PH-toggled DNA architectures: Reversible assembly of three-way junctions into extended 1d architecturesthrough A-motif formation

Small

Volumn 6, Issue 12, 2010, Pages 1288-1292

  Saha, Sonali ^a   Bhatia, Dhiraj ^a   Krishnan, Yamuna ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ENVIRONMENTAL PH; GOLD NANOPARTICLES; NANOARCHITECTURES;

TRANSMISSION ELECTRON MICROSCOPY;

SCANNING ELECTRON MICROSCOPY;

DNA; GOLD; METAL NANOPARTICLE;

ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMISTRY; CIRCULAR DICHROISM; NANOTECHNOLOGY; PH; TRANSMISSION ELECTRON MICROSCOPY; ULTRASTRUCTURE;

CIRCULAR DICHROISM; DNA; GOLD; HYDROGEN-ION CONCENTRATION; METAL NANOPARTICLES; MICROSCOPY, ATOMIC FORCE; MICROSCOPY, ELECTRON, TRANSMISSION; NANOTECHNOLOGY;

EID: 77953443658     PISSN: 16136810     EISSN: 16136829     Source Type: Journal    
DOI: 10.1002/smll.201000330     Document Type: Article

References (53)

1. a) N. C. Seeman, Biochemistry 2003, 42, 7259-7269
2. b) F. A. Aldaye, A. L. Palmer, H. F. Sleiman, Science 2008, 321, 1795-1799
3. c) S. Pitchiaya, Y. Krishnan, Chem. Soc. Rev. 2006, 35, 1111-1121;
4. d) I. Willner, B. Shlyahovsky, M. Jayats, B. Willner, Chem. Soc. Rev. 2008, 37, 1153-1165.
5. Linear DNA scaffold constructions include: a) X. Yang, L. A. Wenzler, J. Qi, X. Li, N. C. Seeman, J. Am. Chem. Soc. 1998, 120, 9779-9786
6. b) F. A. Aldaye, P. K. Lo, P. Karam, C. K. McLaughlin, G. Cosa, H. F. Sleiman, Nat. Nanotechnol. 2009, 4, 349-352;
7. c) S. H. Park, R. Barish, H. Li, J. H. Reif, G. Finkelstein, H. Yan, T. H. LaBean, Nano Lett. 2005, 5, 693-696.
8. a) E. Winfree, F. Liu, L. A. Wenzler, N. C. Seeman, Nature 1998, 394, 539-544
9. b) R. P. Goodman, I. A. T. Schaap, C. F. Tardin, C. M. Erben, R. M. Berry, C. F. Schmidt, A. J. Turberfield, Science 2005, 310, 1661-1665
10. c) W. M. Shih, J. D. Quispe, G. F. Joyce, Nature 2004, 427, 618-621
11. d) F. F. Andersen, B. Knudsen, C. L. P. Oliveira, R. F. Frøhlich, D. Kru″ger, J. Bungert, M. Agbandje-McKenna, R. Mckenna, S. Juul, C. Veigaard, J. Koch, J. L. Rubinstein, B. Guldbrandtsen, M. S. Hede, G. Karlsson, A. H. Andersen, J. S. Pedersen, B. R. Knudsen, Nucleic Acids Res. 2008, 36, 1113-119;
12. e) B. Yurke, A. J. Turberfield, A. P. Mills, Jr, F. C. Simmel, J. L. Neumann, Nature 2000, 406, 605-608;
13. f) H. B. Ghodke, R. Krishnan, K. Vignesh, G. V. P. Kumar, C. Narayana, Y. Krishnan, Angew. Chem. 2007, 119, 2700-2703;
14. Angew. Chem. Int. Ed. 2007, 46, 2646-2649;
15. g) P. Alberti, J.-L. Mergny, Proc. Natl Acad. Sci. USA 2003, 100, 1569-1573;
16. h) C. Zhang, Y. He, M. Su, S. H. Ko, T. Ye, Y. Leng, X. Sun, A. E. Ribbe, W. Jiang, C. Mao, Faraday Discuss. 2009, 143, 221-233.
17. Y. Ke, S. Lindsay, Y. Chang, Y. Liu, H. Yan, Science 2008, 319, 180-183.
18. Z. Deng, C. Mao, Angew. Chem. 2004, 116, 4160-4162;
19. Angew. Chem. Int. Ed. 2004, 43, 4068-4070.
20. a) D. Bhatia, S. Mehtab, R. Krishnan, S. S. Indi, A. Basu, Y. Krishnan, Angew. Chem. 2009, 121, 4198-4201
21. Angew. Chem. Int. Ed. 2009, 48, 4134-4137;
22. b) C. M. Erben, R. P. Goodman, A. J. Turberfield, Angew. Chem. 2006, 118, 7574-7577;
23. Angew. Chem. Int. Ed. 2006, 45, 7414-7417.
