Biomod/2012/UT/Nanowranglers/References

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== Please fill out references ==
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=Related work=
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# Barish, R. D., Rothemund, P. W. K., & Winfree, E. (2005). Two computational primitives for algorithmic self-assembly: copying and counting. Nano letters, 5(12), 2586–92. doi:10.1021/nl052038l
+
 
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# Bath, J., Green, S. J., Allen, K. E., & Turberfield, A. J. (2009). Mechanism for a directional, processive, and reversible DNA motor. Small (Weinheim an der Bergstrasse, Germany), 5(13), 1513–6. doi:10.1002/smll.200900078
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For prior work on designing DNA walkers, please see [2][3][10][21][23][24][30][35][43][44][50][51][53][56][62].
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# Bath, J., Green, S. J., & Turberfield, A. J. (2005). A Free-Running DNA Motor Powered by a Nicking Enzyme. Angewandte Chemie, 117(28), 4432–4435. doi:10.1002/ange.200501262
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# Birac, J. J., Sherman, W. B., Kopatsch, J., Constantinou, P. E., & Seeman, N. C. (2006). Architecture with GIDEON, a program for design in structural DNA nanotechnology. Journal of molecular graphics & modelling, 25(4), 470–80. doi:10.1016/j.jmgm.2006.03.005
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For functional biological motors in cells, please see Myosins [40][39][30], Kinesins [61][8], dyneins [54][19][7], bacterial flagella motors [5][18][52],ATP synthases [42][57][25].
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# Block, S., Blair, D., & Berg, H. (1989). Compliance of bacterial flagella measured with optical tweezers. Nature, 338, 514.
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# Brun, Y. (2008). Solving NP-complete problems in the tile assembly model. Theoretical Computer Science, 395(1), 31–46. doi:10.1016/j.tcs.2007.07.052
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For CHA please see [9][15][62].
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# Carter, A., Garbarino, J. E., Wilson-Kubalek, E. M., Shipley, W. E., Cho, C., Milligan, R. A., Vale, R. D., et al. (2008). Structure and Functional Role of Dynein’s Microtubule-Binding Domain. Science, 322(December), 1691–1695.
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# Carter, N. J., & Cross, R. a. (2005). Mechanics of the kinesin step. Nature, 435(7040), 308–12. doi:10.1038/nature03528
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For software used, please see GIDEON [4] and Kintek [26].
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# Chen, X., & Ellington, A. D. (2010). Shaping up nucleic acid computation. Current opinion in biotechnology, 21(4), 392–400. doi:10.1016/j.copbio.2010.05.003
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# Chhabra, R., Sharma, J., Liu, Y., & Yan, H. (2006). Addressable molecular tweezers for DNA-templated coupling reactions. Nano letters, 6(5), 978–83. doi:10.1021/nl060212f
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=References=
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# Choi, H. M. T., Chang, J. Y., Trinh, L. a, Padilla, J. E., Fraser, S. E., & Pierce, N. a. (2010). Programmable in situ amplification for multiplexed imaging of mRNA expression. Nature biotechnology, 28(11), 1208–12. doi:10.1038/nbt.1692
+
 
