Biomod/2012/UCSD/tRiton Nano Architects/Literature

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<div id='cssmenu'> <ul>

  <li class='active has-sub '><a href=''><span>Home</span></a>
        <li><a href=''><span>Abstract</span></a></li>
        <li><a href=''><span>Video</span></a></li>
  <li class='has-sub '><a href=''><span>Project Introduction</span></a>
        <li><a href=''><span>Concepts</span></a></li>
  <li class='has-sub '><a href=''><span>Experiment</span></a>
        <li><a href=''><span>Methods</span></a></li>
  <li class='has-sub '><a href=''><span>Supplementary Resources</span></a>
        <li><a href=''><span>DNA Architecture Log</span></a></li>
        <li><a href=''><span>Project Ideas</span></a></li>
        <li><a href=''><span>Literature</span></a></li>
  <li><a href=''><span>Team</span></a></li>

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List of selected literature

  • Akinori Kuzuya and Makoto Komiyama. Design and construction of a box-shaped 3D-DNA origami. Chemical communications (Cambridge, England), 45(28):4182–4, July 2009.
  • Akinori Kuzuya and Makoto Komiyama. DNA origami: Fold, stick, and beyond, Nanoscale, Issue 3, 2010,2, 310-322.
  • Anthony J. Genot, David Yu Zhang, Jonathan Bath, and Andrew J. Turberfield. Remote Toehold: A Mechanism for Flexible Control of DNA Hybridization Kinetics. Journal of the American Chemical Society 2011 133 (7), 2177-2182.
  • 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).
  • Bingling Li, Andrew D. Ellington and Xi Chen. Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic acids research 39, e110 (2011).
  • Chhabra, R., Sharma, J., Liu, Y. & Yan, H. Addressable molecular tweezers for DNA-templated coupling reactions. Nano letters 6, 978–83 (2006).
  • Christoph M. Erben, Russell P. Goodman, and Andrew J. Turberfield. A self-assembled DNA bipyramid. Journal of the American Chemical Society, 129(22):6992–3, June 2007.
  • Claudia Höbartner, Scott K. Silverman. Recent advances in DNA catalysis. Biopolymers. Volume 87, Issue 5-6, pages 279–292, 5 - 15 December 2007.
  • David Yu Zhang, Andrew J. Turberfield, Bernard Yurke, and Erik Winfree. Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA. Science 16 November 2007: 318 (5853), 1121-1125.
  • 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).
  • Dinh T Tran, Janssen KPF, Pollet J, et al. Selection and characterization of DNA aptamers for egg white lysozyme[J]. Molecules, 2010, 15(3):1127-1140.
  • Douglas, S. M., Marblestone, A. H., Teerapittayanon, S., Vazquez, A., Church, G. M., & Shih, W. M. (2009). Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research, 37(15), 5001-5006
  • Douglas, S. M., Dietz, H., Liedl, T., Högberg, B., Graf, F., Shih, W.M., Self-assembly of DNA into nanoscale three-dimensional shapes. Nature. 2009 May 21; 459(7245):414-8.
  • Ebbe S. Andersen, Mingdong Dong, Morten M. Nielsen, Kasper Jahn, Allan Lind-Thomsen,Wael Mamdouh, Kurt V. Gothelf, Flemming Besenbacher, and Jø rgen Kjems. DNA origami design of dolphin-shaped structures with flexible tails. ACS nano, 2(6):1213–8, June 2008.
  • Ebbe S. Andersen, Mingdong Dong, Morten M. Nielsen, Kasper Jahn, Ramesh Subramani, Wael Mamdouh, Monika M. Golas, Bjoern Sander, Holger Stark, Cristiano L. P. Oliveira, Jan Skov Pedersen, Victoria Birkedal, Flemming Besenbacher, Kurt V. Gothelf, and Jø rgen Kjems. Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 459(7243):73–6, 2009.
  • Elizabeth a Jares-Erijman and Thomas M. Jovin. FRET imaging. Nature biotechnology, 21(11):1387–95, November 2003.
  • Endo, M.; Sugiyama, H. Chemical approaches to DNA nanotechnology. ChemBioChem 2009, 10, 2420–2443.
  • Endo M, Sugiyama H. Recent progress in DNA origami technology. Current Protocols in Nucleic Acid Chemistry. Published Online: 1 JUN 2011
  • Haiping Huang, Guifen Jie, Rongjing Cui, Jun-Jie Zhu, DNA aptamer-based detection of lysozyme by an electrochemiluminescence assay coupled to quantum dots, Electrochemistry Communications, Volume 11, Issue 4, April 2009, Pages 816-818, ISSN 1388-2481, 10.1016/j.elecom.2009.01.009.
