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. 2009 Apr;37(7):2164-75.
doi: 10.1093/nar/gkp005. Epub 2009 Feb 18.

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

Jinhao Zhu  1 , Bryan Wei, Yuan Yuan, Yongli Mi
Affiliations

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

Jinhao Zhu et al. Nucleic Acids Res. 2009 Apr.

Abstract

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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Figures

Figure 1.
Figure 1.
System hierarchy.
Figure 2.
Figure 2.
The graphics of the structural components of different levels. (a) Three DNA base pairs. (b) A DNA double helix. (c) A sticky end. (d) A motif (4 × 4 tile). (e) A motif array.
Figure 3.
Figure 3.
Valid and invalid closing operations.
Figure 4.
Figure 4.
Parametric curve h+(t) of a single helix.
Figure 5.
Figure 5.
Illustration of the smoothness term.
Figure 6.
Figure 6.
Energy minimization. (a) Two distorted DNA double-helical domains before energy minimization. (b) Two refined DNA double-helical domains after energy minimization. (c) Two distorted DNA double-helical domains with crossover before energy minimization. (d) Two refined DNA double-helical domains with crossover after energy minimization.
Figure 7.
Figure 7.
Base pair matching. Sequences shown in the box are subjected to complementary region.
Figure 8.
Figure 8.
Mismatching prevention. Sequences shown in the box are two repetitive segments of 4 bp.
Figure 9.
Figure 9.
Algorithm for the sequence generation.
Figure 10.
Figure 10.
Hybridization errors. (a) Two segments of strand 1 bind together. (b) Two unintended segments of the strands 1 and 2 bind together.
Figure 11.
Figure 11.
DX motifs. (a) DAE structure (21 bp between crossovers). (b) DAE structure with DNA nodes rendered (21 bp between crossovers). (c) DAE structure (10 bp between crossovers). (d) DAE structure with DNA nodes rendered (10 bp between crossovers). (e) DPON structure (16 bp between crossovers). (f) DPON structure with DNA nodes rendered (16 bp between crossovers).
Figure 12.
Figure 12.
Tetrahedron structure. (a) Structure without DNA nodes rendered. (b) Structure with DNA nodes rendered.
Figure 13.
Figure 13.
Cube structure. (a) Structure without DNA nodes rendered. (b) Structure with DNA nodes rendered.
Figure 14.
Figure 14.
The stepwise design of a soccer ball structure.
Figure 15.
Figure 15.
Soccer ball structure rendered without sequence generation.
Figure 16.
Figure 16.
Soccer ball structure rendered with sequence generation.
See this image and copyright information in PMC

References

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