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# Dietz, H., Douglas, S. M., & Shih, W. M. (2009). Folding DNA into twisted and curved nanoscale shapes. Science (New York, N.Y.), 325(5941), 725–30. doi:10.1126/science.1174251
+
# Barish, R. D., Rothemund, P. W. K. & Winfree, E. Two computational primitives for algorithmic self-assembly: copying and counting. Nano letters 5, 2586–92 (2005).
-
# Dimroth, P., Wang, H., Grabe, M., & Oster, G. (1999). Energy transduction in the sodium F-ATPase of Propionigenium modestum. Proceedings of the National Academy of Sciences of the United States of America, 96(9), 4924–9. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=21793&tool=pmcentrez&rendertype=abstract
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#  Bath, J., Green, S. J. & Turberfield, A. J. A Free-Running DNA Motor Powered by a Nicking Enzyme. Angewandte Chemie 117, 4432–4435 (2005).
-
# Ding, B., Deng, Z., Yan, H., Cabrini, S., Zuckermann, R. N., & Bokor, J. (2010). Gold nanoparticle self-similar chain structure organized by DNA origami. Journal of the American Chemical Society, 132(10), 3248–9. doi:10.1021/ja9101198
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# Bath, J., Green, S. J., Allen, K. E. & Turberfield, A. J. Mechanism for a directional, processive, and reversible DNA motor. Small (Weinheim an der Bergstrasse, Germany) 5, 1513–6 (2009).
-
# Dirks, R. M., & Pierce, N. a. (2004). Triggered amplification by hybridization chain reaction. Proceedings of the National Academy of Sciences of the United States of America, 101(43), 15275–8. doi:10.1073/pnas.0407024101
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# Birac, J. J., Sherman, W. B., Kopatsch, J., Constantinou, P. E. & Seeman, N. C. Architecture with GIDEON, a program for design in structural DNA nanotechnology. Journal of molecular graphics & modelling 25, 470–80 (2006).
-
# Douglas, S. M., Bachelet, I., & Church, G. M. (2012). A logic-gated nanorobot for targeted transport of molecular payloads. Science (New York, N.Y.), 335(6070), 831–4. doi:10.1126/science.1214081
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# Block, S., Blair, D. & Berg, H. Compliance of bacterial flagella measured with optical tweezers. Nature 338, 514 (1989).
-
# Douglas, S. M., Dietz, H., Liedl, T., Högberg, B., Graf, F., & Shih, W. M. (2009). Self-assembly of DNA into nanoscale three-dimensional shapes. Nature, 459(7245), 414–8. doi:10.1038/nature08016
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# Brun, Y. Solving NP-complete problems in the tile assembly model. Theoretical Computer Science 395, 31–46 (2008).
-
# Fahrner, K., Ryu, W. S., & Berg, H. C. (2003). Bacterial flagellar switching under load. Nature, 423(June), 938.
+
# Carter, A. et al. Structure and Functional Role of Dynein’s Microtubule-Binding Domain. Science 322, 1691–1695 (2008).
-
# Gennerich, A., Carter, A. P., Reck-Peterson, S. L., & Vale, R. D. (2007). Force-induced bidirectional stepping of cytoplasmic dynein. Cell, 131(5), 952–65. doi:10.1016/j.cell.2007.10.016
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# Carter, N. J. & Cross, R. a Mechanics of the kinesin step. Nature 435, 308–12 (2005).
-
# Glotzer, S. C. (2004). Self-Assembly of Patchy Particles. Nano Letters, 4(8), 1407–1413. doi:10.1021/nl0493500
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# Chen, X. & Ellington, A. D. Shaping up nucleic acid computation. Current opinion in biotechnology 21, 392–400 (2010).
-
# Green, S., Bath, J., & Turberfield, a. (2008). Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion. Physical Review Letters, 101(23), 20–23. doi:10.1103/PhysRevLett.101.238101
+
# Chhabra, R., Sharma, J., Liu, Y. & Yan, H. Addressable molecular tweezers for DNA-templated coupling reactions. Nano letters 6, 978–83 (2006).
-
# Grierer, A. (1966). Model for DNA and Protein Interaction and the Function of the Operator. Nature, 212(December), 1480.
+
# Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nature biotechnology 28, 1208–12 (2010).
-
# Gu, H., Chao, J., Xiao, S.-J., & Seeman, N. C. (2010). A proximity-based programmable DNA nanoscale assembly line. Nature, 465(7295), 202–5. doi:10.1038/nature09026
+
