A protein adaptor to locate a functional protein dimer on molecular switchboard

Methods

Volumn 67, Issue 2, 2014, Pages 142-150

  Ngo, Tien Anh ^a   Nakata, Eiji ^a,b   Saimura, Masayuki ^a   Kodaki, Tsutomu ^a   Morii, Takashi ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Atomic force microscopy; Basic leucine zipper protein; DNA origami; DNA binding protein; Self assembly

Indexed keywords

ADAPTOR PROTEIN; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; DNA BINDING PROTEIN; NANOMATERIAL; SINGLE STRANDED DNA; IMMOBILIZED NUCLEIC ACID; PROTEIN BINDING;

AMINO ACID SEQUENCE; ARTICLE; ATOMIC FORCE MICROSCOPY; BACTERIAL CELL; DNA ORIGAMI; DNA SEQUENCE; DNA STRUCTURE; ESCHERICHIA COLI; EXPRESSION VECTOR; NANOTECHNOLOGY; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION SYSTEM; PRIORITY JOURNAL; BINDING SITE; CHEMISTRY;

BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; BINDING SITES; IMMOBILIZED NUCLEIC ACIDS; MICROSCOPY, ATOMIC FORCE; NANOSTRUCTURES; PROTEIN BINDING;

EID: 84899744980     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.10.014     Document Type: Article

References (59)

