ננוטכנולוגיית DNA
הערות שוליים

1 2  DNA polyhedra: Goodman, Russel P.; Schaap, Iwan A. T.; Tardin, C. F.; Erben, Christof M.; Berry, Richard M.; Schmidt, C.F.; Turberfield, Andrew J. (9 December 2005). "Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication". Science 310 (5754): 1661–1665. Bibcode 2005Sci...310.1661G. doi:10.1126/science.1120367. PMID 16339440
1 2 3  Overview: Mao, Chengde (December 2004). "The emergence of complexity: lessons from DNA". PLoS Biology 2 (12): 2036–2038. doi:10.1371/journal.pbio.0020431. PMC 535573. PMID 15597116.
^ a b c d e Overview: Seeman, Nadrian C. (June 2004). "Nanotechnology and the double helix". Scientific American 290 (6): 64–75. doi:10.1038/scientificamerican0604-64. PMID 15195395.
1 2 3 4 5  Overview: Seeman, Nadrian C. (June 2004). "Nanotechnology and the double helix". Scientific American 290 (6): 64–75. doi:10.1038/scientificamerican0604-64. PMID 15195395.
↑  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.
1 2 3 4 5 6  Overview: Seeman, Nadrian C. (2010). "Nanomaterials based on DNA". Annual Review of Biochemistry 79: 65–87. doi:10.1146/annurev-biochem-060308-102244. PMID 20222824.
↑  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.
1 2 3 4  Dynamic DNA nanotechnology: Zhang, David Y.; Seelig, Georg (February 2011). "Dynamic DNA nanotechnology using strand-displacement reactions". Nature Chemistry 3 (2): 103–113. doi:10.1038/nchem.957. PMID 21258382
1 2 3 4 5  Structural DNA nanotechnology: Seeman, Nadrian C. (November 2007). "An overview of structural DNA nanotechnology". Molecular Biotechnology 37 (3): 246–257. doi:10.1007/s12033-007-0059-4. PMID 17952671
↑  Dynamic DNA nanotechnology: Lu, Yi; Liu, Juewen (December 2006). "Functional DNA nanotechnology: Emerging applications of DNAzymes and aptamers". Current Opinion in Biotechnology 17 (6): 580–588. doi:10.1016/j.copbio.2006.10.004. PMID 17056247
1 2 3  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.
↑  History: See "Current crystallization protocol". Nadrian Seeman Lab. for a statement of the problem, and "DNA cages containing oriented guests". Nadiran Seeman Laboratory. for the proposed solution.
1 2 3 4 5 6 7 8  Overview: Pinheiro, Andre V.; Han, Dongran; Shih, William M.; Yan, Hao (December 2011). "Challenges and opportunities for structural DNA nanotechnology". Nature Nanotechnology 6 (12): 763–772. doi:10.1038/nnano.2011.187. PMID 22056726.
1 2 3 4 5  History/applications: Service, Robert F. (3 June 2011). "DNA nanotechnology grows up". Science 332 (6034): 1140–1143. doi:10.1126/science.332.6034.1140.
1 2 3 4  DNA machines: Bath, Jonathan; Turberfield, Andrew J. (May 2007). "DNA nanomachines". Nature Nanotechnology 2 (5): 275–284. Bibcode 2007NatNa...2..275B. doi:10.1038/nnano.2007.104. PMID 18654284.
↑  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. doi:10.1093/protein/1.4.295. PMID 3508280.
1 2  Overview: Endo, Masayuki; Sugiyama, Hiroshi (12 October 2009). "Chemical approaches to DNA nanotechnology". ChemBioChem 10 (15): 2420–2443. doi:10.1002/cbic.200900286. PMID 19714700.
↑  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. doi:10.1007/3-540-30296-4_1. ISBN 978-3-540-30295-7.
1 2 3  DNA origami: Rothemund, Paul W. K. (16 March 2006). "Folding DNA to create nanoscale shapes and patterns". Nature 440 (7082): 297–302. Bibcode 2006Natur.440..297R. doi:10.1038/nature04586. PMID 16541064.
1 2  DNA origami: Douglas, Shawn M.; Dietz, Hendrik; Liedl, Tim; H?gberg, Bj?rn; Graf, Franziska; Shih, William M. (21 May 2009). "Self-assembly of DNA into nanoscale three-dimensional shapes". Nature 459 (7245): 414–418. Bibcode 2009Natur.459..414D. doi:10.1038/nature08016. PMC 2688462. PMID 19458720.
↑  History: Hopkin, Karen (August 2011). "Profile: 3-D seer". The Scientist. Retrieved 8 August 2011.
1 2 3  History: Seeman, Nadrian (9 June 2010). "Structural DNA nanotechnology: growing along with Nano Letters". Nano Letters 10 (6): 1971–1978. Bibcode 2010NanoL..10.1971S. doi:10.1021/nl101262u. PMC 2901229. PMID 20486672.
