Читать книгу DNA Origami - Группа авторов - Страница 51

1 1 Seeman, N.C. (1982). Nucleic‐acid junctions and lattices. Journal of Theoretical Biology 99: 237–247.

2 2 Seeman, N.C. (2003). DNA in a material world. Nature 421: 427–431.

3 3 Endo, M. and Sugiyama, H. (2009). Chemical approaches to DNA nanotechnology. Chembiochemistry: A European Journal of Chemical Biology 10: 2420–2443.

4 4 Rajendran, A., Endo, M., and Sugiyama, H. (2012). Single‐molecule analysis using DNA origami. Angewandte Chemie 51: 874–890.

5 5 Torring, T., Voigt, N.V., Nangreave, J. et al. (2011). DNA origami: a quantum leap for self‐assembly of complex structures. Chemical Society Reviews 40: 5636–5646.

6 6 Rothemund, P.W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature 440: 297–302.

7 7 Fu, T.J. and Seeman, N.C. (1993). DNA double‐crossover molecules. Biochemistry‐US 32: 3211–3220.

8 8 Yurke, B., Turberfield, A.J., Mills, A.P. Jr. et al. (2000). A DNA‐fuelled molecular machine made of DNA. Nature 406: 605–608.

9 9 Yan, H., Zhang, X., Shen, Z., and Seeman, N.C. (2002). A robust DNA mechanical device controlled by hybridization topology. Nature 415: 62–65.

10 10 Winfree, E., Liu, F.R., Wenzler, L.A., and Seeman, N.C. (1998). Design and self‐assembly of two‐dimensional DNA crystals. Nature 394: 539–544.

11 11 LaBean, T.H., Yan, H., Kopatsch, J. et al. (2000). Construction, analysis, ligation, and self‐assembly of DNA triple crossover complexes. Journal of the American Chemical Society 122: 1848–1860.

12 12 Ding, B.Q., Sha, R.J., and Seeman, N.C. (2004). Pseudohexagonal 2D DNA crystals from double crossover cohesion. Journal of the American Chemical Society 126: 10230–10231.

13 13 Liu, D., Wang, M., Deng, Z. et al. (2004). Tensegrity: construction of rigid DNA triangles with flexible four‐arm DNA junctions. Journal of the American Chemical Society 126: 2324–2325.

14 14 Yan, H., Park, S.H., Finkelstein, G. et al. (2003). DNA‐templated self‐assembly of protein arrays and highly conductive nanowires. Science 301: 1882–1884.

15 15 Mathieu, F., Liao, S., Kopatsch, J. et al. (2005). Six‐helix bundles designed from DNA. Nano Letters 5: 661–665.

16 16 Bath, J. and Turberfield, A.J. (2007). DNA nanomachines. Nature Nanotechnology 2: 275–284.

17 17 Mao, C., Sun, W., Shen, Z., and Seeman, N.C. (1999). A nanomechanical device based on the B‐Z transition of DNA. Nature 397: 144–146.

18 18 Endo, M., Sugita, T., Katsuda, Y. et al. (2010). Inside cover: programmed‐assembly system using DNA jigsaw pieces. Chemistry 16: 5228.

19 19 Woo, S. and Rothemund, P.W. (2011). Programmable molecular recognition based on the geometry of DNA nanostructures. Nature Chemistry 3: 620–627.

20 20 Rajendran, A., Endo, M., Katsuda, Y. et al. (2011). Programmed two‐dimensional self‐assembly of multiple DNA origami jigsaw pieces. ACS Nano 5: 665–671.

21 21 Zhao, Z., Liu, Y., and Yan, H. (2011). Organizing DNA origami tiles into larger structures using preformed scaffold frames. Nano Letters 11: 2997–3002.

22 22 Liu, W., Zhong, H., Wang, R., and Seeman, N.C. (2011). Crystalline two‐dimensional DNA‐origami arrays. Angewandte Chemie International Edition 50: 264–267.

23 23 Suzuki, Y., Endo, M., and Sugiyama, H. (2015). Lipid‐bilayer‐assisted two‐dimensional self‐assembly of DNA origami nanostructures. Nature Communications 6: 8052.

24 24 Endo, M., Sugita, T., Rajendran, A. et al. (2011). Two‐dimensional DNA origami assemblies using a four‐way connector. Chemical Communications 47: 3213–3215.

25 25 Douglas, S.M., Dietz, H., Liedl, T. et al. (2009a). Self‐assembly of DNA into nanoscale three‐dimensional shapes. Nature 459: 414–418.

