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Key Experimental Approaches in DNA Nanotechnology

dc.contributor.authorSeeman, Nadrian C.
dc.date.accessioned2018-05-15T20:15:15Z
dc.date.available2018-05-15T20:15:15Z
dc.date.issued2002-06
dc.identifier.citationSeeman, Nadrian C. (2002). "Key Experimental Approaches in DNA Nanotechnology." Current Protocols in Nucleic Acid Chemistry 9(1): 12.1.1-12.1.14.
dc.identifier.issn1934-9270
dc.identifier.issn1934-9289
dc.identifier.urihttps://hdl.handle.net/2027.42/143741
dc.description.abstractDNA nanotechnology combines unusual DNA motifs with sticky‐ended cohesion to build polyhedral objects, topological targets, nanomechanical devices, and both crystalline and aperiodic arrays. The goal of DNA nanotechnology is control of the structure of macroscopic matter on the finest possible scale. Applications are expected to arise in the areas of X‐ray crystallography, nanoelectronics, nanorobotics, and DNA‐based computation. DNA and its close molecular relatives appear extremely well suited for these goals. This overview covers the generation of new DNA motifs, construction methods (synthesis, hybridization, phosphorylation, ligation), and a variety of methods for characterization of motifs, devices, and arrays. Finally, the use of DNA nanotechnology as a tool in biochemistry is discussed.
dc.publisherAlan R. Liss
dc.publisherWiley Periodicals, Inc.
dc.titleKey Experimental Approaches in DNA Nanotechnology
dc.typeArticleen_US
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelBiological Chemistry
dc.subject.hlbsecondlevelChemical Engineering
dc.subject.hlbsecondlevelChemistry
dc.subject.hlbsecondlevelPublic Health
dc.subject.hlbtoplevelHealth Sciences
dc.subject.hlbtoplevelScience
dc.subject.hlbtoplevelEngineering
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/143741/1/cpnc1201.pdf
dc.identifier.doi10.1002/0471142700.nc1201s09
dc.identifier.sourceCurrent Protocols in Nucleic Acid Chemistry
dc.identifier.citedreferenceShi, J. and Bergstrom, D.E. 1997. Assembly of novel DNA cycles with rigid tetrahedral linkers. Angew Chem. Int. Ed. Engl. 36: 111 ‐ 113.
dc.identifier.citedreferenceSeeman, N.C., Rosenberg, J.M., and Rich, A. 1976. Sequence specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. U.S.A. 73: 804 ‐ 808.
dc.identifier.citedreferenceSeeman, N.C., Maestre, M.F., Ma, R.‐I., and Kallenbach, N.R. 1985. Physical characterization of a nucleic acid junction. In Progress in Clinical and Biological Research, Vol. 172A: The Molecular Basis of Cancer ( R. Rein ed.) pp. 99 ‐ 108. Alan R. Liss, New York.
dc.identifier.citedreferenceSha, R., Liu, F., Bruist, M.F., and Seeman, N.C. 1999. Parallel helical domains in DNA branched junctions containing 5′,5′ and 3′,3′ linkages. Biochemistry 38: 2832 ‐ 2841.
dc.identifier.citedreferenceSha, R., Liu, F., Millar, D.P., and Seeman, N.C. 2000a. Atomic force microscopy of parallel DNA branched junction arrays. Chem. Biol. 7: 743 ‐ 751.
dc.identifier.citedreferenceSha, R., Liu, F., and Seeman, N.C. 2000b. Direct evidence for spontaneous branch migration in antiparallel DNA Holliday junctions. Biochemistry 39: 11514 ‐ 11522.
dc.identifier.citedreferenceSha, R., Iwasaki, H., Liu, F., Shinagawa, H., and Seeman, N.C. 2000c. Cleavage of symmetric immobile DNA junctions by Ruv C. Biochemistry 39: 11982 ‐ 11988.
dc.identifier.citedreferenceSun, W., Mao, C., Liu, F., and Seeman, N.C. 1998. Sequence dependence of branch migratory minima. J. Mol. Biol. 282: 59 ‐ 70.
dc.identifier.citedreferenceWang, Y.L., Mueller, J.E., Kemper, B., and Seeman, N.C. 1991. Assembly and characterization of five‐arm and six‐arm DNA branched junctions. Biochemistry 30: 5667 ‐ 5674.
dc.identifier.citedreferenceWang, H., Di Gate, R.J., and Seeman, N.C. 1996. An RNA topoisomerase. Proc. Natl. Acad. Sci. U.S.A. 93: 9477 ‐ 9482.
dc.identifier.citedreferenceWang, H., Di Gate, R.J., and Seeman, N.C. 1998. The construction of an RNA knot and its role in demonstrating that E. coli DNA topoisomerase III is an RNA topoisomerase. In Structure, Motion, Interaction and Expression of Biological Macromolecules ( R.H. Sarma and M.H. Sarma, eds.) pp. 103 ‐ 116. Adenine Press, Schenectady, New York.
dc.identifier.citedreferenceWells, A.F. 1977. Three‐dimensional nets and polyhedra. John Wiley & Sons, New York.
dc.identifier.citedreferenceWinfree, E. 1996. On the computational power of DNA annealing and ligation. In DNA Based Computing ( R.J. Lipton and E.B. Baum, eds.) pp. 199 ‐ 219. American Math Society,Providence,R.I.
dc.identifier.citedreferenceWinfree, E., Liu, F., Wenzler, L.A., and Seeman, N.C. 1998. Design and self‐assembly of two‐dimensional DNA crystals. Nature 394: 539 ‐ 544.
dc.identifier.citedreferenceYan, H., Zhang, X., Shen, Z., and Seeman, N.C. 2002. A robust DNA mechanical device controlled by hybridization topology. Nature 415: 62 ‐ 65.
dc.identifier.citedreferenceYang, X., Wenzler, L.A., Qi, J., Li, X., and Seeman, N.C. 1998. Ligation of DNA triangles containing double crossover molecules. J. Am. Chem. Soc. 120: 9779 ‐ 9786.
dc.identifier.citedreferenceYurke, B., Turberfield, A.J., Mills, A.P. Jr., Simmel, F.C., and Neumann, J.L. 2000. A DNA‐fueled molecular machine made of DNA. Nature 406: 605 ‐ 608.
dc.identifier.citedreferenceZhang, S. and Seeman, N.C. 1994. Symmetric Holliday junction crossover isomers. J. Mol. Biol. 238: 658 ‐ 668.
dc.identifier.citedreferenceZhang, Y. and Seeman, N.C. 1992. A solid‐support methodology for the construction of geometrical objects from DNA. J. Am. Chem. Soc. 114: 2656 ‐ 2663.
dc.identifier.citedreferenceZhang, Y. and Seeman, N.C. 1994. The construction of a DNA truncated octahedron. J. Am. Chem. Soc. 116: 1661 ‐ 1669.
dc.identifier.citedreferenceAdleman, L. 1994. Molecular computation of solutions to combinatorial problems. Science 266: 1021 ‐ 1024.
dc.identifier.citedreferenceAlivisatos, A.P., Johnsson, K.P., Peng, X., Wilson, T.E., Loweth, C.J., Bruchez, M.P., and Schultz, P.G. 1996. Organization of ’nanocrystal molecules’ using DNA. Nature 382: 609 ‐ 611.
dc.identifier.citedreferenceBalasubramanian, B., Pogozelski, W.K., and Tullius, T.D. 1998. DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. U.S.A. 95: 9738 ‐ 9743.
dc.identifier.citedreferenceCaruthers, M.H. 1985. Gene synthesis machines: DNA chemistry and its uses. Science 230: 281 ‐ 285.
dc.identifier.citedreferenceChen, J. and Seeman, N.C., 1991a. The synthesis from DNA of a molecule with the connectivity of a cube. Nature 350: 631 ‐ 633.
dc.identifier.citedreferenceChen, J. and Seeman, N.C., 1991b. The electrophoretic properties of a DNA cube and its sub‐structure catenanes. Electrophoresis 12: 607 ‐ 611.
dc.identifier.citedreferenceChurchill, M.E.A., Tullius, T.D., Kallenbach, N.R., and Seeman, N.C. 1988. A Holliday recombination intermediate is twofold symmetric. Proc. Natl. Acad. Sci. U.S.A. 85: 4653 ‐ 4656.
dc.identifier.citedreferenceCooper, J.P. and Hagerman, P.J. 1987. Gel electrophoretic analysis of the geometry of a DNA four‐way junction. J. Mol. Biol. 198: 711 ‐ 719.
dc.identifier.citedreferenceCooper, J.P. and Hagerman, P.J. 1989. Geometry of a branched DNA structure in solution. Proc. Natl. Acad. Sci. U.S.A. 86: 7336 ‐ 7340.
dc.identifier.citedreferenceDu, S.M. and Seeman, N.C. 1994. The construction of a trefoil knot from a DNA branched junction motif. Biopolymers 34: 31 ‐ 37.
dc.identifier.citedreferenceDu, S.M., Zhang, S., and Seeman, N.C. 1992. DNA junctions, antijunctions and mesojunctions. Biochemistry 31: 10955 ‐ 10963.
dc.identifier.citedreferenceDu, S.M., Stollar, B.D., and Seeman, N.C. 1995a. A synthetic DNA molecule in three knotted topologies. J. Am. Chem. Soc. 117: 1194 ‐ 1200.
dc.identifier.citedreferenceDu, S.M., Wang, H., Tse‐Dinh, Y.‐C., and Seeman, N.C. 1995b. Topological transformations of synthetic DNA knots. Biochemistry 34: 673 ‐ 682.
dc.identifier.citedreferenceDuckett, D.R., Murchie, A.I., Diekmann, S., von Kitzing, E., Kemper, B., and Lilley, D.M.J. 1988. The structure of the Holliday junction, and its resolution. Cell 55: 79 ‐ 89.
dc.identifier.citedreferenceEis, P.S. and Millar, D.P. 1993. Conformational distributions of a four‐way DNA junction revealed by time‐resolved fluorescence resonance energy transfer. Biochemistry 32: 13852 ‐ 13860.
dc.identifier.citedreferenceFischer, S.G. and Lerman, L.S. 1979. Length‐independent separation of DNA restriction fragments in two‐dimensional gel electrophoresis. Cell 16: 191 ‐ 200.
dc.identifier.citedreferenceFu, T.‐J. and Seeman, N.C. 1993. DNA double crossover structures. Biochemistry 32: 3211 ‐ 3220.
dc.identifier.citedreferenceFu, T.‐J., Tse‐Dinh, Y.‐C., and Seeman, N.C. 1994a. Holliday junction crossover topology. J. Mol. Biol. 236: 91 ‐ 105.
dc.identifier.citedreferenceFu, T.‐J., Kemper, B., and Seeman, N.C. 1994b. Endonuclease VII cleavage of DNA double crossover molecules. Biochemistry 33: 3896 ‐ 3905.
dc.identifier.citedreferenceHagerman, P.J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17: 265 ‐ 286.
dc.identifier.citedreferenceHolliday, R. 1964. A mechanism for gene conversion in fungi. Genet. Res. 5: 282 ‐ 304.
dc.identifier.citedreferenceKallenbach, N.R., Ma, R.‐I., and Seeman, N.C. 1983. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305: 829 ‐ 831.
dc.identifier.citedreferenceKimball, A., Guo, Q., Lu, M., Kallenbach, N.R., Cunningham, R.P., Seeman, N.C., and Tullius, T.D. 1990. Conformational isomers of Holliday junctions. J. Biol. Chem. 265: 6544 ‐ 6547.
dc.identifier.citedreferenceLaBean, T., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H., and Seeman, N.C. 2000. The construction, analysis, ligation and self‐assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122: 1848 ‐ 1860.
dc.identifier.citedreferenceLi, X., Yang, X., Qi, J., and Seeman, N.C. 1996. Antiparallel DNA double crossover molecules as components for nanoconstruction. J. Am. Chem. Soc. 118: 6131 ‐ 6140.
dc.identifier.citedreferenceLi, X., Wang, H., and Seeman, N.C. 1997. Direct evidence for Holliday junction crossover isomerization. Biochemistry 36: 4240 ‐ 4247.
dc.identifier.citedreferenceLiu, F., Sha, R., and Seeman, N.C. 1999. Modifying the surface features of two‐dimensional DNA crystals. J. Am. Chem. Soc. 121: 917 ‐ 922.
dc.identifier.citedreferenceMa, R.‐I., Kallenbach, N.R., Sheardy, R.D., Petrillo, M.L., and Seeman, N.C. 1986. Three‐arm nucleic acid junctions are flexible. Nucl. Acids Res. 14: 9745 ‐ 9753.
dc.identifier.citedreferenceMao, C., Sun, W., and Seeman, N.C. 1997. Assembly of Borromean rings from DNA. Nature 386: 137 ‐ 138.
dc.identifier.citedreferenceMao, C., Sun, W., Shen, Z., and Seeman, N.C. 1999a. A DNA nanomechanical device based on the B‐Z transition. Nature 397: 144 ‐ 146.
dc.identifier.citedreferenceMao, C., Sun, W., and Seeman, N.C. 1999b. Designed two‐dimensional DNA Holliday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc. 121: 5437 ‐ 5443.
