Biomod/2012/UT/Nanowranglers/References

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== Related Work ==
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=Related work=
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For prior work on designing DNA walkers, please see [Cite He, Y. 2005][Cite Bath, J. 2008 & 2009][Cite Peng, Y. 2008][Cite Green, 2008][Cite Gu, H. 2010][Cite He, Y., 2010][Cite Kinbara, K. 2005][Cite Lund, K, 2010][Cite Omabegho, T., 2009][Cite Sherman, W.B., 2004][Cite Shin, J.S., 2004][Cite Tian, Y., 2005][Cite Venkataraman, S., 2007].
+
For prior work on designing DNA walkers, please see [2][3][10][21][23][24][30][35][43][44][50][51][53][56][62].
-
== References ==
+
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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<pre style="color:red; font-size:127%">
+
For CHA please see [9][15][62].
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Note to NanoWranglers - to cite any of the below references, please say [Cite NAME, YEAR].
+
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Note to Ben - Before wiki freeze, replace all [Cite NAME, YEAR] 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. Two computational primitives for algorithmic self-assembly: copying and counting. Nano letters 5, 2586–92 (2005).
+
For software used, please see GIDEON [4] and Kintek [26].
-
# Bath, J., Green, S. J. & Turberfield, A. J. A Free-Running DNA Motor Powered by a Nicking Enzyme. Angewandte Chemie 117, 4432–4435 (2005).
+
 
-
# 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).
+
=References=
-
# 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).
+
 
-
# Block, S., Blair, D. & Berg, H. Compliance of bacterial flagella measured with optical tweezers. Nature 338, 514 (1989).
+
# 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).
-
# Brun, Y. Solving NP-complete problems in the tile assembly model. Theoretical Computer Science 395, 31–46 (2008).
+
# Bath, J., Green, S. J. & Turberfield, A. J. A Free-Running DNA Motor Powered by a Nicking Enzyme. Angewandte Chemie 117, 4432–4435 (2005).
-
# Carter, A. et al. Structure and Functional Role of Dynein’s Microtubule-Binding Domain. Science 322, 1691–1695 (2008).
+
# 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).
-
# Carter, N. J. & Cross, R. a Mechanics of the kinesin step. Nature 435, 308–12 (2005).
+
# 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).
-
# Chen, X. & Ellington, A. D. Shaping up nucleic acid computation. Current opinion in biotechnology 21, 392–400 (2010).
+
# Block, S., Blair, D. & Berg, H. Compliance of bacterial flagella measured with optical tweezers. Nature 338, 514 (1989).
-
# Chhabra, R., Sharma, J., Liu, Y. & Yan, H. Addressable molecular tweezers for DNA-templated coupling reactions. Nano letters 6, 978–83 (2006).
+
# Brun, Y. Solving NP-complete problems in the tile assembly model. Theoretical Computer Science 395, 31–46 (2008).
-
# Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nature biotechnology 28, 1208–12 (2010).
+
# Carter, A. et al. Structure and Functional Role of Dynein’s Microtubule-Binding Domain. Science 322, 1691–1695 (2008).
-
# 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).
+
# Carter, N. J. & Cross, R. a Mechanics of the kinesin step. Nature 435, 308–12 (2005).
-
# 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).
+
# Chen, X. & Ellington, A. D. Shaping up nucleic acid computation. Current opinion in biotechnology 21, 392–400 (2010).
-
# Ding, B. et al. Gold nanoparticle self-similar chain structure organized by DNA origami. Journal of the American Chemical Society 132, 3248–9 (2010).
+
# Chhabra, R., Sharma, J., Liu, Y. & Yan, H. Addressable molecular tweezers for DNA-templated coupling reactions. Nano letters 6, 978–83 (2006).
-
# 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).
+
# Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nature biotechnology 28, 1208–12 (2010).
-
# 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).
+
# 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).
-
# Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–8 (2009).
+
# 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).
-
# Fahrner, K., Ryu, W. S. & Berg, H. C. Bacterial flagellar switching under load. Nature 423, 938 (2003).
+
# Ding, B. et al. Gold nanoparticle self-similar chain structure organized by DNA origami. Journal of the American Chemical Society 132, 3248–9 (2010).
-
# Gennerich, A., Carter, A. P., Reck-Peterson, S. L. & Vale, R. D. Force-induced bidirectional stepping of cytoplasmic dynein. Cell 131, 952–65 (2007).
+
# 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).
-
# Glotzer, S. C. Self-Assembly of Patchy Particles. Nano Letters 4, 1407–1413 (2004).
+
# 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).
-
# Green, S., Bath, J. & Turberfield, a. Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion. Physical Review Letters 101, 20–23 (2008).
+
# Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–8 (2009).
-
# Grierer, A. Model for DNA and Protein Interaction and the Function of the Operator. Nature 212, 1480 (1966).
+
# Fahrner, K., Ryu, W. S. & Berg, H. C. Bacterial flagellar switching under load. Nature 423, 938 (2003).
-
# Gu, H., Chao, J., Xiao, S.-J. & Seeman, N. C. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–5 (2010).
+
# Gennerich, A., Carter, A. P., Reck-Peterson, S. L. & Vale, R. D. Force-induced bidirectional stepping of cytoplasmic dynein. Cell 131, 952–65 (2007).
-
# 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).
+
# Glotzer, S. C. Self-Assembly of Patchy Particles. Nano Letters 4, 1407–1413 (2004).
-
# Itoh, H. et al. Mechanically driven ATP synthesis by F 1 -ATPase. Nature 427, 465–468 (2004).
+
# Green, S., Bath, J. & Turberfield, a. Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion. Physical Review Letters 101, 20–23 (2008).
-
# Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829 (1983).
+
# Grierer, A. Model for DNA and Protein Interaction and the Function of the Operator. Nature 212, 1480 (1966).
-
# Kallenbach, N. R., Petrillol, M. L. & Laboratories, L. Three-arm nucleic acid junctions are flexible. Nucleic acids research 14, 9745–9753 (1986).
+
# Gu, H., Chao, J., Xiao, S.-J. & Seeman, N. C. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–5 (2010).
-
# Kinbara, K. & Aida, T. Toward intelligent molecular machines: directed motions of biological and artificial molecules and assemblies. Chemical reviews 105, 1377–400 (2005).
+
# 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).
-
# 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).
+
# Itoh, H. et al. Mechanically driven ATP synthesis by F 1 -ATPase. Nature 427, 465–468 (2004).
-
# Liu, C., Jonoska, N. & Seeman, N. C. Reciprocal DNA nanomechanical devices controlled by the same set strands. Nano letters 9, 2641–7 (2009).
+
# Johnson, K. A. Transient state kinetic analysis of enzyme reaction pathways. The Enzymes XX, 1-61 (1992).
-
# 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).
+
Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829 (1983).
-
# Lu, Y. & Liu, J. Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Current opinion in biotechnology 17, 580–8 (2006).
+
# Kallenbach, N. R., Petrillol, M. L. & Laboratories, L. Three-arm nucleic acid junctions are flexible. Nucleic acids research 14, 9745–9753 (1986).
-
# Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–10 (2010).
+
# Kelly, T. R. Molecular motors: synthetic DNA-based walkers inspired by kinesin. Angewandte Chemie (International ed. in English) 44, 4124–7 (2005).
-
# Macfarlane, R. J. et al. Nanoparticle superlattice engineering with DNA. Science (New York, N.Y.) 334, 204–8 (2011).
+
Kinbara, K. & Aida, T. Toward intelligent molecular machines: directed motions of biological and artificial molecules and assemblies. Chemical reviews 105, 1377–400 (2005).
-
# 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).
+
# 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).
-
# 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).
+
# Liu, C., Jonoska, N. & Seeman, N. C. Reciprocal DNA nanomechanical devices controlled by the same set strands. Nano letters 9, 2641–7 (2009).
-
# Mehta, a D. et al. Myosin-V is a processive actin-based motor. Nature 400, 590–3 (1999).
+
# 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).
-
# Mermall, V., Post, P. L. & Mooseker, M. S. Unconventional Myosins in Cell Movement, Memrane Traffic, and Signal Transduction. Science 279, 527 (1998).
+
# Lu, Y. & Liu, J. Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Current opinion in biotechnology 17, 580–8 (2006).
-
# 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).
+
# Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–10 (2010).
-
# Noji, H., Yasuda, R., Yoshida, M. & Kinosita, K. J. Direct observation of the rotation of F1-ATPase. Nature 386, 299 (1997).
+
# Macfarlane, R. J. et al. Nanoparticle superlattice engineering with DNA. Science (New York, N.Y.) 334, 204–8 (2011).
-
# Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science (New York, N.Y.) 324, 67–71 (2009).
+
# 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).
-
# 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).
+
# 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).
-
# Peng, X. et al. A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays. Analytical biochemistry 388, 220–8 (2009).
+
# Mehta, a D. et al. Myosin-V is a processive actin-based motor. Nature 400, 590–3 (1999).
-
# Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
+
# Mermall, V., Post, P. L. & Mooseker, M. S. Unconventional Myosins in Cell Movement, Memrane Traffic, and Signal Transduction. Science 279, 527 (1998).
-
# Seeman, N. C. The use of branched DNA for nanoscale fabrication. Nanotechnology 149 (1991).
+
# 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).
-
# Seeman, N. C. DNA engineering and its application to nanotechnology. Trends in Biotechnology 7799, 437–443 (1999).
+
# Noji, H., Yasuda, R., Yoshida, M. & Kinosita, K. J. Direct observation of the rotation of F1-ATPase. Nature 386, 299 (1997).
-
# Seeman, N. C. & Kallenbach, N. R. Design of immobile nucleic acid junctions. Biophysics 44, 201–209 (1983).
+
# Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science (New York, N.Y.) 324, 67–71 (2009).
-
# Sherman, W. B. & Seeman, N. C. A Precisely Controlled DNA Biped Walking Device. Nano Letters 4, 1203–1207 (2004).
+
# 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).
-
# Shin, J.-S. & Pierce, N. a A synthetic DNA walker for molecular transport. Journal of the American Chemical Society 126, 10834–5 (2004).
+
# Peng, X. et al. A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays. Analytical biochemistry 388, 220–8 (2009).
-
# Sowa, Y. et al. Direct observation of steps in rotation of the bacterial flagellar motor. Nature 437, 916–9 (2005).
+
# Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
-
# 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).
+
# Seeman, N. C. The use of branched DNA for nanoscale fabrication. Nanotechnology 149 (1991).
-
# Vale, R. D. The molecular motor toolbox for intracellular transport. Cell 112, 467–80 (2003).
+
# Seeman, N. C. DNA engineering and its application to nanotechnology. Trends in Biotechnology 7799, 437–443 (1999).
-
# Vale, R. D., Funatsu, T., Pierce, D. W. & Romberg, L. Direct observation of single kinesin molecules moving along microtubules. Nature 380, 451–453 (1996).
+
# Seeman, N. C. & Kallenbach, N. R. Design of immobile nucleic acid junctions. Biophysics 44, 201–209 (1983).
-
# 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).
+
# Sherman, W. B. & Seeman, N. C. A Precisely Controlled DNA Biped Walking Device. Nano Letters 4, 1203–1207 (2004).
-
# Watson, J. D. & Crick, F. H. C. A Structure for Deoxyribose Nucleic Acid. Nature 171, 738 (1953).
+
# Shin, J.-S. & Pierce, N. a A synthetic DNA walker for molecular transport. Journal of the American Chemical Society 126, 10834–5 (2004).
-
# Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–6 (2012).
+
# Sowa, Y. et al. Direct observation of steps in rotation of the bacterial flagellar motor. Nature 437, 916–9 (2005).
-
# 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).
+
# 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).
-
# Woo, S. & Rothemund, P. W. K. Programmable molecular recognition based on the geometry of DNA nanostructures. Nature chemistry 3, 620–7 (2011).
