; ORDERED ARRAY; PH-RESPONSIVE; SECONDARY STRUCTURES; TEMPLATE STRUCTURES;

BIOLOGICAL MATERIALS; DNA; SCAFFOLDS; THREE DIMENSIONAL;

CRYSTAL STRUCTURE;

DNA; GUANINE QUADRUPLEX;

ARTICLE; BASE PAIRING; CHEMICAL INTERACTION; CONFORMATION; CRYSTAL; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA BINDING MOTIF; DNA HELIX; DRUG DESIGN; PH; REACTOR DESIGN; THREE DIMENSIONAL IMAGING;

BASE PAIRING; BASE SEQUENCE; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DNA; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION;

EID: 84864459607     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja3025033     Document Type: Article

References (62)

1. Winfree, E.; Liu, F.; Wenzler, L. A.; Seeman, N. C. Nature 1998, 394, 539-44
2. Shih, W. M.; Quispe, J. D.; Joyce, G. F. Nature 2004, 427, 618-21
3. Ding, B.; Sha, R.; Seeman, N. C. J. Am. Chem. Soc. 2004, 126, 10230-1
4. Mitchell, J. C.; Harris, J. R.; Malo, J.; Bath, J.; Turberfield, A. J. J. Am. Chem. Soc. 2004, 126, 16342-3
5. He, Y.; Chen, Y.; Liu, H.; Ribbe, A. E.; Mao, C. J. Am. Chem. Soc. 2005, 127, 12202-3
6. Liu, Y.; Ke, Y.; Yan, H. J. Am. Chem. Soc. 2005, 127, 17140-1
7. Liu, H.; Chen, Y.; He, Y.; Ribbe, A. E.; Mao, C. Angew. Chem., Int. Ed. 2006, 45, 1942-5
8. Lin, C.; Liu, Y.; Rinker, S.; Yan, H. ChemPhysChem 2006, 7, 1641-7
9. Zheng, J.; Birktoft, J. J.; Chen, Y.; Wang, T.; Sha, R.; Constantinou, P. E.; Ginell, S. L.; Mao, C.; Seeman, N. C. Nature 2009, 461, 74-77
10. Rothemund, P. W. K.; Papadakis, N.; Winfree, E. PLoS Biol 2004, 2, e424
11. Mao, C.; LaBean, T. H.; Relf, J. H.; Seeman, N. C. Nature 2000, 407, 493-6
12. Yan, H.; Feng, L.; LaBean, T. H.; Reif, J. H. J. Am. Chem. Soc. 2003, 125, 14246-7
13. Barish, R. D.; Rothemund, P. W. K.; Winfree, E. Nano Lett 2005, 5, 2586-92
14. Yan, H.; Park, S. H.; Finkelstein, G.; Reif, J. H.; LaBean, T. H. Science 2003, 301, 1882-4
15. Mitra, D.; Di Cesare, N.; Sleiman, H. F. Angew. Chem., Int. Ed. 2004, 43, 5804-8
16. Sharma, J.; Chhabra, R.; Liu, Y.; Ke, Y.; Yan, H. Angew. Chem., Int. Ed. 2006, 45, 730-5
17. Chhabra, R.; Sharma, J.; Liu, Y.; Yan, H. Adv. Exp. Med. Biol. 2007, 620, 107-16
18. Stearns, L. A.; Chhabra, R.; Sharma, J.; Liu, Y.; Petuskey, W. T.; Yan, H.; Chaput, J. C. Angew. Chem., Int. Ed. 2009, 48, 8494-8496
19. Seeman, N. C. J. Theor. Biol. 1982, 99, 237-47
20. Ariga, K.; Hill, J. P.; Ji, Q. Macromol. Biosci. 2008, 8, 981-990
21. You, J.-O.; Almeda, D.; Ye, G. J.; Auguste, D. T. J. Biol. Eng. 2010, 4, 15
22. Stuart, M. A. C.; Huck, W. T. S.; Genzer, J.; Müller, M.; Ober, C.; Stamm, M.; Sukhorukov, G. B.; Szleifer, I.; Tsukruk, V. V.; Urban, M.; Winnik, F.; Zauscher, S.; Luzinov, I.; Minko, S. Nat. Mater. 2010, 9, 101-113
23. Costa, D.; Miguel, M. G.; Lindman, B. Adv. Colloid Interface Sci. 2010, 158, 21-31
24. Sun, T.; Qing, G. Adv. Mater. Weinheim 2011, 23, H57-77
25. Seeman, N. C. Nature 2003, 421, 427-31
26. Seeman, N. C. Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 225-48
27. Rothemund, P. W. K. Nature 2006, 440, 297-302
28. Andersen, E. S.; Dong, M.; Nielsen, M. M.; Jahn, K.; Subramani, R.; Mamdouh, W.; Golas, M. M.; Sander, B.; Stark, H.; Oliveira, C. L. P.; Pedersen, J. S.; Birkedal, V.; Besenbacher, F.; Gothelf, K. V.; Kjems, J. Nature 2009, 459, 73-76