1 2 3  Design: Brenneman, Arwen; Condon, Anne (25 September 2002). "Strand design for biomolecular computation". Theoretical Computer Science 287: 39–58. doi:10.1016/S0304-3975(02)00135-4.
1 2 3  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. doi:10.1093/nar/gkh291. PMC 390280. PMID 14990744.
↑  Methods: Ellington, Andrew; Pollard, Jr., Jack D. (1 May 2001). "Synthesis and purification of oligonucleotides". Current Protocols in Molecular Biology. doi:10.1002/0471142727.mb0211s42. ISBN 0471142727.
↑  Methods: Ellington, A.; Pollard, Jr., J. D. (1 May 2001). "Purification of oligonucleotides using denaturing polyacrylamide gel electrophoresis". Current Protocols in Molecular Biology. doi:10.1002/0471142727.mb0212s42. ISBN 0471142727.
↑  Methods: Gallagher, S. R.; Desjardins, P. (1 July 2011). "Quantitation of nucleic acids and proteins". Current Protocols Essential Laboratory Techniques. doi:10.1002/9780470089941.et0202s5. ISBN 0470089938.
↑  Methods: Chory, Joanne; Pollard, Jr., Jack D. (1 May 2001). "Separation of small DNA fragments by conventional gel electrophoresis". Current Protocols in Molecular Biology. doi:10.1002/0471142727.mb0207s47. ISBN 0471142727.
↑  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. doi:10.1002/0471142700.nc1110s11. ISBN 0471142700.
↑  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 Samor?, B. DNA Nanotechnology: Methods and Protocols. Methods in Molecular Biology. 749. pp. 1–11. doi:10.1007/978-1-61779-142-0_1. ISBN 978-1-61779-141-3.
↑  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.
1 2 3 4  Design: Feldkamp, Udo; Niemeyer, Christof M. (13 March 2006). "Rational design of DNA nanoarchitectures". Angewandte Chemie International Edition 45 (12): 1856–1876. doi:10.1002/anie.200502358. PMID 16470892.
↑  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. doi:10.1002/cphc.200600260. PMID 16832805.
1 2 3  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. Bibcode 2008Natur.451..318Y. doi:10.1038/nature06451. PMID 18202654.
↑  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. Bibcode 1998Natur.394..539W. doi:10.1038/28998. PMID 9707114.
↑  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. doi:10.1021/ja982824a.
↑  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. doi:10.1021/ja9900398.
↑  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. doi:10.1039/b605212f. PMID 17036134.
↑  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. Bibcode 2005NanoL...5..661M. doi:10.1021/nl050084f. PMID 15826105.
1 2  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. doi:10.1371/journal.pbio.0020424. PMC 534809. PMID 15583715.
↑  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. Bibcode 2005NanoL...5.2586B. doi:10.1021/nl052038l. PMID 16351220.
↑  Other arrays: Strong, Michael (March 2004). "Protein Nanomachines". PLoS Biology 2 (3): e73. doi:10.1371/journal.pbio.0020073. PMC 368168. PMID 15024422.
↑  Yan, Hao; Park, Sung Ha; Finkelstein, Gleb; Reif, John H.; Labean, Thomas H. (26 September 2003). "DNA-templated self-assembly of protein arrays and highly conductive nanowires". Science 301 (5641): 1882–1884. doi:10.1126/science.1089389. PMID 14512621.
↑  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. doi:10.1021/ja044319l. PMID 15600335.
↑  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. Bibcode 2009Natur.461...74Z. doi:10.1038/nature08274. PMC 2764300. PMID 19727196.
↑  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. doi:10.1021/ja00084a006.
↑  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. doi:10.1038/nature02307. PMID 14961116.
1 2  DNA boxes: Andersen, Ebbe S.; Dong, Mingdong; Nielsen, Morten M.; Jahn, Kasper; Subramani, Ramesh; Mamdouh, Wael; Golas, Monika M.; Sander, Bjoern; Stark, Holger (7 May 2009). "Self-assembly of a nanoscale DNA box with a controllable lid". Nature 459 (7243): 73–76. Bibcode 2009Natur.459...73A. doi:10.1038/nature07971. PMID 19424153.
↑  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. Bibcode 2009NanoL...9.2445K. doi:10.1021/nl901165f. PMID 19419184.
↑  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. Bibcode 2006NanoL...6.1502Z. doi:10.1021/nl060994c. PMID 16834438.
↑  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. doi:10.1002/ange.200690141.
↑  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. doi:10.1002/anie.200702767. PMID 17763481.
↑  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. Bibcode 2010NatNa...5...61M. doi:10.1038/nnano.2009.311. PMID 19898497.
