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Nucleic Acids Research Advance Access originally published online on February 18, 2009
Nucleic Acids Research 2009 37(7):2164-2175; doi:10.1093/nar/gkp005
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Nucleic Acids Research, 2009, Vol. 37, No. 7 2164-2175
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation

Jinhao Zhu1,2, Bryan Wei2, Yuan Yuan1 and Yongli Mi2,*

1Department of Computer Science and Engineering and 2Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Hong Kong

*To whom correspondence should be addressed. Tel: +00852 2358 7127; Fax: +00852 2358 0054; Email: keymix{at}ust.hk

Received July 19, 2008. Revised January 5, 2009. Accepted January 5, 2009.

A user-friendly software system, UNIQUIMER 3D, was developed to design DNA structures for nanotechnology applications. It consists of 3D visualization, internal energy minimization, sequence generation and construction of motif array simulations (2D tiles and 3D lattices) functionalities. The system can be used to check structural deformation and design errors under scaled-up conditions. UNIQUIMER 3D has been tested on the design of both existing motifs (holiday junction, 4 x 4 tile, double crossover, DNA tetrahedron, DNA cube, etc.) and nonexisting motifs (soccer ball). The results demonstrated UNIQUIMER 3D's capability in designing large complex structures. We also designed a de novo sequence generation algorithm. UNIQUIMER 3D was developed for the Windows environment and is provided free of charge to the nonprofit research institutions.


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