Biomod/2012/UT/Nanowranglers/References

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== References ==
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=Related work=
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<pre style="color:red; font-size:127%">
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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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Note to NanoWranglers - to cite any of the below references, please say [Cite XXX, 2007].
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Note to Ben - Before wiki freeze, replace all [Cite XXX, 2007] with their appropriate numbers and delete
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all uncited sources.
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</pre>
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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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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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# 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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# 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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For CHA please see [9][15][62].
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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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# Block, S., Blair, D., & Berg, H. (1989). Compliance of bacterial flagella measured with optical tweezers. Nature, 338, 514.
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For software used, please see GIDEON [4] and Kintek [26].
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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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# 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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=References=
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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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# 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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# 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).
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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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#  Bath, J., Green, S. J. & Turberfield, A. J. A Free-Running DNA Motor Powered by a Nicking Enzyme. Angewandte Chemie 117, 4432–4435 (2005).
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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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# 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).
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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
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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).
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# 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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# Block, S., Blair, D. & Berg, H. Compliance of bacterial flagella measured with optical tweezers. Nature 338, 514 (1989).
-
# 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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# Brun, Y. Solving NP-complete problems in the tile assembly model. Theoretical Computer Science 395, 31–46 (2008).
-
# 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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# Carter, A. et al. Structure and Functional Role of Dynein’s Microtubule-Binding Domain. Science 322, 1691–1695 (2008).
-
# 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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# Carter, N. J. & Cross, R. a Mechanics of the kinesin step. Nature 435, 308–12 (2005).
-
# 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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# Chen, X. & Ellington, A. D. Shaping up nucleic acid computation. Current opinion in biotechnology 21, 392–400 (2010).
-
# Fahrner, K., Ryu, W. S., & Berg, H. C. (2003). Bacterial flagellar switching under load. Nature, 423(June), 938.
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# Chhabra, R., Sharma, J., Liu, Y. & Yan, H. Addressable molecular tweezers for DNA-templated coupling reactions. Nano letters 6, 978–83 (2006).
-
# 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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# Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nature biotechnology 28, 1208–12 (2010).
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# Glotzer, S. C. (2004). Self-Assembly of Patchy Particles. Nano Letters, 4(8), 1407–1413. doi:10.1021/nl0493500
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# 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).
-
# 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
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# 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).
-
# Grierer, A. (1966). Model for DNA and Protein Interaction and the Function of the Operator. Nature, 212(December), 1480.
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# Ding, B. et al. Gold nanoparticle self-similar chain structure organized by DNA origami. Journal of the American Chemical Society 132, 3248–9 (2010).
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# 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
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# 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).
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# 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
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# 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).
-
# 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.
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# Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–8 (2009).
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# Kallenbach, N. R., Ma, R.-I., & Seeman, N. C. (1983). An immobile nucleic acid junction constructed from oligonucleotides. Nature, 305(27), 829.
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# Fahrner, K., Ryu, W. S. & Berg, H. C. Bacterial flagellar switching under load. Nature 423, 938 (2003).
-
# Kallenbach, N. R., Petrillol, M. L., & Laboratories, L. (1986). Three-arm nucleic acid junctions are flexible. Nucleic acids research, 14(24), 9745–9753.
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# Gennerich, A., Carter, A. P., Reck-Peterson, S. L. & Vale, R. D. Force-induced bidirectional stepping of cytoplasmic dynein. Cell 131, 952–65 (2007).
-
# 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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# Glotzer, S. C. Self-Assembly of Patchy Particles. Nano Letters 4, 1407–1413 (2004).
-
# 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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# Green, S., Bath, J. & Turberfield, a. Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion. Physical Review Letters 101, 20–23 (2008).
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# 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
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# Grierer, A. Model for DNA and Protein Interaction and the Function of the Operator. Nature 212, 1480 (1966).
-
# 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
+
# Gu, H., Chao, J., Xiao, S.-J. & Seeman, N. C. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–5 (2010).
-
# 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
+
# 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).
-
# 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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# Itoh, H. et al. Mechanically driven ATP synthesis by F 1 -ATPase. Nature 427, 465–468 (2004).
-
# 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
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#  Johnson, K. A. Transient state kinetic analysis of enzyme reaction pathways. The Enzymes XX, 1-61 (1992).
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# 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
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# Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829 (1983).
