Difference between revisions of "Biomod/2012/UT/Nanowranglers/References"

From OpenWetWare
Jump to: navigation, search
(Please fill out references)
Line 4: Line 4:
<pre style="color:red; font-size:127%">
<pre style="color:red; font-size:127%">
Note to NanoWranglers - to cite any of the below references, please say [Cite XXX, 2007].  
Note to NanoWranglers - to cite any of the below references, please say [Cite NAME, YEAR].  
Note to Ben - Before wiki freeze, replace all [Cite XXX, 2007] with their appropriate numbers and delete
Note to Ben - Before wiki freeze, replace all [Cite NAME, YEAR] with their appropriate numbers and delete
all uncited sources.
all uncited sources.

Revision as of 09:58, 22 October 2012

<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{


} /* 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>


Note to NanoWranglers - to cite any of the below references, please say [Cite NAME, YEAR]. 
Note to Ben - Before wiki freeze, replace all [Cite NAME, YEAR] with their appropriate numbers and delete
all uncited sources.
  1. 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
  2. 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
  3. 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
  4. 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
  5. Block, S., Blair, D., & Berg, H. (1989). Compliance of bacterial flagella measured with optical tweezers. Nature, 338, 514.
  6. 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
  7. 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.
  8. Carter, N. J., & Cross, R. a. (2005). Mechanics of the kinesin step. Nature, 435(7040), 308–12. doi:10.1038/nature03528
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. Fahrner, K., Ryu, W. S., & Berg, H. C. (2003). Bacterial flagellar switching under load. Nature, 423(June), 938.
  19. 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
  20. Glotzer, S. C. (2004). Self-Assembly of Patchy Particles. Nano Letters, 4(8), 1407–1413. doi:10.1021/nl0493500
  21. 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
  22. Grierer, A. (1966). Model for DNA and Protein Interaction and the Function of the Operator. Nature, 212(December), 1480.
  23. 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
  24. 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
  25. 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.
  26. Kallenbach, N. R., Ma, R.-I., & Seeman, N. C. (1983). An immobile nucleic acid junction constructed from oligonucleotides. Nature, 305(27), 829.
  27. Kallenbach, N. R., Petrillol, M. L., & Laboratories, L. (1986). Three-arm nucleic acid junctions are flexible. Nucleic acids research, 14(24), 9745–9753.
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. Mermall, V., Post, P. L., & Mooseker, M. S. (1998). Unconventional Myosins in Cell Movement, Memrane Traffic, and Signal Transduction. Science, 279(January), 527.
  39. 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.
  40. Noji, H., Yasuda, R., Yoshida, M., & Kinosita, K. J. (1997). Direct observation of the rotation of F1-ATPase. Nature, 386, 299.
  41. 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
  42. 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.
  43. 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
  44. Rothemund, P. W. K. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297–302. doi:10.1038/nature04586
  45. Seeman, N. C. (1991). The use of branched DNA for nanoscale fabrication. Nanotechnology, 149.
  46. Seeman, N. C. (1999). DNA engineering and its application to nanotechnology. Trends in Biotechnology, 7799(99), 437–443.
  47. Seeman, N. C., & Kallenbach, N. R. (1983). Design of immobile nucleic acid junctions. Biophysics, 44(November), 201–209.
  48. Sherman, W. B., & Seeman, N. C. (2004). A Precisely Controlled DNA Biped Walking Device. Nano Letters, 4(7), 1203–1207. doi:10.1021/nl049527q
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. Watson, J. D., & Crick, F. H. C. (1953). A Structure for Deoxyribose Nucleic Acid. Nature, 171(April), 738.
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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.
  62. 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
  63. 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
  64. 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
  65. 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