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DNA Origami Design of Dolphin-Shaped Structures with Flexible Tails

Supporting Info

Ebbe S. Andersen†‡, Mingdong Dong†§, Morten M. Nielsen†‡, Kasper Jahn†‡, Allan Lind-Thomsen

, Wael Mamdouh†§, Kurt V. Gothelf†

, Flemming Besenbacher†§ and Jørgen Kjems†‡*

^† Danish National Research Foundation, Centre for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, DK-8000 Aarhus, Denmark

^‡ Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus, Denmark

^§ Department of Physics and Astronomy, University of Aarhus, DK-8000 Aarhus, Denmark

Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark

Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark

ACS Nano, 2008, 2 (6), pp 1213–1218

DOI: 10.1021/nn800215j

Publication Date (Web): June 10, 2008

* Address correspondence to jk@mb.au.dk.

Abstract

The DNA origami method allows the folding of long, single-stranded DNA sequences into arbitrary two-dimensional structures by a set of designed oligonucleotides. The method has revealed an unexpected strength and efficiency for programmed self-assembly of molecular nanostructures and makes it possible to produce fully addressable nanostructures with wide-reaching application potential within the emerging area of nanoscience. Here we present a user-friendly software package for designing DNA origami structures (http://www.cdna.dk/origami) and demonstrate its use by the design of a dolphin-like DNA origami structure that was imaged by high-resolution AFM in liquid. The software package provides automatic generation of DNA origami structures, manual editing, interactive overviews, atomic models, tracks the design history, and has a fully extendable toolbox. From the AFM images, it was demonstrated that different designs of the dolphin tail region provided various levels of flexibility in a predictable fashion. Finally, we show that the addition of specific attachment sites promotes dimerization between two independently self-assembled dolphin structures, and that these interactions stabilize the flexible tail.

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