Biomod/2012/UT/Nanowranglers/References

From OpenWetWare
Jump to navigationJump to search

<html> <style type="text/css"> //<!--

//Get the playbill font by Hank Gillette, 1992, public domain @font-face { 

 font-family: Playbill2;  
 src: url( 'http://openwetware.org/images/e/e6/PLAYBILL.eot' ); /* IE */  
 src: local(Playbill), 
      url( 'http://openwetware.org/images/a/a1/PLAYBILL.TTF' ) format('truetype'),
      url( 'http://openwetware.org/images/b/ba/PLAYBILL.svg#font' ) format('svg'); /* non-IE */

} /* Define the background of the whole page */ @media screen { 

   body { background: #c5d0ea 0 0 no-repeat; }

} /* Define the div holding the page contents */

  1. globalWrapper{
 left: 50%;
 height: 100%;
 background-color: #FFFFFF;
 width: 900px;
 margin-left: -450px; /* Should be width / 2 */
 margin-top: 0px;
 margin-bottom: 0px;
 margin-right: 0px;
 padding: 0 0 0 0;   
 position: absolute;

} .toc{ 

 display:none;

} /* Hide the page heading at top */ .firstHeading {display:none;} /* Hide the bar at the left */

  1. column-one {display:none;}

/* Define the div holding the page contents (this div is inside globalWrapper. We override its default margins) */

  1. content{
 margin: 0 0 0 0;
 font: normal 100% sans-serif;
 color: #000033;
 padding: 12px 12px 12px 12px;
 background-image: url(http://openwetware.org/images/3/38/FortDavis-Pano-Cropped.jpg); background-repeat: no-repeat; 
 border: 0;

} /* Miscellaneous stuff. Feel free to add style definitions. */ h3 { 

 /*
 color: #CC5500;
 font: normal 3em sans-serif;
 letter-spacing: 1px; 
 margin-bottom: 0; 
 */
 color: #000000;
 font-style: normal;
 font-size: 39px;
 font-family: 'Playbill2', 'Playbill', sans-serif;
 //font-stretch: ultra-expanded;
 letter-spacing: 1px; 
 margin-bottom: -10px;
 line-height: 25px;
 padding-bottom: 0px;

} h2 { 

 color: #000000;
 font-style: normal;
 font-size: 39px;
 font-family: 'Playbill2', 'Playbill', sans-serif;
 //font-stretch: ultra-expanded;
 letter-spacing: 1px; 
 margin-bottom: -10px;
 line-height: 25px;
 padding-bottom: 0px;

} h1 { 

 /*
 color: #CC5500;
 font: normal 3em sans-serif;
 letter-spacing: 1px; 
 margin-bottom: 0; 
 */
 color: #000000;
 font-style: normal;
 font-size: 39px;
 font-family: 'Playbill2', 'Playbill', sans-serif;
 //font-stretch: ultra-expanded;
 letter-spacing: 1px; 
 margin-bottom: -10px;
 line-height: 25px;
 padding-bottom: 0px;

}

.scriptFont { 

  color: #0;
  padding-top: 5px;
  font: normal 1em Georgia;

}

/* Code taken from publicly available css tutorials at onderhond.com */ .linkconcept a {background:url("http://openwetware.org/images/0/03/Concept-bright.png") left top no-repeat;} .linkmembers a {background:url("http://openwetware.org/images/2/24/Members-bright.png") left top no-repeat;} .linkresults a {background:url("http://openwetware.org/images/a/ac/Results-bright.png") left top no-repeat;} .linkmethods a {background:url("http://openwetware.org/images/0/02/Methods-bright.png") left top no-repeat;} .linkrefs a {background:url("http://openwetware.org/images/2/28/References-bright.png") left top no-repeat;}

.linkgeneral {float:left; padding-right:3px; } .linkgeneral a {display:block; width:141px; height:52px;} .linkgeneral a:hover img {position:absolute; left:-999em; top:-999em;} .linkgeneral a:hover {zoom:1;} //--> </style> <div style="text-align:center" /> <img src="http://openwetware.org/images/5/59/NanoWranglers.png"/><br /> <div class="scriptFont"> Undergraduate DNA nanotechnology research group from the University of Texas at Austin </div> <img src="http://openwetware.org/images/e/e6/NanoWranglersDNAStripe.png"/><br /> <!-- links at top --> <div style="float:left; width:85px; height:52px; display:block" > </div> <div class="linkconcept linkgeneral"> 

 <a href="http://openwetware.org/wiki/Biomod/2012/UT/Nanowranglers"><img src="http://openwetware.org/images/c/ce/Concept-dull.png" alt="" /></a>

</div> <div class="linkmethods linkgeneral"> 

 <a href="http://openwetware.org/wiki/Biomod/2012/UT/Nanowranglers/Methods"><img src="http://openwetware.org/images/b/be/Methods-dull.png" alt="" /></a>

</div> <div class="linkresults linkgeneral"> 

 <a href="http://openwetware.org/wiki/Biomod/2012/UT/Nanowranglers/Results"><img src="http://openwetware.org/images/8/8f/Results-dull.png" alt="" /></a>

</div> <div class="linkmembers linkgeneral"> 

 <a href="http://openwetware.org/wiki/Biomod/2012/UT/Nanowranglers/Members"><img src="http://openwetware.org/images/4/47/Members-dull.png" alt="" /></a>