29. Douglas, S. M.; Dietz, H.; Liedl, T.; Hogberg, B.; Graf, F.; Shih, W. M. Nature 2009, 459, 414-418
30. Dietz, H.; Douglas, S. M.; Shih, W. M. Science 2009, 325, 725-730
31. Endo, M.; Hidaka, K.; Kato, T.; Namba, K.; Sugiyama, H. J. Am. Chem. Soc. 2009, 131, 15570-15571
32. Ke, Y.; Douglas, S. M.; Liu, M.; Sharma, J.; Cheng, A.; Leung, A.; Liu, Y.; Shih, W. M.; Yan, H. J. Am. Chem. Soc. 2009, 131, 15903-15908
33. Liedl, T.; Hogberg, B.; Tytell, J.; Ingber, D. E.; Shih, W. M. Nat. Nano. 2010, 5, 520-524
34. Han, D.; Pal, S.; Nangreave, J.; Deng, Z.; Liu, Y.; Yan, H. Science 2011, 332, 342-346
35. Seeman, N. C. Nat. Comput. 2002, 1, 53-84
36. Westhof, E.; Fritsch, V. Structure 2000, 8, R55-65
37. Sundquist, W. I.; Klug, A. Nature 1989, 342, 825-9
38. Siddiqui-Jain, A.; Grand, C. L.; Bearss, D. J.; Hurley, L. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11593-8
39. Alberti, P.; Mergny, J.-L. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1569-73
40. Chen, Y.; Lee, S.-H.; Mao, C. Angew. Chem., Int. Ed. 2004, 116, 5449-5452
41. Surana, S.; Bhat, J. M.; Koushika, S. P.; Krishnan, Y. Nat. Commun. 2011, 2, 340
42. Saha, S.; Chakraborty, K.; Krishnan, Y. Chem. Commun. (Camb.) 2012, 48, 2513-2515
43. Paukstelis, P. J.; Nowakowski, J.; Birktoft, J. J.; Seeman, N. C. Chem. Biol. 2004, 11, 1119-26
44. Paukstelis, P. J. J. Am. Chem. Soc. 2006, 128, 6794-5
45. Kettani, A.; Bouaziz, S.; Skripkin, E.; Majumdar, A.; Wang, W.; Jones, R. A.; Patel, D. J. Structure 1999, 7, 803-15
46. Sunami, T.; Kondo, J.; Kobuna, T.; Hirao, I.; Watanabe, K.; Miura, K.; Takénaka, A. Nucleic Acids Res. 2002, 30, 5253-60
47. Robinson, H.; van der Marel, G. A.; van Boom, J. H.; Wang, A. H. Biochemistry 1992, 31, 10510-7
48. Robinson, H.; Wang, A. H. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5224-8
49. Kobuna, T.; Sunami, T.; Kondo, J.; Takénaka, A. Nucleic Acids Res. Suppl. 2002, 179-80
50. Lu, X.-J.; Olson, W. K. Nat. Protoc. 2008, 3, 1213-1227
51. Franklin, R. E.; Gosling, R. G. Nature 1953, 171, 740-741
52. Braunlin, W. H.; Xu, Q. Biopolymers 1992, 32, 1703-1711
53. Xu, Q.; Shoemaker, R. K.; Braunlin, W. H. Biophys. J. 1993, 65, 1039-1049
54. Robinson, H.; Wang, A. H. Nucleic Acids Res. 1996, 24, 676-682
55. Bauer, C.; Wang, A. H. J. Inorg. Biochem. 1997, 68, 129-135
56. Yingling, Y. G.; Shapiro, B. A. Nano Lett. 2007, 7, 2328-2334
57. Bindewald, E.; Grunewald, C.; Boyle, B.; O'Connor, M.; Shapiro, B. A. J. Mol. Graph. Model. 2008, 27, 299-308
58. Bindewald, E.; Hayes, R.; Yingling, Y. G.; Kasprzak, W.; Shapiro, B. A. Nucleic Acids Res. 2008, 36, D392-397
59. Otwinowski, Z.; Minor, W. Methods Enzymol. 1997, 276, 307-326
60. Adams, P. D.; Afonine, P. V.; Bunkóczi, G.; Chen, V. B.; Echols, N.; Headd, J. J.; Hung, L.-W.; Jain, S.; Kapral, G. J.; Grosse Kunstleve, R. W.; McCoy, A. J.; Moriarty, N. W.; Oeffner, R. D.; Read, R. J.; Richardson, D. C.; Richardson, J. S.; Terwilliger, T. C.; Zwart, P. H. Methods 2011, 55, 94-106
61. Emsley, P.; Lohkamp, B.; Scott, W. G.; Cowtan, K. Acta Crystallogr., Sect. D 2010, 66, 486-501
62. Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallogr., Sect. D 1997, 53, 240-255