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

Nucleic Acids Research

Volumn 37, Issue 7, 2009, Pages 2164-2175

  Zhu, Jinhao ^a   Wei, Bryan ^a   Yuan, Yuan ^a   Mi, Yongli ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SYSTEM; DNA DETERMINATION; DNA SEQUENCE; DNA STRUCTURE; MATHEMATICAL ANALYSIS; NANOTECHNOLOGY; PRIORITY JOURNAL; PROTEIN MOTIF; SCALE UP; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

BASE PAIR MISMATCH; BASE SEQUENCE; COMPUTER GRAPHICS; DNA; NANOSTRUCTURES; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; SOFTWARE;

EID: 65549158772     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp005     Document Type: Article

References (24)

1. Seeman,N.C. (2003 DNA in a material world. Nature, 421, 427-431.
2. Seeman,N.C., (1999) DNA engineering and its application to nanotechnology. Trends Biotechnol., 17, 437-42.
3. Kallenbach,N.R.. Ma.R.I. and Seeman,N.C. (1983) An immobile nucleic acid junction constructed from oligonucleotides. Nature, 305, 829-831.
4. Li,X., Yang,X., Qi.J., and Seeman,N.C. (1996) Antiparallel DNA double crossover molecules as components for nanoconstruction. J. Am. Chem. Soc., 118, 6131-6140.
5. LaBean,T.H., Yan.H., Kopatsch,U., Liu,F., Winfree,E., Reif,J.H. and Seeman,N.C. (2000) Construction. analysis. ligation. and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc., 122, 1848-1860.
6. Seeman,N.C. (2001) DNA Kicks and nodes and nanotechnology. Nano Lett. 1, 22-26.
7. Zhang.X., Yan,H., Shen.Z., and Seeman,N.C. (2002) A robust DNA mechanical device controlled by hybridization topologt. J. Am. Chem. Soc., 124, 12940-12941.
8. Shen,Z., Yan,H., Wang,J. and Seeman,N.C. (2004) Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology. J. Am. Chem. Soc., 126, 1666-1674.
9. Yan,H., Park,S-H., Finkelstein,G., Reil,J.H. and LaBean,T.H. (2003) DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science, 301, 1882-1884.
10. Rothemund,P.W.K. (2006) Folding DNA to create nanoscale shapes and pattern. Nature, 440, 297-302.
11. Seeman,N.C. (1990) De novo design of sequences for nucleic acid structural engineering. J. Biomol. Struct. Dyn., 8. 573-581.
12. Busa,S.R. (2003) 3D Computer Graphics: A Mathematical Introduction with OpenGL. Cambridge University Press. Cambridge, England.
13. Powell, M.I.D. (1977). A fast algorithm for nonlinearly constrained optimization calculation. Proc. Numer. Anal., 630, 144-157.
14. Seeman,N.C. (1990) De novo design of sequences for nucleic acid structural engineering. J. Biomol. Struct. Dyn., 8, 573-581.
15. Willianis,S., Lund,K., Lin,C., Wonka,P., Lindsay,S. and Yan,H. (2008) Tiamat: A three-dimensional editing tool for complec DNA structure. In: Goel,A., Simmel,F.C., and Sosik,P. The 14th International Meeting on DNA Computing Proceedings. Silesian University in Opava. Czech Republic. pp. 112-121.
16. Boyer,R.S. and Moore. J.S. (1977) A fast string searching algorithm. Commun. ACM 20. 10, 762-772.
17. Fu,T.-J. and Seeman,N.C. (1993) DNA double-crossover molecules. Biochemistry, 32, 3211-3220.
18. Goodman,R.P. Berry,R.M. and Turberfield, A.J. (2004) The single-step synthesis of a DNA tetrahedron. Chem. Commun., 12, 1372-1373.
19. Chen,J. and Seeman,N.C. (1991) Synthesis from DNA of a molecule with the connectivity of a cube. Nature, 350, 631-633.
20. Tung,C.-S. and Carter,H.E.S. (1994) Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures. Comput. Appls. Biosci., 10, 422-433.
21. Carter,E.S., II and Tung, C.-S. (1996) NAMOT2-a redesigned nucleic acid modeling tool: Construction of non-canonical DNA structures. Comput. Apps. Biosci., 12, 25-30.
22. Birac,J.J., Sherman,W.B., Kopatsch,J., Constantinou,P.E. and Seeman,N.C. (2006) Architecture with GIDEON, a program for design in structural DNA nanotechnology. J. Mol. Graph. Model., 25, 470-480.
23. Bindewald,E., Grunewald,G., Boyle,B., O'Connor,M. and Shapiro,B.A., (2008) Computational strategies for the automated design of RNA nanoscale structures from building blocks using NonoTiler. J. Mol. Graph. Model., 27, 299-308.
24. Wei,B., Wang,Z. and Mi,Y. (2007) Uniquimer: Software of de novo DNA sequence generation for DNA self-assembly-an introduction and the related applications in DNA self-assembly. J. Comput. Theor. Nanosci. 4, 133-146.