Biomod/2012/Harvard/BioDesign/References

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A list of great literature<br><br><br>
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Afonin, K. a, Bindewald, E., Yaghoubian, A. J., Voss, N., Jacovetty, E., Shapiro, B. a, & Jaeger, L. (2010). In vitro assembly of cubic RNA-based scaffolds designed in silico. Nature nanotechnology, 5(9), 676–82. doi:10.1038/nnano.2010.160
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Some papers here<br><br><br><br><br>
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Delebecque, C. J., Lindner, A. B., Silver, P. a, & Aldaye, F. a. (2011). Organization of intracellular reactions with rationally designed RNA assemblies. Science (New York, N.Y.), 333(6041), 470–4. doi:10.1126/science.1206938
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Useful websites<br><br><br>
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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. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2737683&tool=pmcentrez&rendertype=abstract
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Douglas, S. M., Bachelet, I., & Church, G. M. (2012a). 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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Douglas, S. M., Bachelet, I., & Church, G. M. (2012b). A logic-gated nanorobot for targeted transport of molecular payloads. (SUPPLEMENTAL). Science (New York, N.Y.), 335(6070), 831–4. doi:10.1126/science.1214081
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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. Retrieved from http://dx.doi.org/10.1038/nature08016
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Hauser, N. C., Martinez, R., Jacob, A., Rupp, S., Hoheisel, J. D., & Matysiak, S. (2006). Utilising the left-helical conformation of L-DNA for analysing different marker types on a single universal microarray platform. Nucleic acids research, 34(18), 5101–11. doi:10.1093/nar/gkl671
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Kim, D.-N., Kilchherr, F., Dietz, H., & Bathe, M. (2011). Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic acids research, 1–7. doi:10.1093/nar/gkr1173
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Kim, Y., Yang, C. J., & Tan, W. (2007). Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem. Nucleic acids research, 35(21), 7279–87. doi:10.1093/nar/gkm771
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Lee, H., Lytton-Jean, A. K. R., Chen, Y., Love, K. T., Park, A. I., Karagiannis, E. D., Sehgal, A., et al. (2012). Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery. Nature Nanotechnology, (June), 6–10. doi:10.1038/nnano.2012.73
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Liedl, T., Högberg, B., Tytell, J., Ingber, D. E., & Shih, W. M. (2010). Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nature nanotechnology, 5(7), 520–4. doi:10.1038/nnano.2010.107
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Lin, C., Rinker, S., Wang, X., Liu, Y., Seeman, N. C., & Yan, H. (2008). In vivo cloning of artificial DNA nanostructures. Proceedings of the National Academy of Sciences of the United States of America, 105(46), 17626–31. doi:10.1073/pnas.0805416105
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Mei, Q., Wei, X., Su, F., Liu, Y., Youngbull, C., Johnson, R., Lindsay, S., et al. (2011). Stability of DNA origami nanoarrays in cell lysate. Nano letters, 11(4), 1477–82. doi:10.1021/nl1040836
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Nolte, A., Bald, R., & Erdmann, V. (1996). Mirror-design of L-oligonucleotide ligands binding to L-arginine. Nature. Retrieved from http://www.nature.com/nbt/journal/v14/n9/abs/nbt0996-1116.html
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Noy, A., & Golestanian, R. (2010). the Influence of Ionic Strength, 8022–8031.
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Pinheiro, A. V., Han, D., Shih, W. M., & Yan, H. (2011). Challenges and opportunities for structural DNA nanotechnology. Nature nanotechnology, 6(12), 763–72. doi:10.1038/nnano.2011.187
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Rajendran, A., Endo, M., Katsuda, Y., Hidaka, K., & Sugiyama, H. (2011). Photo-cross-linking-assisted thermal stability of DNA origami structures and its application for higher-temperature self-assembly. Journal of the American Chemical Society, 133(37), 14488–91. doi:10.1021/ja204546h
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Rothemund, P. W. K. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297–302. Retrieved from http://dx.doi.org/10.1038/nature04586
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Shih, W. M., Quispe, J. D., & Joyce, G. F. (2004). A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature, 427(6975), 618–21. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/14961116
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Wei, B., Dai, M., & Yin, P. (2012a). Complex shapes self-assembled from single-stranded DNA tiles. Nature, 485(7400), 623–626. Retrieved from http://dx.doi.org/10.1038/nature11075
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Wei, B., Dai, M., & Yin, P. (2012b). Complex shapes self-assembled from single-stranded DNA tiles (SUPPLEMENTAL). Nature, 485(7400), 623–626. doi:10.1038/nature11075
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Wlotzka, B., Leva, S., Eschgfäller, B., Burmeister, J., Kleinjung, F., Kaduk, C., Muhn, P., et al. (2002). In vivo properties of an anti-GnRH Spiegelmer: an example of an oligonucleotide-based therapeutic substance class. Proceedings of the National Academy of Sciences of the United States of America, 99(13), 8898–902. doi:10.1073/pnas.132067399
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Yin, P., Hariadi, R. F., Sahu, S., Choi, H. M. T., Park, S. H., Labean, T. H., & Reif, J. H. (2008a). Programming DNA tube circumferences. Science (New York, N.Y.), 321(5890), 824–6. Retrieved from http://www.sciencemag.org/content/321/5890/824.abstract
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Yin, P., Hariadi, R. F., Sahu, S., Choi, H. M. T., Park, S. H., Labean, T. H., & Reif, J. H. (2008b). Programming DNA tube circumferences. (SUPPLEMENTAL). Science (New York, N.Y.), 321(5890), 824–6. doi:10.1126/science.1157312