26 26 Andersen, E.S., Dong, M., Nielsen, M.M. et al. (2009). Self‐assembly of a nanoscale DNA box with a controllable lid. Nature 459: 73–76.

27 27 Han, D., Pal, S., Nangreave, J. et al. (2011). DNA origami with complex curvatures in three‐dimensional space. Science 332: 342–346.

28 28 Douglas, S.M., Marblestone, A.H., Teerapittayanon, S. et al. (2009b). Rapid prototyping of 3D DNA‐origami shapes with caDNAno. Nucleic Acids Research 37: 5001–5006.

29 29 Dietz, H., Douglas, S.M., and Shih, W.M. (2009). Folding DNA into twisted and curved nanoscale shapes. Science 325: 725–730.

30 30 Kuzuya, A. and Komiyama, M. (2009). Design and construction of a box‐shaped 3D‐DNA origami. Chemical Communications 4182–4184.

31 31 Endo, M., Hidaka, K., and Sugiyama, H. (2011). Direct AFM observation of an opening event of a DNA cuboid constructed via a prism structure. Organic & Biomolecular Chemistry 9: 2075–2077.

32 32 Ke, Y., Sharma, J., Liu, M. et al. (2009). Scaffolded DNA origami of a DNA tetrahedron molecular container. Nano Letters 9: 2445–2447.

33 33 Endo, M., Hidaka, K., Kato, T. et al. (2009). DNA prism structures constructed by folding of multiple rectangular arms. Journal of American Chemical Society 131: 15570–15571.

34 34 Sharma, J., Chhabra, R., Andersen, C.S. et al. (2008). Toward reliable gold nanoparticle patterning on self‐assembled DNA nanoscaffold. Journal of the American Chemical Society 130: 7820–7821.

35 35 Ding, B., Deng, Z., Yan, H. et al. (2010). Gold nanoparticle self‐similar chain structure organized by DNA origami. Journal of the American Chemical Society 132: 3248–3249.

36 36 Sacca, B., Meyer, R., Erkelenz, M. et al. (2010). Orthogonal protein decoration of DNA origami. Angewandte Chemie International Edition 49: 9378–9383.

37 37 Fu, J., Liu, M., Liu, Y. et al. (2012). Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures. Journal of the American Chemical Society 134: 5516–5519.

38 38 Stein, I.H., Steinhauer, C., and Tinnefeld, P. (2011). Single‐molecule four‐color FRET visualizes energy‐transfer paths on DNA origami. Journal of American Chemical Society 133: 4193–4195.

39 39 Chhabra, R., Sharma, J., Ke, Y. et al. (2007). Spatially addressable multiprotein nanoarrays templated by aptamer‐tagged DNA nanoarchitectures. Journal of American Chemical Society 129: 10304–10305.

40 40 Shen, W., Zhong, H., Neff, D., and Norton, M.L. (2009). NTA directed protein nanopatterning on DNA Origami nanoconstructs. Journal American Chemical Society 131: 6660–6661.

41 41 Rinker, S., Ke, Y., Liu, Y. et al. (2008). Self‐assembled DNA nanostructures for distance‐dependent multivalent ligand‐protein binding. Nature Nanotechnology 3: 418–422.

42 42 Kuzuya, A., Kimura, M., Numajiri, K. et al. (2009). Precisely programmed and robust 2D streptavidin nanoarrays by using periodical nanometer‐scale wells embedded in DNA origami assembly. Chembiochem: A European Journal of Chemical Biology 10: 1811–1815.

43 43 Mandell, J.G. and Barbas, C.F. 3rd. (2006). Zinc finger tools: custom DNA‐binding domains for transcription factors and nucleases. Nucleic Acids Research 34: W516–W523.

44 44 Sander, J.D., Zaback, P., Joung, J.K. et al. (2007). Zinc finger targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Research 35: W599–W605.

45 45 Nakata, E., Liew, F.F., Uwatoko, C. et al. (2012). Zinc‐finger proteins for site‐specific protein positioning on DNA‐origami structures. Angewandte Chemie 51: 2421–2424.

46 46 Bando, T. and Sugiyama, H. (2006). Synthesis and biological properties of sequence‐specific DNA‐alkylating pyrrole‐imidazole polyamides. Accounts of Chemical Research 39: 935–944.

47 47 Yoshidome, T., Endo, M., Kashiwazaki, G. et al. (2012). Sequence‐selective single‐molecule alkylation with a pyrrole‐imidazole polyamide visualized in a DNA nanoscaffold. Journal of the American Chemical Society 134: 4654–4660.

48 48 Ke, Y., Lindsay, S., Chang, Y. et al. (2008). Self‐assembled water‐soluble nucleic acid probe tiles for label‐free RNA hybridization assays. Science 319: 180–183.

