Abstract
Crystallization is periodic self-assembly onthe molecular scale. Individual DNA componentshave been used several times to achieveself-assembled crystalline arrangements in twodimensions. The design of a fractal system isa much more difficult goal to achieve withmolecular components. We present DNAcomponents whose cohesive portions arecompatible with a fractal assembly. Thesecomponents are DNA parallelograms that havebeen used previously to produce two dimensionalarrays. To obtain a fractal arrangement,however, we find it necessary to combine theseparallelograms with glue-like constructs. Theassembly of the individual parallelograms and aseries of glues and protecting groups appear toensure the fractal growth of the system in twodimensions. Synthetic protocols are suggestedfor the implementation of this approach tofractal assembly.
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References
Cohen SN, Chang ACY, Boyer HW and Helling RB (1973) Construction of biologically functional bacterial plasmids in vitro. Proc. Nat. Acad. Sci. (USA) 70: 3240–3244
Eichman BF, Vargason JM, Mooers BHM and Ho PS (2000) The holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions. Proc. Nat. Acad. Sci. USA 97: 3971–3976
LaBean T, Yan H, Kopatsch J, Liu F, Winfree E, Reif JH and Seeman NC (2000) The construction, analysis, ligation and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122: 1848–1860
Mao C, Sun W and Seeman NC (1999) Designed two-dimensional DNA holliday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc. 121: 5437–5443
Mao C, LaBean T, Reif JH and Seeman NC (2000) Logical computation using algorithmic self-assembly of DNA triple crossover molecules. Nature 407: 493–496
Qi J, Li X, Yang X and Seeman NC (1996) The ligation of triangles built from bulged threearm DNA branched junctions. J. Am. Chem. Soc. 118: 6121–6130
Qiu H, Dewan JC and Seeman NC (1997) A DNA decamer with a sticky end: The crystal structure of d-CGACGATCGT. J. Mol. Biol. 267: 881–898
Seeman NC (1982) Nucleic acid junctions and lattices. J. Theor. Biol. 99: 237–247
Seeman NC (1999) DNA engineering and its application to nanotechnology. Trends Biotech. 17: 437–443
Sha R, Liu F, Millar DP and Seeman NC (2000) Atomic force microscopy of parallel DNA branched junction arrays. Chem. & Biol. 7: 743–751
Sha R, Liu F and Seeman NC (2002) Atomic force microscopic measurement of the interdomain angle in symmetric holliday junctions. Biochem. 41: 5950–5955
Winfree E (1996) On the computational power of DNA annealing and ligation. In: Lipton EJ and Baum EB (eds) DNA Based Computing, pp. 199–219. Am. Math. Soc. Providence
Winfree E, Liu F, Wenzler LA and Seeman NC (1998a) Design and self-assembly of twodimensional DNA crystals. Nature 394: 539–544
Winfree E, Yang X and Seeman NC (1998b) Universal computation via self-assembly of DNA: Some theory and experiments. In: Landweber LF and Baum EB (eds) DNA Based Computers II, pp. 191–213. Am. Math. Soc. Providence
Yan H, Zhang X, Shen Z and Seeman NC (2002) A robust DNA mechanical device controlled by hybridization topology. Nature 415: 62–65
Yang X, Wenzler LA, Qi J, Li X and Seeman NC (1998) Ligation of DNA triangles containing double crossover molecules. J. Am. Chem. Soc. 120: 9779–9786
Yurke B, Turberfield AJ, Mills AP, Jr., Simmel FC and Neumann JL (2000) A DNA-fueled molecular machine made of DNA. Nature 406: 605–608
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Carbone, A., Seeman, N.C. A route to fractal DNA-assembly. Natural Computing 1, 469–480 (2002). https://doi.org/10.1023/A:1021323017415
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DOI: https://doi.org/10.1023/A:1021323017415