Architecture with GIDEON, a program for design in structural DNA nanotechnology

Jeffrey J. Birac, William B. Sherman, Jens Kopatsch, Pamela E. Constantinou, Nadrian C. Seeman

Research output: Contribution to journalArticlepeer-review


We present geometry based design strategies for DNA nanostructures. The strategies have been implemented with GIDEON-a graphical integrated development environment for oligonucleotides. GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein. Models are built on a simple model of undistorted B-DNA double-helical domains. Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between these domains and the identification of any steric clashes that might occur as a result. Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes. We have carried out experiments that confirm that 3D triangles form well only when their geometrical strain is less than 4% deviation from the estimated relaxed structure. Thus geometry-based techniques alone, without detailed energetic considerations, can be used to explain certain general trends in DNA structure formation. We have used GIDEON to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction misalignments. Computer modeling using a graphical user interface overcomes the limited precision of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software.

Original languageEnglish (US)
Pages (from-to)470-480
Number of pages11
JournalJournal of Molecular Graphics and Modelling
Issue number4
StatePublished - Dec 2006


  • DNA
  • DNA double crossover
  • DNA models
  • DNA tensegrity triangle
  • DNA triple crossover
  • Geometrical molecular modeling
  • Graphical user interface

ASJC Scopus subject areas

  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry


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