dc.identifier.citedreferenceMao, C., LaBean, T., Reif, J.H., and Seeman, N.C. 2000. Logical computation using algorithmic self‐assembly of DNA triple crossover molecules. Nature 407: 493 ‐ 496.
dc.identifier.citedreferenceMarky, L.A., Kallenbach, N.R., McDonough, K.A., Seeman, N.C., and Breslauer, K.J. 1987. The melting behavior of a nucleic acid junction: A calorimetric and spectroscopic study. Biopolymers 26: 1621 ‐ 1634.
dc.identifier.citedreferenceMathieu, F., Mao, C., and Seeman, N.C. 2001. A DNA nanotube based on a six‐helix bundle motif. J. Biomol. Struct. Dyn. 18: 907 ‐ 908.
dc.identifier.citedreferenceMirkin, C.A., Letsinger, R.L., Mucic, R.C., and Storhoff, J.J. 1996. A DNA‐based method for rationally assembling nanoparticles into macroscopic materials. Nature 382: 607 ‐ 609.
dc.identifier.citedreferenceMueller, J.E., Du, S.M., and Seeman, N.C. 1991. The design and synthesis of a knot from single‐stranded DNA. J. Am. Chem. Soc. 113: 6306 ‐ 6308.
dc.identifier.citedreferenceMurchie, A.I., Clegg, R.M., von Kitzing, E., Duckett, D.R., Diekmann, S., and Lilley, D.M.J. 1989. Fluorescence energy transfer shows that the four‐way DNA junction is a right‐handed cross of antiparallel molecules. Nature 341: 763 ‐ 766.
dc.identifier.citedreferenceNeilsen, P.E. 1995. DNA analogs with non‐phosphodiester backbones. Annu. Rev. Biophys. Biophys. Chem. 14: 167 ‐ 183.
dc.identifier.citedreferenceNiemeyer, C.M., Sano, T., Smith, C.L., and Cantor, C.R. 1994. Oligonucleotide‐directed self‐assembly of proteins. Nucl. Acids Res. 22: 5530 ‐ 5539.
dc.identifier.citedreferencePetrillo, M.L., Newton, C.J., Cunningham, R.P., Ma, R.‐I., Kallenbach, N.R., and Seeman, N.C. 1988. The ligation and flexibility of four‐arm DNA junctions. Biopolymers 27: 1337 ‐ 1352.
dc.identifier.citedreferencePodtelezhnikov, A., Mao, C., Seeman, N.C., and Vologodskii, A.V. 2000. Multimerization‐cyclization of DNA fragments as a method of conformational analysis. J. Biophys. 79: 2692 ‐ 2704.
dc.identifier.citedreferenceQiu, H., Dewan, J.C., and Seeman, N.C. 1997. A DNA decamer with a sticky end: The crystal structure of d‐CGACGATCGT. J. Mol. Biol. 267: 881 ‐ 898.
dc.identifier.citedreferenceRobinson, B.H. and Seeman, N.C. 1987. The design of a biochip: A self‐assembling molecular‐scale memory device. Protein Eng. 1: 295 ‐ 300.
dc.identifier.citedreferenceRodbard, D. and Chrambach, A. 1971. Estimation of molecular radius, free mobility, and valence using polyacrylamide gel electrophoresis. Anal. Biochem. 40: 95 ‐ 134.
dc.identifier.citedreferenceSeeman, N.C. 1982. Nucleic acid junctions and lattices. J. Theor. Biol. 99: 237 ‐ 247.
dc.identifier.citedreferenceSeeman, N.C. 1990. De novo design of sequences for nucleic acid structure engineering. J. Biomol. Struct. Dyn. 8: 573 ‐ 581.
dc.identifier.citedreferenceSeeman, N.C. 1992. The design of single‐stranded nucleic acid knots. Mol. Eng. 2: 297 ‐ 307.
dc.identifier.citedreferenceSeeman, N.C. 2000. In the nick of space: Generalized nucleic acid complementarity and the development of DNA nanotechnology. Synlett 1536 ‐ 1548.
dc.identifier.citedreferenceSeeman, N.C. 2001. DNA nicks and nodes and nanotechnology. NanoLetters 1: 22 ‐ 26.
dc.identifier.citedreferenceSeeman, N.C. and Kallenbach, N.R. 1983. Design of immobile nucleic acid junctions. J. Biophys. 44: 201 ‐ 209.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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