DNA nanotechnology | references

References

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  2. ^ a b c Overview: Mao, Chengde (December 2004). "The emergence of complexity: lessons from DNA". PLoS Biology. 2 (12): 2036–2038. 10.1371/journal.pbio.0020431. 535573Freely accessible. 15597116. 
  3. ^ a b c d e Overview: Seeman, Nadrian C. (June 2004). "Nanotechnology and the double helix". Scientific American. 290 (6): 64–75. 2004SciAm.290f..64S. 10.1038/scientificamerican0604-64. 15195395. 
  4. ^ Background: Pelesko, John A. (2007). Self-assembly: the science of things that put themselves together. New York: Chapman & Hall/CRC. pp. 5, 7. ISBN 978-1-58488-687-7. 
  5. ^ a b c d e Overview: Seeman, Nadrian C. (2010). "Nanomaterials based on DNA". Annual Review of Biochemistry. 79: 65–87. 10.1146/annurev-biochem-060308-102244. 3454582Freely accessible. 20222824. 
  6. ^ Background: Long, Eric C. (1996). "Fundamentals of nucleic acids". In Hecht, Sidney M. Bioorganic chemistry: nucleic acids. New York: Oxford University Press. pp. 4–10. ISBN 0-19-508467-5. 
  7. ^ RNA nanotechnology: Chworos, Arkadiusz; Severcan, Isil; Koyfman, Alexey Y.; Weinkam, Patrick; Oroudjev, Emin; Hansma, Helen G.; Jaeger, Luc (2004). "Building Programmable Jigsaw Puzzles with RNA". Science. 306 (5704): 2068–2072. 2004Sci...306.2068C. 10.1126/science.1104686. 15604402. 
  8. ^ RNA nanotechnology: Guo, Peixuan (2010). "The Emerging Field of RNA Nanotechnology". Nature Nanotechnology. 5 (12): 833–842. 2010NatNa...5..833G. 10.1038/nnano.2010.231. 3149862Freely accessible. 21102465. 
  9. ^ a b c d Dynamic DNA nanotechnology: Zhang, D. Y.; Seelig, G. (February 2011). "Dynamic DNA nanotechnology using strand-displacement reactions". Nature Chemistry. 3 (2): 103–113. 2011NatCh...3..103Z. 10.1038/nchem.957. 21258382. 
  10. ^ a b c d e Structural DNA nanotechnology: Seeman, Nadrian C. (November 2007). "An overview of structural DNA nanotechnology". Molecular Biotechnology. 37 (3): 246–257. 10.1007/s12033-007-0059-4. 3479651Freely accessible. 17952671. 
  11. ^ Dynamic DNA nanotechnology: Lu, Y.; Liu, J. (December 2006). "Functional DNA nanotechnology: Emerging applications of DNAzymes and aptamers". Current Opinion in Biotechnology. 17 (6): 580–588. 10.1016/j.copbio.2006.10.004. 17056247. 
  12. ^ Other arrays: Strong, Michael (March 2004). "Protein Nanomachines". PLoS Biology. 2 (3): e73. 10.1371/journal.pbio.0020073. 368168Freely accessible. 15024422. 
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  14. ^ a b Algorithmic self-assembly: Rothemund, Paul W. K.; Papadakis, Nick; Winfree, Erik (December 2004). "Algorithmic self-assembly of DNA Sierpinski triangles". PLoS Biology. 2 (12): 2041–2053. 10.1371/journal.pbio.0020424. 534809Freely accessible. 15583715. 
  15. ^ DX arrays: Winfree, Erik; Liu, Furong; Wenzler, Lisa A.; Seeman, Nadrian C. (6 August 1998). "Design and self-assembly of two-dimensional DNA crystals". Nature. 394 (6693): 529–544. 1998Natur.394..539W. 10.1038/28998. 9707114. 
  16. ^ DX arrays: Liu, Furong; Sha, Ruojie; Seeman, Nadrian C. (10 February 1999). "Modifying the surface features of two-dimensional DNA crystals". Journal of the American Chemical Society. 121 (5): 917–922. 10.1021/ja982824a. 