1. Rothemund P.W. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440:297-302.
2. 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., Pdersen J.S., Birkedal V., Besenbacher F., Gothelf K.V., Kjems J. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 2009, 459:73-76.
3. Douglas S.M., Detz H., Liedl T., Högberg B., Graf F., Shih W.M. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 2009, 459:414-418.
4. Seeman N.C. An overview of structural DNA nanotechnology. Mol. Biotechnol. 2007, 37:246-257.
5. Lin C., Liu Y., Yan H. Designer DNA nanoarchitectures. Biochemistry 2009, 48:1663-1674.
6. Endo M., Sugiyama H. Chemical approaches to DNA nanotechnology. ChemBioChem 2009, 10:2420-2443.
7. Kuzuya A., Komiyama M. DNA origami: fold, stick, and beyond. Nanoscale 2010, 2:310-322.
8. Nangreave J., Han D., Liu Y., Yao H. DNA origami: a history and current perspective. Curr. Opin. Biotechnol. 2010, 14:608-615.
9. Torring T., Voigt N.V., Nangreave J., Yan H., Gothelf K.V. DNA origami: a quantum leap for self-assembly of complex structures. Chem. Soc. Rev. 2011, 40:5606-5646.
10. Pinheiro A.V., Han D., Shih W.M., Yan H. Challenges and opportunities for structural DNA nanotechnology. Nat. Nanotech. 2011, 6:763-771.
11. Rajiendran A., Endo M., Sugiyama H. Single-molecule analysis using DNA origami. Angew. Chem. Int. Ed. 2012, 51:874-890.
12. Ding B., Deng Z., Yan H., Cabrini S., Zuckermann R.N., Bokor J. Gold nanoparticle self-similar chain structure organized by DNA origami. J. Am. Chem. Soc. 2010, 132:3248-3249.
13. Maune H.T., Han S., Barish R.D., Bockrath M., Goddard W.A., Rothemund P.W.K., Winfree E. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nat. Nanotech. 2010, 5:61-66.
14. Stephanopoulos N., Liu M., Tong G.J., Li Z., Liu Y., Yan H., Francis M.B. Immobilization and one-dimensional arrangement of virus capsids with nanoscale precision using DNA origami. Nano Lett. 2010, 10:2714-2720.
15. Niemeyer C.M., Birger W., Peplies J. Covalent DNA-streptavidin conjugates as building blocks for novel biometallic nanostructures. Angew. Chem. Int. Ed. 1998, 37:2265-2268.
16. Cohen J.D., Sadowski J.P., Dervan P.B. Addressing single molecules on DNA nanostructures. Angew. Chem. Int. Ed. 2007, 46:7956-7959.
17. Cohen J.D., Sadowski J.P., Dervan P.B. Programming multiple protein patterns on a single DNA nanostructure. J. Am. Chem. Soc. 2008, 130:402-403.
18. Willner O.I., Weizmann Y., Gill R., Lioubashevski O., Freeman R., Willner I. Enzyme cascades activated on topologically programmed DNA scaffolds. Nat. Nanotechnol. 2009, 4:249-254.
19. Saccà B., Meyer R., Erkelenz M., Kiko K., Arndt A., Schroeder H., Rabe K.S., Niemeyer C.M. Orthogonal protein decoration of DNA origami. Angew. Chem. Int. Ed. 2010, 49:9378-9383.
20. Jahn K., Tørring T., Voigt N.V., Sørensen R.S., Kodal A.L.B., Andersen E.S., Gothelf K.V., Kjems J. Functional patterning of DNA origami by parallel enzymatic modification. Bioconjugate Chem. 2011, 22:819-823.
21. Fu J., Liu M., Liu Y., Woodbury N.W., Yan H. Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures. J. Am. Chem. Soc. 2012, 134:5516-5519.
22. Nakata E., Lew F.F., Uwatoko C., Kiyonaka S., Mori Y., Katsuda Y., Endo M., Sugiyama H., Morii T. Zinc-finger proteins for site-specific protein positioning on DNA-origami structures. Angew. Chem. Int. Ed. 2012, 51:2421-2424.
23. Yoshidome T., Endo M., Kashiwazaki G., Hidaka K., Bando T., Sugiyama H. Sequence-selective single-molecule alkylation with a pyrrole-imidazole polyamide visualized in a DNA nanoscaffold. J. Am. Chem. Soc. 2012, 134:4654-4660.
24. Niemeyer C.M., Koehler J., Wuerdemann C. DNA-directed assembly of bienzymic complexes from in vivo biotinylated NAD(P)H: FMN oxidoreductase and luciferase. ChemBioChem 2002, 02-03:242-245.
25. Meyer R., Niemeyer C.M. Orthogonal protein decoration of DNA nanostructures. Small 2011, 7:3211-3218.
26. Erkelenz M., Kuo C.H., Niemeyer C.M. DNA-mediated assembly of cytochrome P450 BM3 subdomains. J. Am. Chem. Soc. 2011, 133:16111-16118.
27. Teller C., Willner I. Organizing protein-DNA hybrids as nanostructures with programmed functionalities. Trends Biotechnol. 2010, 28:619-628.
28. Saccà B., Niemeyer C.M. Functionalization of DNA nanostructures with proteins. Chem. Soc. Rev. 2011, 40:5910-5912.
29. He Y., Tian Y., Ribbe A.E., Mao C. Antibody nanoarrays with a pitch of ~20nm. J. Am. Chem. Soc. 2006, 128:12664-12665.
30. Williams B.A.R., Lund K., Liu Y., Yan H., Chaput J.C. Self-Assembled peptide nanoarrays: an approach to studying protein-protein interactions. Angew. Chem. Int. Ed. 2007, 46:3051-3054.
