DNA rendering of polyhedral meshes at the nanoscale

DNA rendering of polyhedral meshes at the nanoscale It was suggested 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. The starting point of the method we present here is a 3D mesh representing the geometry one wishes to realize at the nanoscale. Focusing only on polyhedral meshes, http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nature Nature Publishing Group (NPG)

DNA rendering of polyhedral meshes at the nanoscale

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Publisher
Nature Publishing Group (NPG)
Copyright
Copyright © 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
ISSN
0028-0836
eISSN
1476-4687
D.O.I.
10.1038/nature14586
Publisher site
See Article on Publisher Site

Abstract

It was suggested 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. The starting point of the method we present here is a 3D mesh representing the geometry one wishes to realize at the nanoscale. Focusing only on polyhedral meshes,

Journal

NatureNature Publishing Group (NPG)

Published: Jul 22, 2015

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