  17. ^ Other arrays: Mao, Chengde; Sun, Weiqiong; Seeman, Nadrian C. (16 June 1999). "Designed two-dimensional DNA Holliday junction arrays visualized by atomic force microscopy". Journal of the American Chemical Society. 121 (23): 5437–5443. 10.1021/ja9900398. 
  18. ^ Other arrays: Constantinou, Pamela E.; Wang, Tong; Kopatsch, Jens; Israel, Lisa B.; Zhang, Xiaoping; Ding, Baoquan; Sherman, William B.; Wang, Xing; Zheng, Jianping; Sha, Ruojie; Seeman, Nadrian C. (21 September 2006). "Double cohesion in structural DNA nanotechnology". Organic and Biomolecular Chemistry. 4 (18): 3414–3419. 10.1039/b605212f. 3491902Freely accessible. 17036134. 
  19. ^ Other arrays: Mathieu, Frederick; Liao, Shiping; Kopatsch, Jens; Wang, Tong; Mao, Chengde; Seeman, Nadrian C. (April 2005). "Six-helix bundles designed from DNA". Nano Letters. 5 (4): 661–665. 2005NanoL...5..661M. 10.1021/nl050084f. 3464188Freely accessible. 15826105. 
  20. ^ a b c History: Seeman, Nadrian (9 June 2010). "Structural DNA nanotechnology: growing along with Nano Letters". Nano Letters. 10 (6): 1971–1978. 2010NanoL..10.1971S. 10.1021/nl101262u. 2901229Freely accessible. 20486672. 
  21. ^ Algorithmic self-assembly: Barish, Robert D.; Rothemund, Paul W. K.; Winfree, Erik (December 2005). "Two computational primitives for algorithmic self-assembly: copying and counting". Nano Letters. 5 (12): 2586–2592. 2005NanoL...5.2586B. 10.1021/nl052038l. 16351220. 
  22. ^ a b c d Design: Feldkamp, U.; Niemeyer, C. M. (13 March 2006). "Rational design of DNA nanoarchitectures". Angewandte Chemie International Edition. 45 (12): 1856–1876. 10.1002/anie.200502358. 16470892. 
  23. ^ DNA nanotubes: Rothemund, Paul W. K.; Ekani-Nkodo, Axel; Papadakis, Nick; Kumar, Ashish; Fygenson, Deborah Kuchnir & Winfree, Erik (22 December 2004). "Design and Characterization of Programmable DNA Nanotubes". Journal of the American Chemical Society. 126 (50): 16344–16352. 10.1021/ja044319l. 15600335. 
  24. ^ DNA nanotubes: Yin, P.; Hariadi, R. F.; Sahu, S.; Choi, H. M. T.; Park, S. H.; Labean, T. H.; Reif, J. H. (8 August 2008). "Programming DNA Tube Circumferences". Science. 321 (5890): 824–826. 2008Sci...321..824Y. 10.1126/science.1157312. 18687961. 
  25. ^ Three-dimensional arrays: Zheng, Jianping; Birktoft, Jens J.; Chen, Yi; Wang, Tong; Sha, Ruojie; Constantinou, Pamela E.; Ginell, Stephan L.; Mao, Chengde; Seeman, Nadrian C. (3 September 2009). "From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal". Nature. 461 (7260): 74–77. 2009Natur.461...74Z. 10.1038/nature08274. 2764300Freely accessible. 19727196. 
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  27. ^ DNA polyhedra: Zhang, Yuwen; Seeman, Nadrian C. (1 March 1994). "Construction of a DNA-truncated octahedron". Journal of the American Chemical Society. 116 (5): 1661–1669. 10.1021/ja00084a006. 
  28. ^ DNA polyhedra: Shih, William M.; Quispe, Joel D.; Joyce, Gerald F. (12 February 2004). "A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron". Nature. 427 (6975): 618–621. 2004Natur.427..618S. 10.1038/nature02307. 14961116. 
  29. ^ a b c DNA origami: Rothemund, Paul W. K. (16 March 2006). "Folding DNA to create nanoscale shapes and patterns". Nature. 440 (7082): 297–302. 2006Natur.440..297R. 10.1038/nature04586. 16541064. 
  30. ^ Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu (December 2017). "Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns". Nature. 552 (7683): 67–71. 10.1038/nature24655. 1476-4687. 29219965. 