24. X. Liang, T. Mochizuki, H. Asanuma, Small 2009, 5, 1761-1768.
25. a) R. P. Goodman, M. Heilemann, S. Doose, C. M. Erben, A. N. Kapanidis, A. J. Turberfield, Nat. Nanotechnol. 2008, 3, 93-96;
26. a) F. A. Aldaye, H. F. Sleiman, J. Am. Chem. Soc. 2007, 129, 13376-13377;
27. b) In addition, metal-ion induced rigidification of a pre-formed DNA architecture has been shown. See D. Miyoshi, H. Karimata, Z. M. Wang, K. Koumoto, N. Sugimoto, J. Am. Chem. Soc. 2007, 129, 5919-5925
28. H. Yang, C. K. McLaughlin, F. A. Aldaye, G. D. Hamblin, A. Z. Rys, I. Rouiller, H. F. Sleiman, Nat. Chem. 2009, 1, 390-396.
29. a) S. Modi, A. H. Wani, Y. Krishnan, Nucleic Acids Res. 2006, 34, 4354-4363;
30. b) S. Chakraborty, S. Modi, Y. Krishnan, Chem. Commun. 2008, 70-72;
31. c) Y. Krishnan-Ghosh, E. Stephens, S. Balasubramanian, Chem. Commun. 2005, 5278-5280;
32. d) Y. Krishnan-Ghosh, D. Liu, S. Balasubramanian, J. Am. Chem. Soc. 2004, 126, 11009-11016.
33. S. Modi, M. G. Swetha, D. Goswami, G. D. Gupta, S. Mayor, Y. Krishnan, Nat. Nanotechnol. 2009, 4, 325-330.
34. S. Chakraborty, S. Sharma, P. K. Maiti, Y. Krishnan, Nucleic Acids Res. 2009, 37, 2810-2817.
35. A. Akcasu, C. C. Han, Macromolecules 1979, 12, 276-280.
36. 0 is the intensity of scattered light of a monomer (A. Lomakin, G. B. Benedek, D. B. Teplow, Methods Enzymol. 1999, 309, 429-459). Since I and I0 are directly measurable by DLS, it was possible to obtain the degree of oligomerization of 123A at any given concentration.
37. 123A and 123T is a bicomponent system. A very small shift from an exact 1:1 ratio can lead to inefficient polymerization (self-assembly). 123A always produces larger HOS as it is a single-component system.
38. J. Kypr, I. Kejnovská, D. Renčiuk, M. Vorlíč ková, Nucleic Acids Res. 2009, 37, 61713-61725.
39. As CD and DLS are monitoring two different properties in a related phenomenon, the rate of their increase need not be the same (S. Jain, J. B. Udgaonkar, J. Mol. Biol. 2008, 382, 1228-1241).
40. C. A. Mirkin, Inorg. Chem. 2000, 39, 2258-2272.
41. a) Z. Deng, Y. Tian, S.-H. Lee, A. E. Ribbe, C. Mao, Angew. Chem. 2005, 117, 3648-3651;
42. Angew. Chem. Int. Ed. 2005, 44, 3582- 3585;
43. b) I. Cheng, B. Wei, X. Zhang, Y. Wang, Y. Mi, Res. Lett. Nanotechnol. DOI:10.1155/2008/827174;
44. c) H. Li, S. H. Park, J. H. Reif, T. H. LaBean, H. Yan, J. Am. Chem. Soc. 2004, 126, 418-419;
45. d) G. Braun, K. Inagaki, R. A. Estabrook, D. K. Wood, E. Levy, A. N. Cleland, G. F. Strouse, N. O. Reich, Langmuir 2005, 21, 10699- 10701;
46. e) M. G. Warner, J. E. Huchison, Nat. Mater. 2003, 2, 272- 277;
47. f) J. Sharma, R. Chhabra, Y. Liu, Y. Ke, H. Yan, Angew. Chem. 2006, 118, 744-749;
48. Angew. Chem. Int. Ed. 2006, 45, 730-735.
49. As each cycle resulted in a 10% dilution of monomer, this was corrected by supplementing 10% 123A in the solution at the end of each working cycle.
50. a) J. S. Shin, N. A. Pierce, J. Am. Chem. Soc. 2004, 126, 10834- 10845;
51. b) P. Yin, H. M. T. Choi, C. R. Calvert, N. A. Pierce, Nature 2008, 451, 318-322.
52. D. Lubrich, J. Lin, J. Yan, Angew. Chem. 2008, 120, 7134-7136;
53. Angew. Chem. Int. Ed. 2008, 47, 7026-7028.