title: UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation.
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.
authors.affiliation: Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Hong Kong.
authors.forename: Jinhao
authors.initials: J
authors.lastname: Zhu
authors.forename: Bryan
authors.initials: B
authors.lastname: Wei
authors.forename: Yuan
authors.initials: Y
authors.lastname: Yuan
authors.forename: Yongli
authors.initials: Y
authors.lastname: Mi
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry*; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D012984:Software
chemical_list: D004247:DNA