49 49 Voigt, N.V., Torring, T., Rotaru, A. et al. (2010). Single‐molecule chemical reactions on DNA origami. Nature Nanotechnology 5: 200–203.

50 50 Kuzuya, A., Sakai, Y., Yamazaki, T. et al. (2011). Nanomechanical DNA origami 'single‐molecule beacons' directly imaged by atomic force microscopy. Nature Communications 2: 449.

51 51 Koirala, D., Shrestha, P., Emura, T. et al. (2014). Single‐molecule mechanochemical sensing using DNA origami nanostructures. Angewandte Chemie International Edition 53: 8137–8141.

52 52 Endo, M., Yang, Y., and Sugiyama, H. (2013). DNA origami technology for biomaterials applications. Biomaterials Science 1: 347–360.

53 53 Ando, T., Kodera, N., Takai, E. et al. (2001). A high‐speed atomic force microscope for studying biological macromolecules. Proceedings of the National Academy of Sciences of the United States of America 98: 12468–12472.

54 54 Ando, T. and Kodera, N. (2012). Visualization of mobility by atomic force microscopy. Methods in Molecular Biology 896: 57–69.

55 55 Uchihashi, T., Kodera, N., and Ando, T. (2012). Guide to video recording of structure dynamics and dynamic processes of proteins by high‐speed atomic force microscopy. Nature Protocols 7: 1193–1206.

56 56 Rajendran, A., Endo, M., and Sugiyama, H. (2014). State‐of‐the‐art high‐speed atomic force microscopy for investigation of single‐molecular dynamics of proteins. Chemical Reviews 114: 1493–1520.

57 57 Walters, D.A., Cleveland, J.P., Thomson, N.H. et al. (1996). Short cantilevers for atomic force microscopy. Review of Scientific Instruments 67: 3583–3590.

58 58 Schitter, G., Astrom, K.J., DeMartini, B.E. et al. (2007). Design and modeling of a high‐speed AFM‐scanner. IEEE Transactions of Control Systems Technology 15: 906–915.

59 59 Sannohe, Y., Endo, M., Katsuda, Y. et al. (2010). Visualization of dynamic conformational switching of the G‐quadruplex in a DNA nanostructure. Journal of the American Chemical Society 132: 16311–16313.

60 60 Rajendran, A., Endo, M., Hidaka, K., and Sugiyama, H. (2013). Direct and real‐time observation of rotary movement of a DNA nanomechanical device. Journal of American Chemical Society 135: 1117–1123.

61 61 Suzuki, Y., Endo, M., Katsuda, Y. et al. (2014a). DNA origami based visualization system for studying site‐specific recombination events. Journal of American Chemical Society 136: 211–218.

62 62 Endo, M., Katsuda, Y., Hidaka, K., and Sugiyama, H. (2010). Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure. Journal of American Chemical Society 132: 1592–1597.

63 63 Xu, Y., Sato, H., Sannohe, Y. et al. (2008). Stable lariat formation based on a G‐quadruplex scaffold. Journal of American Chemical Society 130: 16470–16471.

64 64 Youngblood, B. and Reich, N.O. (2006). Conformational transitions as determinants of specificity for the DNA methyltransferase EcoRI. The Journal of Biological Chemistry 281: 26821–26831.

65 65 Bruner, S.D., Norman, D.P., and Verdine, G.L. (2000). Structural basis for recognition and repair of the endogenous mutagen 8‐oxoguanine in DNA. Nature 403: 859–866.

66 66 Morikawa, K., Matsumoto, O., Tsujimoto, M. et al. (1992). X‐ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer. Science 256: 523–526.

67 67 Guo, F., Gopaul, D.N., and Van Duyne, G.D. (1997). Structure of Cre recombinase complexed with DNA in a site‐specific recombination synapse. Nature 389: 40–46.

68 68 Van Duyne, G.D. (2001). A structural view of cre‐loxp site‐specific recombination. Annual Review of Biophysics and Biomolecular Structure 30: 87–104.

69 69 Suzuki, Y., Endo, M., Canas, C. et al. (2014b). Direct analysis of Holliday junction resolving enzyme in a DNA origami nanostructure. Nucleic Acids Research 42: 7421–7428.

70 70 Kobayashi, Y., Misumi, O., Odahara, M. et al. (2017). Holliday junction resolvases mediate chloroplast nucleoid segregation. Science 356: 631–634.

71 71 Rajendran, A., Endo, M., Hidaka, K., and Sugiyama, H. (2014). Direct and single‐molecule visualization of the solution‐state structures of G‐hairpin and G‐triplex intermediates. Angewandte Chemie International Edition 53: 4107–4112.