  31. ^ a b DNA origami: Douglas, Shawn M.; Dietz, Hendrik; Liedl, Tim; Högberg, Björn; Graf, Franziska; Shih, William M. (21 May 2009). "Self-assembly of DNA into nanoscale three-dimensional shapes". Nature. 459 (7245): 414–418. 2009Natur.459..414D. 10.1038/nature08016. 2688462Freely accessible. 19458720. 
  32. ^ a b DNA boxes: Andersen, Ebbe S.; Dong, Mingdong; Nielsen, Morten M.; Jahn, Kasper; Subramani, Ramesh; Mamdouh, Wael; Golas, Monika M.; Sander, Bjoern; et al. (7 May 2009). "Self-assembly of a nanoscale DNA box with a controllable lid". Nature. 459 (7243): 73–76. 2009Natur.459...73A. 10.1038/nature07971. 19424153. 
  33. ^ DNA boxes: Ke, Yonggang; Sharma, Jaswinder; Liu, Minghui; Jahn, Kasper; Liu, Yan; Yan, Hao (10 June 2009). "Scaffolded DNA origami of a DNA tetrahedron molecular container". Nano Letters. 9 (6): 2445–2447. 2009NanoL...9.2445K. 10.1021/nl901165f. 19419184. 
  34. ^ Overview: Endo, M.; Sugiyama, H. (12 October 2009). "Chemical approaches to DNA nanotechnology". ChemBioChem. 10 (15): 2420–2443. 10.1002/cbic.200900286. 19714700. 
  35. ^ Nanoarchitecture: Zheng, Jiwen; Constantinou, Pamela E.; Micheel, Christine; Alivisatos, A. Paul; Kiehl, Richard A.; Seeman Nadrian C. (July 2006). "2D Nanoparticle Arrays Show the Organizational Power of Robust DNA Motifs". Nano Letters. 6 (7): 1502–1504. 2006NanoL...6.1502Z. 10.1021/nl060994c. 3465979Freely accessible. 16834438. 
  36. ^ Nanoarchitecture: Park, Sung Ha; Pistol, Constantin; Ahn, Sang Jung; Reif, John H.; Lebeck, Alvin R.; Dwyer, Chris; LaBean, Thomas H. (October 2006). "Finite-size, fully addressable DNA tile lattices formed by hierarchical assembly procedures". Angewandte Chemie. 118 (40): 749–753. 10.1002/ange.200690141. 
  37. ^ Nanoarchitecture: Cohen, Justin D.; Sadowski, John P.; Dervan, Peter B. (22 October 2007). "Addressing single molecules on DNA nanostructures". Angewandte Chemie International Edition. 46 (42): 7956–7959. 10.1002/anie.200702767. 17763481. 
  38. ^ Nanoarchitecture: Maune, Hareem T.; Han, Si-Ping; Barish, Robert D.; Bockrath, Marc; Goddard III, William A.; Rothemund, Paul W. K.; Winfree, Erik (January 2009). "Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates". Nature Nanotechnology. 5 (1): 61–66. 2010NatNa...5...61M. 10.1038/nnano.2009.311. 19898497. 
  39. ^ Nanoarchitecture: Liu, J.; Geng, Y.; Pound, E.; Gyawali, S.; Ashton, J. R.; Hickey, J.; Woolley, A. T.; Harb, J. N. (22 March 2011). "Metallization of branched DNA origami for nanoelectronic circuit fabrication". ACS Nano. 5 (3): 2240–2247. 10.1021/nn1035075. 21323323. 
  40. ^ Nanoarchitecture: Deng, Z.; Mao, C. (6 August 2004). "Molecular lithography with DNA nanostructures". Angewandte Chemie International Edition. 43 (31): 4068–4070. 10.1002/anie.200460257. 
  41. ^ a b c d DNA machines: Bath, Jonathan; Turberfield, Andrew J. (May 2007). "DNA nanomachines". Nature Nanotechnology. 2 (5): 275–284. 2007NatNa...2..275B. 10.1038/nnano.2007.104. 18654284. 