# Dietz, H., Douglas, S. M. & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science (New York, N.Y.) 325, 725–30 (2009).
-
# He, Y., & Liu, D. R. (2010). Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker. Nature nanotechnology, 5(11), 778–82. doi:10.1038/nnano.2010.190
+
# Dimroth, P., Wang, H., Grabe, M. & Oster, G. Energy transduction in the sodium F-ATPase of Propionigenium modestum. Proceedings of the National Academy of Sciences of the United States of America 96, 4924–9 (1999).
-
# Itoh, H., Takahashi, A., Adachi, K., Noji, H., Yasuda, R., Yoshida, M., & Kinosita, K. J. (2004). Mechanically driven ATP synthesis by F 1 -ATPase. Nature, 427(January), 465–468. doi:10.1038/nature02229.1.
+
# Ding, B. et al. Gold nanoparticle self-similar chain structure organized by DNA origami. Journal of the American Chemical Society 132, 3248–9 (2010).
-
# Kallenbach, N. R., Ma, R.-I., & Seeman, N. C. (1983). An immobile nucleic acid junction constructed from oligonucleotides. Nature, 305(27), 829.
+
# Dirks, R. M. & Pierce, N. a Triggered amplification by hybridization chain reaction. Proceedings of the National Academy of Sciences of the United States of America 101, 15275–8 (2004).
-
# Kallenbach, N. R., Petrillol, M. L., & Laboratories, L. (1986). Three-arm nucleic acid junctions are flexible. Nucleic acids research, 14(24), 9745–9753.
+
# Douglas, S. M., Bachelet, I. & Church, G. M. A logic-gated nanorobot for targeted transport of molecular payloads. Science (New York, N.Y.) 335, 831–4 (2012).
-
# Kinbara, K., & Aida, T. (2005). Toward intelligent molecular machines: directed motions of biological and artificial molecules and assemblies. Chemical reviews, 105(4), 1377–400. doi:10.1021/cr030071r
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# Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–8 (2009).
-
# Li, B., Ellington, A. D., & Chen, X. (2011). Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic acids research, 39(16), e110. doi:10.1093/nar/gkr504
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# Fahrner, K., Ryu, W. S. & Berg, H. C. Bacterial flagellar switching under load. Nature 423, 938 (2003).
-
# Liu, C., Jonoska, N., & Seeman, N. C. (2009). Reciprocal DNA nanomechanical devices controlled by the same set strands. Nano letters, 9(7), 2641–7. doi:10.1021/nl901008k
+
# Gennerich, A., Carter, A. P., Reck-Peterson, S. L. & Vale, R. D. Force-induced bidirectional stepping of cytoplasmic dynein. Cell 131, 952–65 (2007).
-
# Liu, H., Chen, Y., He, Y., Ribbe, A. E., & Mao, C. (2006). Approaching The Limit: Can One DNA Oligonucleotide Assemble into Large Nanostructures? Angewandte Chemie, 118(12), 1976–1979. doi:10.1002/ange.200504022
+
# Glotzer, S. C. Self-Assembly of Patchy Particles. Nano Letters 4, 1407–1413 (2004).
-
# Lu, Y., & Liu, J. (2006). Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Current opinion in biotechnology, 17(6), 580–8. doi:10.1016/j.copbio.2006.10.004
+
# Green, S., Bath, J. & Turberfield, a. Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion. Physical Review Letters 101, 20–23 (2008).
-
# Lund, K., Manzo, A. J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., et al. (2010). Molecular robots guided by prescriptive landscapes. Nature, 465(7295), 206–10. doi:10.1038/nature09012
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# Grierer, A. Model for DNA and Protein Interaction and the Function of the Operator. Nature 212, 1480 (1966).
-
# Macfarlane, R. J., Lee, B., Jones, M. R., Harris, N., Schatz, G. C., & Mirkin, C. a. (2011). Nanoparticle superlattice engineering with DNA. Science (New York, N.Y.), 334(6053), 204–8. doi:10.1126/science.1210493
+
# Gu, H., Chao, J., Xiao, S.-J. & Seeman, N. C. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–5 (2010).
-
# Mao, C., Sun, W., Shen, Z., & Seeman, N. C. (1999). A nanomechanical device based on the B-Z transition of DNA. Nature, 397(6715), 144–6. doi:10.1038/16437
+
# He, Y. & Liu, D. R. Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker. Nature nanotechnology 5, 778–82 (2010).
-