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# 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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# Kallenbach, N. R., Petrillol, M. L. & Laboratories, L. Three-arm nucleic acid junctions are flexible. Nucleic acids research 14, 9745–9753 (1986).
-
# 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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#  Kelly, T. R. Molecular motors: synthetic DNA-based walkers inspired by kinesin. Angewandte Chemie (International ed. in English) 44, 4124–7 (2005).
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# Mermall, V., Post, P. L., & Mooseker, M. S. (1998). Unconventional Myosins in Cell Movement, Memrane Traffic, and Signal Transduction. Science, 279(January), 527.
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# Kinbara, K. & Aida, T. Toward intelligent molecular machines: directed motions of biological and artificial molecules and assemblies. Chemical reviews 105, 1377–400 (2005).
-
# 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.
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# 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).
-
# Noji, H., Yasuda, R., Yoshida, M., & Kinosita, K. J. (1997). Direct observation of the rotation of F1-ATPase. Nature, 386, 299.
+
# Liu, C., Jonoska, N. & Seeman, N. C. Reciprocal DNA nanomechanical devices controlled by the same set strands. Nano letters 9, 2641–7 (2009).
-
# 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
+
# 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).
-
# 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.
+
# Lu, Y. & Liu, J. Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Current opinion in biotechnology 17, 580–8 (2006).
-
# 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
+
# Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–10 (2010).
-
# Rothemund, P. W. K. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297–302. doi:10.1038/nature04586
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# Macfarlane, R. J. et al. Nanoparticle superlattice engineering with DNA. Science (New York, N.Y.) 334, 204–8 (2011).
-
# Seeman, N. C. (1991). The use of branched DNA for nanoscale fabrication. Nanotechnology, 149.
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# 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).
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# Seeman, N. C. (1999). DNA engineering and its application to nanotechnology. Trends in Biotechnology, 7799(99), 437–443.
+
# 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).
-
# Seeman, N. C., & Kallenbach, N. R. (1983). Design of immobile nucleic acid junctions. Biophysics, 44(November), 201–209.
+
# Mehta, a D. et al. Myosin-V is a processive actin-based motor. Nature 400, 590–3 (1999).
-
# Sherman, W. B., & Seeman, N. C. (2004). A Precisely Controlled DNA Biped Walking Device. Nano Letters, 4(7), 1203–1207. doi:10.1021/nl049527q
+
# Mermall, V., Post, P. L. & Mooseker, M. S. Unconventional Myosins in Cell Movement, Memrane Traffic, and Signal Transduction. Science 279, 527 (1998).
-
# 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
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# 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).
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# 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
+
# Noji, H., Yasuda, R., Yoshida, M. & Kinosita, K. J. Direct observation of the rotation of F1-ATPase. Nature 386, 299 (1997).
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# 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
+
# Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science (New York, N.Y.) 324, 67–71 (2009).
-
# 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
+
# 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).
-
# 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
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# Peng, X. et al. A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays. Analytical biochemistry 388, 220–8 (2009).
-
# 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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# Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
-
# Watson, J. D., & Crick, F. H. C. (1953). A Structure for Deoxyribose Nucleic Acid. Nature, 171(April), 738.
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# Seeman, N. C. The use of branched DNA for nanoscale fabrication. Nanotechnology 149 (1991).
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# 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
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# Seeman, N. C. DNA engineering and its application to nanotechnology. Trends in Biotechnology 7799, 437–443 (1999).
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# 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
+
# Seeman, N. C. & Kallenbach, N. R. Design of immobile nucleic acid junctions. Biophysics 44, 201–209 (1983).
-
# 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
+
# Sherman, W. B. & Seeman, N. C. A Precisely Controlled DNA Biped Walking Device. Nano Letters 4, 1203–1207 (2004).
-
# 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
+
# Shin, J.-S. & Pierce, N. a A synthetic DNA walker for molecular transport. Journal of the American Chemical Society 126, 10834–5 (2004).
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# 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
+
# Sowa, Y. et al. Direct observation of steps in rotation of the bacterial flagellar motor. Nature 437, 916–9 (2005).
-
# 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.
+
# 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).
-
# 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
+
# Vale, R. D. The molecular motor toolbox for intracellular transport. Cell 112, 467–80 (2003).
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# 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
+
# Vale, R. D., Funatsu, T., Pierce, D. W. & Romberg, L. Direct observation of single kinesin molecules moving along microtubules. Nature 380, 451–453 (1996).
-
# 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
+
# 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).
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# 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
+
# 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].

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