Single molecule visualization and characterization of Sox2-Pax6 complex formation on a regulatory DNA element using a DNA origami frame

Nano Letters

Volumn 14, Issue 5, 2014, Pages 2286-2292

  Yamamoto, Seigi ^a   De, Debojyoti ^b   Hidaka, Kumi ^c   Kim, Kyeong Kyu ^b   Endo, Masayuki ^c,d   Sugiyama, Hiroshi ^a,c,d  

^a KYOTO UNIVERSITY   (Japan)

^b Sungkyunkwan University School of Medicine   (South Korea)

^c KYOTO UNIVERSITY   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

AFM; DNA origami; Pax6; protein DNA; single molecule; Sox2

Indexed keywords

ATOMIC FORCE MICROSCOPY; MOLECULES;

AFM; DNA ORIGAMIS; PAX6; PROTEIN-DNA; SINGLE MOLECULE; SOX2;

DNA;

DNA; DNA BINDING PROTEIN; EYE PROTEIN; HOMEODOMAIN PROTEIN; MULTIPROTEIN COMPLEX; PAIRED BOX TRANSCRIPTION FACTOR; PROTEIN BINDING; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR PAX6; TRANSCRIPTION FACTOR SOX;

ATOMIC FORCE MICROSCOPY; CHEMISTRY; NANOTECHNOLOGY; NUCLEOTIDE SEQUENCE; PROCEDURES; ULTRASTRUCTURE;

BASE SEQUENCE; DNA; DNA-BINDING PROTEINS; EYE PROTEINS; HOMEODOMAIN PROTEINS; MICROSCOPY, ATOMIC FORCE; MULTIPROTEIN COMPLEXES; NANOTECHNOLOGY; PAIRED BOX TRANSCRIPTION FACTORS; PROTEIN BINDING; REPRESSOR PROTEINS; SOXB1 TRANSCRIPTION FACTORS;

EID: 84900505871     PISSN: 15306984     EISSN: 15306992     Source Type: Journal    
DOI: 10.1021/nl4044949     Document Type: Article

References (50)

