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      Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices

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      Proceedings of the National Academy of Sciences

      Proceedings of the National Academy of Sciences

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          Abstract

          The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applications for nanofabrication of complex structures and useful devices. Here we report the construction of an aperiodic patterned DNA lattice (barcode lattice) by a self-assembly process of directed nucleation of DNA tiles around a scaffold DNA strand. The input DNA scaffold strand, constructed by ligation of shorter synthetic oligonucleotides, provides layers of the DNA lattice with barcode patterning information represented by the presence or absence of DNA hairpin loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles around the scaffold strand was shown to result in a patterned lattice containing barcode information of 01101. We have also demonstrated the reprogramming of the system to another patterning. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands composing each tile. A ribbon lattice, consisting of repetitions of the barcode pattern with expected periodicity, was also constructed by the addition of sticky ends. The patterning of both classes of lattices was clearly observable via atomic force microscopy. These results represent a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques. A functioning visual output method would not only increase the readout speed of DNA-based computers, but may also find use in other sequence identification techniques such as mutation or allele mapping.

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          Most cited references 29

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          DNA in a material world.

          The specific bonding of DNA base pairs provides the chemical foundation for genetics. This powerful molecular recognition system can be used in nanotechnology to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information. The exploitation of DNA for material purposes presents a new chapter in the history of the molecule.
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            Design and self-assembly of two-dimensional DNA crystals.

            Molecular self-assembly presents a 'bottom-up' approach to the fabrication of objects specified with nanometre precision. DNA molecular structures and intermolecular interactions are particularly amenable to the design and synthesis of complex molecular objects. We report the design and observation of two-dimensional crystalline forms of DNA that self-assemble from synthetic DNA double-crossover molecules. Intermolecular interactions between the structural units are programmed by the design of 'sticky ends' that associate according to Watson-Crick complementarity, enabling us to create specific periodic patterns on the nanometre scale. The patterned crystals have been visualized by atomic force microscopy.
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              Molecular computation of solutions to combinatorial problems

               L Adleman (1994)
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                Author and article information

                Journal
                Proceedings of the National Academy of Sciences
                PNAS
                Proceedings of the National Academy of Sciences
                0027-8424
                1091-6490
                July 08 2003
                July 08 2003
                July 08 2003
                June 23 2003
                : 100
                : 14
                : 8103-8108
                10.1073/pnas.1032954100
                166189
                12821776
                © 2003

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