↑  Nanoarchitecture: Liu, Jianfei; Geng, Yanli; Pound, Elisabeth; Gyawali, Shailendra; Ashton, Jeffrey R.; Hickey, John; Woolley, Adam T.; Harb, John N. (22 March 2011). "Metallization of branched DNA origami for nanoelectronic circuit fabrication". ACS Nano 5 (3): 2240–2247. doi:10.1021/nn1035075. PMID 21323323.
↑  Nanoarchitecture: Deng, Zhaoxiang; Mao, Chengde (6 August 2004). "Molecular lithography with DNA nanostructures". Angewandte Chemie International Edition 43 (31): 4068. doi:10.1002/anie.200460257.
↑  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. Bibcode 1999Natur.397..144M. doi:10.1038/16437. PMID 9923675.
↑  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. Bibcode 2000Natur.406..605Y. doi:10.1038/35020524. PMID 10949296.
↑  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. Bibcode 2002Natur.415...62Y. doi:10.1038/415062a. PMID 11780115.
↑  DNA machines: Feng, Liping; Park, Sung Ha; Reif, John H.; Yan, Hao (22 September 2003). "A two-state DNA lattice switched by DNA nanoactuator". Angewandte Chemie 115 (36): 4478. doi:10.1002/ange.200351818.
↑  DNA machines: Goodman, Russell P.; Heilemann, Mike; Doose, S?ren; Erben, Cristoph M.; Kapanidis, Achillefs N.; Turberfield, Andrew J. (February 2008). "Reconfigurable, braced, three-dimensional DNA nanostructures". Nature Nanotechnology 3 (2): 93–96. doi:10.1038/nnano.2008.3. PMID 18654468.
↑  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. doi:10.1126/science.1214081.
↑  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. doi:10.1021/ja047543j. PMID 15339155.
↑  DNA walkers: Sherman, William B.; Seeman, Nadrian C. (July 2004). "A precisely controlled DNA biped walking device". Nano Letters 4 (7): 1203–1207. Bibcode 2004NanoL...4.1203S. doi:10.1021/nl049527q.
↑  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. doi:10.1002/ange.200500703.
↑  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. doi:10.1002/anie.200501262.
↑  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. Bibcode 2010Natur.465..206L. doi:10.1038/nature09012. PMC 2907518. PMID 20463735.
↑  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. Bibcode 2010NatNa...5..778H. doi:10.1038/nnano.2010.190. PMC 2974042. PMID 20935654.
↑  Strand displacement cascades: Seelig, Georg; Soloveichik, David; Zhang, David Y.; Winfree, Erik (8 December 2006). "Enzyme-free nucleic acid logic circuits". Science 314 (5805): 1585–1588. doi:10.1126/science.1132493. PMID 17158324.
↑  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. doi:10.1126/science.1200520. PMID 21636773.
↑  Applications: Rietman, Edward A. (2001). Molecular engineering of nanosystems. Springer. pp. 209–212. ISBN 978-0-387-98988-4. Retrieved 17 April 2011.
↑  Applications: Jungmann, Ralf; Renner, Stephan; Simmel, Friedrich C. (March 2008). "From DNA nanotechnology to synthetic biology". HFSP journal 2 (2): 99–109. doi:10.2976/1.2896331. PMC 2645571. PMID 19404476.
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בקרת זהויות :  NLI: 987012402016005171  LCCN: sh2020006318 
צומת Holliday: ארבעת הגדילים שייכים לצומת ה־DNA- בעל 4 זרועות, מבנה זה ממקסם את מספר זוגות הבסיסים המתאימים ביו ארבעת הגדילים, כאשר A נקשר ל-T ו-C נקשר ל-G. ראה תמונה זו כדי לקבל מודל יותר ריאלי של צומת 4 זרועות, המראה את המבנה השלישוני שלו.
הקומפלקס הסופרמולקולרי DX) double-crossover) מורכב מ-5 גדילי DNA שיוצרים 2 סלילים דו גדיליים, במחצית העליונה והתחתונה של התמונה. ישנן 2 נקודות חיתוך בהן הגדילים עוברים מסליל אחד לסליל השני.
יצירת מערך DX. תמונה של המערך המורכב במיקרוסקופ כח אטומי. ניתן לראות את האריחים המרכיבים את המערך.
יצירת מערך DX באופן סכמתי. כל לבנה מייצגת סליל דו גדילי של DNA, כאשר הקצוות שלהם דביקים. קומפלקס ה-DX למעלה יתחבר לקומפלקס שמופיע למטה
משמאל: מודל של אריח DNA המשמש ליצירת סריג זמני. מימין: תמונה של הסריג המורכב במיקרוסקופ כח אטומי
דוגמה לסריג דו־ממדי קבוע שיוצר תבנית של פרקטל: ה-Sierpinski gasket
דוגמה לסריג דו־ממדי קבוע שיוצר תבנית של פרקטל: מערכי DNA המציגים Sierpinski gasket