# McNaughton, B. R., Cronican, J. J., Thompson, D. B., & Liu, D. R. (2009). Mammalian cell penetration, siRNA transfection, and DNA transfection by supercharged proteins. Proceedings of the National Academy of Sciences of the United States of America, 106(15), 6111–6. doi:10.1073/pnas.0807883106
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# Itoh, H. et al. Mechanically driven ATP synthesis by F 1 -ATPase. Nature 427, 465–468 (2004).
-
# Mehta, a D., Rock, R. S., Rief, M., Spudich, J. a, Mooseker, M. S., & Cheney, R. E. (1999). Myosin-V is a processive actin-based motor. Nature, 400(6744), 590–3. doi:10.1038/23072
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#  Johnson, K. A. Transient state kinetic analysis of enzyme reaction pathways. The Enzymes XX, 1-61 (1992).
-
# Mermall, V., Post, P. L., & Mooseker, M. S. (1998). Unconventional Myosins in Cell Movement, Memrane Traffic, and Signal Transduction. Science, 279(January), 527.
+
# Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829 (1983).
-
# Mirkin, C. A. (2000). Programming the Assembly of Two- and Three-Dimensional Architectures with DNA and Nanoscale Inorganic Building Blocks. Inorg. Chem., 39, 2258–2272.
+
# Kallenbach, N. R., Petrillol, M. L. & Laboratories, L. Three-arm nucleic acid junctions are flexible. Nucleic acids research 14, 9745–9753 (1986).
-
# Noji, H., Yasuda, R., Yoshida, M., & Kinosita, K. J. (1997). Direct observation of the rotation of F1-ATPase. Nature, 386, 299.
+
#  Kelly, T. R. Molecular motors: synthetic DNA-based walkers inspired by kinesin. Angewandte Chemie (International ed. in English) 44, 4124–7 (2005).
-
# Omabegho, T., Sha, R., & Seeman, N. C. (2009). A bipedal DNA Brownian motor with coordinated legs. Science (New York, N.Y.), 324(5923), 67–71. doi:10.1126/science.1170336
+
# Kinbara, K. & Aida, T. Toward intelligent molecular machines: directed motions of biological and artificial molecules and assemblies. Chemical reviews 105, 1377–400 (2005).
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# Pei, R., Taylor, S. K., Stefanovic, D., Rudchenko, S., Mitchell, T. E., & Stojanovic, M. N. (2006). Behavior of Polycatalytic Assemblies in a Substrate-Displaying Matrix Nanoassembly Incorporating Catalytic Kinesis because they couple diffusion ( movement ) to a catalytic process . For example ,. Journal of the American Chemical Society, 128, 12693–12699.
+
# Li, B., Ellington, A. D. & Chen, X. Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic acids research 39, e110 (2011).
-
# Peng, X., Chen, H., Draney, D. R., Volcheck, W., Schutz-Geschwender, A., & Olive, D. M. (2009). A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays. Analytical biochemistry, 388(2), 220–8. doi:10.1016/j.ab.2009.02.024
+
# Liu, C., Jonoska, N. & Seeman, N. C. Reciprocal DNA nanomechanical devices controlled by the same set strands. Nano letters 9, 2641–7 (2009).
-
# Rothemund, P. W. K. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297–302. doi:10.1038/nature04586
+
# Liu, H., Chen, Y., He, Y., Ribbe, A. E. & Mao, C. Approaching The Limit: Can One DNA Oligonucleotide Assemble into Large Nanostructures? Angewandte Chemie 118, 1976–1979 (2006).
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# Seeman, N. C. (1991). The use of branched DNA for nanoscale fabrication. Nanotechnology, 149.
+
# Lu, Y. & Liu, J. Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Current opinion in biotechnology 17, 580–8 (2006).
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# Seeman, N. C. (1999). DNA engineering and its application to nanotechnology. Trends in Biotechnology, 7799(99), 437–443.
+
# Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–10 (2010).
-
# Seeman, N. C., & Kallenbach, N. R. (1983). Design of immobile nucleic acid junctions. Biophysics, 44(November), 201–209.
+
# Macfarlane, R. J. et al. Nanoparticle superlattice engineering with DNA. Science (New York, N.Y.) 334, 204–8 (2011).
-
# Sherman, W. B., & Seeman, N. C. (2004). A Precisely Controlled DNA Biped Walking Device. Nano Letters, 4(7), 1203–1207. doi:10.1021/nl049527q
+
# Mao, C., Sun, W., Shen, Z. & Seeman, N. C. A nanomechanical device based on the B-Z transition of DNA. Nature 397, 144–6 (1999).
-