  42. ^ DNA machines: Mao, Chengde; Sun, Weiqiong; Shen, Zhiyong; Seeman, Nadrian C. (14 January 1999). "A DNA nanomechanical device based on the B-Z transition". Nature. 397 (6715): 144–146. 1999Natur.397..144M. 10.1038/16437. 9923675. 
  43. ^ DNA machines: Yurke, Bernard; Turberfield, Andrew J.; Mills, Allen P., Jr; Simmel, Friedrich C.; Neumann, Jennifer L. (10 August 2000). "A DNA-fuelled molecular machine made of DNA". Nature. 406 (6796): 605–609. 2000Natur.406..605Y. 10.1038/35020524. 10949296. 
  44. ^ DNA machines: Yan, Hao; Zhang, Xiaoping; Shen, Zhiyong; Seeman, Nadrian C. (3 January 2002). "A robust DNA mechanical device controlled by hybridization topology". Nature. 415 (6867): 62–65. 2002Natur.415...62Y. 10.1038/415062a. 11780115. 
  45. ^ DNA machines: Feng, L.; Park, S. H.; Reif, J. H.; Yan, H. (22 September 2003). "A two-state DNA lattice switched by DNA nanoactuator". Angewandte Chemie. 115 (36): 4478–4482. 10.1002/ange.200351818. 
  46. ^ DNA machines: Goodman, R. P.; Heilemann, M.; Doose, S. R.; Erben, C. M.; Kapanidis, A. N.; Turberfield, A. J. (February 2008). "Reconfigurable, braced, three-dimensional DNA nanostructures". Nature Nanotechnology. 3 (2): 93–96. 2008NatNa...3...93G. 10.1038/nnano.2008.3. 18654468. 
  47. ^ Applications: Douglas, Shawn M.; Bachelet, Ido; Church, George M. (17 February 2012). "A logic-gated nanorobot for targeted transport of molecular payloads". Science. 335 (6070): 831–834. 2012Sci...335..831D. 10.1126/science.1214081. 22344439. 
  48. ^ DNA walkers: Shin, Jong-Shik; Pierce, Niles A. (8 September 2004). "A synthetic DNA walker for molecular transport". Journal of the American Chemical Society. 126 (35): 10834–10835. 10.1021/ja047543j. 15339155. 
  49. ^ DNA walkers: Sherman, William B.; Seeman, Nadrian C. (July 2004). "A precisely controlled DNA biped walking device". Nano Letters. 4 (7): 1203–1207. 2004NanoL...4.1203S. 10.1021/nl049527q. 
  50. ^ DNA walkers: Tian, Ye; He, Yu; Chen, Yi; Yin, Peng; Mao, Chengde (11 July 2005). "A DNAzyme that walks processively and autonomously along a one-dimensional track". Angewandte Chemie. 117 (28): 4429–4432. 10.1002/ange.200500703. 
  51. ^ DNA walkers: Bath, Jonathan; Green, Simon J.; Turberfield, Andrew J. (11 July 2005). "A free-running DNA motor powered by a nicking enzyme". Angewandte Chemie International Edition. 44 (28): 4358–4361. 10.1002/anie.200501262. 15959864. 
  52. ^ Functional DNA walkers: Lund, Kyle; Manzo, Anthony J.; Dabby, Nadine; Michelotti, Nicole; Johnson-Buck, Alexander; Nangreave, Jeanette; Taylor, Steven; Pei, Renjun; Stojanovic, Milan N.; Walter, Nils G.; Winfree, Erik; Yan, Hao (13 May 2010). "Molecular robots guided by prescriptive landscapes". Nature. 465 (7295): 206–210. 2010Natur.465..206L. 10.1038/nature09012. 2907518Freely accessible. 20463735. 
  53. ^ Functional DNA walkers: He, Yu; Liu, David R. (November 2010). "Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker". Nature Nanotechnology. 5 (11): 778–782. 2010NatNa...5..778H. 10.1038/nnano.2010.190. 2974042Freely accessible. 20935654. 
  54. ^ Pan, J; Li, F; Cha, TG; Chen, H; Choi, JH (2015). "Recent progress on DNA based walkers". Current Opinion in Biotechnology. 34: 56–64. 10.1016/j.copbio.2014.11.017. 25498478. Retrieved 2015-09-28. 