  • Hao Yan, Thomas H. LaBean, Liping Feng, and John H. Reif, Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices. Proc. Nat. Acad. Sci. USA, 100(14):8103{8108, 2003.
  • Hieu Bui, Craig Onodera, Carson Kidwell, YerPeng Tan, Elton Graugnard, Wan Kuang, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, and William L. Hughes. Programmable Periodicity of Quantum Dot Arrays with DNA Origami Nanotubes, Nano Letters 2010 10 (9), 3367-3372.
  • Hui, D. et al. (2003) Hybridization-based unquenching of DNA hairpins on Au surfaces: prototypical “molecular beacon” biosensors. J. Am. Chem. Soc. 125, 4012–4013.
  • I. Willner, B. Shlyahovsky, M. Zayats and B. Willner, "DNAzymes for Sensing, Nanobiotechnology and Logic Gate Applications", Chem. Soc. Rev., 37, 1153-1165 (2008)
  • Jaswinder Sharma, Rahul Chhabra, Yan Liu Dr., Yonggang Ke, Hao Yan Prof., DNA templated self-assembly of two-dimensional and periodical gold nanoparticle arrays, Angew. Chem. Int. Ed. 45, 730-735 (2006).
  • Joseph Wang, Gustavo Rivas,Mian Jiang, and, and Xueji Zhang, Induced Release of DNA from Gold Ultramicroelectrodes, Langmuir 1999 15 (19), 6541-6545
  • Jong-Shik Shin and Niles A. Pierce. A synthetic DNA walker for molecular transport. Journal of the American Chemical Society, 126(35):10834–5, September 2004.
  • Jun Qian, Sicheng Liao1, Song Xu, Michael A. Stroscio1, and Mitra Dutta1, Direct measurement of electrical transport through DNA molecules, Nature 403, 635-638 (10 February 2000)
  • Katsuhiko Ariga, Jonathan P. Hill and Qingmin Ji, Layer-by-layer assembly as a versatile bottom-up nanofabrication technique for exploratory research and realistic application, Phys Chem Chem Phys. 9(19):2319-40, 2007 May 21.
  • Ke Y, Douglas SM, Liu M, Sharma J, Cheng A, Leung A, Liu Y, Shih WM, Yan H. Multilayer DNA origami packed on a square lattice. J Am Chem Soc. 2009 Nov 4; 131(43):15903-8.
  • Kyle Lund, Anthony J. Manzo, Nadine Dabby, Nicole Michelotti, Alexander Johnson-Buck, Jeanette Nangreave, Steven Taylor, Renjun Pei, Milan N. Stojanovic, Nils G. Walter, Erik Winfree, and Hao Yan. Molecular robots guided by prescriptive landscapes, Nature, 465, 206–210,(13 May 2010).
  • Lee, J.B., Campolongo, M.J., Kahn, J.S., Roh, Y.H., Hartman, M.R. & Luo, D. DNA-based nanostructures for molecular sensing. Nanoscale 2, 188-197 (2010).
  • Lee, J.B.; Hong, J.; Bonner, D.K.; Poon, Z.; Hammond, P.T. Self-assembled RNA interference microsponges for efficient siRNA delivery. Nature Materials. 2012.
  • Lin, C., Ke, Y., Liu, Y., Mertig, M., Gu, J., & Yan, H. (2007). Functional DNA nanotube arrays: bottom-up meets top-down. Angew Chem Int Ed, 46(32), 6089–6092.
  • Lin, C., Liu, Y., Rinker, S. & Yan, H. DNA tile based self-assembly: building complex nanoarchitectures. ChemPhysChem 7, 1641–1647 (2006).
  • Lu, Y. & Liu, J. Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Current opinion in biotechnology 17, 580–8 (2006).
  • Lulu Qian and Erik Winfree. 2009. A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits. In DNA Computing, Ashish Goel, Friedrich C. Simmel, and Petr Sos\&\#237;k (Eds.). Lecture Notes In Computer Science, Vol. 5347. Springer-Verlag, Berlin, Heidelberg 70-89.
  • Mastroianni, A.J., Claridge, S.A. & Alivisatos, A.P. Pyramidal and chiral groupings of gold nanocrystals assembled using DNA scaffolds. J. Am. Chem. Soc. 131, 8455-8459 (2009).
