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DNA Rendering of Polyhedral Meshes At the Nanoscale

Erik Benson, Abdulmelik Mohammed, Johan Gardell, Sergej Masich, Eugen Czeizler, Pekka Orponen, Bjorn Hogberg, DNA Rendering of Polyhedral Meshes At the Nanoscale. Nature 523(7561), 4, 2015.

http://dx.doi.org/10.1038/nature14586

Abstract:

It was suggested1 more than thirty years ago that Watson–Crick base pairing might be used for the rational design of nanometre-scale structures from nucleic acids. Since then, and especially since the introduction of the origami technique, DNA nanotechnology has enabled increasingly more complex structures. But although general approaches for creating DNA origami polygonal meshes and design software are available, there are still important constraints arising from DNA geometry and sense/antisense pairing, necessitating some manual adjustment during the design process. Here we present a general method of folding arbitrary polygonal digital meshes in DNA that readily produces structures that would be very difficult to realize using previous approaches. The design process is highly automated, using a routeing algorithm based on graph theory and a relaxation simulation that traces scaffold strands through the target structures. Moreover, unlike conventional origami designs built from close-packed helices, our structures have a more open conformation with one helix per edge and are therefore stable under the ionic conditions usually used in biological assays.

BibTeX entry:

@ARTICLE{jBeMoGaMaCzOrHo15a,
  title = {DNA Rendering of Polyhedral Meshes At the Nanoscale},
  author = {Benson, Erik and Mohammed, Abdulmelik and Gardell, Johan and Masich, Sergej and Czeizler, Eugen and Orponen, Pekka and Hogberg, Bjorn},
  journal = {Nature},
  volume = {523},
  number = {7561},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  pages = {4},
  year = {2015},
  keywords = {DNA nanostructures; Computer science; Self-assembly},
  ISSN = {0028-0836},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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