+
# Vale, R. D. The molecular motor toolbox for intracellular transport. Cell 112, 467–80 (2003).
-
# Yildiz, A., Tomishige, M., Vale, R. D. & Selvin, P. R. Kinesin walks hand-over-hand. Science (New York, N.Y.) 303, 676–8 (2004).
+
# Vale, R. D., Funatsu, T., Pierce, D. W. & Romberg, L. Direct observation of single kinesin molecules moving along microtubules. Nature 380, 451–453 (1996).
-
# Yin, P., Choi, H. M. T., Calvert, C. R. & Pierce, N. a Programming biomolecular self-assembly pathways. Nature 451, 318–22 (2008).
+
# 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).
-
# 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).
+
# Wang H, Oster G. 1998. Energy transduction in the F1 motor of ATP synthase. Nature 396:279–82
-
# 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).
+
# Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–6 (2012).
-
# Zhang, D. Y. & Winfree, E. Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society 131, 17303–14 (2009).
+
# 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).
-
# Zhang, D. Y. & Winfree, E. Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic acids research 38, 4182–97 (2010).
+
# Woo, S. & Rothemund, P. W. K. Programmable molecular recognition based on the geometry of DNA nanostructures. Nature chemistry 3, 620–7 (2011).
-
# Zheng, J. et al. From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal. Nature 461, 74–77 (2009).
+
# 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

  1. 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).
  2. Bath, J., Green, S. J. & Turberfield, A. J. A Free-Running DNA Motor Powered by a Nicking Enzyme. Angewandte Chemie 117, 4432–4435 (2005).
  3. 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).
  4. 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).
  5. Block, S., Blair, D. & Berg, H. Compliance of bacterial flagella measured with optical tweezers. Nature 338, 514 (1989).
  6. Brun, Y. Solving NP-complete problems in the tile assembly model. Theoretical Computer Science 395, 31–46 (2008).
  7. Carter, A. et al. Structure and Functional Role of Dynein’s Microtubule-Binding Domain. Science 322, 1691–1695 (2008).
  8. Carter, N. J. & Cross, R. a Mechanics of the kinesin step. Nature 435, 308–12 (2005).
  9. Chen, X. & Ellington, A. D. Shaping up nucleic acid computation. Current opinion in biotechnology 21, 392–400 (2010).
  10. Chhabra, R., Sharma, J., Liu, Y. & Yan, H. Addressable molecular tweezers for DNA-templated coupling reactions. Nano letters 6, 978–83 (2006).
  11. Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nature biotechnology 28, 1208–12 (2010).
  12. 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).
  13. 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).
  14. Ding, B. et al. Gold nanoparticle self-similar chain structure organized by DNA origami. Journal of the American Chemical Society 132, 3248–9 (2010).
  15. 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).
  16. 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).
  17. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–8 (2009).
  18. Fahrner, K., Ryu, W. S. & Berg, H. C. Bacterial flagellar switching under load. Nature 423, 938 (2003).
  19. Gennerich, A., Carter, A. P., Reck-Peterson, S. L. & Vale, R. D. Force-induced bidirectional stepping of cytoplasmic dynein. Cell 131, 952–65 (2007).
  20. Glotzer, S. C. Self-Assembly of Patchy Particles. Nano Letters 4, 1407–1413 (2004).
  21. Green, S., Bath, J. & Turberfield, a. Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion. Physical Review Letters 101, 20–23 (2008).
  22. Grierer, A. Model for DNA and Protein Interaction and the Function of the Operator. Nature 212, 1480 (1966).
  23. Gu, H., Chao, J., Xiao, S.-J. & Seeman, N. C. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–5 (2010).
  24. 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).
  25. Itoh, H. et al. Mechanically driven ATP synthesis by F 1 -ATPase. Nature 427, 465–468 (2004).
  26. Johnson, K. A. Transient state kinetic analysis of enzyme reaction pathways. The Enzymes XX, 1-61 (1992).
  27. Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829 (1983).