1. Levine, M.; Tjian, R. Nature 2003, 424, 147-151
2. Vaquerizas, J. M.; Kummerfeld, S. K.; Teichmann, S. A.; Luscombe, N. M. Nat. Rev. Genet. 2009, 10, 252-263
3. Petti, A. A.; McIsaac, R. S.; Ho-Shing, O.; Bussemaker, H. J.; Botstein, D. Mol. Biol. Cell 2012, 15, 3008-3024
4. Bonn, S.; Furlong, E. E. Curr. Opin. Genet. Dev. 2008, 6, 513-520
5. Cunha, P. M. F.; Sandmann, T.; Gustafson, E. H.; Ciglar, L.; Eichenlaub, M. P.; Furlong, E. E. M. PLoS Genet. 2010, 6, e1001014
6. Boyer, L. A. Cell 2005, 122, 947-956
7. Loh, Y. H. Nat. Genet. 2006, 38, 431-440
8. Lodato, M. A.; Ng, C. W.; Wamstad, J. A.; Cheng, A. W.; Thai, K. K.; Fraenkel, E.; Jaenisch, R.; Boyer, L. A. PLoS Genet. 2013, 9, e1003288
9. Kamachi, Y.; Uchikawa, M.; Tanouchi, A.; Sekido, R.; Kondoh, H. Genes Dev. 2001, 15, 1272-1286
10. Danno, H.; Michiue, T.; Hitachi, K.; Yukita, A.; Ishiura, S.; Asashima, M. Proc. Natl. Acad. Sci. 2008, 105, 5408-5013
11. Shimozaki, K.; Zhang, C. L.; Suh, H.; Denli, A. M.; Evans, R. M.; Gage, F. H. J. Biol. Chem. 2012, 287, 5969-5978
12. Bustamante, C. Q. Rev. Biophys. 2005, 38, 291-301
13. Rajendran, A.; Endo, M.; Sugiyama, H. Angew. Chem., Int. Ed. 2012, 51, 874-890
14. Kuhn, J. R.; Pollard, T. D. J. Biol. Chem. 2007, 282, 28014-28024
15. Park, J.; Jeon, Y.; In, D.; Fishel, R.; Ban, C.; Lee, J.-B. PLoS One 2010, 5, e15496
16. Camacho, A. J. Biotechnol. 2004, 107, 107-114
17. Hasse, J. J. Genome Res. 2006, 16, 1041-1045
18. Twist, C. R.; Winson, M. K.; Rowland, J. J.; Kell, D. B. Anal. Biochem. 2004, 327, 35-44
19. Sung, J.; Sivaramakrishnan, S.; Dunn, A. R.; Spudich, J. A. Methods Enzymol. 2010, 475, 321-375
20. Miranda, T. B.; Kelly, T. K.; Bouazoune, K.; Jones, P. A. Curr. Protoc. Mol. Biol. 2010, 89, 21.17.1-21.17.16
21. Hintersteiner, M.; Auer, M. Ann. N.Y. Acad. Sci. 2008, 1130, 1-11
22. Skinner, G. M.; Visscher, K. Assay Drug Dev. Technol. 2004, 2, 397-405
23. Schomburg, D.; Schomburg, I. Springer Handbook of Enzymes, 2 nd ed.; Springer: New York, 2001.
24. Rajendran, A.; Endo, M.; Sugiyama, H. Chem. Rev. 2014, 114, 1493-1520
25. Engel, A.; Gaub, H. E. Annu. Rev. Biochem. 2008, 77, 127-148
26. Scheuring, S.; Fotiadis, D.; Möller, C.; Müller, S. A.; Engel, A.; Müller, D. J. Single Mol. 2001, 2, 59-67
27. Rothemund, P. W. Nature 2006, 440, 297-302
28. Andersen, E. S.; Dong, M.; Nielsen, M. M.; Jahn, K.; Lind-Thomsen, A.; Mamdouh, W.; Gothelf, K. V.; Besenbacher, F.; Kjems, J. ACS Nano 2008, 2, 1213-1218
29. Douglas, S. M.; Chou, J. J.; Shih, W. M. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 6644-6648
30. Kuzuya, A.; Komiyama, M. Chem. Commun. 2009, 4182-4184
31. Ke, Y.; Sharma, J.; Liu, M.; Jahn, K.; Liu, Y.; Yan, H. Nano Lett. 2009, 9, 2445-2447
32. Endo, M.; Hidaka, K.; Kato, T.; Namba, K.; Sugiyama, H. J. Am. Chem. Soc. 2009, 131, 15570-15571
33. Douglas, S. M.; Dietz, H.; Liedl, T.; Högberg, B.; Graf, F.; Shih, W. M. Nature 2009, 459, 414-418
34. Voigt, N. V. Nat. Nanotechnol. 2010, 5 (3) 200-203
35. Helmig, S. ACS Nano 2010, 4, 7475-7480
36. Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. J. Am. Chem. Soc. 2010, 132, 1592-1597
37. Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. Angew. Chem., Int. Ed. 2010, 49, 9412-9416
38. Suzuki, Y.; Endo, M.; Katsuda, Y.; Ou, K.; Hidaka, K.; Sugiyama, H. J. Am. Chem. Soc. 2014, 136, 211-218
39. Subramanian, H. K.; Chakraborty, B.; Sha, R.; Seeman, N. C. Nano Lett. 2011, 11, 910-913
40. Sannohe, Y.; Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. J. Am. Chem. Soc. 2010, 132, 16311-16313
41. Ranjendran, A.; Endo, M.; Hidaka, K.; Sugiyama, H. J. Am. Chem. Soc. 2013, 135, 1117-1123
42. Aota, S.; Nakajima, N.; Sakamoto, R.; Watanabe, S.; Ibaraki, N.; Okazaki, K. Dev. Biol. 2003, 257, 1-13
43. Glaser, T.; Jepeal, L.; Edwards, J. G.; Young, S. R.; Favor, J.; Mass, R. L. Nat. Genet. 1994, 7, 463-471
44. Hill, R. E. Nature 1991, 354, 522-525
45. Simpson, T. I.; Price, D. J. Bioessays 2002, 24, 1041-1051
46. Shandilya, J.; Roberts, S. G. Biochem. Biophys. Acta 2012, 19, 391-400
47. Scaffidi, P.; Bianchi, M. E. J. Biol. Chem. 2001, 276, 47296-47302
48. Shimada, N.; Aya-Murata, T.; Reza, H. M.; Yasuda, K. Mech. Dev. 2003, 120, 455-465
49. Reményi, A.; Lins, K.; Nissen, L. J.; Reinbold, R.; Schöler, H. R.; Wilmanns, M. Genes Dev. 2003, 17, 2048-2059
50. Shlyakhtenko, L. S.; Gilmore, J.; Portillo, A.; Tamulaitis, G.; Siksnys, V.; Lyubchenko, Y. L. Biochemistry 2007, 46, 11128-11136