# Shin, J.-S., & Pierce, N. a. (2004). A synthetic DNA walker for molecular transport. Journal of the American Chemical Society, 126(35), 10834–5. doi:10.1021/ja047543j
+
# McNaughton, B. R., Cronican, J. J., Thompson, D. B. & Liu, D. R. Mammalian cell penetration, siRNA transfection, and DNA transfection by supercharged proteins. Proceedings of the National Academy of Sciences of the United States of America 106, 6111–6 (2009).
-
# Sowa, Y., Rowe, A. D., Leake, M. C., Yakushi, T., Homma, M., Ishijima, A., & Berry, R. M. (2005). Direct observation of steps in rotation of the bacterial flagellar motor. Nature, 437(7060), 916–9. doi:10.1038/nature04003
+
# Mehta, a D. et al. Myosin-V is a processive actin-based motor. Nature 400, 590–3 (1999).
-
# Tian, Y., He, Y., Chen, Y., Yin, P., & Mao, C. (2005). A DNAzyme that walks processively and autonomously along a one-dimensional track. Angewandte Chemie (International ed. in English), 44(28), 4355–8. doi:10.1002/anie.200500703
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# Mermall, V., Post, P. L. & Mooseker, M. S. Unconventional Myosins in Cell Movement, Memrane Traffic, and Signal Transduction. Science 279, 527 (1998).
-
# Vale, R. D. (2003). The molecular motor toolbox for intracellular transport. Cell, 112(4), 467–80. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/12600311
+
# Mirkin, C. A. Programming the Assembly of Two- and Three-Dimensional Architectures with DNA and Nanoscale Inorganic Building Blocks. Inorg. Chem. 39, 2258–2272 (2000).
-
# Vale, R. D., Funatsu, T., Pierce, D. W., & Romberg, L. (1996). Direct observation of single kinesin molecules moving along microtubules. Nature, 380(6573), 451–453. doi:10.1038/380451a0.Direct
+
# Noji, H., Yasuda, R., Yoshida, M. & Kinosita, K. J. Direct observation of the rotation of F1-ATPase. Nature 386, 299 (1997).
-
# Venkataraman, S., Dirks, R. M., Rothemund, P. W. K., Winfree, E., & Pierce, N. a. (2007). An autonomous polymerization motor powered by DNA hybridization. Nature nanotechnology, 2(8), 490–4. doi:10.1038/nnano.2007.225
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# Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science (New York, N.Y.) 324, 67–71 (2009).
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# Watson, J. D., & Crick, F. H. C. (1953). A Structure for Deoxyribose Nucleic Acid. Nature, 171(April), 738.
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# Pei, R. et al. Behavior of Polycatalytic Assemblies in a Substrate-Displaying Matrix Nanoassembly Incorporating Catalytic Kinesis because they couple diffusion ( movement ) to a catalytic process . For example ,. Journal of the American Chemical Society 128, 12693–12699 (2006).
-
# Wei, B., Dai, M., & Yin, P. (2012). Complex shapes self-assembled from single-stranded DNA tiles. Nature, 485(7400), 623–6. doi:10.1038/nature11075
+
# Peng, X. et al. A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays. Analytical biochemistry 388, 220–8 (2009).
-
# Wendt, T. G., Volkmann, N., Skiniotis, G., Goldie, K. N., Müller, J., Mandelkow, E., & Hoenger, A. (2002). Microscopic evidence for a minus-end-directed power stroke in the kinesin motor ncd. The EMBO journal, 21(22), 5969–78. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=137211&tool=pmcentrez&rendertype=abstract
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# Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
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# Woo, S., & Rothemund, P. W. K. (2011). Programmable molecular recognition based on the geometry of DNA nanostructures. Nature chemistry, 3(8), 620–7. doi:10.1038/nchem.1070
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# Seeman, N. C. The use of branched DNA for nanoscale fabrication. Nanotechnology 149 (1991).
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# Yildiz, A., Tomishige, M., Vale, R. D., & Selvin, P. R. (2004). Kinesin walks hand-over-hand. Science (New York, N.Y.), 303(5658), 676–8. doi:10.1126/science.1093753
+
# Seeman, N. C. DNA engineering and its application to nanotechnology. Trends in Biotechnology 7799, 437–443 (1999).
-