  55. ^ a b c Kinetic assembly: Yin, Peng; Choi, Harry M. T.; Calvert, Colby R.; Pierce, Niles A. (17 January 2008). "Programming biomolecular self-assembly pathways". Nature. 451 (7176): 318–322. 2008Natur.451..318Y. 10.1038/nature06451. 18202654. 
  56. ^ Fuzzy and Boolean logic gates based on DNA: Zadegan, R. M.; Jepsen, M. D. E.; Hildebrandt, L. L.; Birkedal, V.; Kjems, J. R. (2015). "Construction of a Fuzzy and Boolean Logic Gates Based on DNA". Small. 11 (15): 1811–7. 10.1002/smll.201402755. 25565140. 
  57. ^ Strand displacement cascades: Seelig, G.; Soloveichik, D.; Zhang, D. Y.; Winfree, E. (8 December 2006). "Enzyme-free nucleic acid logic circuits". Science. 314 (5805): 1585–1588. 2006Sci...314.1585S. 10.1126/science.1132493. 17158324. 
  58. ^ Strand displacement cascades: Qian, Lulu; Winfree, Erik (3 June 2011). "Scaling up digital circuit computation with DNA strand displacement cascades". Science. 332 (6034): 1196–1201. 2011Sci...332.1196Q. 10.1126/science.1200520. 21636773. 
  59. ^ a b c d e History/applications: Service, Robert F. (3 June 2011). "DNA nanotechnology grows up". Science. 332 (6034): 1140–1143. 10.1126/science.332.6034.1140. 21636754. 
  60. ^ Applications: Rietman, Edward A. (2001). Molecular engineering of nanosystems. Springer. pp. 209–212. ISBN 978-0-387-98988-4. Retrieved 17 April 2011. 
  61. ^ M. Zadegan, Reza; et, al. (2012). "Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami". ACS Nano. 6 (11): 10050–10053. 10.1021/nn303767b. 
  62. ^ Applications: Jungmann, Ralf; Renner, Stephan; Simmel, Friedrich C. (March 2008). "From DNA nanotechnology to synthetic biology". HFSP journal. 2 (2): 99–109. 10.2976/1.2896331. 2645571Freely accessible. 19404476. 
  63. ^ Lovy, Howard (5 July 2011). "DNA cages can unleash meds inside cells". fiercedrugdelivery.com. Retrieved 22 September 2013. 
  64. ^ Walsh, Anthony; Yin, Hai; Erben, Christoph; Wood, Matthew; Turberfield, Andrew (2011). "DNA Cage Delivery to Mammalian Cells". ACS Nano. ACS Publications. 5 (7): 5427–5432. 10.1021/nn2005574. 21696187. 
  65. ^ Trafton, Anne (4 June 2012). "Researchers achieve RNA interference, in a lighter package". MIT News. Retrieved 22 September 2013. 
  66. ^ Lee, Hyukjin; Lytton-Jean, Abigail; Chen, Yi; Love, Kevin; Park, Angela; Karagiannis, Emmanouil; Sehgal, Alfica; Querbes, William; et al. (2012). "Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery" (PDF). Nature Nanotechnology. Nature. 7 (6): 389–393. 2012NatNa...7..389L. 10.1038/NNANO.2012.73. 
  67. ^ Kim, Kyoung-Ran; Kim, Da-Rae; Lee, Taemin; Yhee, Ji Young; Kim, Byeong-Su; Kwon, Ick Chan; Ahn, Dae-Ro (2013). "Drug delivery by a self-assembled DNA tetrahedron for overcoming drug resistance in breast cancer cells". Chemical Communications. 49 (20): 2010. 10.1039/c3cc38693g. 1359-7345. 23380739. 
  68. ^ a b c Design: Brenneman, Arwen; Condon, Anne (25 September 2002). "Strand design for biomolecular computation". Theoretical Computer Science. 287: 39–58. 10.1016/S0304-3975(02)00135-4. 
  69. ^ Overview: Lin, Chenxiang; Liu, Yan; Rinker, Sherri; Yan, Hao (11 August 2006). "DNA tile based self-assembly: building complex nanoarchitectures". ChemPhysChem. 7 (8): 1641–1647. 10.1002/cphc.200600260. 16832805. 