72 72 Endo, M., Yang, Y., Suzuki, Y. et al. (2012). Single‐molecule visualization of the hybridization and dissociation of photoresponsive oligonucleotides and their reversible switching behavior in a DNA nanostructure. Angewandte Chemie International Edition 51: 10518–10522.

73 73 Yamagata, Y., Emura, T., Hidaka, K. et al. (2016). Triple helix formation in a topologically controlled DNA nanosystem. Chemistry 22: 5494–5498.

74 74 Endo, M., Xing, X., Zhou, X. et al. (2015). Single‐molecule manipulation of the duplex formation and dissociation at the G‐quadruplex/i‐Motif site in the DNA nanostructure. ACS Nano 9: 9922–9929.

75 75 Endo, M., Katsuda, Y., Hidaka, K., and Sugiyama, H. (2010). A versatile DNA nanochip for direct analysis of DNA base‐excision repair. Angewandte Chemie International Edition 49: 9412–9416.

76 76 Lee, A.J., Endo, M., Hobbs, J.K., and Walti, C. (2018). Direct single‐molecule observation of mode and geometry of RecA‐mediated homology search. ACS Nano 12: 272–278.

77 77 Raz, M.H., Hidaka, K., Sturla, S.J. et al. (2016). Torsional constraints of DNA substrates impact Cas9 cleavage. Journal of American Chemical Society 138: 13842–13845.

78 78 Xing, X., Sato, S., Wong, N.K. et al. (2020). Direct observation and analysis of TET‐mediated oxidation processes in a DNA origami nanochip. Nucleic Acids Research 48: 4041–4051.

79 79 Yamamoto, S., De, D., Hidaka, K. et al. (2014). Single molecule visualization and characterization of Sox2‐Pax6 complex formation on a regulatory DNA element using a DNA origami frame. Nano Letters 14: 2286–2292.

80 80 Raghavan, G., Hidaka, K., Sugiyama, H., and Endo, M. (2019). Direct observation and analysis of the dynamics of the photoresponsive transcription factor GAL4. Angewandte Chemie International Edition 58: 7626–7630.

81 81 Mino, T., Iwai, N., Endo, M. et al. (2019). Translation‐dependent unwinding of stem‐loops by UPF1 licenses Regnase‐1 to degrade inflammatory mRNAs. Nucleic Acids Research 47: 8838–8859.

82 82 Steinhauer, C., Jungmann, R., Sobey, T.L. et al. (2009). DNA origami as a nanoscopic ruler for super‐resolution microscopy. Angewandte Chemie International Edition 48: 8870–8873.

83 83 Jungmann, R., Steinhauer, C., Scheible, M. et al. (2010). Single‐molecule kinetics and super‐resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Letters 10: 4756–4761.

84 84 Lin, C., Jungmann, R., Leifer, A.M. et al. (2012). Submicrometre geometrically encoded fluorescent barcodes self‐assembled from DNA. Nature Chemistry 4: 832–839.

85 85 Gu, H., Chao, J., Xiao, S.J., and Seeman, N.C. (2009). Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate. Nature Nanotechnology 4: 245–248.

86 86 Gu, H.Z., Chao, J., Xiao, S.J., and Seeman, N.C. (2010). A proximity‐based programmable DNA nanoscale assembly line. Nature 465: 202–205.

87 87 Lund, K., Manzo, A.J., Dabby, N. et al. (2010). Molecular robots guided by prescriptive landscapes. Nature 465: 206–210.

88 88 Wickham, S.F.J., Endo, M., Katsuda, Y. et al. (2011). Direct observation of stepwise movement of a synthetic molecular transporter. Nature Nanotechnology 6: 166–169.

89 89 Bath, J., Green, S.J., and Turberfield, A.J. (2005). A free‐running DNA motor powered by a nicking enzyme. Angewandte Chemie International Edition 44: 4358–4361.

90 90 Wickham, S.F., Bath, J., Katsuda, Y. et al. (2012). A DNA‐based molecular motor that can navigate a network of tracks. Nature Nanotechnology 7: 169–173.

91 91 Kuzuya, A., Koshi, N., Kimura, M. et al. (2010). Programmed nanopatterning of organic/inorganic nanoparticles using nanometer‐scale wells embedded in a DNA origami scaffold. Small 6: 2664–2667.

92 92 Endo, M., Yang, Y., Emura, T. et al. (2011). Programmed placement of gold nanoparticles onto a slit‐type DNA origami scaffold. Chemical Communications 47: 10743–10745.

