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Computer-Aided Design of DNA Origami Structures

  • Denis Selnihhin
  • Ebbe Sloth Andersen
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1244)

Abstract

The DNA origami method enables the creation of complex nanoscale objects that can be used to organize molecular components and to function as reconfigurable mechanical devices. Of relevance to synthetic biology, DNA origami structures can be delivered to cells where they can perform complicated sense-and-act tasks, and can be used as scaffolds to organize enzymes for enhanced synthesis. The design of DNA origami structures is a complicated matter and is most efficiently done using dedicated software packages. This chapter describes a procedure for designing DNA origami structures using a combination of state-of-the-art software tools. First, we introduce the basic method for calculating crossover positions between DNA helices and the standard crossover patterns for flat, square, and honeycomb DNA origami lattices. Second, we provide a step-by-step tutorial for the design of a simple DNA origami biosensor device, from schematic idea to blueprint creation and to 3D modeling and animation, and explain how careful modeling can facilitate later experimentation in the laboratory.

Key words

DNA Nanotechnology Origami Biosensor CAD Software 

Notes

Acknowledgement

This work was supported by a Sapere Aude Starting Grant from the Danish Council for Independent Research (DFF-0602-01772) and the Centre for DNA Nanotechnology (http://cdna.au.dk/) funded by the Danish National Research Foundation (DNRF81).

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Center for DNA Nanotechnology, Interdisciplinary Nanoscience Center, Department of Molecular Biology & GeneticsAarhus UniversityAarhusDenmark
  2. 2.Center for DNA Nanotechnology, Interdisciplinary Nanoscience Center, Department of Molecular Biology & GeneticsAarhus UniversityAarhusDenmark

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