  70. ^ a b c Design: Dirks, Robert M.; Lin, Milo; Winfree, Erik; Pierce, Niles A. (15 February 2004). "Paradigms for computational nucleic acid design". Nucleic Acids Research. 32 (4): 1392–1403. 10.1093/nar/gkh291. 390280Freely accessible. 14990744. 
  71. ^ Methods: Ellington, A.; Pollard, J. D. (1 May 2001). "Synthesis and purification of oligonucleotides". Current Protocols in Molecular Biology. 10.1002/0471142727.mb0211s42. ISBN 0471142727. 
  72. ^ Methods: Ellington, A.; Pollard, J. D. (1 May 2001). "Purification of oligonucleotides using denaturing polyacrylamide gel electrophoresis". Current Protocols in Molecular Biology. 10.1002/0471142727.mb0212s42. ISBN 0471142727. 
  73. ^ Methods: Gallagher, S. R.; Desjardins, P. (1 July 2011). "Quantitation of nucleic acids and proteins". Current Protocols Essential Laboratory Techniques. 10.1002/9780470089941.et0202s5. ISBN 0470089938. 
  74. ^ Methods: Chory, J.; Pollard, J. D. (1 May 2001). "Separation of small DNA fragments by conventional gel electrophoresis". Current Protocols in Molecular Biology. 10.1002/0471142727.mb0207s47. ISBN 0471142727. 
  75. ^ Methods: Walter, N. G. (1 February 2003). "Probing RNA structural dynamics and function by fluorescence resonance energy transfer (FRET)". Current Protocols in Nucleic Acid Chemistry. 10.1002/0471142700.nc1110s11. ISBN 0471142700. 
  76. ^ Methods: Lin, C.; Ke, Y.; Chhabra, R.; Sharma, J.; Liu, Y.; Yan, H. (2011). "Synthesis and Characterization of Self-Assembled DNA Nanostructures". In Zuccheri, G. and Samorì, B. DNA Nanotechnology: Methods and Protocols. Methods in Molecular Biology. 749. pp. 1–11. 10.1007/978-1-61779-142-0_1. ISBN 978-1-61779-141-3. 
  77. ^ Methods: Bloomfield, Victor A.; Crothers, Donald M.; Tinoco, Jr., Ignacio (2000). Nucleic acids: structures, properties, and functions. Sausalito, Calif: University Science Books. pp. 84–86, 396–407. ISBN 0-935702-49-0. 
  78. ^ a b c History: Pelesko, John A. (2007). Self-assembly: the science of things that put themselves together. New York: Chapman & Hall/CRC. pp. 201, 242, 259. ISBN 978-1-58488-687-7. 
  79. ^ History: See "Current crystallization protocol". Nadrian Seeman Lab.  for a statement of the problem, and "DNA cages containing oriented guests". Nadrian Seeman Laboratory.  for the proposed solution.
  80. ^ a b DNA origami: Rothemund, Paul W. K. (2006). "Scaffolded DNA origami: from generalized multicrossovers to polygonal networks". In Chen, Junghuei; Jonoska, Natasha; Rozenberg, Grzegorz. Nanotechnology: science and computation. Natural Computing Series. New York: Springer. pp. 3–21. 10.1007/3-540-30296-4_1. ISBN 978-3-540-30295-7. 
  81. ^ Nanoarchitecture: Robinson, Bruche H.; Seeman, Nadrian C. (August 1987). "The design of a biochip: a self-assembling molecular-scale memory device". Protein Engineering. 1 (4): 295–300. 10.1093/protein/1.4.295. 3508280. 
  82. ^ Nanoarchitecture: Xiao, Shoujun; Liu, Furong; Rosen, Abbey E.; Hainfeld, James F.; Seeman, Nadrian C.; Musier-Forsyth, Karin; Kiehl, Richard A. (August 2002). "Selfassembly of metallic nanoparticle arrays by DNA scaffolding". Journal of Nanoparticle Research. 4 (4): 313–317. 2002JNR.....4..313X. 10.1023/A:1021145208328. 
  83. ^ History: Hopkin, Karen (August 2011). "Profile: 3-D seer". The Scientist. Retrieved 8 August 2011. 
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