  • Niels V. Voigt, Thomas Tørring, Alexandru Rotaru, Mikkel F. Jacobsen, Jens B. Ravnsbæk, Ramesh Subramani, Wael Mamdouh1, Jørgen Kjems1, Andriy Mokhir, Flemming Besenbacher, and Kurt Vesterager Gothelf1, Single-molecule chemical reactions on DNA origami, Nature Nanotechnology 5, 200 - 203 (2010)
  • Nobuko Hamaguchi, Andrew Ellington, Martin Stanton, Aptamer Beacons for the Direct Detection of Proteins, Analytical Biochemistry, Volume 294, Issue 2, 15 July 2001, Pages 126-131, ISSN 0003-2697, 10.1006/abio.2001.5169.
  • O.A. Shenderova, V.V. Zhirnov, and D.W. Brenner, Carbon Nanostructures, Critical Reviews in Solid State and Materials Sciences, 27(3/4):227–356 (2002)
  • P. W. K. Rothemund, “Folding DNA to create nanoscale shapes and patterns,” Nature, vol. 440, no. 7082, pp. 297–302, 2006.
  • Pik Kwan Lo, Kimberly L Metera, Hanadi F Sleiman, Self-assembly of three-dimensional DNA nanostructures and potential biological applications, Current Opinion in Chemical Biology, Volume 14, Issue 5, October 2010, Pages 597-607, ISSN 1367-5931, 10.1016/j.cbpa.2010.08.002.
  • Prigodich AE et al. Nano-Flares for mRNA Regulation and Detection. ACS Nano. 2009 August 25; 3(8): 2147–2152.
  • Prigodich AE et al. Multiplexed nanoflares: mRNA detection in live cells. Anal Chem. 2012 Feb 21;84(4):2062-6.
  • R. Chhabra, J. Sharma, Y. Liu, S. Rinker, and H. Yan, “DNA self-assembly for nanomedicine,” Advanced Drug Delivery Reviews, vol. 62, no. 6, pp. 617–625, 2010.
  • R. P. Goodman, R. M. Berry, A. J. Turberfield, The single-step synthesis of a DNA tetrahedron, Chem. Commun. 12 (2004) 1372–1373. [5].
  • Rasvan Nutiu, Li Y. Structure-switching signaling aptamers: transducing molecular recognition into fluorescence signaling. Chemistry. 2004 Apr 19;10(8):1868-76.
  • Ronald R Breaker, DNA aptamers and DNA enzymes, Current Opinion in Chemical Biology, Volume 1, Issue 1, June 1997, Pages 26-31, ISSN 1367-5931, 10.1016/S1367-5931(97)80105-6.
  • Russell P. Goodman, Mike Heilemann, Sören Doose, Christoph M. Erben, Achillefs N. Kapanidis, and Andrew J. Turberfield. Reconfigurable, braced, three-dimensional DNA nanostructures. Nature nanotechnology, 3(2):93–6, February 2008.
  • S. M. Douglas, I. Bachelet, G. M. Church. A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads. Science, 2012
  • S.Woo (2011). "Programmable molecular recognition based on the geometry of DNA nanostructures" Nature Chemistry (VOL 3) :620-627
  • Shih, W. M., Quispe, J. D. & Joyce, G. F. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618–621 (2004).
  • 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).
  • Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–6 (2012).
  • William B. Sherman and Nadrian C. Seeman. A Precisely Controlled DNA BipedWalking Device. Nano Letters, 4(7):1203–1207, July 2004.
  • William M. Shih, J.D. Quispe, and G.F. Joyce. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature, 427(6975):618–621, 2004.
  • William M Shih, Chenxiang Lin, Knitting complex weaves with DNA origami, Current Opinion in Structural Biology, Volume 20, Issue 3, June 2010, Pages 276-282, ISSN 0959-440X, 10.1016/
  • Woltman SJ, Jay GD, Crawford GP, “Liquid-crystal materials find a new order in biomedical applications”, Nature Materials 2007, vol.6, p.929-38.
  • Xiaogang Han , Zihao Zhou , Fan Yang and Zhaoxiang Deng, Catch and release. DNA tweezers that can capture, hold, and release an object under control. J Am Chem Soc 2008;130:14414–5.
  • Yi Lu, Juewen Liu, Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers, Current Opinion in Biotechnology, Volume 17, Issue 6, December 2006, Pages 580-588, ISSN 0958-1669, 10.1016/j.copbio.2006.10.004.
  • Yonggang Ke, Jaswinder Sharma, Minghui Liu, Kasper Jahn, Yan Liu, and Hao Yan. Scaffolded DNA origami of a DNA tetrahedron molecular container. Nano letters, 9(6):2445–7, June 2009.
  • Yossi Weizmann, Adam B. Braunschweig, Ofer I. Wilner, Zoya Cheglakov, Itamar Willner. A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures PNAS 2008 105 (14) 5289-5294, April 7, 2008.