  28. Kallenbach, N. R., Petrillol, M. L. & Laboratories, L. Three-arm nucleic acid junctions are flexible. Nucleic acids research 14, 9745–9753 (1986).
  29. Kelly, T. R. Molecular motors: synthetic DNA-based walkers inspired by kinesin. Angewandte Chemie (International ed. in English) 44, 4124–7 (2005).
  30. Kinbara, K. & Aida, T. Toward intelligent molecular machines: directed motions of biological and artificial molecules and assemblies. Chemical reviews 105, 1377–400 (2005).
  31. 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).
  32. Liu, C., Jonoska, N. & Seeman, N. C. Reciprocal DNA nanomechanical devices controlled by the same set strands. Nano letters 9, 2641–7 (2009).
  33. 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).
  34. Lu, Y. & Liu, J. Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Current opinion in biotechnology 17, 580–8 (2006).
  35. Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–10 (2010).
  36. Macfarlane, R. J. et al. Nanoparticle superlattice engineering with DNA. Science (New York, N.Y.) 334, 204–8 (2011).
  37. 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).
  38. 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).
  39. Mehta, a D. et al. Myosin-V is a processive actin-based motor. Nature 400, 590–3 (1999).
  40. Mermall, V., Post, P. L. & Mooseker, M. S. Unconventional Myosins in Cell Movement, Memrane Traffic, and Signal Transduction. Science 279, 527 (1998).
  41. 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).
  42. Noji, H., Yasuda, R., Yoshida, M. & Kinosita, K. J. Direct observation of the rotation of F1-ATPase. Nature 386, 299 (1997).
  43. Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science (New York, N.Y.) 324, 67–71 (2009).
  44. 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).
  45. Peng, X. et al. A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays. Analytical biochemistry 388, 220–8 (2009).
  46. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
  47. Seeman, N. C. The use of branched DNA for nanoscale fabrication. Nanotechnology 149 (1991).
  48. Seeman, N. C. DNA engineering and its application to nanotechnology. Trends in Biotechnology 7799, 437–443 (1999).
  49. Seeman, N. C. & Kallenbach, N. R. Design of immobile nucleic acid junctions. Biophysics 44, 201–209 (1983).
  50. Sherman, W. B. & Seeman, N. C. A Precisely Controlled DNA Biped Walking Device. Nano Letters 4, 1203–1207 (2004).
  51. Shin, J.-S. & Pierce, N. a A synthetic DNA walker for molecular transport. Journal of the American Chemical Society 126, 10834–5 (2004).
  52. Sowa, Y. et al. Direct observation of steps in rotation of the bacterial flagellar motor. Nature 437, 916–9 (2005).
  53. 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).
  54. Vale, R. D. The molecular motor toolbox for intracellular transport. Cell 112, 467–80 (2003).
  55. Vale, R. D., Funatsu, T., Pierce, D. W. & Romberg, L. Direct observation of single kinesin molecules moving along microtubules. Nature 380, 451–453 (1996).
  56. 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).
  57. Wang H, Oster G. 1998. Energy transduction in the F1 motor of ATP synthase. Nature 396:279–82
  58. Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–6 (2012).
  59. 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).
  60. Woo, S. & Rothemund, P. W. K. Programmable molecular recognition based on the geometry of DNA nanostructures. Nature chemistry 3, 620–7 (2011).
  61. Yildiz, A., Tomishige, M., Vale, R. D. & Selvin, P. R. Kinesin walks hand-over-hand. Science (New York, N.Y.) 303, 676–8 (2004).
  62. Yin, P., Choi, H. M. T., Calvert, C. R. & Pierce, N. a Programming biomolecular self-assembly pathways. Nature 451, 318–22 (2008).
  63. 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).
  64. 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).
  65. Zhang, D. Y. & Winfree, E. Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society 131, 17303–14 (2009).
  66. Zhang, D. Y. & Winfree, E. Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic acids research 38, 4182–97 (2010).
  67. Zheng, J. et al. From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal. Nature 461, 74–77 (2009).
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