</div> <div class="linkrefs linkgeneral"> 

 <a href="http://openwetware.org/wiki/Biomod/2012/UT/Nanowranglers/References"><img src="http://openwetware.org/images/4/49/References-dull.png" alt="" /></a>

</div> <div style="clear: both;" ></div> <img src="http://openwetware.org/images/e/e6/NanoWranglersDNAStripe.png"/><br />

</div> </html>

Related Work

For prior work on designing DNA walkers, please see [Cite Bath et al., 2005 & 2009][Cite Green et al., 2008][Cite Gu et al., 2010][Cite He et al., 2010][Cite Kinbara et al., 2005][Cite Lund et al., 2010][Cite Omabegho et al., 2009][Cite Pei et al., 2006][Cite Sherman et al., 2004][Cite Shin et al., 2004][Cite Tian et al., 2005][Cite Venkataraman et al., 2007][Cite Yin et al., 2004 & 2008].

References

Note to NanoWranglers - to cite any of the below references, please say [Cite Last name et al., YEAR]. 
Note to Ben - Before wiki freeze, replace all [Cite Last name et al., YEAR] with their appropriate numbers 
and delete all uncited sources.
  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. Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829 (1983).
  27. Kallenbach, N. R., Petrillol, M. L. & Laboratories, L. Three-arm nucleic acid junctions are flexible. Nucleic acids research 14, 9745–9753 (1986).
  28. Kelly, T. R. Molecular motors: synthetic DNA-based walkers inspired by kinesin. Angewandte Chemie (International ed. in English) 44, 4124–7 (2005).
  29. Kinbara, K. & Aida, T. Toward intelligent molecular machines: directed motions of biological and artificial molecules and assemblies. Chemical reviews 105, 1377–400 (2005).
  30. 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).
  31. Liu, C., Jonoska, N. & Seeman, N. C. Reciprocal DNA nanomechanical devices controlled by the same set strands. Nano letters 9, 2641–7 (2009).
  32. 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).
  33. Lu, Y. & Liu, J. Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Current opinion in biotechnology 17, 580–8 (2006).
  34. Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–10 (2010).
  35. Macfarlane, R. J. et al. Nanoparticle superlattice engineering with DNA. Science (New York, N.Y.) 334, 204–8 (2011).
  36. 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).
  37. 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).
  38. Mehta, a D. et al. Myosin-V is a processive actin-based motor. Nature 400, 590–3 (1999).
  39. Mermall, V., Post, P. L. & Mooseker, M. S. Unconventional Myosins in Cell Movement, Memrane Traffic, and Signal Transduction. Science 279, 527 (1998).
  40. 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).
  41. Noji, H., Yasuda, R., Yoshida, M. & Kinosita, K. J. Direct observation of the rotation of F1-ATPase. Nature 386, 299 (1997).
  42. Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science (New York, N.Y.) 324, 67–71 (2009).
  43. 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).
  44. Peng, X. et al. A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays. Analytical biochemistry 388, 220–8 (2009).
  45. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
  46. Seeman, N. C. The use of branched DNA for nanoscale fabrication. Nanotechnology 149 (1991).
  47. Seeman, N. C. DNA engineering and its application to nanotechnology. Trends in Biotechnology 7799, 437–443 (1999).
  48. Seeman, N. C. & Kallenbach, N. R. Design of immobile nucleic acid junctions. Biophysics 44, 201–209 (1983).
  49. Sherman, W. B. & Seeman, N. C. A Precisely Controlled DNA Biped Walking Device. Nano Letters 4, 1203–1207 (2004).
  50. Shin, J.-S. & Pierce, N. a A synthetic DNA walker for molecular transport. Journal of the American Chemical Society 126, 10834–5 (2004).
  51. Sowa, Y. et al. Direct observation of steps in rotation of the bacterial flagellar motor. Nature 437, 916–9 (2005).
  52. 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).
  53. Vale, R. D. The molecular motor toolbox for intracellular transport. Cell 112, 467–80 (2003).
  54. Vale, R. D., Funatsu, T., Pierce, D. W. & Romberg, L. Direct observation of single kinesin molecules moving along microtubules. Nature 380, 451–453 (1996).
  55. 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).
  56. Watson, J. D. & Crick, F. H. C. A Structure for Deoxyribose Nucleic Acid. Nature 171, 738 (1953).
  57. Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–6 (2012).
  58. 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).
  59. Woo, S. & Rothemund, P. W. K. Programmable molecular recognition based on the geometry of DNA nanostructures. Nature chemistry 3, 620–7 (2011).
  60. Yildiz, A., Tomishige, M., Vale, R. D. & Selvin, P. R. Kinesin walks hand-over-hand. Science (New York, N.Y.) 303, 676–8 (2004).
  61. Yin, P., Choi, H. M. T., Calvert, C. R. & Pierce, N. a Programming biomolecular self-assembly pathways. Nature 451, 318–22 (2008).
  62. 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).
  63. 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).
  64. Zhang, D. Y. & Winfree, E. Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society 131, 17303–14 (2009).
  65. Zhang, D. Y. & Winfree, E. Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic acids research 38, 4182–97 (2010).
  66. Zheng, J. et al. From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal. Nature 461, 74–77 (2009).
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2012/UT/Nanowranglers/References&oldid=643482"