31. Chhabra R., Sharma J., Ke Y., Liu Y., Rinker S., Lindsay S., Yan H. Spatially addressable multiprotein nanoarrays templated by aptamer-tagged DNA nanoarchitectures. J. Am. Chem. Soc. 2007, 129:10304-10305.
32. Rinker S., Ke Y., Liu Y., Chhabra R., Yan H. Self-assembled DNA nanostructures for distance dependent multivalent ligand-protein binding. Nat. Nanotechnol. 2008, 418-422.
33. Shen W., Zhong H., Neff D., Norton M.L. Nanopatterning on DNA origami nanoconstructs. J. Am. Chem. Soc. 2009, 131:6660-6661.
34. Goodman R.P., Erben C.M., Malo J., Ho W.M., McKee M.L., Kapanidis A.N., Turberfield A.J. A facile method for reversibly linking a recombinant protein to DNA. ChemBioChem 2009, 10:1551-1557.
35. Selmi D.N., Adamson R.J., Attrill H., Goddard A.D., Gilbert R.J.C., Watts A., Turberfield A.J. DNA-templated protein arrays for single-molecule imaging. Nano Lett. 2011, 11:657-660.
36. Yan H., Park S.H., Finkelstein G., Reif J.H., LaBean T.H. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 2003, 301:1882-1884.
37. Li H., Park S., Reif J.H., LaBean T.H., Yan H. DNA templated self-assembly of protein and nanoparticle linear arrays. J. Am. Chem. Soc. 2004, 126:418-419.
38. Lund K., Liu Y., Lindsay S., Yan H. Self-assembling molecular pegboard. J. Am. Chem. Soc. 2005, 127:17606-17607.
39. Kuzuya A., Kimura M., Numajiri K., Koshi N., Ohnishi T., Okada F., Komiyama M. Precisely programmed and robust 2D streptavidin nanoarrays by using periodical nanometer-scale wells embedded in DNA origami assembly. ChemBioChem 2009, 10:1811-1815.
40. Voigt N.V., Torring T., Rotaru A., Jacobsen M.F., Ravnsbaek J.B., Subramani R., Mamdouh W., Kjems J., Mokhir A., Besenbacher F., Gothelf K.V. Single-molecule chemical reactions on DNA origami. Nat. Nanotech. 2010, 5:200-203.
41. Numajiri K., Yamazaki T., Kimura M., Kuzuya A., Komiyama M. Discrete and active enzyme nanoarrays on DNA origami scaffolds purified by affinity tag separation. J. Am. Chem. Soc. 2010, 132:9937-9939.
42. Aldaye F.A., Senapedis W.T., Silver P.A., Way J.C. A structurally tunable DNA-based extracellular matrix. J. Am. Chem. Soc. 2010, 132:14727-14729.
43. Fu Y., Zeng D., Chao J., jin Y., Zhang Z., Liu H., Li D., Ma H., Huang Q., Gothelf K.V., Fan C. Single-step rapid assembly of DNA origami nanostructures for addressable nanoscale bioreactors. J. Am. Chem. Soc. 2013, 135:696-702.
44. Pavletich N.P., Pabo C.O. Zinc finger--DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 1991, 252:809-817.
45. Klug A., Schwabe J.W.R. Protein motifs 5. Zinc fingers. FASEB J. 1995, 9:597-601.
46. Elrod-Erickson M., Benson T.E., Pabo C.O. High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Structure 1998, 6:451-464.
47. Brayer K.J., Segal D. Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. Cell Biochem. Biophys. 2008, 50:111-131.
48. O'Shea E.K., Rutkowski R., Kim P.S. Evidence that the leucine zipper is a coiled coil. Science 1989, 243:538-542.
49. Ellenberger T.E., Brandl C.J., Struhl K., Harrison S.C. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. Cell 1992, 71:1223-1237.
50. König P., Richmond T.J. The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility. J. Mol. Biol. 1993, 233:139-154.
51. Keller W., König P., Richmond T.J. Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition. J. Mol. Biol. 1995, 254:657-667.
52. Mei G., Venere A.D., Rosato N., Finazzi-Agrò A. The importance of being dimeric. FEBS J. 2005, 272:16-27.
53. Watanabe S., kodaki T., Makino K. Complete reversal of coenzyme specificity of xylitol dehydrogenase and increase of thermostability by the introduction of structural zinc. J. Biol. Chem. 2005, 280:10340-10349.
54. Morii T., Saimei Y., Okagami M., Makino K., Sugiura Y. Factors governing the sequence-selective DNA binding of geometrically constrained peptide dimers. J. Am. Chem. Soc. 1997, 119:3649-3655.
55. Morii T., Sato S., Hagihara M., Mori Y., Imoto K., Makino K. Structure-based design of a leucine zipper protein with new DNA contacting region. Biochemistry 2002, 41:2177-2183.
56. Pabo C.O., Peisach E., Grant R.A. Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem. 2001, 70:313-340.
57. Sellers J.W., Vincent A.C., Struhl K. Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites. Mol. Cell. Biol. 1990, 10:5077-5086.
58. Metallo S.J., Schepartz A. Distribution of labor among bZIP segments in the control of DNA affinity and specificity. Chem. Biol. 1994, 1:143-151.
59. Watanabe S., Saleh A.A., Pack S.P., Annaluru N., Kodaki T., Makino K. Ethanol production from xylose by recombinant Saccharomyces cerevisiae expressing protein-engineered NADH-preferring xylose reductase from Pichia stipitis. Microbiology 2007, 153:3044-3054.