Revision as of 23:51, 26 October 2012

Afonin, K. a, Bindewald, E., Yaghoubian, A. J., Voss, N., Jacovetty, E., Shapiro, B. a, & Jaeger, L. (2010). In vitro assembly of cubic RNA-based scaffolds designed in silico. Nature nanotechnology, 5(9), 676–82. doi:10.1038/nnano.2010.160

Delebecque, C. J., Lindner, A. B., Silver, P. a, & Aldaye, F. a. (2011). Organization of intracellular reactions with rationally designed RNA assemblies. Science (New York, N.Y.), 333(6041), 470–4. doi:10.1126/science.1206938

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. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2737683&tool=pmcentrez&rendertype=abstract Douglas, S. M., Bachelet, I., & Church, G. M. (2012a). A logic-gated nanorobot for targeted transport of molecular payloads. Science (New York, N.Y.), 335(6070), 831–4. doi:10.1126/science.1214081 Douglas, S. M., Bachelet, I., & Church, G. M. (2012b). A logic-gated nanorobot for targeted transport of molecular payloads. (SUPPLEMENTAL). Science (New York, N.Y.), 335(6070), 831–4. doi:10.1126/science.1214081 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. Retrieved from http://dx.doi.org/10.1038/nature08016 Hauser, N. C., Martinez, R., Jacob, A., Rupp, S., Hoheisel, J. D., & Matysiak, S. (2006). Utilising the left-helical conformation of L-DNA for analysing different marker types on a single universal microarray platform. Nucleic acids research, 34(18), 5101–11. doi:10.1093/nar/gkl671 Kim, D.-N., Kilchherr, F., Dietz, H., & Bathe, M. (2011). Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic acids research, 1–7. doi:10.1093/nar/gkr1173 Kim, Y., Yang, C. J., & Tan, W. (2007). Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem. Nucleic acids research, 35(21), 7279–87. doi:10.1093/nar/gkm771 Lee, H., Lytton-Jean, A. K. R., Chen, Y., Love, K. T., Park, A. I., Karagiannis, E. D., Sehgal, A., et al. (2012). Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery. Nature Nanotechnology, (June), 6–10. doi:10.1038/nnano.2012.73 Liedl, T., Högberg, B., Tytell, J., Ingber, D. E., & Shih, W. M. (2010). Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nature nanotechnology, 5(7), 520–4. doi:10.1038/nnano.2010.107 Lin, C., Rinker, S., Wang, X., Liu, Y., Seeman, N. C., & Yan, H. (2008). In vivo cloning of artificial DNA nanostructures. Proceedings of the National Academy of Sciences of the United States of America, 105(46), 17626–31. doi:10.1073/pnas.0805416105 Mei, Q., Wei, X., Su, F., Liu, Y., Youngbull, C., Johnson, R., Lindsay, S., et al. (2011). Stability of DNA origami nanoarrays in cell lysate. Nano letters, 11(4), 1477–82. doi:10.1021/nl1040836 Nolte, A., Bald, R., & Erdmann, V. (1996). Mirror-design of L-oligonucleotide ligands binding to L-arginine. Nature. Retrieved from http://www.nature.com/nbt/journal/v14/n9/abs/nbt0996-1116.html Noy, A., & Golestanian, R. (2010). the Influence of Ionic Strength, 8022–8031. Pinheiro, A. V., Han, D., Shih, W. M., & Yan, H. (2011). Challenges and opportunities for structural DNA nanotechnology. Nature nanotechnology, 6(12), 763–72. doi:10.1038/nnano.2011.187 Rajendran, A., Endo, M., Katsuda, Y., Hidaka, K., & Sugiyama, H. (2011). Photo-cross-linking-assisted thermal stability of DNA origami structures and its application for higher-temperature self-assembly. Journal of the American Chemical Society, 133(37), 14488–91. doi:10.1021/ja204546h Rothemund, P. W. K. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297–302. Retrieved from http://dx.doi.org/10.1038/nature04586 Shih, W. M., Quispe, J. D., & Joyce, G. F. (2004). A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature, 427(6975), 618–21. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/14961116 Wei, B., Dai, M., & Yin, P. (2012a). Complex shapes self-assembled from single-stranded DNA tiles. Nature, 485(7400), 623–626. Retrieved from http://dx.doi.org/10.1038/nature11075 Wei, B., Dai, M., & Yin, P. (2012b). Complex shapes self-assembled from single-stranded DNA tiles (SUPPLEMENTAL). Nature, 485(7400), 623–626. doi:10.1038/nature11075 Wlotzka, B., Leva, S., Eschgfäller, B., Burmeister, J., Kleinjung, F., Kaduk, C., Muhn, P., et al. (2002). In vivo properties of an anti-GnRH Spiegelmer: an example of an oligonucleotide-based therapeutic substance class. Proceedings of the National Academy of Sciences of the United States of America, 99(13), 8898–902. doi:10.1073/pnas.132067399 Yin, P., Hariadi, R. F., Sahu, S., Choi, H. M. T., Park, S. H., Labean, T. H., & Reif, J. H. (2008a). Programming DNA tube circumferences. Science (New York, N.Y.), 321(5890), 824–6. Retrieved from http://www.sciencemag.org/content/321/5890/824.abstract

Yin, P., Hariadi, R. F., Sahu, S., Choi, H. M. T., Park, S. H., Labean, T. H., & Reif, J. H. (2008b). Programming DNA tube circumferences. (SUPPLEMENTAL). Science (New York, N.Y.), 321(5890), 824–6. doi:10.1126/science.1157312
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