93 93 Maune, H.T., Han, S.P., Barish, R.D. et al. (2010). Self‐assembly of carbon nanotubes into two‐dimensional geometries using DNA origami templates. Nature Nanotechnology 5: 61–66.

94 94 Kuzyk, A., Schreiber, R., Fan, Z. et al. (2012). DNA‐based self‐assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483: 311–314.

95 95 Acuna, G.P., Moller, F.M., Holzmeister, P. et al. (2012). Fluorescence enhancement at docking sites of DNA‐directed self‐assembled nanoantennas. Science 338: 506–510.

96 96 Kershner, R.J., Bozano, L.D., Micheel, C.M. et al. (2009). Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nature Nanotechnology 4: 557–561.

97 97 Hung, A.M., Micheel, C.M., Bozano, L.D. et al. (2010). Large‐area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nature Nanotechnology 5: 121–126.

98 98 Castro, C.E., Su, H.J., Marras, A.E. et al. (2015). Mechanical design of DNA nanostructures. Nanoscale 7: 5913–5921.

99 99 Marras, A.E., Zhou, L., Su, H.J., and Castro, C.E. (2015). Programmable motion of DNA origami mechanisms. Proceedings of the National Academy of Sciences of the United States of America 112: 713–718.

100 100 Gerling, T., Wagenbauer, K.F., Neuner, A.M., and Dietz, H. (2015). Dynamic DNA devices and assemblies formed by shape‐complementary, non‐base pairing 3D components. Science 347: 1446–1452.

101 101 Kuzyk, A., Yang, Y., Duan, X. et al. (2016). A light‐driven three‐dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function. Nature Communications 7: 10591.

102 102 Kuzyk, A., Schreiber, R., Zhang, H. et al. (2014). Reconfigurable 3D plasmonic metamolecules. Nature Materials 13: 862–866.

103 103 Langecker, M., Arnaut, V., Martin, T.G. et al. (2012). Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338: 932–936.

104 104 Yang, Y., Wang, J., Shigematsu, H. et al. (2016). Self‐assembly of size‐controlled liposomes on DNA nanotemplates. Nature Chemistry 8: 476–483.

105 105 Zhang, Z., Yang, Y., Pincet, F. et al. (2017). Placing and shaping liposomes with reconfigurable DNA nanocages. Nature Chemistry 9: 653–659.

106 106 Castro, C.E., Kilchherr, F., Kim, D.N. et al. (2011). A primer to scaffolded DNA origami. Nature Methods 8: 221–229.

107 107 Mei, Q., Wei, X., Su, F. et al. (2011). Stability of DNA origami nanoarrays in cell lysate. Nano Letters 11: 1477–1482.

108 108 Jiang, Q., Song, C., Nangreave, J. et al. (2012). DNA origami as a carrier for circumvention of drug resistance. Journal of the American Chemical Society 134: 13396–13403.

109 109 Zhao, Y.X., Shaw, A., Zeng, X. et al. (2012). DNA origami delivery system for cancer therapy with tunable release properties. ACS Nano 6: 8684–8691.

110 110 Perrault, S.D. and Shih, W.M. (2014). Virus‐inspired membrane encapsulation of DNA nanostructures to achieve in vivo stability. ACS Nano 8: 5132–5140.

111 111 Ponnuswamy, N., Bastings, M.M.C., Nathwani, B. et al. (2017). Oligolysine‐based coating protects DNA nanostructures from low‐salt denaturation and nuclease degradation. Nature Communications 8: 15654.

112 112 Zhang, Q., Jiang, Q., Li, N. et al. (2014). DNA origami as an in vivo drug delivery vehicle for cancer therapy. ACS Nano 8: 6633–6643.

113 113 Rahman, M.A., Wang, P., Zhao, Z. et al. (2017). Systemic delivery of Bc12‐targeting siRNA by DNA nanoparticles suppresses cancer cell growth. Angewandte Chemie 56: 16023–16027.

114 114 Takenaka, T., Endo, M., Suzuki, Y. et al. (2014). Photoresponsive DNA nanocapsule having an open/close system for capture and release of nanomaterials. Chemistry—A European Journal 20: 14951–14954.

115 115 Douglas, S.M., Bachelet, I., and Church, G.M. (2012). A logic‐gated nanorobot for targeted transport of molecular payloads. Science 335: 831–834.

116 116 Hu, Q., Li, H., Wang, L. et al. (2018). DNA nanotechnology‐enabled drug delivery systems. Chemical Reviews.

117 117 Li, S., Jiang, Q., Liu, S. et al. (2018). A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. Nature Biotechnology 36: 258–264.