# Yin, P., Choi, H. M. T., Calvert, C. R., & Pierce, N. a. (2008). Programming biomolecular self-assembly pathways. Nature, 451(7176), 318–22. doi:10.1038/nature06451
+
# Seeman, N. C. & Kallenbach, N. R. Design of immobile nucleic acid junctions. Biophysics 44, 201–209 (1983).
-
# Yurke, B., Turber, A. J., Jr, A. P. M., Simmel, F. C., & Neumann, J. L. (2000). A DNA-fuelled molecular machine made of DNA. Nature, 406(August), 605–608.
+
# Sherman, W. B. & Seeman, N. C. A Precisely Controlled DNA Biped Walking Device. Nano Letters 4, 1203–1207 (2004).
-
# Zhang, D. Y., Turberfield, A. J., Yurke, B., & Winfree, E. (2007). Engineering entropy-driven reactions and networks catalyzed by DNA. Science (New York, N.Y.), 318(5853), 1121–5. doi:10.1126/science.1148532
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# Shin, J.-S. & Pierce, N. a A synthetic DNA walker for molecular transport. Journal of the American Chemical Society 126, 10834–5 (2004).
-
# Zhang, D. Y., & Winfree, E. (2009). Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society, 131(47), 17303–14. doi:10.1021/ja906987s
+
# Sowa, Y. et al. Direct observation of steps in rotation of the bacterial flagellar motor. Nature 437, 916–9 (2005).
-
# Zhang, D. Y., & Winfree, E. (2010). Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic acids research, 38(12), 4182–97. doi:10.1093/nar/gkq088
+
# Tian, Y., He, Y., Chen, Y., Yin, P. & Mao, C. A DNAzyme that walks processively and autonomously along a one-dimensional track. Angewandte Chemie (International ed. in English) 44, 4355–8 (2005).
-
# Zheng, J., Birktoft, J. J., Chen, Y., Wang, T., Sha, R., Pamela, E., Ginell, S. L., et al. (2009). From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal. Nature, 461(7260), 74–77. doi:10.1038/nature08274.From
+
# Vale, R. D. The molecular motor toolbox for intracellular transport. Cell 112, 467–80 (2003).
 +
# Vale, R. D., Funatsu, T., Pierce, D. W. & Romberg, L. Direct observation of single kinesin molecules moving along microtubules. Nature 380, 451–453 (1996).
 +
# Venkataraman, S., Dirks, R. M., Rothemund, P. W. K., Winfree, E. & Pierce, N. a An autonomous polymerization motor powered by DNA hybridization. Nature nanotechnology 2, 490–4 (2007).
 +
# Wang H, Oster G. 1998. Energy transduction in the F1 motor of ATP synthase. Nature 396:279–82
 +
# Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–6 (2012).
 +
# Wendt, T. G. et al. Microscopic evidence for a minus-end-directed power stroke in the kinesin motor ncd. The EMBO journal 21, 5969–78 (2002).
 +
# Woo, S. & Rothemund, P. W. K. Programmable molecular recognition based on the geometry of DNA nanostructures. Nature chemistry 3, 620–7 (2011).
 +
# Yildiz, A., Tomishige, M., Vale, R. D. & Selvin, P. R. Kinesin walks hand-over-hand. Science (New York, N.Y.) 303, 676–8 (2004).
 +
# Yin, P., Choi, H. M. T., Calvert, C. R. & Pierce, N. a Programming biomolecular self-assembly pathways. Nature 451, 318–22 (2008).
 +
# Yurke, B., Turber, A. J., Jr, A. P. M., Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000).
 +
# Zhang, D. Y., Turberfield, A. J., Yurke, B. & Winfree, E. Engineering entropy-driven reactions and networks catalyzed by DNA. Science (New York, N.Y.) 318, 1121–5 (2007).
 +
# Zhang, D. Y. & Winfree, E. Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society 131, 17303–14 (2009).
 +
# Zhang, D. Y. & Winfree, E. Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic acids research 38, 4182–97 (2010).
 +
# Zheng, J. et al. From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal. Nature 461, 74–77 (2009).

Current revision


Undergraduate DNA nanotechnology research group from the University of Texas at Austin



Related work

For prior work on designing DNA walkers, please see [2][3][10][21][23][24][30][35][43][44][50][51][53][56][62].

For functional biological motors in cells, please see Myosins [40][39][30], Kinesins [61][8], dyneins [54][19][7], bacterial flagella motors [5][18][52],ATP synthases [42][57][25].

For CHA please see [9][15][62].

For software used, please see GIDEON [4] and Kintek [26].

References

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