Design and test of noncrosshybridizing oligonucleotide building blocks for DNA computers and nanostructures

Deaton, Russell; Kim, Jin-Woo; Chen, Junghuei
February 2003
Applied Physics Letters;2/24/2003, Vol. 82 Issue 8, p1305
Academic Journal
DNA oligonucleotides that anneal to form duplexes in specific, planned configurations are a basic construction material for DNA-based computers and nanotechnology. Unplanned duplex configurations introduce errors in computations and defects in structures, and thus, the sequences must be designed to minimize these effects. A software design tool has been developed that uses thermodynamic models of DNA duplex thermal stability and algorithms from graph theory to select good sets of oligonucleotides. An example set was tested in the laboratory, and the designed sequences formed no unplanned duplexes and had no detectable secondary structure.


Related Articles

  • Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides. Ducani, Cosimo; Kaul, Corinna; Moche, Martin; Shih, William M; Högberg, Björn // Nature Methods;Jul2013, Vol. 10 Issue 7, p647 

    Single-stranded oligonucleotides are important as research tools, as diagnostic probes, in gene therapy and in DNA nanotechnology. Oligonucleotides are typically produced via solid-phase synthesis, using polymer chemistries that are limited relative to what biological systems produce. The number...

  • Assembly Of G-Quartet Based DNA Superstructures (G-Wires). Sondermann, Anett; Holste, Claudia; Möller, Robert; Fritzsche, Wolfgang // AIP Conference Proceedings;2002, Vol. 640 Issue 1, p93 

    G-wires are DNA superstructures based on the intermolecular interactions of four Guanine bases. They allow the fabrication of structures reaching the micrometer scale using only short DNA oligonucleotides, what makes them potentially interesting for molecular nanotechnology. We investigated the...

  • A DNA Origami of Slovenia in Nano Dimensions. Jerala, Miha; Jerala, Roman; Hafner-Bratkovič, Iva // Acta Chimica Slovenica;2011, Vol. 58 Issue 1, p181 

    The principle of the rapidly evolving DNA nanotechnology is the design of nanostructures based only on the Watson-Crick base pairing and the oligonucleotide sequence. DNA origami technique is able to produce a variety of different shapes by constraining a long single stranded DNA molecule with a...

  • Site-specific positioning of dendritic alkyl chains on DNA cages enables their geometry-dependent self-assembly. Edwardson, Thomas G. W.; Carneiro, Karina M. M.; McLaughlin, Christopher K.; Serpell, Christopher J.; Sleiman, Hanadi F. // Nature Chemistry;Oct2013, Vol. 5 Issue 10, p868 

    Nature uses a combination of non-covalent interactions to create a hierarchy of complex systems from simple building blocks. One example is the selective association of the hydrophobic side chains that are a strong determinant of protein organization. Here, we report a parallel mode of assembly...

  • Coupling G-Wires To Metal Nanoparticles. Holste, Claudia; Sondermann, Anett; Möller, Robert; Fritzsche, Wolfgang // AIP Conference Proceedings;2004, Vol. 725 Issue 1, p53 

    G-wires are DNA superstructures based on quartet formation by four guanine (G) bases. These molecular structures reach the micrometer size scale by assembling short oligonucleotides of a guanine rich sequence. Physico-chemical parameters were optimized to achieve optimal superstructure assembly....

  • Applications of nanotechnology for immunology. Smith, Douglas M.; Simon, Jakub K.; Baker, James R. // Nature Reviews Immunology;Aug2013, Vol. 13 Issue 8, p592 

    Nanotechnology uses the unique properties of objects that function as a unit within the overall size range of 1-1,000 nanometres. The engineering of nanostructure materials, including nanoparticles, nanoemulsions or nanotubules, holds great promise for the development of new immunomodulatory...

  • Biosensors based on a method for determining the conductance matrix of multiterminal semiconductor nanostructures. Danilovskii, E.; Bagraev, N.; Chernev, A.; Getz, D.; Klyachkin, L.; Malyarenko, A. // Semiconductors;Nov2014, Vol. 48 Issue 11, p1512 

    A method for determining the conductance matrix is analyzed to study the properties of silicon nanostructures fabricated within Hall geometry on an n-type Si(100) surface as ultra-narrow p-type silicon quantum wells bounded by δ barriers heavily doped with boron. Within the proposed approach,...

  • Generating Aptamers by Cell-SELEX for Applications in Molecular Medicine. Mao Ye; Jun Hu; Minyuan Peng; Jing Liu; Jun Liu; Huixia Liu; Xielan Zhao; Weihong Tan // International Journal of Molecular Sciences;Mar2012, Vol. 13 Issue 3, p3341 

    Aptamers are single-stranded oligonucleotides of DNA or RNA that bind to target molecules with high affinity and specificity. Typically, aptamers are generated by an iterative selection process, called systematic evolution of ligands by exponential enrichment (SELEX). Recent advancements in...

  • Synthetic Oligonucleotide Modifications for the Investigation of Charge Transfer and Migration Processes in DNA. Wagenknecht, Hans-Achim // Current Organic Chemistry;Feb2004, Vol. 8 Issue 3, p251 

    With respect to the biological role during DNA damaging and to potential applications in DNA chip and nanotechnology, the DNA-mediated charge transfer phenomena attracted a lot of attention in the scientific community during the last 15 years. Most research groups have focused their work on the...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics